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A Phylogeny of Begoniaceae
Bercht. & J.Presl.
A thesis submitted to the University of Glasgow
for the degree of Doctor of Philosophy
Laura Lowe Forrest
Division of Environmental and Evolutionary Biology
December 2000
ProQuest Num ber: 10656230
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Declaration
I hereby declare that this thesis is composed of work carried out by
myself unless otherwise acknowledged and cited and that this
thesis is of my own composition. The research was carried out in
the period of April 1997 to December 2000. This dissertation has
not in whole or in part been previously presented for any other
degree.
“I see a rose, that strange thing, and what’s there
But a seeming coloured something on the air
With the transparencies that make up me.
Thickened to existence by my notice”
Norman McCaig, 'Ego’
II
Abstract
Begonia is one of the largest angiosperm genera, with 1400 species currently
recognised. These were placed into 63 sections in the most recent
taxonomic treatment. However, there is considerable uncertainty in both
section inter-relationships and sectional composition, and there is no
formalised phylogenetic hypothesis for the genus. Using the nuclear internal
transcribed spacers (ITS) and partial large subunit (268) sequences of
ribosomal DMA, I have produced phylogenetic trees to form the basis of a
cladistic framework for the interpretation of the evolution and sectional level
systematics of Begonia.
Maximum parsimony, maximum likelihood and minimum evolution
cladograms were produced for 35 Begonia, one Symbegonia and two Datisca
species, for partial 268, ITS and combined sequence data. The results of the
analyses suggest that African taxa are basal in Begonia, but that there is not
sufficient information to elucidate the precise relationships among these
basal lineages. The genus Symbegonia is nested deeply within Begonia.
A far larger data set was constructed by sequencing the ITS region for 153
species. Different alignment methods (automated, elision and manual) were
tested on these sequences, as were different search strategies. The topology
which was taken to be the best estimate of the ITS phylogeny of Begoniaceae
was constructed using manual alignment, culled of ambiguous regions, and
adjusted to reflect the topologies of smaller, localised, compartment
analyses. In the resulting tree, the African species of Begonia resolve as
paraphyletic, with both Asian species (including Socotra) and American
species (sister to southern African species) monophyletic.
Comparisons were made between the ITS sequence data and trees
produced from the chloroplast trnC - trnD inter-genic spacer. Parsimony
analyses of trnC - trnD sequences support African taxa as basal in Begonia\
however, in contrast to the ITS data, trnC - trnD suggests polyphyly / paraphyly
of American taxa, albeit with little bootstrap support.
A morphological data matrix (67 characters for 159 taxa) did not produce a
phylogenetic hypothesis for Begonia that was congruent with any other
Hi
available data. Using a combined morphology - ITS analysis, the fit of
individual morphological characters to a fundamental tree was examined.
Some characters fitted the combined topology well, although some of the
characters which have traditionally been considered important in Begonia
taxonomy (e.g. the number of placental branches) proved misleading.
The ITS tree was used as a framework for reviewing chromosome evolution in
the genus (604 published counts from 239 species). In contrast to sequence
divergence, which was greatest among African species, chromosome
number diversity was greatest among American species.
The correlation between phylogenetic relationships implied by the ITS tree
and the geographical distributions of species was explored to obtain
biogeographic hypotheses which may explain the present-day distribution of
Begonia. As a general rule, related species are geographically proximal,
suggesting limited dispersal of lineages. This finding contradicts
observations made on morphology, where the close affinities of
morphologically disparate (but geographically proximal) taxa were previously
unsuspected.
Mechanisms responsible for the evolution of large genera were discussed,
and Willis’ ‘age and area’ hypothesis compared to the ‘relict’ hypothesis of
Cronk. In Begonia, the morphological diversity of the genus, and most of the
species, are encompassed among the putatively derived lineages, favouring
the ‘relict’ hypothesis.
IV
Acknowledgements
As must be the case with any work of this kind, I owe thanks to a large number
of people.
Firstly, there are all the people who helped me organise my field work in south
west China, 1997, and who assisted when I got there. Particular thanks are
due to Mark Tebbitt, Zoe Badcock, Mark Watson, David Chamberlain, Pete
Hollingsworth, Jim Dickson, Nick Turland and Rod Taylor. From Kunming,
Yunnan, I would like to thank Guan Kaiun, and most specially Tian Dai’ke and
Li Di-Xi (who both accompanied me down to the Vietnamese border and
across to Nanning, Guangxi; I am particularly grateful to them for taking such
care to find me vegetarian things to eat, to Tian for interpretation, to Driver Li
for keeping the jeep on the goat-tracks which appear to pass for roads, and to
both of them for spotting many Begonia that I would have trotted blithely past).
Wei Yi Gang looked after me very well in Guilin, Guangxi and showed me a
golden Camilia (which otherwise I would probably still not know existed). In
Beijing, Fu De-Zhe, Qin Hai-Nin, Ban Qin, Song Shu-Yin, Sun Qi-Gao (who
sorted out my paperwork, and made sure I left the country), Jin Xiao-Bai (who
kindly provided me with living material of B. morsei, which survived just long
enough for me to get some DNA out of it), Liu Zhao-Hua (who very kindly acted
as interpreter, personal shopper and general dogsbody) and Jason Hilton
(who gamely assisted in some spectacular hangovers) all deserve
acknowledgement.
I am very grateful to Malcolm Wilkins and the MacIntyre Begonia Trust
Trustees for funding my collecting trip.
People who have provided me with information about Begonia include Jan
Doorenbos, Marc Sosef and Ferry Bouman in the Netherlands (I am
particularly grateful to Ferry for taking me to visit the herbarium in Leiden, and
for being good-natured when we found that the specimen we had gone to see
was on loan to a 'L. Forrest’ in Glasgow....), Martin Sands in Kew, Tracy
McLellan, South Africa, and Susan Swensen in Ithaca, New York.
Friends and colleagues who have brought back living or silica dried material
of Begonia from their travels include Peter Wilkie, Mary Mendum, George
Argent, Toby Pennington, Philip Thomas, Nick Turland, Colin Pendry, Bill
Baker, Mark Hughes and Michael Moller.
There are several people who have been involved in keeping the living
collections of Begonia going. They include John Stevensen, Euan
Donaldson, David Menzies, Paul Mathews and many others at Glasgow
Botanic Garden. Also Fiona Inches, Allister Reid, Fred Mobeck, Louise
Galloway, Andrea Fowler, Steve Scott and Neil Watherston in Horticulture, and
Becky Govier (for help with accessioning), at the Royal Botanic Garden
Edinburgh.
Essential Begonia advice has been provided by Zoe Badcock, Mark Tebbitt,
Mark Hughes and Vanessa Plana. The Begonia group meetings in the
Marina have been a very valuable source of ideas....
General advice has come from numerous sources, including Cymon Cox,
Terry Hedderson, Ken Johnson, Richard Bateman, Quentin Cronk, James
Richardson, Rod Page, Vince Smith, Diana Percy, Michael Moller, Kwiton
Jong, Hans Sluiman, Pete Hollingsworth and Toby Pennington (for whom I
summarise that chapter on species concepts which I spared everyone the
ordeal of: Species are progress reports in the history of life (Eldridge, 1995).
Fin.)
My attempts in the laboratory have been inevitably assisted by Caroline
Guihal, Jill Preston, Michelle Hollingsworth, Alex Ponge and James
Richardson. I am very grateful to Jill Harrison, Andy Hudson and other folk at
the University of Edinburgh for lab space, chemicals and advice on cloning.
Other people who deserve a mention include the Library staff at the Royal
Botanic Garden, Edinburgh. Furthermore, Steve Cafferty has raided the BM
library for me on a few occasions, when I've had trouble getting hold of
papers.
David Ingram and Richard Bateman kindly allowed me to move my studies
across to the Royal Botanic Garden Edinburgh (and Steve Blackmore and
Mary Gibby haven’t objected yet). I would like to thank everyone at the Gardens
(including Antonia) for providing a supportive, enthusiastic and friendly place
to study.
VI
Both my supervisors, Pete Hollingsworth and Jim Dickson, have provided
support and encouragement where required. The MacIntyre Begonia Trust
funded the bulk of this work. I hope that this thesis fullfills at least some of its
expectations, and that it continues to support basic Begonia taxonomy and
phylogenetic work. Molecular studies were also supported by a NERC
Glasgow Taxonomy Initiative grant.
Jan Doorenbos kindly checked over the reports of chromosome numbers in
the table on the CD-ROM. I owe particular thanks to Vanessa Plana and Mark
Hughes for talking over ideas, Mark Hughes for manfully trudging his way
through entire chapters of thesis, and Pete Hollingsworth for actually reading
The Lot, and improving most of it. (Thanks are also due to Michelle
Hollingsworth for her tolerance of house invasions and for pasta.) Without
Pete's help and advice this thesis would have been significantly less
interesting (which I am sure he will find hard to believe) and I am very grateful
for all he has done (which I suspect he will find even harder to believe
).
I must also thank my family for believing that a botanical PhD is some sort of
worthwhile investment (and for the river of money).
I intended to put the following quote in somewhere as a reminder that, when
talking on evolutionary timescales, unlikely events can happen. It seems,
however, that there are people out there (Mark) who consider it equally
relevant to the final completion of this thesis (and thanks to Silvia for making
perfection unnecessary).
“the improbable is possible and ... the possible can occur”
Siddall and Kluge, 1997
VII
Table of Contents
1.
Large genera
1.1
Introduction
1
1.2
Genus size
1
1.3
The hollow curve
1.3.1 Behaviour of taxonomists
A
Genus size and importance to man
B.
Historical correlations
0.
Taxonomic pragmatism
D.
Conservation and politics
1.3.2 Natural phenomina
A
Age and Area
B.
Relict Hypothesis
C.
Partitioning of diverstiy
D.
Summary
1.3.3 Combination
2
3
3
3
4
4
5
5
5
6
6
6
1.4
Phylogenetic inputs
1.4.1 The need for monophyly
1.4.2 The shape of phylogenetic trees
A
Terminology
B.
Evolutionary scenarios
i.
balance
ii.
stemminess
iii.
hypothetical example
C.
Caveats
D.
Summary
1.4.3 Are big genera real?
1.4.4 Are big genera old or young?
A
Fossil record
B.
Clade position
7
7
7
7
11
11
11
12
13
14
15
15
16
17
1.5
Biological factors
1.5.1 Diversification
1.5.2 Extinction
1.5.3 Distribution
A
Dispersal
B.
Vicariance
18
18
20
21
22
23
1.6
Summary
24
VI II
2.
Using molecules to reconstruct evolutionary history
2.1
Why morphology is not enough
2.1.1 Contrast between molecularphylogenies and
traditional classification
2.1.2 Contrast between molecular andmorphological
phylogenies
25
2.2
Molecular phylogenies
2.2.1 Which gene for which question?
2.2.2 Evolutionary rates and molecular clocks
28
28
31
2.3
Ribosomal DNA
2.3.1 ITS
2.3.1.1
2.3.1.2
2.3.1.3
2.3.1.4
2.3.2 5.8S
2.3.3 26S (LSU)
2.3.3.1
2.3.3.2
2.3.3.3
A
B
C
D
2.3.3.4
2.3.3.5
32
32
33
33
34
35
36
36
36
36
37
37
37
37
38
39
A
B
ITS function
Taxonomic level
Secondary structure
Intra-individual polymorphism
26S function
Taxonomic level
Expansion segments
Description and definition
Cryptic simplicity
Compensatory slippage
Function
Secondary structure and weighting
Practical applications to phylogeny
reconstruction
Animals
Plants
i.
Deep level
ii.
Family and generic groups
26
27
39
39
39
40
41
2.4
Homology assessment in molecular data sets
2.4.1 Culling
2.4.2 Elision
2.4.3 Optimal alignment
2.4.4 Using the entire data set
2.4.5 Secondary structure
2.4.6 Treatment of gaps
42
45
45
46
47
48
48
2.5
Summary
50
IX
3.
Analysis of large data sets using parsimony
3.1
Addition of data
51
3.2
Adding taxa and tree confidence measures
53
3.3
Rapid searches using confidence measures
54
3.4
Using better programs and methods
55
3.5
Supertrees
56
3.6
Compartmentalization
56
3.7
Summary
57
4.
Begoniaceae
4.1
Size and distribution
58
4.2
Taxonomic history
4.2.1 Begoniaceae
4.2.2 Begonia
58
Taxonomic problems within Begonia
4.3.1 Homoplasy
4.3.2 Genus size
a.
Morphological splits
b.
Molecular splits
60
60
60
60
61
4.4
Why are there so many species of Begonia?
61
4.5
Summary
63
4.6
Aims of thesis
64
4.3
58
59
5.
Establishing the backbone - ITS and 265
5.1
Introduction - obtaining molecular-based cladograms for
Begoniaceae
65
5.2
Material and methods
5.2.1 Plant material
5.2.2 Molecular methods
A
DNA extraction
B.
Sequence amplification and purification
C.
Cloning reactions
D.
DNA sequencing
5.2.3 Alignment
A
268
B.
ITS
5.2.4 Analyses
A
Maximum parsimony (MP)
B.
Maximum likelihood (ML
C.
Minimum evolution (ME)
65
65
67
67
67
69
69
70
70
70
70
71
71
72
5.3
Results
5.3.1 The 26S data set
5.3.1.1
Data set
5.3.1.2
MP
5.3.1.3
ML
5.3.1.4
ME
5.3.2 The ITS data set
5.3.2.1
Data set
5.3.22
MP
5.3.2.3
ML
5.32.4
ME
5.3.3 The combined 26S / ITS data set
5.3.3.1
Data set
5.3.32
MP
5.3.3.3
ML
5.3.3.4
ME
5.3.4 General results
5.3.5 Molecular evolution in ITS and 26S data sets
72
72
72
73
75
75
77
77
77
79
79
81
81
81
83
83
85
86
5.4
268 analysis and taxon sampling
5.4.1 Introduction
5.4.2 Material and methods
5.4.3 Results
5.4.4 Discussion, taxon sampling
5.4.4.1
Characters
5.4.42
Indices
5.4.4.3
Skewedness
5.4.4.4
Permutation tail probabilities (PTP)
5.4.4.5
Bootstrap
XI
88
88
88
89
90
90
90
91
91
92
5.5
General discussionand conclusions
5.5.1 Taxonomy
5.5.2 Analysis method
93
93
93
5.6
Summary
97
6.
268 - The wider picture - adding GenBank taxa
6.1
Introduction
98
6.2
Material and methods
98
6.3
Results
99
6.4
Discussion
101
7.
Building the cladogram - ITS
Introduction
102
7.2
Material and methods
7.2.1 Plant material
7.2.2 Molecular methods
7.2.3 Sequence alignment
Automated alignments
7.2.3.1
7.2.32
Manual alignment
7.2.4 Phylogenetic analyses
Automated alignments
7.2.4.1
7.2.4.2
Elision alignment
7.2.4.3 Manual alignment
A
Unculled
B.
Culled
7.2.4.4
Tree comparisons
102
102
103
103
103
104
104
105
105
105
105
105
106
7.3
Results
7.3.1 Statistics
7.3.2 Trees
7.3.2.1
Topology
Tree distance measures
7.32.2
7.3.3 Compartmentalization
Methods
A
B.
Results
Compartment 1: Loasibegonia
7.3.3.1
Compartment 2: Tetraphila
7.3.3.2
107
107
108
121
123
123
123
125
126
127
XII
7.3.33
7.3.3.4
7.3.3.5
7.3.3.6
7.3.3.7
7.3.3.8
7.3.3.9
a.
b.
c.
d.
Compartment 3: Madagascar
Compartment 4: Coelocentrum
Compartment 5: Petermannia
Compartment 6: Platycentrum
Compartment 7: Begonia
Compartment 8: Pritzelia
The remaining taxa
Introduction
Material and methods
Results and discussion
The Jigsaw Tree
129
130
132
133
136
137
140
140
142
143
147
7.4
Gaps
149
7.5
General discussion and conclusions
152
7.6
Summary
158
8.
Secondary structure
8.1
Introduction
8.1.1 Length of ITS regions
8.1.2 Secondary structure
159
159
159
8.2
Material and methods
160
8.3
Results
161
8.4
Discussion
169
9.
trnC - trnD
9.1
Introduction
171
9.2
Material and methods
9.2.1 Taxa included in this study
9.2.2 Analyses
A
MP (Maximum parsimony)
B.
ML (Maximum likelihood)
C.
ME (Minimum evolution)
171
172
173
173
173
173
9.3
Results
9.3.1 trnC -trnD
174
174
xiii
9.3.2 ITS
A
Data
B.
Trees
9.3.3 Combined trnC - trnD and ITS analyses
A
Data
B.
Trees
9.3.4 General comments
9.3.5 Gaps
9.3.6 Molecular evolution
174
174
174
175
177
177
177
178
180
180
180
181
182
184
Discussion
186
Summary
187
A
B.
Data matrix
Trees
i.
MP
ii.
ML
iii.
ME
10. Morphology
10.1 Introduction
10.1.1 Previousmorphological studies
10.1.2 Vegetative characters
Perenniating organs
10.1.2.1
10.1.2.2
Stipules
Leaves
10.1.2.3
Leaf colour
A
Leaf venation
B.
Stomata
C.
10.1.2.4
Hairs
.3 Sexual characters
Sexual separation and inflorescence
10.1.3.1
architecture
10.1.3.2
Inflorescence size
Bracts
10.1.3.3
10.1.3.4
Bracteoles
Flowers
10.1.3.5
Tepal colour
A
Stigma and anther colour
B.
Tepals
C.
Scent
D.
E.
Size
Male flower
F.
i.
Androecium
ii.
Bud and tepal shape
Female flower
G.
i.
Styles
xiv
188
189
190
190
191
192
193
194
194
194
195
195
196
198
198
199
199
199
199
201
201
201
201
203
203
203
ii.
Ovary
iii.
Fruit
Material and methods
10.2.1 Plant material
10.2.2 Non-DNA character coding
10.2.3 Cladistic analyses
10.2.3.1
Data sets
10.2.3.3
Analyses
203
205
206
206
206
10.3
Results
10.3.1 Non-DNA data set
10.3.2 ITS data set
10.3.3 Combined ITS / non-DNA data set
10.3.4 Tree comparisons
10.3.5 Character performance
10.3.6 Character evolution - some case studies
A
Leaf characters
B.
Tepal characters
C.
Ovary characters
212
212
217
222
227
229
230
230
233
235
10.4
Micromorphology - congruence with other data sets
10.4.1 Introduction
10.4.2 The data sets
Anther endothecial cells
10.4.2.1
10.4.2.2
Stigmatic papillae
Seed
10.4.2.3
Pollen
10.4.2.4
10.4.3 Results
Anther endothecial cells
10.4.3.1
10.4.3.2
Stigmatic papillae
Seed
10.4.3.3
Pollen
10.4.3.4
The Map
10.4.3.5
10.4.4 Discussion
Anther endothecial cells
10.4.3.1
Seed
10.4.3.2
Pollen
10.4.3.3
237
237
238
238
238
238
239
240
240
240
240
242
242
244
244
245
245
211
211
211
10.5 Discussion
246
10.6 Summary
249
XV
11.
Cytology
11.1
Introduction
255
11.2
Material and methods
255
11.3
Results
257
11.4
Discussion
11.4.1 Africa
11.4.2 America
11.4.3 Asia
11.4.4 Summary of cytologicalpatterns
11.4.5 Hybridisation in Begonia
260
260
262
265
267
269
11.5
Summary
271
12.
Evolution, Biogeography and the Begoniaceae
12.2
Introduction
272
12.2
Geology through time
12.2.1 Cretaceous
12.2.2 Palaeogene
12.2.3 Neogene
12.2.4 Summary of main points
272
273
273
274
276
12.3
Geographic origins
12.3.1 Introduction
12.3.2 Daf/sca
^2.3.3 Hillebrandia
12.3.4 Segon/a - relationships from the cladograms
12.3.4.1
Continental relationships
12.3.4.2
African clades
12.3.4.3
American clades
12.3.4.4
Asian clades
277
277
280
281
285
285
291
296
303
12.4
Why is Begonia a large genus?
313
12.5
Overview - the evolution of Begonia
320
12.6
Taxonomic changes recommended
12.6.1 Genera
12.6.2 Madagascan species
12.6.3 African species
323
323
325
325
12.7
Summary
327
xvi
13.
References
328
14.
Appendices
359
14.1
A
B.
List of large genera - by family
List of large genera - by size
360
361
14.2
Families which contain large genera
362
14.3
List of fossil record for large genera
363
14.4
Comparison between ITS tree, Loasibegonia I Scutobegoniaj
and Sosef s (1994) tree
365
14.5
Herbarium specimens included in morphological
analysis
XVI I
370
List of Figures
Figure 1.1
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
1.2
1.3
1.4
1.5
1.6
1.7
1.8
1.9
1.10
2.1
4.1
5.1
5.2
5.3
5.4
5.5
5.6
5.7
5.8
Figure 5.9
Figure 5.10
Figure 5.11
Figure
Figure
Figure
Figure
Figure
5.12
5.13
5.14
5.15
5.16
Figure 6.1
Figure 7.1
Figure 7.2
Figure 7.3
Figure 7.4
Figure
Figure
Figure
Figure
Figure
Figure
Figure
7.5
7.6
7.7
7.8
7.9
7.10
7.11
The hollow curve distribution (number of species per genus for a
family)
Balanced unstemmy tree
Balanced stemmy tree
Pectinate unstemmy tree
Pectinate stemmy tree
How rooting can affect tree symmetry
Symmetry and tree balance
Outgroups and tree balance
Hypothetical phylogenetic tree
The Markov model of evolution
The rDNA cistron
The number of species per section for Begonia
Primer positions
MP strict consensus of 18 MPTs and phylogram, 26S data set
ML, 26S data set
ME, 26S data set
Strict consensus of three MPTs and phylogram, ITS data set
Single ML tree, ITS data set
Single ME tree, ITS data set
ITS and 26S combined, MP strict consensus of 22 MPTs and
phylogram
ML tree, combined data set
ME tree, combined data set
Strict consensus of MP, ML and ME trees for 26S, ITS and
combined data sets
ITS 1, 5.8S and ITS 2 changes per site for one MPT
26S change per site for one MPT
Base composition, 26S and ITS
Transitions/transversions, 26S and ITS
26S and ITS phylogeny for 36 Begoniaceae taxa, produced using
ML
Bootstrap consensus tree for 26S D1, D2, D3 and linking
regions
Phylogram from analysis of ITS elision matrix
Majority rule of strict consensus trees from the16 automated
alignments
Strict consensus of 10,000 MPTs, culled manual ITS alignment
Phylogram for the culled manual ITS alignment, one of 10,000
MPTs
Strict consensus of 100 MPTs, unculled manual alignment
Phylogram for unculled manual ITS alignment, one of 100 MPTs
Phylogram of single MPT for culled 'Loasibegonia' data set
Phylogram of single MPT for ‘Tetraphila’ matrix
First phylogram (of two MPTs) for Madagascan matrix
Second phylogram (of two MPTs) for Madagascan matrix
Single MPT for Coelocentrum matrix
xviii
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
7.12
7.13
7.14
7.15
7.16
7.17
7.18
7.19
7.20
Figure 7.21
Figure 7.22
Figure 7.23
Figure 7.24
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
8.1
8.2
8.3
8.4
8.5
8.6
8.7
8.8
Figure 8.9
Figure 8.10
Figure 8.11
Figure 8.12
Figure
Figure
Figure
Figure
9.1
9.2
9.3
9.4
Figure 9.5
Figure
Figure
Figure
Figure
9.6
9.7
9.8
9.9
Figure 9.10
Figure
Figure
Figure
Figure
Figure
10.1
10.2
10.3
10.4
10.5
strict consensus of four MPTs, Petermannia matrix
Phylogram for Petermannia matrix, one of four MPTs
Strict consensus of 10 MPTs for ‘Platycentrum’ matrix
Phylogram for ‘Platycentrum’ matrix, one of 10 MPTs
Single MPT for ‘Begonia’ matrix
Strict consensus of two MPTs for ‘Pritzelia’ matrix
Phylogram for ‘Pritzelia’ matrix, one of two MPTs
Chosing exemplar taxa
Strict consensus of 554 MPts, compartment-removed ITS data
set
Pruned strict consensus of 10,000 MPYs, culled ITS data set
The ‘Jigsaw’ tree: ITS phylogeny of Begoniaceae
ITS phylogeny (the Jigsaw tree) for African and American taxa,
with coded ITS gaps mapped on
Tree shape (phylograms) for manual (culled and unculled) and
elision data sets
Schematic summary diagram of ITS 2 secondary structure
Datisca glomerata ITS 2 secondary structure (free energy -102.8)
6. nossibea ITS 2 secondary structure (free energy -103.9)
B. gabonensis ITS 2 secondary structure (free energy -145.5)
B. socotrana ITS 2 secondary structure (free energy -175.3)
B. hemsleyana ITS 2 secondary structure (free energy -140.0)
B. aequata ITS 2 secondary structure (free energy -119.5)
B. masoniana ITS 2 secondary structure (3’ end cut short)
(free energy -130.1)
Symbegonia sp. 136 ITS 2 secondary structure (free energy
-131.8)
B. fissistyla ITS 2 secondary structure (free energy -120.3)
B. oxyphylla ITS 2 secondary structure (free energy -115.8)
Schematic diagram of stem C showing conserved secondary
structure
trnC - trnD, MP strict consensus of 186 MPTs and phylogram
trnC - trnD, ML and ME trees
ITS, strict consensus of 16 MPTs and phylogram
Combined trnC - trnD and ITS strict consensus of 4 MPTs and
phylogram
trnC - trnD indels mapped onto trnC - trnD and ITS strict
consensus trees
trnC - trnD: number of steps per position for one MPT
ITS: number of steps per position for one MPT
Base compositions of the two matrices
Proportion of transitions and transversions in the different
matrices
Sectional treatment and geographic distribution, trnC - trnD strict
consensus tree
Symmetric and asymmetric inflorescence structure
Bracts and bracteoles
Tepal symmetry planes in male flowers
Tepal arrangement in B. masoniana female flowers
Anther arrangement
xix
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
Figure
10.6 Placentation types
10.7 Majority rule cladogram from 1000 MPTs, non-DNA data set
10.8 Phylogram of one of 1000 MPTs, non-DNA
10.9 Strict consensus of 1000 MPTs, ITS data set
10.10 Phylogram, ITS data set, one of 1000 MPTs
10.11 Strict consensus of 1000 MPTs, combined non-DNA and ITS
10.12 Phylogram, one of 1000 MPTs, combined non-DNA and ITS
10.13 Agreement subtree tree, non-DNA and ITS analyses
10.14 Leaf characters, ACCTRAN optimisation
10.15 Male and female tepal number, ACCTRAN optimisation
10.16 Ovary characters, ACCTRAN optimisation
10.17 ITS phylogeny, with endothecial call types and seed types
mapped on
10.18 Begonia leaves (colour plate)
10.19 Gegon/a inflorescences (colour plate)
10.20 Begonia male flowers (colour plate)
10.21 Begonia female flowers (colour plate)
10.11 Begonia fruits (colour plate)
11.1 Chromosome counts across an ITS phylogeny
11.2 Clade 1 (Africa)
11.3 Clade 2 (Africa)
11.4 Clade 3 (Africa)
11.5 Clade 4 (southern Africa)
11.6 Clades 5 and 6 (America)
11.7 Clade 7 (America)
11.8 Clade 8 (America)
11.9 Clade 9 (America)
11.10 Clade 10 (Asia / Socotra)
11.11 Clade 11 (Asia)
11.12 Clade 12 (Asia)
12.1 ITS phylogeny, wtih geography marked on
12.2 Molecular clock - based estimates of lineage age
12.3 An rbcL phylogeny of Coriariaceae, Corynocarpaceae,
Tetramelaceae, Datiscaceae and Begoniacae
12.4 ITS-based geographic relationships of Begonia species
12.5 Geographic origins of Begonia lineages
a.
Cladograms
b.
Block diagrams
12.6 Begonia biogeography, hypothesis one
a.
Fitting lineages across a modern-day map
b.
Fitting dates onto the cladogram
12.7 Begonia biogeography, hypothesis two
a.
Fitting lineages across a modern-day map
b.
Fitting dates onto the cladogram
12.8 Asian and Socotran Begonia lineages
12.9 ITS based relationships of African Begonia taxa
12.10 Map of geographic distribution of species in Clade 1 and Clade
1 (Africa)
12.11 Map of geographic distribution of species in Clade 2 and Clade
2 (Africa)
XX
Figure 12.12 Map of geographic distribution of species in Clade 3 and Clade
3 (Africa)
Figure 12.13 Map of geographic distribution of species in Clade 4 and Clade
4 (Africa)
Figure 12.14 ITS based relationships of American Begonia taxa
Figure 12.15 Map of geographic distribution of species in Clade 5 and Clade
5 (America)
Figure 12.16 Map of geographic distribution of species in Clade 6 and Clade
6 (America)
Figure 12.17 Map of geographic distribution of species in Clade 7 and Clade
7 (America)
Figure 12.18 Map of geographic distribution of species in Clade 8 and Clade
8 (America)
Figure 12.19 Map of geographic distribution of species in Clade 9 and Clade
9 (America)
Figure 12.20 ITS based relationships of Asian Begonia taxa
Figure 12.21 Map of geographic distribution of species in Clade 10 and Clade
10 (Asia / Socotra)
Figure 12.22 Map of geographic distribution of species in Clade 11 and Clade
11 (Asia)
Figure 12.23 Map of geographic distribution of species in Clade 12 and Clade
12 (Asia)
Figure 12.24 Phylogram for Platycentrum clade compartment analysis
(copied from Figure 7.14)
Figure 12.25 T.S., two-locular fruit, section Platycentrum
Figure 12.26 The number of species per section for Begonia (from Figure 4.1)
Figure 12.27 Tree shape, from a phylogram produced by analysis of the
manually aligned, culled ITS data set (reproduced from Figure
7.24)
Figure 12.28 ITS phylogeny of Begoniaceae, with approximate species
numbers marked on
Figure 12.29 Summary diagram of species number per clade, for the 12
clades described previously
XXI
List of Tables
Table
Table
Table
Table
Table
Table
Table
Table
Table
5.1
5.2
5.3
5.4
5.5
5.6
6.1
7.1
7.2
Table 7.3
Table 7.4
Table 7.5
Table 7.6
Table 7.7
Table 8.1
Table 8.2
Table
Table
Table
Table
Table
Table
9.1
9.2
9.3
10.1
10.2
10.3
Table 10.4
Table 11.1
Table 12.1
Table 12.2
Taxa used in 26S and ITS analysis
Primer sequences for ITS and 26S
MP tree statistics
Taxa included in different analysis, changing taxon number
Tree statistics for different sized matrices, 26S
Tree statistics for different sized matrices, ITS
GenBank sequences for 26S analysis
Automated alignment parameters
Statistics for the various automated alignments and for the
elision, the manual culled, and the manual unculled alignments
The effect of alignment on characters
Topological features of the cladograms produced by different
alignments
Tree statistics for compartment analyses
Summary of comparisons between compartment analysis
topologies and 177-sequence analysis topologies for different
alignments
Unambiguous gaps in ITS manual alignment
The length of ITS 1, 5.8S and ITS 2 for representative taxa
Lengths of the first, second and third stems from secondary
structure reconstructions for ITS 2
Taxa included in trnC - trnD / ITS study
Summary: statistics for MP analyses, three different data sets
Unambiguous gaps in trnC - trnD alignment
Number of flowers in different sized inflorescences
Summary of non-DNA characters and their states
Data and tree statistics for the non-DNA, ITS and combined
analyses
Statistics for individual morpholgical characters, over a tree
produced by analysis of the combined ITS / non-DNA data set
Chromosome trends: summary of CD-ROM Table
Geological time scale
Molecular clock-based estimated of clade ages, ITS
XXI I
1.
WHY ARE SOME GENERA LARGE?
1.1
Taxonomists have long been intrigued by very large and very small
genera. The extreme variation which exists in genus size (which ranges from 1
to around 2000 species in vascular plants) prompts several questions. Is this
size distribution indicative of some natural phenomenon / phenomena, or is it
an artifact of the way we produce our classifications? Are we consistent in the
way we perceive morphological discontinuities (and do we view some
characters as more important than others in delimitation of taxonomic rank)?
Are very large (or very small) genera useful to the consumers of taxonomic
output? This thesis is an exploration into patterns of species diversity in large
genera, focusing on Begonia L. (Begoniaceae Bercht. & J.Presl.) and is
intended to address some of these issues.
It is first worth defining what a large genus is. Species number per genus is
one way of measuring this, although it is not necessarily a measure of
successfulness but presumably of morphological discontinuity, as the genus
may be made up of many rare species. A large genus is a genus with a lot of
species in it, but could equally be a genus with a lot of individuals in it. In this
thesis, a large genus is arbitrarily defined as one including 400 or more
species.
1.2
Genus size
Among the largest genera of vascular plants are Euphorbia L. (Euphorbiaceae
Juss., c. 2000 species). Piper L. (Piperaceae Giseke, c. 2000), Carex L.
(Cyperaceae Juss., c. 2000), Astragalus L. (Fabaceae Lindley, c. 1750),
Solanum L. (Solanaceae Juss., c. 1700), Senecio L. (Asteraceae Martinov., c.
1250), Psychotria L. (Rubiaceae Juss., 800-1500), Acacia Miller (Fabaceae
Lindley, c. 1200), Pleurothallis R.Br. (Orchidaceae Juss., c. 1120),
Bulbophyllum Thouars (Orchidaceae, c. 1000), Miconia Ruiz & Pavon
(Melastomataceae Juss., c. 1000) and Syzygium Gaertner (Myrtaceae Juss., c.
1000) (figures from Mabberly, 1997; for a more complete list of large genera
(taken from Minelli, 1993) see Appendix 14.1 a, b). Begonia is estimated at
900 species (Mabberly, 1997), although the more reliable estimate of at least
1400 (Doorenbos et al., 1998) certainly places the genus well within the ten
largest vascular plant genera.
Some families include more than one large genus, prompting the question, do
they have some biological attributes which make them more liable to include
large genera, or are they just large families? There are 71 genera with 400 or
more species and they are contained in 42 families (see Appendix 14.2).
Dividing the total number of species by the total number of genera for each
family to get a mean species number per genus allows a very rough
comparison with values given by Clayton (1974) of an average of 18 species
per genus for the angiosperms overall. Values for the large-genus-containing
families (given in Appendix 14.2) are frequently higher than Clayton’s figures,
with 38 of the 42 families having a mean genus size of over 20 species. 23 of
the 71 large genera are contained in only four families (Orchidaceae,
Asteraceae, Fabaceae and Euphorbiaceae), suggesting a non-random
distribution of large genera.
The number of large genera included in a family is positively correlated with the
total species number for the family. (Obviously, small families cannot have
many large genera - Aquifoliaceae A.Rich. has a total size of c. 420 species.
Aquifoliaceae could include a maximum of 1 large genus, while Asteraceae
could include a maximum of 56.)
1.3
The hollow curve
Several authors have explored the distribution of genus size within plant
families. Plotting the number of species in a genus against the number of
genera for a given family gives a characteristic ‘hollow curve’ distribution. The
right-skewed shape of this curve is due to an excess of monotypic taxa and a
dearth of larger taxa (Clayton, 1974) (see Figure 1.1).
^ The figures are not directly comparable, as Clayton took his values from Shaw ’s Dictionary of
the Flowering Plants and Ferns (1966), while mine come from Mabberly (1997).
2
Figure 1.1:
The hollow curve distribution (number of species per genus for a
family)
many
smaller
genera
Number of
species per
genus
few
larger
genera
Number of genera
Explanations for this taxonomic pattern focus on either:
1.
The behaviour of taxonomists (pragmatic decision making, folk history
and chaining)
2.
Natural phenomena
or a combination of these factors.
1.3.1 Behaviour of taxonomists
A.
Genus size and the importance to man:
Walters (1986) considers
the size distributions of plant genera and families to be taxonomic artifacts.
The average number of species per genus in the Poaceae Caruel is 15.5,
while in the Cyperaceae it is 44.5. These families are similarly widespread in
Europe and present similar problems in identification (with reduced complex
flowers). Walters (1986) suggests that the difference in treatment between
them reflects Linnaeus’ formalisation of an extensive ‘folk taxonomy’ resulting
from economic usage of grasses in Europe; this folk taxonomy is absent from
the economically less important sedges.
B.
Historical correlation:
According to Walters (1986), looking for some
natural law to explain the ‘hollow curve’ distribution overlooks the fact that many
large genera are old historically (as opposed to biologically). Genus sizes
follow the same pattern in any “reasonably large modern Angiosperm family”: a
few large genera and a lot of small genera (Walters, 1986, p. 535). The large
genera are “nearly always” in Species Piantarum (Linnaeus, 1753) (i.e.
historically older), while the smaller ones tend to be nineteenth century
creations (i.e. historically more recent) (Walters, 1986). Effectively his
argument was that subsequent taxonomists have been more likely to add to
existing Linnaean genera than to create new ones (this is described as
‘chaining’, which is people’s tendency to add to taxa which already exist in
preference to creating new ones). However, Cronk (1989) points out a flaw in
Walters’ (1986) argument: that the genera Linnaeus knew would most often be
widespread therefore often large; monotypic genera would thus be expected to
be found more recently.
C.
Taxonomic pragmatism: Taxonomists deliberately try to keep large taxa
small - probably as they try to keep a classification usable, while the creation of
small taxa is due to taxonomists’ “obvious predilection for the excision of
solitary outliers” (Clayton, 1974, p. 278). Clayton believes the sizes of genera
to have been influenced by convenience, in favour of simple circumscription
and easy identification (Clayton, 1983). Cronk (1989) also finds that
“[o]versized taxa and monotypic taxa make plant taxonomy irredeemably
inefficient” (Cronk, 1989, p. 368). However, Cronk (1990) describes a general
trend in classifications of the Fabaceae to, in practice, retain a similar median
genus size over time (from Linnaeus in 1753 through to Hutchinson, 1964)
despite range changes in genus size - large genera are growing bigger
(through chaining) but very small genera are also being created.
Taxonomists may also consider the ‘principle of ease of identification’
(Backlund & Bremer, 1998) - big genera like Begonia and Rhododendron L.
(Ericaceae Juss.) are currently very easy to identify to genus level; some of that
utility may be lost by splitting.
D.
Conservation and politics:
A recent Nature paper (Myers et al.,
2000) argued for targeted areas of the world for ‘silver bullet’ conservation
money, based partly on consideration of the numbers of endemic genera in
each region, with priority given to regions richest in such taxa. Counts of
endemic genera per region would be inflated by splitting large genera. If this
approach is adopted then there may be the temptation for taxonomists to bias
taxonomies towards the creation of endemic genera when they feel that a
geographical region is in need of greater conservation recognition.
1.3.2 Natural phenomena:
It is difficult to disagree with Minelli: “Raikow
(1986) feels that only the vagaries of taxonomy explain the higher number of
species belonging to the passerine birds, compared with the non-passerine
birds
I cannot agree with Raikow’s views, as it is difficult to disprove the fact
that there are more types of cats than there are types of elephants and more
types of cone shells than there are types of nautilus. Despite the vagaries of
systematics, there are, in a taxonomic sense, many dense clusters of biotic
diversity” (Minelli, 1993, p. 185).
A.
Age and Area:
Willis (1922), who first described the hollow curve
phenomenon, argued that it had a natural basis. He explained it by his ‘Age
and Area’ hypothesis, namely, that younger taxa are less species rich and less
widely distributed, while older taxa have had more time to diversify into species.
B.
Relict Hypothesis: Cronk’s Relict Hypothesis (1989) also provides a
natural explanation for the observed pattern. Cronk (1989) explains the
monotypic endemic genera of St Helena as ancient relicts. They are
taxonomically and geographically isolated and he feels that such a pattern is
better explained by widespread extinction than by some “special evolutionary
syndrome” (Cronk, 1989, p. 359). He describes three factors to explain the
phylogenetic patterns of species richness over time:
1. A bloom period, when groups diversify in species.
2. Evolutionary stasis.
3. Extinction, at more or less constant rate (approximating exponential decay).
The world’s flora will always consist of groups at different stages in this
progression; in general large genera are young and monotypic genera old; for
example, on average the Magnoliidae have far lower numbers of species in
their families than the dicotyledons as a whole, while the Asteridae have higher
species’ numbers per family (Cronk, 1989). Recent angiosperm phylogenies
(e.g. Soltis, Soltis & Chase, 1999) certainly put the magnoliids as a more basal
clade than the asterids. Within the Fabaceae, subfamily Caesalpinoideae has
a low median genus size (Cronk, 1990), so, following this argument, is an
ancient relict group. However, interpreting legume phylogeny in this manner is
extremely problematic, as phylogenetic study (Doyle et al., 1997) has revealed
the Caesalpinoideae to be paraphyletic and so not suitable for consideration
as a single evolutionary unit.
C.
Partitioning of Biodiversity:
The relict hypothesis affects the
partitioning of taxonomic diversity for two reasons (Cronk, 1989):
1. Groups in ‘bloom’ phase may be recognised as a single taxon because
diversity produces intermediates and discontinuities are not evident.
2. Groups depleted by extinction may have “large areas of empty phenetic
space” (Cronk, 1989, p. 368) so taxonomic boundaries are clear.
Therefore new groups will be poorly divided and old groups, well divided:
“Spéciation tends to fill phenetic space, extinction to empty it. Although
spéciation produces clades, extinction produces taxa ” (Cronk, 1989, p. 368).
D.
Summary:
Despite observations which attribute to psychological or
historical factors the numbers of species in genera, and the observation
(Cronk, 1990) that taxonomists are usually happier to describe new species
than new genera, the role of evolutionary process in the generation of patterns
of biological diversity cannot be ruled out; one or a few subtaxa often account
for much of the diversity in higher taxa - most mammals are rodents, most
birds are passerines and most insects are beetles (Heard, 1992).
1.3.3 Combination:
Clayton (1974) thought hollow curve frequency
distributions to be due to a combination of natural and psychological
phenomena. Cronk (1989) also believes that both factors contribute; he found
that he could explain about half the ‘hollowness’ of hollow curves by
psychological and historical factors, while the other half is due to biological
reality.
1.4
Phylogenetic inputs
1.4.1 The need for monophyly: In the light of a phylogeny, the question ‘What
is a genus?’ is one of rank, not of monophyly (Wojciechowski, Sanderson &
Hu, 1999). If a reliable phylogeny is not available, influences of taxonomic
grouping can be misleading as recent molecular data have shown that some
traditional genera are paraphyletic, or actually consist of phylogenetically
disparate taxa. For instance,
Eupatorium L. (Asteraceae) was once
considered a very large genus with about 1200 species (Mabberly, 1998). A
recent ITS phylogeny (Schmidt & Schilling, 2000) found that many of the
species included in Eupatorium s.I. are scattered across several clades; the
characters used to define the genus were sympleisiomorphies which occur
throughout the tribe Eupatoriinae. Restricting Eupatorium to the 42 species
which form a monophyletic assemblage allied to the type species allowed
generic synapomorphies to be identified.
Guyer and Slowinski (1993) express concern that studies which count the
distribution of units within larger taxa (e.g. species within genera) may indicate
more about how taxonomists delimit these taxa (as discussed above) than
about evolutionary pattern. Phylogenetic trees, which have now more or less
replaced the use of taxonomic lists of genus or family size to extrapolate
macroevolution, represent histories of the diversification of clades (Mooers &
Heard, 1997) (i.e. real events) and negate the potential problems caused by
arbitrary taxonomic decision-making.
1.4.2 The shape of phylogenetic trees:
Before discussing inferences
from phylogenetic trees it is worth discussing terminology and some
theoretical issues regarding their interpretation. Any phylogeny can be
separated into 3 distinct parts (Lapointe & Cucumel, 1997);
1. topology (tree shape)
2. branch length (difference in evolutionary change between clades)
3. label position (the phylogenetic relationships).
A.
Terminology:
Terminology can be confusing; the topology of trees
which are not symmetric (or ‘balanced’) is varyingly referred to as comb-like
(which may also be used to describe unresolved trees), an Hennigian comb,
7
unbalanced or pectinate. In a pectinate tree only one of the two descendant
species continue to speciate after a splitting event; in a balanced tree, all extant
lineages participate equally in cladogenesis (Kirkpatrick & Slatkin, 1993).
‘Stemminess’ is a measure of the relative amount of change, such as branch
length differences within and between clades. A ‘stemmy’ tree is one where
there is more opportunity for change before spéciation events than after
(Salisbury, 1999) (see Figures 1.2 - 1.5).
-ig. 1.2: Balanced, unstemmy tree
Fig. 1.3: Balanced, stemmy tree
Fig. 1.4: Pectinate, unstemmy tree
Fig. 1.5: Pectinate, stemmy tree
The relative symmetry (or lack of) is a function of a rooted tree; a fully pectinate
rooted tree is produced from a symmetric network. The same network, with
different rooting, can produce a balanced tree (see Figure 1.6).
8
Figurel .6:
How rooting can affect tree symmetry
Rooted
at B
Rooted
at A
It is also vital to consider sampling strategy in any consideration of tree shape;
frequently in phylogenetic analyses taxa serve as exemplars for other similar
species. Often the tree shape as reconstructed is not the primary concern. For
example a tree may appear perfectly balanced, but if, in biological reality, there
is (for example) one taxon in clade A, one in clade B, 1 in clade 0 and 10 in
clade D, the real situation is unbalanced (see Figure 1.7):
Figure 1.7:
OG
Symmetry and Tree Balance
D
Tree reconstructed through sampling
OG
Real clade sizes
Therefore a balanced tree shape can represent an ‘unbalanced’ (pectinate)
reality, where one lineage (that leading to D) is far more species rich than the
others (those leading to A, B and to C). The outgroup should not be
considered in questions of balance because of differences in sampling
strategy. Even where a small outgroup is used, and 100% of the taxa within it
are sampled, it is important to ensure that it is the monophyletic closest sister
to the ingroup. For example. Figure 1.8 shows a situation where sampling
could lead to the supposition that the outgroup is considerably less speciesrich than the ingroup, but when the entire monophyletic assemblage is
considered it is evident that the ingroup is of comparable size to the outgroup
and its sister group:
Figure 1.8:
Outgroup
Outgroups and tree balance
Ingroup
'Sister
Tree reconstructed through sampling
'O utgroup
Ingroup
Real clade sizes
This could be equivalent to rooting an analysis of Violaceae Batsch. (c. 800
species) on the smaller family, Turneraceae Kunth ex DC (c. 100 species);
phylogenetic analysis (Savolainen et al., 2000; combined afpB-rbcL) shows
that Passifloraceae Juss. ex DC is sister to Turneraceae; it contains
approximately 575 species and so balances the larger Violaceae.
10
B.
Evolutionary Scenarios:
i.
Balance:
Balance correlates with relative diversification or extinction
rates in different parts of the cladogram. In a balanced tree, either the rates are
the same in all clades, or one clade may have a higher spéciation rate AND a
higher extinction rate (or vice versa) than the others. In a pectinate tree, rates of
spéciation and extinction can vary independently in different clades.
The balanced topology represented by the tree in Figure 1.2 is often regarded
as the norm, and model systems have aimed to reconstruct this topology (e.g.
Hillis et al., 1992). For any given scenario, however, it seems unlikely that every
lineage should speciate as often as every other (producing a fully balanced
tree); the reverse situation, where only one of each lineage pair speciates
(producing a fully pectinate tree, as in Figures 1.4 and 1.5) is also improbable.
Certainly some sort of favourable mutation (like a ‘key innovation’) along one
branch of a tree could cause it to speciate more than other branches, thus
causing some asymmetry. Kirkpatrick and Slatkin (1993) suggest one
scenario which could lead to a symmetric tree: where there is “synchronous
spéciation caused by vicariance events that affect most of all of the species in a
clade" (Kirkpatrick & Slatkin, 1993, p. 1179). However, published phylogenies
are seldom either fully balanced or fully pectinate.
ii.
Stemminess:
Where trees contain more and less stemmy clades,
the more stemmy clades have built up a series of unique characters, either
through remaining undiversified for a long time (perhaps through a period of
climatic or geological stability), or through the extinction of more basal
members (the Relict Hypothesis).
11
iii.
Hypothetical example:
Figure 1.9:
Hypothetical phylogenetic tree
Clade A
Clade B
i~
~i r
- — I
Clade C
r
Clade D
...
E3
?
KEY:
Balanced clade
Pectinate clade
Stemmy clade
Y //À Unstemmy clade
JL,
\
With a phylogenetic tree, we can make some inferences about the relative
ages of clades. In Figure 1.9, clade A is old compared to clade D, and can be
described as basal relative to it. Sister groups are always the same age clade A is the same age as clade (B, C, D), clade B is the same age as (C, D)
and clade C is the same age as clade D.
One could hypothesis that the smaller number of taxa in clade C (5) than in the
sister group D (15) is due to some form of key innovation (e.g. the angiosperm
flower) in the ancestor of clade D. A beneficial morphological innovation (such
as the angiosperm flower) is liable to produce an unbalanced tree where the
clade which possesses the innovation has a greater rate of spéciation (or
lower rate of extinction) than the clade which is without it.
Phylogenetic trees which contain long, undivided branches interspersed with
short branches (e.g. clade C) are notoriously difficult to reconstruct. Such
12
topologies exist when rates of evolution vary greatly among lineages, or where
the timing of cladogenesis varies (Hillis & Bull, 1993), or where there is a lot of
extinction in some lineages.
C.
Caveats:
There are several confounding variables which contribute
to tree shape but tell us nothing about evolutionary process. Topology is due to
a combination of three factors - noise (stochastic effects), bias (analytical
method, taxon choice and definition) and signal (macroevolutionary process)
(Mooes & Heard, 1997). We need to be able to isolate the effects of signal
from those of noise and bias.
Guyer and Slowinski (1993) point out that, because phylogenetic trees must
take some shape, species-rich clades can appear which require no adaptive
explanation, and so a null model must be invoked to tell us whether our
observed tree shape deviates from what is expected. The simplest null model
of evolution is the Markovian model, which involves equal rates and random
spéciation (Heard, 1992). The growing branches of a phylogeny diverge at
random. One species can progress to four terminal branches by six routes
(Figure 1.10).
Figure 1.10: The Markovian model of evolution
or
or
or
or
13
Four of these routes produce a pectinate tree; two produce a balanced
cladogram. Thus the null probability of a pectinate tree is 4/6 (0.67), and of a
balanced tree, is 2/6 (0.33) (Guyer & Slowinski, 1993). The Markov model is
only one of several which can be used; another is the Proportional-todistinguishable-arrangements model, wherein each possible tree is assumed
to be equally likely. Given four terminals (and allowing all combinations of taxa
across the terminals), there are 15 possible arrangements. 12 of these are
pectinate, which makes the null probability of a pectinate tree 12/15 (0.80)
(Guyer & Slowinski, 1993).
Studies which have sought to recover trees from simulated data have revealed
that phylogenetic methods can bias the shape of the recovered trees towards
asymmetry, particularly in cases where the (simulated) evolutionary rates are
high (Huelsenbeck & Kirkpatrick, 1996). Heard (1996) also found that, under
most simulations and using different models of spéciation rate variation, the
amount of imbalance increases as spéciation rate increases. However,
various studies (reviewed in Mooes & Heard, 1997) indicate that although
noise and bias do contribute to tree shape, macroevolution also plays a part
and can be invoked in the explanation. Thus the prevalence of pectinate trees
in the literature (Pearson, 1999) is not an entirely artificial phenomenon but
reflects some natural pattern. Pearson (1999) explains it as “the result of the
relative success of apomorphic taxa over their more pleisiomorphic sisters,
where success is measured in terms of resistance to extinction or propensity
for spéciation” (Pearson, 1999, p. 405).
D.
Summary:
It is important to remember that sister clades the same
size are no more likely than sister clades of very different sizes (in fact, under
the two models discussed here, they are far less likely); a null model must be
invoked in order to distinguish any significance in observed differences (Mooes
& Heard, 1997). The simplest model is the Markovian model of equal rate
random spéciation (Heard, 1992); departure from this can be tested by
evaluating whether each internal node in a tree is balanced or unbalanced
(Bond & Open, 1998).
14
1.4.3 Are big genera real?:
One question which should be answerable
given the relevant phylogenies is, ‘Are big genera real?' If similar cladogram
shapes and sequence divergence rates could be found for groups with very
different hierarchical positions, we could conclude them to be a case of
inconsistency in the application of taxonomic rank.
However, there are several variables which complicate such comparisons.
One is that sequence divergence rates are known to differ in different groups.
For example, in the monocots, rbcL is fastest in grasses and slowest in palms
(Gaut, 1998). Another is that decisions about plant taxonomy are (or have
traditionally been) made on the basis of plant morphological, not of molecular,
distinction, and morphological and molecular evolution are uncoupled. Indeed,
Bateman (1999) suggests that both track different facets of evolution, with “the
vast majority of morphological character-state transitions occur[ing] during
spéciation events and the vast majority of molecular character-state transitions
occur[ing] between them” (Bateman, 1999, p. 446).
Ideally, we would have a same-gene phylogeny for two related groups with
similar life history characteristics, together with comparable morphological
phylogenies to guard against differential rates of morphological evolution due,
for example, to key innovations. This (perhaps rather unlikely) combination of
data sets would allow comparison of the taxonomic treatment of two groups;
for example, one could throw some light on whether the smaller average
genus size of Poaceae (668 genera, 9500 species) over Cyperaceae (98
genera, 4350 species) is real or is an artifact of folk taxonomy, as has been
suggested previously (figures from Mabberly, 1998).
1.4.4 Are big genera old or young?:
The question of whether large genera
are ancient (as expected from the Age and Area hypothesis), or the results of
bloom phase groups (as expected by the Relict hypothesis) should be testable
by two methods: one, by the physical evidence of when taxa appear in the fossil
record, and the other, by evidence from phylogenetic trees.
15
A.
Fossil Record:
The Plant Fossil Record (http://ibs.uel.ac.uk/palaeo/
pfr2/pfr.htm) only lists fossil records for 23 of the 71 large vascular plant genera
listed in the Appendix (14.3). 9 genera have records which predate the Eocene
{Acacia, Palaeocene; Asplénium L., Cretaceous; Diospyros L., Cretaceous;
Eucalyptus L'Herit., Cretaceous; Ficus L., Palaeocene; Ilex L., Cretaceous;
Litsea Lam., Cretaceous; Quercus L., Palaeocene, Selaginella Pal.,
Cretaceous). That no records were found for Huperzia Bernh. does not,
however, indicate a lack of fossils; a thorough search would need to include
any relevant form genera. There are two problems with interpreting this fossil
evidence as evidence of the age of genera.
Firstly, it is noteworthy that all seven of the angiosperm genera listed above are
predominantly trees. This is more likely to reflect a bias in the fossil record
(such as: larger plants, producing huge quantities of pollen; woody tissue
preserving better than, for example, succulent tissue) than any natural reality.
Secondly, evidence about the age of a lineage is not the same as evidence
about the age of the species which make up the genus today. A lineage may
be very old, yet be made up entirely of young species. The fern Asplénium,
despite having a fossil record, does not belong to a very old lineage compared
to other ferns (M. Gibby, pens, comm., 2000; R.M. Bateman, pers. comm.,
2000). Selaginella has a fossil record which dates back to the lower
Carboniferous, but although the genus is old its component species are young
(R.M. Bateman, pens, comm., 2000). The conifer genus Araucaria Juss.
(Araucariaceae Henkel & Hochst) is old; there are good fossil records for the
Jurassic. However, all 13 species on New Caledonian have near-identical
rbcL sequences (pairwise differences between 0 and 0.5%, with 10 of the
species having identical sequences) (Setoguchi et al., 1998), suggesting that
they may be the results of comparatively recent spéciation events. Setoguchi et
al. (1998) suggest that rapid differentiation of Araucaria occurred after the
Eocene, when a large part of New Caledonia, with predominately ultramafic
soils, was formed. Therefore even in what are ancient lineages {Selaginella
and Araucaria ), there is evidence that the extant species are comparatively
recent.
What is required to show the existence of ancient large genera is a large
16
genus with a fossil record which shows high taxon diversity over a relatively
long time period.
B.
Clade position:
As more genus-level phylogenies are being
produced, the relative ages of larger genera can be estimated from their
positions on the phylogeny.
Begonia has a derived position (relative to the far smaller families Datiscaceae
Bercht. & J.Presl., Corynocarpaceae Engl, and Coriariaceae DC) in the rbcL
phylogeny of Wagstaff and Dawson (2000). In the combined afpB - rbcL trees
of Savolainen et al. (2000), none of the larger genera included in the analyses
take obviously basal positions. Also, in the 589 taxon rbcL phylogeny
(Savolainen et al., 2000) many large genera including Salix L., Passifiora L.,
Euphorbia, Viola L., Ficus and Rhododendron all appear in derived positions.
Likewise, Astragalus does not take a basal branch within an ITS phylogeny of
temperate herbaceous legumes (Sanderson & Wojciechowski, 1996).
Although broad generalisations are unlikely to apply to all large genera, the
evidence from the position of these taxa in wider phylogenies suggests that
many large genera are not very old.
If the diversity in a large genus is very young, one would expect the extant taxa
to show little sequence divergence, while if the diversity is old, there would be
high levels of divergence between extant taxa. Azuma et al. (2000) used rbcL to
examine relationships between Salix species. Their phylogeny produced a
polytomy with zero-length branches for 9 of the 19 Salix species they included;
9 other species were also on zero length branches. This result suggests that it
is more likely that the species in this lineage are comparatively recent, and as
such, disproves Willis’ Age and Area hypothesis (Willis, 1922), that older taxa
tend to be more speciose.
17
1.5
Biological factors
Before moving on, it is worth considering the biology which gives rise to the
shapes of trees. The evolutionary patterns we reconstruct in our phylogenies
are essentially the result of two processes, spéciation (diversification) and
extinction. Naturally large genera may be large because they have an aboveaverage rate of spéciation, or a below-average rate of extinction (or a
combination of both). The most vital tool to test hypotheses about these
patterns is phylogeny.
1.5.1 Diversification:
The success of a large clade is often attributed to
one or more ‘key innovations’ unique to that lineage (Bond & Opell, 1998). For
example, changes in the jaw musculature of cichlid fish have led to their highly
speciose lineage (Nee & Harvey, 1994). Dodd, Silvertown and Chase (1999)
argue that if such ‘key innovations’ have opened up new adaptive zones and
led to increased proliferation of species, it should be possible to identify certain
clades which are more species rich than others and wherein this richness
correlates with the presence of “traits that influence spéciation and extinction”
(Dodd, Silvertown & Chase, 1999, p. 732). A key innovation is not, however, a
prerequisite to an adaptive radiation; Nee and Harvey (1994) point out that
there was not necessarily anything special about the first finch to reach the
Galapagos islands.
Sanderson and Wojciechowski (1996) used ITS to look at diversification rates
in Astragalus, assessing whether increases in diversification rate within a
wider group of Fabaceae coincided with the origin of Astragalus and if so,
whether diversification could be tied in to identifiable ‘key innovations’.
Astragalus has several features which have been considered to promote
diversification in angiosperms, namely geographic population structure
consisting of local isolates with restricted gene flow; herbaceousness
(correlating with reduced generation time); chromosomal variability; a tendency
to parallelism and reversal associated with ecological specialisation; and
lastly, morphological novelties (Sanderson & Wojciechowski, 1996).
However,
Sanderson and Wojciechowski (1996) found no significant difference in
diversity between Astragalus and its sister groups; they did however find a
significant increase in diversification in the branch which leads to this
18
Astragalean clade (Astragalus and its sister groups, which together comprise
about 3000 to 3500 species of generally xerophytic, generally herbaceous
perennials; often with high degrees of endemism ). Thus there may well be no
key innovations to be found for Astragalus alone; given the tree shape it seems
more likely that the key innovations would belong to the Astragalean clade in its
entirety, although no obvious morphological novelties coincide with the origin of
the Astragalean clade or its increase in species diversity. In this clade, “similar
morphological adaptations to extreme environmental conditions have evolved
countless times in parallel ...[therefore]... species represent endless variation
on an essentially constant ground plan” (Sanderson & Wojciechowski, 1996, p.
1499).
Using a molecular clock for ITS, Wojciechowski, Sanderson and Hu (1999)
estimated an age of 11 Myr (t) for Astragalus (c. 2500 species (N)), giving an
average lineage diversification rate of 0.71 spp/Myr (estimated as In N/t). They
argue that this rapid rate of lineage diversification (compared to an estimated
median value of 0.12 spp/Myr for continental plant families - Erikkson &
Bremer, 1992), combined with conventional (or low) rates of morphological
evolution, is what has given rise to this large genus.
Dodd, Silvertown and Chase (1999) were also interested in key innovations
and diversification. They found that species richness in the angiosperms
correlates with evolutionary changes in pollination and in growth form, although
not consistently with changes in dispersal mode. (The loss (not the gain) of
biotic pollination is almost ubiquitous, leading to the suggestion that, as a
significant number of these losses of biotic pollinators has been accompanied
by a subsequent fall in diversification, this could be used as a positive test for
the theory that it was the early evolution of biotic pollination which was
responsible for the original diversification of the angiosperms.)
However, diversification may not be due to any intrinsic biological property of
species. In geologically active areas, for example, higher spéciation rates may
be an incidental side effect of biogeography (habitat fragmentation leading to
vicariant spéciation) (Kirkpatrick & Slatkin, 1993). Many clades in plant
phylogenies have geographical correlations; scenarios which involve
19
increased spéciation or increased extinction in some areas (therefore in some
clades), for example due to climatic change and / or differences in sea level,
are not difficult to imagine.
1.5.2 Extinction:
Species can either die gradually, as the population
dwindles and fails to respond to selective pressures, or suddenly, with the
extinction of all individuals due to an environmental crisis which is beyond prior
experience (Niklas, 1997). Because mass extinctions allow for only 4% of all
extinctions in the fossil record, the geologically sudden loss of formerly
successful species does not seem to be the most frequent mode of extinction.
Although well over 90% of all the species which ever lived are extinct, the
morphological and taxonomic diversity present today represents a surplus of
species birth and survival over death; the taxonomic composition of the Earth’s
flora has changed dramatically in 450 million years (Niklas, 1997). (The
obvious taxonomic bias in the groups suffering extinction should deflate the
otherwise depressing sampling problems for phylogeny reconstruction!)
Extinction is a very difficult hypothesis to prove from a cladogram alone; many
factors can lead to taxa appearing isolated on long branches - Pfosser and
Speta (1999) found such a pattern in Hyacinthaceae Batsch ex Borckh. (a high
number of nucleotide changes before spéciation occurred within the
subfamilies, or ‘stemminess’), which they explain as due to either a) a higher
rate of substitutions during this initial radiation, b) sampling bias because of
extinction, or c) primary radiation occurring very slowly (analogous to the
Punctuated Equilibrium hypothesis of Eldredge and Gould (1972) and the
Turnover-pulse hypothesis of Vrba (1985) which states that “[ejvolution is
normally conservative
[t]hus most lineage turnover in the history of life has
occurred in pulses....in predictable synchrony with changes in the physical
environment” (p. 232)). When there is fossil evidence it becomes easier to
choose between such alternatives.
The fossil record for the genus Ilex L. (Aquifoliaceae) goes back 90 million
years and the genus appears to have been cosmopolitan long before the end
of the Cretaceous (Cuenoud et al., 2000). When comparing mean rates of
nucleotide substitution for rbcL for Ilex with rbcL substitution rates given by
20
other authors for other taxa, the rates for Ilex are low, and a divergence time for
the outgroups (Helwingla Willd. and Phyllonoma Willd.) is estimated as at least
198 Mya. Cuenoud et al. (2000) felt this age to be excessive. They used the
relative test of the rate of nucleotide substitution (Wu & Li, 1985) to test whether
a) the rate of substitution in Ilex is low compared to other lineages or b) the
extant species only represent part of the 90 My old lineage, i.e. whether
divergence rates indicate that the common ancestor of all the extant species of
Ilex is 90 million years old, or whether the common ancestor of the extant
species is more recent. Because the Aquifoliaceae do not appear to have
diverged more slowly than their near relatives Helwingla and Phyllonoma,
Cuenoud et al. (2000) suggest instead that the basal branches of the lineage
are extinct (although equally there could have been little or no spéciation in the
early lineage). Evidence from the fossil record suggests that much
diversification in Ilex occurred in the Eocene; this may be the time of ancestry
for all extant species and so a complete study of the Ilex lineage would have to
include fossil evidence (Cuenoud et al., 2000) as there is no other way around
the sampling bias (due to extinction) among extant taxa.
1.5.3 Distribution: Diversification and extinction deal with the distribution of
species richness through time. Phylogeny can also be used to uncover
patterns of taxonomic richness in space^. Large genera are often widespread.
These patterns of taxon distribution are attributable to dispersal (“the
movement of an organism from one area to another independent of other
organisms and of earth history, which changes the natural distribution of the
organism”; Humphries & Parenti, 1999, p. 172) and vicariance events (the
splitting of a taxon or biota into two or more geographical subdivisions by the
formation of a natural barrier such as mountain building, glaciation, stream
capture”, Humphries & Parenti, 1999, p. 174) and may be complicated by
extinction. Both dispersal and vicariance may be followed by radiation.
^ There is a danger in using a non-phylogenetic approach to such studies - monophyly is a
necessary criterion. For example, phylogenetic analysis of Hyacinthaceae revealed that the
American genus Cam assia Lindley. belongs in its own unrelated family, Camassiaceae
(Pfosser & Speta, 1999). Biogeographers no longer have an unusual disjunction between
the north American endemic Cam assia, and the monotypic Chilean Oziroe Rafin. to explain.
In Eupatorium, redefining the genus according to phylogeny also removes a geographical
disjunction from within the genus (Schmidt & Schilling, 2000).
21
Certainly the vicariance hypothesis is more applicable to older lineages, as it is
most cited in instances of continental drift. Phylogeny can help chose between
these explanations.
A.
Dispersal:
The phylogeny of Astragalus produced by Wojciechowski,
Sanderson and Hu (1999) allowed them to reject a previous hypothesis of
vicariance, that two disjunct groups of Astragalus, one New World and one
Eurasian, had been separate since the Tertiary and undergone independent,
parallel evolution. The Old World Astragalus are not monophyletic; New World
taxa nest clearly within them. The genus appears to contain more recent
(Pleistocene to late Pliocene) immigrants to North America via a Beringian land
bridge.
In the phylogeny of Aeonium Webb & Berth. (Crassulaceae J.St-Hil.) the
distribution pattern is explained entirely by dispersal rather than vicariance
(Jorgensen & Frydenberg, 1999). This genus of succulent, rosulate species is
considered a prime example of adaptive radiation in an island plant group.
Most taxa from the same islands did not form monophyletic groups. This has
led the authors to believe that colonisation of similar ecological zones on
different islands followed by divergence has been important in the spéciation of
these plants.
Corlaria L. (Coriariaceae DC) has a strikingly disjunct geographical
distribution; it occurs in the Mediterranean, continental and insular eastern
Asia, from Papua New Guinea to New Zealand, and from northern Mexico to
southern Chile (Yokoyama et al., 2000) . There have been many suggestions
as to the cause, including: migration north from the southern hemisphere via
the Pacific islands (dispersal); habitat disturbance by Tertiary glaciers (within
hemispheres) and vicariance between hemispheres caused by continental
drift; and rafting north from Gondwanaland on the Indian plate (vicariance).
Yokoyama et al. (2000) produced a phylogeny to test these hypotheses. They
were able to rule out northern expansion via the Pacific Islands, and instead
postulate an Eurasian or North American origin for the genus. They also found
it unlikely that Corlaria migrated from South to Central America. Fossil
evidence suggests that the genus was more widely distributed in the past, at
22
least in Eurasia. They estimated the divergence time for the main clades to be
c. 60 My ago (early Tertiary), when Eurasia and North America were closer and
the Arctic region was warm enough to support temperate species. The
common ancestor for these clades could have expanded its range through this
region. Thus the present disjunct range may well have been caused by the
climatic changes associated with glaciation and drying out during the
Cenozoic. One lineage may have migrated into North America after the land
bridge from South America formed, while another dispersed to the Pacific
Islands and radiated in Papua New Guinea. Central America and the Pacific
Islands were not connected in the Cenozoic, leading Yokoyama et al. (2000) to
postulate long distance dispersal.
B.
Vicariance: Pfosser and Speta (1999) suggest a southern Gondwanic
origin for the Hyacinthaceae, because South African, South American and
Madagascan species occupy the basal branches in their phylogeny. Direct
migration was possible between these landmasses and India until the midCretaceous (c. 100 Mya). The distribution of species within one clade (Africa
south of the Sahara and the Indian subcontinent) suggests that the initial
diversification within the family occurred while India was still connected to
southern Africa. Because another clade has members in the Mediterranean
and in Eurasia but not in North America, they suggest that this clade diversified
after North America separated from Eurasia, which may explain why no
Hyacinthaceae are found in North America, despite its climate being suitable
for the family (Pfosser & Speta, 1999).
However, the phylogeny of extant species cannot always provide
biogeographical answers. When Cuenoud et al. (2000) considered the
geographic distribution of Ilex they found that they could not distinguish
between Asia or South America as its area of origin. North America has been
colonised from East Asia, South America or both areas. Africa and Europe
have been colonised relatively recently from East Asia. As they have dated the
ancestry of the extant species as Tertiary, they point out that we cannot expect
to find evidence for a Gondwanan origin from molecular data alone in this
genus.
23
1.6
Summary
The recognition of the phenomenon of the ‘hollow curve’ predates widespread
used of phylogeny reconstruction, and many of the hypotheses produced to
explain it have become, if not redundant, at least resolvable in the light of
phylogenetic treatment. That the answers to questions about the application of
taxonomic rank are not apparent from the literature reflects a shift in focus
towards subjects like the identification of promoters of diversification (e.g. ‘key
innovations’).
Looking at the shapes of phylogenies and at evidence from the fossil record, it
appears likely that most of the species in the larger genera are the results of
(comparatively) recent radiations, which may, however, bear no correlation with
the ages of the lineages (in this instance, genera) themselves. Shapes and
branch lengths of phylogenies can be used to answer a number of biological
questions about species richness and distribution - whether radiations have
occurred, if key innovations can be identified, if extinction is a likely explanation
for isolated clades, and whether dispersal or disjunction account for presentday ranges. However, the answers we receive can only be as good as the
phylogenies we produce; it is important to consider whether non-biological
factors or homoplasy have affected our hypotheses of relationships.
24
2.
Using Molecules to Reconstruct Evolutionary
History
2.1. Why morphology is not enough
It is becoming increasingly apparent that small changes in single genes can
be responsible for major shifts in plant morphology. Significant
reorganisations of genomes can have little to no effect on the appearance of
organisms, while dramatic morphological changes can result from what
appear to be minor genic or chromosomal alterations. Thus morphological
cladistic analyses can give hypotheses which differ radically from those based
on molecular data. This can be regarded as an example of ‘mosaic evolution’ ■
“the ability of different characters to evolve at different rates and in different
directions” (Niklas, 1997, p. 350).
For example, the gene cycloidea encodes a protein which causes bilateral
symmetry in flowers (by acting on only the upper parts as the flower develops).
If this gene is inactivated by even a single nucleotide substitution, flowers
become peloric (Citerne & Cronk, 1999). Furthermore, if characters used in
morphological phylogeny and / or classification are subject to strong selection
pressures, recurrent evolution and similar forms can lead to misleading
inferences of affinity. A common example of this relates to the evolution of
pollination syndromes. For instance, within Ipomoea L. (Convolvulaceae
Juss.) (Miller, Rausher & Manos, 1999) there have been multiple shifts in
pollination syndrome, from bees to birds (associated with gain of red pigment
in the corollas). There are also numerous independent shifts from pigmented
to white flowers. Clearly classification based on floral similarity in this case
would not reflect evolutionary relationships. If minor mutations causing such
major shifts prove to be a common pattern in plant evolution, and where such
genes belong to gene families, mosaic evolution may be found to riddle
morphology-based phylogenies. In contrast, molecular data gathering and
analysis is becoming increasingly rapid and cost effective and appears to
generate usable (and apparently predictive) phylogenies.
25
2.1.1. Contrast between molecular phylogenles and traditional
classification:
A number of authors have found that the results of
their molecular phylogenetic analyses are incongruent with traditional
classifications. In Viola, ITS sequences uncovered a relationship between an
Hawaiian clade and an amphi-Beringian complex that was not evident from
morphological or cytological data (Ballard, Sytsma & Kowal, 1998).
The
previous placement of the Hawaiian group, with two neotropical sections, was
based on close morphological similarity; the shared traits (the branching
pattern, the woody stems, the leaf shape, the short corolla spur and the simple
style) map on the phylogeny as being homoplastic, and appear to be a
remarkable example of convergence between montane plant groups.
Pfosser and Speta (1999) describe problems with morphological
circumscription in Hyacinthaceae, because characters which are useful in
other families are often highly variable among closely related species, e.g. the
type of embryo sac varies within Scilla L. s.s. Their phylogeny, based on trnL
and trnL-trnF sequence data, disagrees with most of the traditional
morphological treatments. In their opinion, “[f]or no plant family is it more true
than for Hyacinthaceae that the interpretation of single morphological
characters resulted in highly erratic classifications when delineating tribal and
subfamilial relationships. No character, from bulb morphology to pistils or
seeds, or even karyological data, has proved reliable" (Pfosser & Speta, 1999,
p. 865).
In Ilex, the phylogeny inferred from atpB-rbcL spacer chloroplast sequence
data is not congruent with traditional systematics: the infrageneric
classifications of Loesener (in Engler & PrantI, 1942) and used by Hu (who
published in 1949, 1950 and 1967) show “only a few examples of agreement
with the molecular phylogeny” (Cuenoud et al., 2000, p. 121). Molecular
phylogenetic analysis of Ipomoea (Miller, Rausher & Manos, 1999) also failed
to support any previous subgeneric classification.
Similar problems occur in other taxa. Ro, Keener and McPheron (1997) used
26S rDNA to estimate a phylogeny for the Ranunculaceae Juss. Although
chromosome number and karyotype are consistent with this tree (as are
26
chloroplast restriction site data and sequence data from three other genes
{atpB (cp), rbcL (cp) and 18S (nr))), fruit type, which has been considered
critical in subfamilial classification within Ranunculaceae, is not.
Fleshy fruits
have evolved in two, and achenes have evolved in at least three, independent
lineages.
2.1.2. Contrast between molecular and morphological phylogenles:
Baker,
Hedderson and Dransfield (2000) found that their molecular phylogenles are
not very congruent with previous morphological phylogenles (Baker et al.,
1999a). Their molecular phylogeny of subfamily Calamoideae (Arecaceae
C.H.Schultz.), based on nr DNA ITS and cp DNA rpsIB intron sequence data,
supported an Asian clade which has “no conspicuous morphological basis"
(Baker, Hedderson & Dransfield, 2000, p. 213).
Watson, Evans and Boluarte (2000) produced a molecular phylogeny, based
on cpDNA ndhF sequences, for Anthemideae (Asteraceae), to compare with
the morphological phylogeny produced by Bremer and Humphries (1993).
Although the molecular data from their study are congruent with ITS and
chloroplast DNA restriction site data, and with the biogeography of the taxa, the
molecular phylogeny (as in the Calamoideae example) is ‘in general'
incongruent with the morphological phylogeny and with all previously proposed
classifications for the tribe.
There are now numerous examples of disagreement between molecular data
and morphological data. In some cases, reexamination of morphology in the
light of a molecular phylogeny has allowed reciprocal illumination and the
identification of new morphological characters. In addition, while individual
characters can be homoplastic across a given data set, they may be locally
informative and can be useful at lower taxonomic levels (Pennington, 1995).
This being said, there are also increasing reports of cryptic clades, well
supported by molecular data but with no identifiable morphological characters
(e.g. Richardson et al., 2000). Assuming these molecular phylogenles
represent species phylogeny (see later for a discussion of the potential
complicating factors) this indicates that under some circumstances
morphology can be misleading.
27
2.2.
Molecular phylogenles
The use of molecular data in phylogenetic reconstruction is now
commonplace, with direct DNA sequencing the most widely used character
source (Soltis & Soltis, 1998).
There are many DNA regions (coding and non
coding, transcribed and untranscribed) available for sequencing; areas can be
selected with different evolutionary histories, from different genomes, and with
different rates of change. In 1999, papers in Systematic Botany used the
following regions for DNA sequencing:
Chloroplast: matK (gene), ndtiF (gene), rbcL (gene), rp/16 (intron), trnL intron,
trnL-trnF (intergenic spacer).
Nuclear: Adh (gene, alcohol dehydrogenase, low copy number), vicilin (gene,
seed storage proteins, low copy number), waxy (gene, starch synthase; single
copy), 18S (nuclear ribosomal RNA gene; high copy number), ITS (nuclear
ribosomal RNA gene transcribed spacer; high copy number).
2.2.1 Which gene for which question?:
The three genomes of plants
offer genes with differing characteristics and tempos of evolution.
The slowest
substitution rates of all eukaryotic genomes are found in plant mitochondrial
DNA (Li, 1997); chloroplast DNA has a substitution rate of about four times that
of mitochondrial DNA and nuclear DNA has a 10-fold increase. However,
these are broad generalisations based on a narrow range of genes; it would
perhaps be more informative to consider commonly used genes individually.
Perhaps the most widely used genes in plant phylogeny reconstruction (at
least until the late 1990s) are nbcL and 18S. The chloroplast gene rbcL is
alignable over wide phylogenetic distances and has been used to infer the
evolutionary history of the angiosperms. Sequences of rDNA 188 have also
been used for deep level phylogenetic reconstruction; 188 includes slightly
less phylogenetic signal than rbcL, but is also widely alignable and has been
used to provide corroboration of novel deep level angiosperm-wide clades
from a different genome to rbcL (Hershkovitz, Zimmer & Hahn, 1999). These
genes do not, however, evolve quickly enough to resolve relationships at lower
taxonomic levels such as among the species of a genus, or related genera in a
family. Instead, more rapidly evolving regions such as the internal transcribed
spacers (IT8) of nr rDNA and the chloroplast intron / intergenic spacer of trnL
28
have been widely used as a source of characters at this level. Among very
closely related species even these regions are not variable enough, and
attention has recently turned to fragment analyses such as AFLPs or RAPDs,
or sequence data from introns of low copy number protein encoding genes, in
the search for variable characters.
It should be noted that the concept of speed of genes is not straightforward
with regard to the most suitable level for their application. It is clear when a
gene is too slow, as few or no variable characters are present. Determining
when a gene is too fast for the question in hand is more difficult. In some
cases, where the taxonomic distance is too large, the sequences may simply
not be alignable; without a satisfactory alignment, any phylogenetic hypothesis
is hard to justify. However, for those rapidly evolving genes such as matK,
performance over deep levels of evolutionary history can be better than one
might have predicted. For instance, the APG (V. Savolainen pens, comm.,
2000) have, by combining data sets for several genes, produced what they take
to be the closest tree to a ‘true’ phylogeny for the angiosperms and used this
topology to examine the relative contributions of the component genes. The
fastest gene they sampled (matK) produced the ‘best’ tree (it had most nodes
in common with the ‘true’ tree). However, one must note that the number of
nodes in common, on its own, requires some qualification. The majority of
nodes on a tree are near the terminals, and so a tree from a fast gene could be
predicted to most approximate a ‘true’ tree using this criterion. Using a slower
gene however, one would expect to resolve the deeper branching patterns. In
order to obtain good resolution at both the distal and the basal nodes, the ideal
gene / region would include both comparatively conserved and divergent
sequence.
However, Savolainen et al. (2000) point out that rate per se is not a reliable
explanation of how well a gene or region will perform in phylogenetic
reconstruction; a better explanation is ‘decisiveness’. Although more rapid
regions may have more homoplasy, they may also have more signal therefore
be more ‘decisive’. Homoplasy is only a problem in phylogenetic
reconstruction if it covaries (Chase & Cox, 1998), otherwise it should be
swamped by signal.
29
Of course, there are two ways of looking at the rate of a gene or region - one,
simplistically, is the number of sites that vary along its length; the other is how
many changes there are per variable site. While a gene or region may be
described as ‘fast’ because it has a lot of variable sites (and conversely, ‘slow’
if it has only a few), a gene which has a lot of changes at each variable site may
also be described as ‘fast’ (and vice versa). Each nucleotide in a sequence is
not necessarily equally likely to undergo a substitution; for example, in genes
or proteins, substitution rates tend to be highest in third codon positions, and
lowest in second codon positions (Yang, 1996). This sort of pattern can be
modelled using the shape parameter a of the gamma distribution of
substitution rates at sites, where a low value for a indicates extreme rate
variation among sites, and a high value indicates minor rate variation (when all
sites have the same substitution rate, a is infinity) (Yang, 1996).
Where there are many changes at each variable site, multiple hits on the same
base are more likely, which increases the potential for homoplasy to obscure
phylogenetic signal. Thus a measure of the number of variable sites for a
gene or region will not necessarily correlate with the potential levels of
homoplasy, if it does not take some account of the number of changes per site.
Even where variable sites are very variable, and multiple hits are thought to be
a problem, however, signal is not always obscured. Although previous authors
have advised eliminating third codon positions from analyses because they
tend to have more changes per site than other positions and therefore more
potential for homoplasy (e.g. Kitching et al. (1998, p. 103) find it “rational to
downweight or even ignore third position changes’’), Kallersjo, Albert and Farris
(1999) found that the third codon positions in rbcL, although rapidly evolving
and highly homoplastic, contain most of the phylogenetic signal in a 2538taxon green plant matrix. Excluding these regions cuts down the resolving
power of the matrix. Likewise, Chase and Albert (1998, p. 495) found that
eliminating third positions gives “less resolution and weaker measures of
internal support”.
In most studies people seek to resolve not only within-clade relationships, but
also the deeper relationships of the clades to each other. A matrix wherein
30
sites evolve at different rates, although problematic for some phylogeny
reconstruction algorithms, offers the potential for recovering clades at different
hierarchical levels.
2.2.2 Evolutionary rates and molecular clocks:
In reconstructing the
phylogenetic relationships of organsisms, it is clearly desirable for the date,
and not just the order, of branching patterns to be known. A cursory glance at
most DNA sequences shows that the more phylogenetically disparate taxa are,
the more divergent their sequences tend to be. This has led evolutionary
biologists to explore the concept of the molecular clock - using sequence
divergence to estimate times of separation. The molecular clock hypotheses
are based around the Neutral Theory of Molecular Evolution (Kimura, 1968).
The beauty of the neutral theory is the prediction that substitutional change over
time is affected only by the mutation rate. Providing the mutation rate is
constant across the lineages considered in the study group, there is an
expectation that sequence divergence will be linearly related to time. One
confounding variable is that of generation time; longer generation times are
predicted to lead to slower divergence. This is attributable to fewer meiotic
events per unit absolute time, which reduces the opportunity for mutation.
However, in plants this is complicated as mutations may be fixed in vegetative
meristems as well as reproductive cells, and seed banks and clonal
reproduction may have a stabilising effect on the evolutionary rate in herbs
(Baldwin et al., 1995).
In addition, in a less simplified extension to the Neutral Theory, the Nearly
Neutral Theory predicts that many mutations will be slightly deleterious (Ohta
1973). If this is the case, then population size will also affect rates of change,
due to the inefficiency of selection in small populations compared to large
ones.
Various other confounding variables have also been postulated (Gaut, 1998)
and in practice, estimates of relative nucleotide substitution rates among
evolutionary lineages for rbcL and for ITS have shown that there are no timecalibrated clocks for these regions (Bousquet et al., 1992; Gaut et al., 1992;
Baldwin et al., 1995).
31
However, although the issue of whether percentage divergence between a pair
of sequences can be related in some way to the time since the lineages split is
still in many respects under debate, clocks calibrated by known events (e.g.
fossil evidence or geological history) are appearing increasingly in the
literature (e.g. Wagstaff & Dawson, 2000, dating by fossil records; Richardson,
1999, dating through island appearance). Methods to estimate lineagespecific evolutionary rates and / or divergence times are reviewed by
Sanderson (1998).
2.3.
Ribosomal DNA
As the current project is addressing patterns of diversification in a large genus,
a region which offers resolution at the inter- and intra-sectional level was
required. The region I have chosen is a combination of sections of nuclear
ribosomal DNA. A summary of the characteristics and evolutionary dynamics
of this region are given below.
The reasons why the rDNA cistron is so frequently used in phylogeny
reconstruction have been comprehensively reviewed (Soltis & Soltis, 1998, and
references therein). In eukaryotes the rDNA cistron encodes the 18S (SSU),
5.8S and 26S (LSU) rRNAs, which are separated by two internal transcribed
spacers (ITS 1 and ITS 2) and flanked by the 5’ and 3’ external transcribed
spacers (5’ ETS and 3’ ETS). There are thousands of copies of the cistron,
which are each separated by the intergenic spacer (IGS) (see Figure 2.1).
Figure 2.1
IGS
5 ' ETS
2.3.1 ITS:
The rDNA cistron
1 8S
ITS1
5 .8 S
ITS 2
26S
3 ' ETS
IGS
Many authors have found the internal transcribed spacer (ITS) of
nuclear ribosomal DNA to provide useful characters for phylogenetic studies,
particularly at lower phylogenetic levels. The utility of this region was first
demonstrated by Baldwin (1992, 1993) in the Asteraceae and since then there
has been a vast proliferation in studies using ITS (e.g. Yuan & Kupfer, 1997,
Gentiana L., Gentiaceae Juss.; Li et al., 1999, Hamamelidaceae R.Br.).
Baldwin et al. (1995) provide a comprehensive review of the use of the ITS
region in angiosperm phylogeny reconstruction.
32
2.3.1.1
ITS Function:
The two spacers, ITS 1 and 2, have different
evolutionary histories. ITS 1 is homologous to the SSU-LSU spacer in non
eukaryote and organellar rDNA (Hershkovitz, Zimmer & Hahn, 1999), while ITS
2 is missing in prokaryotes (Clark et al., 1984). 5.8S is homologous to the 5’
end of 23S rRNA in E. coli (Clark et al., 1984). ITS 1 is not only unrelated
evolutionarily to ITS 2, but is also distinct structurally and functionally. However,
evolutionary patterns in the two spacers (such as overall rates, and base
composition biases) are usually parallel (Baldwin et al., 1995).
The ITS regions are thought to have a role in the maturation of nuclear rRNAs,
bringing the large and small subunits close within a processing domain.
Deletion of small parts of ITS 1 can inhibit the production of mature small and
large subunit rRNAs in yeast, while some deletions or point mutations in parts
of ITS 2 prevent or reduce the processing of large subunit rRNAs (references
cited by Baldwin et al., 1995). Thus it seems as if there is some evolutionary
constrain on the structure and sequence of ITS 1 and ITS 2. Baldwin et al.
(1995) suggest that the similarity in G and C content between ITS 1 and ITS 2
reflects a degree of coevolution. The ITS regions are inherently G and C rich
(the GC content of angiosperm ITS is almost always over 50% and can in
some cases exceed 75% (Hershkovitz, Zimmer & Hahn, 1999)) and have
some regions which are highly conserved across the angiosperms (Soltis &
Soltis, 1998). Because of the presence of these conserved regions,
Hershkovitz and Zimmer (1996) could align about 50% of the ITS 2 region
above the family level in angiosperms.
2.3.1.2
Taxonomic level:
ITS is considered to be best suited for
“diagnosing relationships among closely related genera and infrageneric
groups” (Hershkovitz, Zimmer & Hahn, 1999, p. 287). Divergence values
between closely related species may be less than 1% (less than 5
substitutions); given that some of these may be autapomorphies, ITS may not
offer much information about relationships at the species level (Hershkovitz,
Zimmer & Hahn, 1999).
The most rapidly-evolving ITS regions are prone to length variation, which can
cause problems with alignment. This means that increased divergence
33
between species is not always accompanied by an “equiproportional increase
in the number of alignable informative sites” (Hershkovitz, Zimmer & Hahn,
1999, p. 287). There is approximately one indel per 2% sequence divergence;
however, because the indel positions vary in different lineages, in many cases
only a small minority of taxa have an indel at any one site (Hershkovitz, Zimmer
& Hahn, 1999).
2.3.1.3
Secondary structure:
A potential problem with analysis of ITS
is non-independence of nucleotide sites. Estimated secondary structures of
ITS 2 for species in the Asteridae (Baldwin et al., 1995) showed high levels of
similarity, with a three-stem / loop structure. Mutations of positions along the
stems may need compensatory mutations at the opposite sites to maintain
structural integrity. This has led to authors suggesting that stem sites should
be weighted over loop sites in analyses (Dixon & Hillis, 1993; Wheeler &
Honeycutt, 1988; Baldwin et al., 1995), and that compensatory mutations
should be downweighted (Hershkovitz & Zimmer, 1996), although such
weighting schemes can be too constrictive. Soltis and Soltis (1998, p. 205)
say: “most efforts to weight stem versus loops and transitions versus
transversions, and even conserved versus variable domains, are probably not
worth the effort or extra computer time required to conduct some of the
analyses”, and Kitching et al. (1998) suggest that any such weighting scheme
may not be generalisable to all organisms and all molecules but should be
investigated with reference to each individual study group and molecule.
Mai and Coleman (1997) produced secondary structures for ITS 2 for several
green algae, and also for some angiosperms. They searched aligned
sequence data for covariants (compensating base changes which change so
as to maintain base pairing).
Most of the ITS 2 region appears to be a self-
contained folding complex, usually with four distinct hairpin loops. Highly
conserved regions within ITS 2(116 positions) were readily alignable across
all of the Volvocales (algae). 85.3% of these positions fell into regions which
base-pair. Despite considerable length heterogeneity, conserved structural
elements consistently form. Mai and Coleman (1997) also found close
structural correspondence between ITS 2 from the Rosaceae Juss. and
Volvocales, although this was not due to similarities in nucleotide sequences.
34
Variations in distal portions of the hairpins, however, occur even among
interbreeding organisms (Mai & Coleman, 1997).
Hershkovitz and Zimmer (1996) also looked for conserved regions of ITS 2;
they identified six regions which are conserved across a wide range of
angiosperms. “The combination of angiosperm-wide sequence conservation
with species-level sequence variability renders ITS a unique window for
examining the behaviour of a rapidly-evolving, homologous, non-coding DNA
sequence through divergence times spanning relatively ancient (90-130 million
years) to the most contemporary” (Hershkovitz & Zimmer, 1996, p. 2866).
Coleman et al. (1998) examined the secondary structure of ITS 1, and
considered its use in primary sequence alignment. In comparison with their
previous work on ITS 2 (Mai & Coleman, 1997) they found a significantly greater
level of primary sequence divergence in Volvocalean ITS 1 sequences; they did
not find any regions of conserved primary sequence across the family or order.
The ITS 1 sequences were most useful at population and species levels
although, in their more conserved portions, they contribute information up to the
family level. ITS 2 provided information at higher taxonomic levels.
2.3.1.4
Intra-individual Polymorphism: In practice, the problem of
polymorphism between the multiple copies of ITS is not whether it exists (it
does, and can be demonstrated by cloning), but whether it can mislead
phylogenetic analyses. Hershkovitz, Zimmer and Hahn (1999) suggest that it
does not: ITS phylogenles are usually congruent with independent evidence.
The levels of divergence are low between closely related species and
paralogues will probably not support the incorrect tree as they are not
differentiated enough; at greater taxonomic distances, homogenisation will fix
the differences (Hershkovitz, Zimmer & Hahn, 1999).
2.3.2 5.88: Much of the variation in the 5.8S gene is in a 24-base helix close
to the 3’ end. The overall variability of the gene is low, but Hershkovitz, Zimmer
and Hahn (1999) suggest that it may be useful in augmenting 18S and / or
26S.
35
2.3.3 26S (LSU):
The ribosomal large subunit gene is different lengths in
different taxa, which means that the homologous region is somewhat
confusingly known as 288 in animals, as 23S in prokaryotes and as 26S in
plants; the region is also sometimes simply called the LSU.
2.3.3.1
263 Function:
Most of the ribosomal large subunit is formed
from 5.8S and 26S (Hershkovitz, Zimmer & Hahn, 1999).
2.3.3 2
Taxonomic level:
Few studies have utilised the entire region,
due in part to its large size (about 3.5kb, made up of around 2.5kb conserved
sites and about Ikb variable regions (Hershkovitz, Zimmer & Hahn, 1999)).
However, phylogenetic analyses of portions of this region have been used in
collaboration with 18S (c. 1800 bp), producing similar topologies to 18S for
termite and fungal taxa (references in Soltis & Soltis, 1998, p. 20) and also the
same plant relationships as those revealed by 18S and rbcL sequences
(Kuzoff et al., 1998). The conserved regions within 26S seem to be more
conserved per unit length of sequence than 18S, while the variable regions
have been thought to be too variable to be used at the same taxonomic
(divergence) level as the conserved regions (Hershkovitz, Zimmer & Hahn,
1999). It appears that the entire 26S region evolves 1.6 to 2.2 times faster than
18S and at about half the rate of rbcL; as 26S is longer than 18S or rbcL, it
provides two to three times as many informative characters as either region
(Kuzoff et al., 1998). The c. 1 kb of variable regions are contained within
expansion segments I divergent domains. As these regions are a source of
many of the phylogenetically informative characters for this gene, their evolution
is discussed in some detail below.
2.3.3 3
A.
Expansion Segments I Divergent Domains
Description and definition:
The first size differences between
prokaryote and eukaryote LSU rRNA were due to a few inserted domains
interspersed among a set of conserved regions. Long tracks of the LSU
molecule have been strongly conserved during evolution; additional
sequences in higher eukaryotes are clustered in a few highly divergent areas
identified as D1 to D12 (mouse 28S rRNA sequence) (Hassouna et al., 1984)
(12 ‘expansion segments’ in the terminology of Clark et al., 1984). Outwith
36
these size-variable areas, the secondary structure between four eukaryotes
and E. coli is almost identical. Variation in the D domains seems to be due to
frequent inverted or direct repeats, possibly through DNA strand slippages
during replication. Hassouna et al. (1984) found that the D domains of 28S
rRNA in higher eukaryotes are closely related to the transcribed spacers of the
ribosomal transcription unit; most if not all the transcripts of D domains are
present in mature 28S rRNA of higher eukaryotes.
B.
Cryptic Simplicity: Tautz et al, (1988) coined the term ‘cryptic simplicity’
for scrambled permutations of direct repetitive short motifs, which are not as
obvious to the eye as tandem runs of a particular motif (pure simplicity). 5.88
and 188 rRNA genes and IT8 2 are not cryptically simple; slippage-like
mechanisms of variation do not seem to occur to any great extent within them.
The regions of high simplicity in the 288 rRNA gene correspond almost exactly
to the expansion segments (or D domains). Despite this, it appears that the
set of expansion segments is coevolving during interspecific divergence,
suggesting that 288 rRNA alone of the rRNAs can remain functional in the
presence of the repetitive and scrambled products of slippage-like events.
C.
Compensatory slippage: ‘Compensatory slippage' occurs when
slippage products accumulate at sites within the DNA in a manner which
conserves overall secondary structure. The main differences between the
longer and shorter expansion segments of highly divergent organisms are the
lengths of certain major secondary structural stems. There is an analogy to be
made with compensatory point mutations. It is possible that slippage might be
more frequent in sequences which have biased base composition therefore
higher concentrations of repetitive motifs. The species which show most
prominent accumulation of slippage-generated products in their expansion
segments also have the expansion segments with the most biased base
composition (Hancock & Dover, 1988).
D.
Function:
Because the expansion segments have higher rates of
sequence variation than the rest of the L8U, it has been suggested that they
may lack function (Hancock & Dover, 1988). However, Hancock and Dover
(1988) point out that, despite suggestions that expansion segments are
37
functionless and tolerated only as they do not interfere with ribosome function,
the interspecific conservation of gross secondary structure found by several
authors suggests that these regions are subject to some sequence constraint.
Expansion segments show sequence similarity patterns in mouse, rat, frog
and human but not in slime mould, yeast, nematode and E. coli. Rice is less
clear-cut, with lower similarities between expansion segments than mouse,
rat, frog or human, and with less obvious regions of localised high simplicity.
Sequence similarities and heightened simplicity could be due to the consistent
bias of base composition of the expansion segments within any one species.
That the expansion segments are found to be coevolving also points to their
having a degree of functional interaction (Hancock & Dover, 1988). Coevolution
could occur by either slippages in short regions producing larger blocks of
related sequence, or intragenic gene conversion. It has been suggested that
expansion segments enlarge in the main by accretion of short tracts of simple
sequence to the tips of secondary-structure stems; this is consistent with the
observation by Hancock et al. (Hancock & Dover, 1988, cited in text) of
conserved secondary structure in expansion segments even between species
which show complete sequence divergence (similar to the results found by Mai
and Coleman (1997) for ITS 2). As far as overall sequence goes, the high
levels of similarities found within but not between species are suggestive of
concerted evolution - the expansion segments of individual species appear to
have diverged and evolved as a unit.
2.3.3.4
Secondary Structure and Weighting:
Dixon and Hillis (1993)
examined the secondary structure of the LSU; they found that the expansion
segments contain significantly more paired bases than the rest of the gene.
Stem base characters supported a conventional (morphology-based)
hypothesis of vertebrate relationship, while loop characters supported
unconventional trees. The best results, however, were obtained when the two
data sets were combined. Although the secondary structure of rRNA reduces
the evolutionary independence of paired nucleotides, weighting these paired
bases by a half overcompensates; Dixon and Hillis (1993) suggest a value of
0.8 (although point out that different data sets may require different weighting
schemes); weighting at 0.8 produces the same tree as equal weighting;
38
weighting at 0.5 produces an unconventional tree (consistent with one
produced from loop data alone).
2.3.3.S
A.
Practical applications to phylogeny reconstruction
Animals:
Most of the cited studies have been on animal 28S.
Several properties of animal 28S (and particularly expansion segments) have
been cited as problematic for phylogenetic reconstruction (Kuzoff et al., 1998):
1. the expansion segments have a higher base substitution rate than the
conserved areas.
2. the base composition is biased (high GC).
3. indels are frequent.
4. there is character non-independance, through compensatory mutations and
sequence coevolution among remote domains. Cryptic sequence similarity
also violates the assumption that characters at different sites evolve
independently.
B.
Plants:
Comparing 7 full-length angiosperm 26S sequences, Bult,
Sweere and Zimmer (1995) found that levels of GC are higher in expansion
segments (65%) than in conserved core segments (52%). This high GC level
may be a problem if the methods of phylogeny reconstruction used assume
equal base frequencies (Kuzoff et al., 1998), but it is not a problem specific to
the 26S region.
Overall sequence variance is much greater in the expansion segments than in
the conserved core regions. Bult, Sweere and Zimmer (1995) found 42% of
nucleotide positions in the expansion segments were variable, while 10%
were variable in the core regions; rates found by Kuzoff et al. (1998), from 15
species of seed plants (basal and higher eudicots and monocots, and
Gnetales), are slightly higher, with expansion segments evolving 6.4 to 10.2
times as fast as the conserved regions. Levels of internal sequence similarity
(motif shuffling through repeated slippage events) within expansion segments,
which can violate assumptions of character independence, are generally low in
plants and are really most problematic for reconstructing deep divergences
(Bult, Sweere & Zimmer, 1995). However, the fact that motif shuffling can
occur, however infrequently, led Bult, Sweere and Zimmer to caution that 26S
39
can present difficulties in the basic assumptions of homology and
independence among characters.
The levels of cryptic sequence similarity are considerably lower in plant 26S
than in animal 28S, and are confined to the expansion segments (Kuzoff et al.,
1998). Plant 26S has an average length of 3.4kb, while animal 28S has an
average length of 4.5kb. Kuzoff et al. (1998) point out that there is a positive
correlation between the length of expansion segments and the cryptic similarity
in the sequence. In plant 26S there is less compensatory slippage and fewer
length mutations; so there may be more phylogenetic signal at higher
taxonomic levels in plants than in animals. This taxonomic correlation could
explain Hancock and Dover’s (1988) results, where expansion segments
showed sequence similarity patterns in vertebrate 28S, less in rice 26S and
none in nematode, yeast, slime mould and E. coli 23S. Further studies are
needed to look for taxonomic correlations with LSU length and expansion
segment sequence similarity.
i.
Deep level:
In a study across the angiosperms, sequence information
from both the conserved core regions and the expansion segments produced
greater internal support, more resolution, and greater congruence with studies
based on other data than using the core regions alone. This has led Kuzoff et
al. (1998) to suggest that the expansion segments have useful data to
contribute to reconstructions of evolutionary events which occurred in the last
100 to 200 million years.
ii.
Family and generic phylogenies:
In a phylogeny of the
Saxifragaceae Juss., expansion segments provide more signal than the core
regions, and the exclusion of core region sequences did not affect the
resolution of a reconstructed phylogeny (Kuzoff et al., 1998).
Oxelman and Liden (1995) used the ITS 2 region and about 800 bases from
the 5’ end of 263 to look at evolution in Circaeaster Maxim. (Circeasteraceae
Hutch.). For the 268 sequence they recovered a single most parsimonious
tree, but the ITS 2 sequences “could not be meaningfully aligned above family
level” (Oxelman & Liden, 1995, p. 191).
40
Ro et al. (1997) sequenced a kilobase long portion of the 5’ end of 26S to test
phylogenetic relationships within the Ranunculaceae, as this region shows the
highest sequence variability in the gene across several angiosperm taxa. A
further aim of their study was to test the phylogenetic utility of partial 26S
sequence data, comparing results with morphology and other molecular
studies. They found that the phylogenies produced were highly congruent with
chloroplast restriction site data and sequence data from other genes and with
karyological characters.
2.4.
Homology assessment in molecular data sets
One of the perceived advantages of molecular data is that there are
homologous characters (4 nucleotides) which are comparable across the
deepest branches of life, over phylogenetic distances where identification of
homologous morphological characters is difficult or impossible. However,
molecular data are not immune from problems of homology assessment. One
initial step is the assumption that the genes or regions under consideration
are orthologous. Gene duplication is a frequent event in plant evolution and the
potential exists for paralogous copies of genes to be sequenced (Page &
Holmes, 1998). For cpDNA genes, where order is relatively conserved,
problems of paralogy are limited (Stoebe et al., 1999). Likewise, for nuclear
rDNA (a multi-gene family), providing homogenisation is efficient, problems
with paralogy can be reduced. The problem is most apparent for low copy
number nuclear genes, when multiple copies of divergent paralogues are often
documented within individuals. (For example. Sang and Zhang (1999) found
two to three diverged types of sequence at each of the AdhIA and Adh2 loci, for
each of 5 putatively hybrid-origin species of Paeonia L. (Paeoniaceae Raf.).) If
mistakenly sequenced, these can confound estimates of phylogeny.
Even when orthologous regions are being analysed, there are further problems
with homology assessment. Sequences of one gene or region for two or more
taxa will not necessarily be homologous at every position, due to the presence
of inserted (or absence of deleted) segments of sequence. When indel events
have occurred in the evolution of the sequences being analysed, then the
sequence data cannot be considered to be a row of characters (a character is
41
a proposed homologue; prior to alignment there is no hypothesis of homology
for nucleotide positions in length-variable sequence, therefore no character
set; the character states are observed prior to character definition). Position
(defined by alignment) is the only useful homology criterion for characters
which have identical ranges of states (Doyle & Davis, 1998). Failure to insert
gaps correctly causes inaccurate associations of states with characters
(analogous to “leaf pubescence a cyme”) (Doyle & Davis, 1998, p. 113).
Morrison and Ellis (1997) seek to distinguish between ‘gaps’, which are
spaces introduced into sequences during the process of alignment, and
‘indels’, which are the actual mutation events. For the purpose of phylogenetic
reconstruction, we often have to hypothesise that gaps do in fact represent
indels.
Choosing between explaining differences by point mutations and explaining
them in terms of indels requires some form of cost assessment. Global
alignment programs look for an optimal alignment which maximises (or
minimises) some overall score over entire sequences. Because it is possible
to align any two sequences so that there is no mismatch (by the addition of a
gap wherever a mismatch would occur) the addition of gaps must be
penalised more than the cost of the mismatch (Doyle & Davis, 1998). The
most commonly used form of cost assessment is the gap penalty, which
specifies the cost of a gap relative to a substitution (Page & Holmes, 1998); it
is also possible to consider the cost of changing the length of gaps. These
gap opening and gap extension penalties influence the number and length of
gaps.
There are several algorithms which will search for the alignment with the
lowest cost for specified penalties. Most algorithms use exact procedures to
align pairs of sequences and then use heuristics to make the pairwise
alignments into a multiple alignment. There are two reasons why this may not
represent the ‘true’ alignment (Morrison & Ellis, 1997):
1. this procedure will find local optima, not necessarily the global optimum.
2. the procedure seeks to maximise similarity, not sequence homology.
42
Sequence similarity may be due to common ancestry (homology),
convergence, parallelism or reversal (all homoplasies).
For a data set with several sequences, Clustal constructs a tree using
distances computed from pairwise alignments of sequences, and then uses
this tree to determine the order of sequence input into the multiple alignment
(Thompson, Higgins & Gibson, 1997). A different method is used in Wheeler
and Gladstein's package (MALIGN, 1992); parsimony is used rather than
distance in the initial tree construction, because the best alignment is that
which produces the most parsimonious cladogram for a given set of gap
costs. Selecting the appropriate costs in MALIGN is simplified in that the
minimum gap cost must be over one half the substitution cost (or a change
from A to gap to G would cost less than a change from A to G), while at the
upper end of the scale all data sets 'asymptote' - a point is reached where
further alterations to the ratios do not alter the alignment(s) (Gatesy, DeSalle &
Wheeler, 1993).
Likewise, if the cost assigned to transversion-transition is
less than 0.5, the cost of A to C to G (where C is not observed) will be less than
the cost of A to G (Wheeler, 1995).
Morrison and Ellis (1997) tested 5 different multiple alignment algorithms
(including Clustal and MALIGN). Each produced different alignments. From
each alignment they produced neighbour-joining, maximum likelihood and
maximum parsimony trees. Although they found that the same “underlying
phylogenetic signal is present in all of the alignments, and ... the phylogeny ...
is thus relatively robust to variation in the sequence alignment process”
(Morrison & Ellis, 1997, p. 433), they got greater variation in the tree topologies
due to their alignment than they did from the different tree-building methods.
It is unlikely that any set of gap costs or algorithm will produce a correct
alignment, because the best estimate will only be best on average and not for
every part of the sequence - the likelihood of mutation varies across a
nucleotide sequence (Doyle & Davis, 1998). Thus Hershkovitz, Zimmer and
Hahn (1999) favour treating computational alignments as heuristic solutions,
subject to réévaluation in the light of further evidence.
43
Alignment of a matrix by eye, although more subjective, also involves some
assessment of relative costs.
Liston et al. (1999) divide the ways of dealing with problematic alignments into
four categories:
1. Culling all ambiguous sites (Swofford et al., 1996).
2. Elision (Wheeler, Gatesy & DeSalle, 1995).
3. Optimal alignment - comparing individual automated alignments using tree
statistics (Bogler & Simpson, 1996).
4. Single manual alignment (this is the most common approach, but is best
used on relatively unambiguous matrices).
The methods of culling and elision represent the extremes of the analytical
procedure.
2.4.1. Culling:
Gatesy, DeSalle and Wheeler (1993) were concerned that
data is usually excluded from analyses on subjective grounds. A priori data
exclusion is an “extreme form of character weighting” (Gatesy, DeSalle &
Wheeler, 1993, p. 155) and should not be determined by the “whim” of
individual researchers. They suggest a repeatable, objective protocol, whereby
alignments are created over a wide range of gap: substitution cost ratios (they
varied settings in MALIGN from 2/3:1 to 300:1, although admitted that this was
extreme). Alignment-invariant nucleotide positions (constant across all
alignments for all taxa) are identified and are used in phylogenetic analyses.
They do point out a problem with this method, which is that, despite its greater
repeatability and subjectivity, much information (contained in the alignmentambiguous sites) can be lost.
Swofford et al. (1996) put forward an alternative viewpoint: that data are
excluded from analyses “from the moment one chooses a particular gene, set
of genes, or gene region to use in a systematic study” (Swofford et al., 1996, p.
500). In the same way that researchers avoid genes they know a priori to be
evolving too fast in their study group, sequence data may also be culled after
being gathered. They believe that “the benefits of excluding clearly unalignable
44
regions - however subjectively determined - outweigh the dangers.”
Culling is the most conservative method, but it can lead to poor resolution of
relationships within clades (Gatesy, DeSalle & Wheeler, 1993; Soltis, Johnson
& Looney, 1996).
2.4.2. Elision:
Eight months after submitting their paper on the use of the
culling method (Gatesy, DeSalle & Wheeler, 1993), the same authors
(Wheeler, Gatesy & DeSalle, 1995) revisited the topic, with the paper ‘Elision: A
Method for Accommodating Multiple Molecular Sequence Alignments with
Alignment-Ambiguous Sites”. They suggest, as a method for including all the
information from a data set, the accumulation of various alignments created
using different gap penalties into one large ‘elision’ set, thus downweighting
positions which vary among alignments and applying a heavier weight to
positions which are consistently aligned. ‘Culling’ (Gatsy, DeSalle & Wheeler,
1993) created robust but rather unresolved hypotheses of relationship,
whereas this new method applies weights in a continuous fashion to
nucleotide positions. While there may be a problem in homology
assessments with data analysed using the elision method (individual bases
must have individual histories, but using elision, each base contributes more
than once as different characters) it allows phylogenetic analysis even of data
sets with sequence alignment ambiguities (Wheeler, Gatesy & DeSalle, 1995).
Of course, the number of different alignments which are added together in the
elision matrix will affect the amount of weighting placed on consistently-aligned
sequence positions; given a sufficient number of matrices, the effect will be
similar to that of culling, with virtually no information from variable positions
filtering though.
Swensen, Luthi and Rieseberg (1998) had difficulty aligning ITS sequences
from the Datiscaceae Bercht. & J.Presl., Begoniaceae and Cucurbitaceae
Juss. They used ten different alignments generated by ClustalX (Thompson,
Higgins & Gibson, 1997) using different gap opening and gap extension
penalties as inputs for phylogenetic analysis and also produced an elision
data set of all ten alignments put together. This strategy was preferred over
‘culling’, which would have removed a large amount of data given that
45
sequences from the outgroup taxa were substantially divergent from the
ingroup.
2.4.3. Optimal alignment: Bogler and Simpson (1996) used ITS to produce a
phylogeny of the Agavaceae Dumort. Because they found simple manual
alignment of the sequences difficult and subjective, they used homoplasy
indices to evaluate different alignments (created by varying the gap penalty in a
computer package.) They considered the alignment which produced
phylograms with the lowest levels of homoplasy (measured using the Cl, Rl
and RO) to be optimal. They found that nearly all the alignments they created
produced trees with similar topologies.
Li et al. (1999) also had difficulty aligning ITS sequences, from 28 genera in the
Hamamelidaceae R.Br., a highly morphologically diverse family. Li et al.
(1999) therefore tested various alignments, selecting the one which created
trees with the highest RO index as being optimal for both ITS 1 and ITS 2.
However, tree statistics are not necessarily the best way to find a ‘true’ tree.
Morrison and Ellis (1997) tested Clustal alignments using 9 gap opening
penalties and 8 gap extension penalties (giving 72 separate alignments).
None of these alignments produced what they considered to be the ‘true’ tree
(which they obtained on the basis of an alignment which included information
from secondary structure, as they expected this to be most likely to have
produced the multiple-sequence alignment closest to the ‘true’ alignment. Of
course, the validity of these assumptions is not testable).
2.4.4. Using the entire data set: Wenzel and Siddall (1999) found that, where
20% of a data matrix was replaced by “noise” (random, signal-free data), or
where a noise matrix the same size as the original matrix was added on to it, if
the original cladogram was supported by one synapomorphy per node, the
original signal was recovered by parsimony over 50% of the time. A pectinate
topology was more stable than a balanced cladogram to this sort of
manipulation. A higher proportion of the trees reported in the literature are
pectinate than would be expected given a Markovian (equal rate random)
branching process of spéciation (Pearson, 1999); if most real trees are
46
pectinate the effects of noise may be less severe. Wenzel and Siddall (1999)
ask: “[i]f including all of the data results in a tree that coincides with
conventional wisdom, would proponents of data triage still advocate the
downweighting or elimination of whole portions of data, even if doing so results
in a radically unconventional hypothesis?
In the very worst case, truly
saturated data will not necessarily be misinformative. They might be
misinformative, uninformative, or even informative
If one knows in advance
what the relationships should be, there is not much point in looking for them”
(Wenzel & Siddall, 1999, p. 62).
2.4.5 Secondary structure:
If there is some a priori model of sequence
secondary structure, the alignment can be constrained by this model (Morrison
& Ellis, 1997).
Hershkovitz, Zimmer and Hahn (1999) detail two ways of using secondary
structural information in alignment, with the proviso that RNA secondary
structure is apparently dynamic in vivo, and presumably also dynamic
evolutionarily:
1. analysing substitution covariance, and using it as evidence of compensatory
mutation, therefore of base pairing in secondary structure.
2. analysing the minimum free energy of folded rRNA, using heuristics
(therefore obtaining estimates).
Hershkovitz and Zimmer (1996) used an heuristic package (MULFOLD) to
produce a set of consensus features for the ITS 2 region. They found that
multiple, radically different, secondary structures may have similar minimum
free-energy values. Also, experimental evidence suggests that in
Chlamydomonas and in yeast, the secondary structures have sub-minimal
free-energy. Thus minimum free energy is not reliable as the sole criterion for
secondary structure prediction. Backing up a secondary structure with
evidence of compensatory mutations in related taxa gives added weight to the
hypothesis (Mai & Coleman, 1997).
47
2.4.6 Treatment of gaps:The gaps inserted during alignment represent
hypothetical evolutionary events; they are thus potential phylogenetic
characters. Although gaps may only be inferred, while nucleotide substitutions
are observed, nucleotides themselves only become characters after alignment
(Doyle & Davis, 1998). Just as there are alternative ways of dealing with
alignments, there are different ways of treating gaps once they have been
inserted:
1. culling all sites with gaps;
2. as a 5th state (A, C, T, G, gap);
3. as missing data / uncertainly (which in most parsimony analyses will be
assigned the most parsimonious solution);
4. coded in a separate matrix.
Many studies include gap matrices to utilise any phylogenetic information.
However, it can be difficult to assess homologies for overlapping or lengthvariable gaps (Doyle & Davis, 1998).
Swensen, Luthi and Rieseberg (1998) treat gaps in 188 as a fifth state
because they consider it likely that the single nucleotide gaps in their
sequence are caused by single evolutionary events, while they treat gaps in ITS
as missing data (as these multiple nucleotide gaps could have been
generated by one or more events). Gaps (treated as missing data) can lead to
“the generation of multiple equally most parsimonious cladograms, to
spurious theories of character evolution, and to lack of resolution by masking
the phylogenetic signal implied by the observed data” (Kitching et al., 1998, p.
80). However, they will not alter the topological relationship of taxa (Kitching et
al., 1998).
48
2.5
Summary
Molecular data can be used to generate phylogenies rapidly and efficiently,
while, in contrast, morphological data suffers problems with homoplasy which
may often tie in with convergence (e.g. habitat in Viola, and pollination
syndrome in Ipomoea).
Selecting the correct gene or region for a problem is one of the most difficult
stages in phylogenetic analysis; there are a wide range to choose from. It is
becoming increasingly apparent that faster genes offer more information at
deeper phylogenetic levels than had previously been supposed and they are
more likely to track rapid spéciation events (although may be more difficult to
align). The ribosomal DNA cistron is very frequently used for phylogenetic
reconstruction; ITS and 26S were selected from it for this present study. The
ITS region is made up of two transcribed spacers (ITS 1 and ITS 2) separated
by a short gene (5.8S). It appears to have some function in the maturation of
nuclear rRNAs, which imposes some evolutionary constraint on it (most
notably on the secondary structure of ITS 2). Although there is intra-individual
polymorphism in ITS, it does not appear to lead to inaccurate phylogenetic
reconstructions.
The ribosomal large subunit (26S in plants) has been used to a lesser extent
in phylogenetics. It is made up of a long, relatively conserved, region which is
broken up by 12 highly divergent regions. These divergent regions are not
present in prokaryotes, and are shorter in the examined plant taxa than in
animal taxa. Particularly within these divergent regions, there are complex
patterns of sequence evolution (cryptic similarity and compensatory slippage),
although these appear less liable to bias phylogenetic analysis in plant taxa
than in animals.
Homoplasy is not restricted to morphological data, and can occur at several
levels in molecular sequence data. First is the issue of orthology / paralogy,
second, that of the alignment of the orthologous sequences by the insertion of
hypothesised indels. Workers have used a variety of means, both more and
less subjective, to obtain their aligned matrices, and have used a variety of
methods to deal with the indel events within their matrices.
49
3.
Analysis of large data sets using parsimony
No efficient algorithm exists to find the optimal tree (using minimum evolution
or maximum parsimony) for over c. 20 sequences; heuristic methods must be
used (Page & Holmes, 1998). Despite recent improvements in the programs
used for maximum likelihood analyses, there is an upper limit of 50-60 taxa on
the size of data set which can be handled (Soltis & Soltis, 2000) so it is not (yet)
practicable for truly large data sets.
A recent review by Soltis and Soltis (2000) summarises the current
methodology for the analysis of large data sets (defined (arbitrarily) as having
over 150 placeholders (leaves / terminals)).
There has been a lot of debate about how feasible large analyses are, given
the size of treespace - for 10 taxa there are over 34 million possible rooted
trees (Page & Holmes, 1998); for 20 taxa there are 8.87 x 1023 possible rooted
trees (Soltis & Soltis, 2000); for 135 taxa there are 2.113 x 10267 different trees,
exceeding the number of particles in the known universe (Page & Holmes,
1998). Recent analyses of large angiosperm data sets have, however, come
up with strikingly similar topologies for different genes, despite searches not
swapping to completion, suggesting that real patterns are being recovered
(Soltis & Soltis, 2000).
3.1. Addition of data
It appears from analyses of the Angiosperm Data Set that adding more taxa
and more characters not only increases the accuracy of tree estimation, but
also reduces the length of time the computer requires to find a solution; this
seems to be because addition of taxa breaks up long branches and disperses
homoplasy (Soltis & Soltis, 2000). Adding more characters will not only make it
less probably that large numbers of trees with different topologies but the
same overall length will exist, but can also reduce the difference between the
length of the starting tree(s) in parsimony analysis and the length of the
shortest tree(s). Chase and Cox (1998) found, for a 141 taxon, 3 gene matrix
(rbcL, atpB and 18S), that this length difference explained the decrease in
analysis time for the combined gene matrix over the single-gene matrices. In
50
fact, they argue that genes or regions with high functional constraints will have
more homoplasy (e.g. convergence), therefore the starting trees will be further
from the shortest tree length than regions with lower constraints (Chase & Cox,
1998).
‘Long branch attraction’ is said to occur when there are large differences in the
rates of evolution among sequences, or where the sequences are quite
divergent. The length of branches per se is not the problem; the difficulty
occurs when the same substitutions occur independently on two long
branches (homoplasy). Intuitively, this is less of a problem if the long branches
are widely separated phylogenetically - closer relatives probably had
similarities to begin with which have been compounded (Page & Holmes,
1998). Adding taxa to regions where there are perceived to be difficulties is
one way of dealing with this problem (up to a point; it is not always possible to
add taxa, e.g. Richardson, 1999, Rhamnaceae Juss. Following a “relict
hypothesis” (Cronk, 1989) one would expect there to be many cases where
data addition was not an option due to extinction.) Maximum likelihood is said
to avoid such problems with homoplasy and so the comparison of trees
produced using both methods is often advocated (but not possible for large
data sets). An alternative (and faster) test, when two taxa are thought to be
exhibiting long branch attraction, is reanalysis of the data, each time including
only one of the two taxa. If the positions of the solitary taxa are invariant, then
long branch attraction can be ruled out as a factor (Siddall & Whiting, 1999).
Inconsistent trees can be made consistent by the addition of taxa (which
shortens the average branch length). Graybeal (1998) looked at whether it is
better to add characters or taxa; she found that it is “always preferable to add
taxa rather than characters” (Graybeal, 1998, p. 13). Trees are reconstructed
most accurately when taxa are added closest to the bases of long branches;
adding taxa near the tips is least efficient. For many real data sets this can be
a problem, because the ‘difficult’ parts of the tree are often those which contain
the most isolated clades, with the least potential for the addition of taxa.
Furthermore, when the sequence data give a polytomy, adding taxa will not
resolve the relationships; only adding more sequence data can give more
resolution.
51
Kim (1996) also gives recommendations for avoiding inconsistency problems
in tree reconstruction, but comes to a different conclusion: to use regions with
a low rate of change and to use fewer rather than more taxa (as larger trees are
more likely to include inconsistent branches).
3.2. Adding taxa and tree confidence measures
Sanderson (1990) discusses the problem of hidden homoplasy (for example,
homoplasy on the same branch or on the branches leading to two sister taxa).
The only way that this can be discovered is by the addition of taxa to the
phylogeny. Sanderson considers there to be a bias in hidden homoplasy
levels - “lineages in which many taxa have been ‘added’ by evolution will tend
to display a larger fraction of the actual homoplasy than depauperate lineages”
(Sanderson, 1990, p. 387). Thus tree lengths for phylogenies created with too
few taxa may be artificially low. Also, tree statistics could be influenced by the
diversification rate of the taxa being examined.
So the addition of taxa to the ingroup can increase measures of homoplasy. A
further effect is the breaking up of branches. While in many ways this is
desirable, reducing analytical problems with long branch attraction and
potentially anchoring inconsistent clades or taxa, our measures of tree support
rely to a greater or lesser extent on absolute branch length. In fact, one of the
most obvious measures is branch length; Bremer values are also strongly
correlated to it. Resampling measures like Bootstrapping and Jackknifing are
also less likely to recover shorter internal branches. The addition of taxa may
give a truer tree; it may also reduce islands of equally parsimonious trees;
however, it will not necessarily lead to improved values for tree confidence
measures.
Adding characters can also lead to decreased confidence values. For
example, with bootstrapping, the expected bootstrap frequency of a group G
which has r uncontradicted characters is 1-p% where p is the probability of any
character being absent from the resampled matrix. If n is the number of
characters, and r is constant, the bootstrap frequency of G is 1-(1-r/n)", a value
which decreases as n increases. Even the addition of autapomorphies to
52
groups irrelevant to G can therefore decrease the bootstrap frequency of G
(Farris et al., 1996). This actually relates directly to the issue of adding taxa to
sequence data matrices, because in many cases the addition of taxa will
increase the number of characters in the matrix, simply by turning some
constant characters into parsimony-uninformative characters (and likewise,
some uninformative characters into informative characters)
With a smaller data set. Wojciechowski, Sanderson and Hu (1999) found high
bootstrap support for a monophyletic clade of New World Astragalus species;
for a far larger data set it became low. Bootstrap proportions are expected to
decline with increased taxon sampling in a large clade, and eventually taxa will
be sampled which, by chance, have reversals at the synapomorphy for the
clade. Thus with the addition of taxa, it becomes more likely that homoplasy
will "knock out’ a clade (Wojciechowski, Sanderson & Hu, 1999). Adding taxa
may also break up internal branches, decreasing the levels of bootstrap
support for the clades at the ends of those branches. Procedures have been
suggested which give better estimates of data support. Using an iterated
bootstrap procedure (Efron et al., 1996), Wojciechowski. Sanderson & Hu
(1999) were able to get corrected values for their large analysis which are very
close to those they received for the smaller study.
3.3.
Rapid searching using confidence measures
Soltis and Soltis (2000) also suggest that, as well-supported clades appear
early-on in long parsimony analyses, it may be more efficient to only resolve
those groups with reasonable support. This can be done using parsimony
jackknifing (Farris et al., 1996). Savolainen et al. (2000) also argue that “[t]he
only relationships that we can be confident about are those that have high
internal support, and performing a bootstrap analysis does not first require
swapping to find the shortest tree”.
53
3.4.
Using better programs and methods
Advances in the programs available for phylogenetic analyses have also
helped the analysis of large data sets. PAUP* 4.0b3a (Swofford, 2000) run on
a G4 Macintosh is many times faster than running PAUP 3.1.1 (Swofford, 1993)
on a Macintosh with a Quadra operating system.
Goloboff (1999) describes the difficulty caused by ‘composite optima’ in large
data sets, which make it unlikely that any search using random taxon addition
and TBR will find a global optimum. Data sets with over 40 to 50 taxa can
exhibit local optima (or ‘islands’); large trees are composed of many sectors
(clades of over 40 to 50 taxa), each of which will have its own local optima. The
globally optimum tree will have all of the sectors at their local optima; Goloboff
estimates that, for the Angiosperm phylogeny data set from Chase et al.
(1993), there are 10 sectors and if each has a 50% chance of hitting its
optimum in any search, the probability of hitting the tree where all 10 sectors
are at their optima is 0.5’°, or less than one in 1000 replicates. However,
identification of this problem of composite optima has led to a number of
analyses methods which are designed to solve it. These methods do not
spend time searching for large numbers of equally parsimonious trees at
different optima, but concentrate on finding the shortest possible trees quickly
(Goloboff, 1999).
One of these is Nixon’s Parsimony Ratchet method (1999, which can be
implemented with the PC based packages DADA and NONA), which is able to
sample many different tree islands. Nixon claims that, compared to previous
search strategies, the parsimony ratchet is more likely to encounter shorter
trees in any given time and collects a broader sample of trees of any given
length. Nixon (1999) reanalysed the Chase et al. (1993) 500 taxon data set.
Chase et al. spent one month TBR swapping on a single tree, using PAUP.
Rice et al. (1997) reanalysed the matrix; they swapped with TBR for 11.6
months, finding trees 5 steps shorter. Using NONA, Nixon found trees the
length of the Chase et al. trees in about 15 minutes, and the length of the Rice
et al. trees in between 30 minutes and one hour (depending on parameters
used). In between one and a quarter and two and a quarter hours, ratchet
analysis found trees two steps shorter than the Rice et al. trees.
54
As long as the search for the shortest tree is a recognised goal of phylogenetic
analysis (but see provisos in Savolainen et al., 2000), such software and
hardware advances will dramatically cut analysis times.
3.5.
Super trees
Most individual cladistic studies only sample a few taxa; thus our knowledge of
the wider tree of life is fragmentary. However, topologies which share several
taxa can be ‘grafted’ together (Sanderson, Purvis & Henze, 1998). A tree which
is made up in such a way is termed a ‘supertree’, and may include trees from
several different types of data set (different genes or morphology). A ‘strict
supertree’ is a supertree which agrees with all the trees from which it was
derived (Sanderson, Purvis & Henze, 1998). Algorithms are also available to
calculate ‘reduced supertrees’, which can be constructed from source trees
which are not completely compatible (Wilkinson & Thorley, 1998).
The supertree approach can be used after a large data set has been analysed
phylogenetically to obtain an overall topology, to graft clades which have been
subjected to more intense sampling onto the main tree (Soltis & Soltis, 2000).
3.6.
Compartmentalization
This method involves partitioning the data to allow subset analysis (Mishler,
1994; Mishler et al., 1998). Known monophyletic groups can be represented in
the analysis by an inferred hypothetical ancestor (with character states based
on the group rather than an exemplar taxon). Alternatively, compartments can
be analysed using constraints imposed from the topologies found by local
analyses. Thus the method would be followed thus: 1. Global analysis to
identify compartments. 2. Local analysis within compartments. 3. Global
analysis, with compartments represented by hypothetical ancestors or as
constraint trees.
Of course, as this technique requires a global analysis in the first instance, it
can still require intensive computer time. However, one benefit is that the
homology assessment within compartments will be much improved from the
55
global analysis; this technique is most likely to be useful in the analyses of
large data sets across large phylogenetic distance (Soltis & Soltis, 2000) or in
data sets which contain conserved and variable regions.
3.7
Summary
Although heuristic searches must be used to analyse large data sets, and it
has previously been supposed that the vast size of treespace makes it
impossible to find the best solutions, current literature seems to be converging
on the view that the problem is not intractable. Adding more characters to a
matrix seems to decrease analysis time by making the length of the starting
tree closer to that of the most parsimonious tree, while adding taxa can negate
problems of homoplasy (‘long branch attraction'). It may not even be
necessary to find the shortest tree for a data set; several-gene studies suggest
that the clades which are rapidly recovered (e.g. by bootstrapping) are those
which are most reliable overall, so we may not then need to spend a long time
searching for further relationships in which we can have little confidence.
56
4.
Begoniaceae Bercht. & J.Presl.
4.1
Size and distribution
The Begoniaceae includes the genera Symbegonia Warb. (c. 12 species, New
Guinea), Hillebrandia Oliver (monotypic, Hawaiian archipelago) and Begonia L.
Begonia is one of the largest genera of vascular plants, with around 1400
named species and certainly much undescribed material from less collected
areas like Sulawesi and the Philippines. Begonia has a near-pantropical
distribution; it is absent only from Australia and New Zealand and extends as
far north as the Western Hills near Beijing. Species in the Begoniaceae are
largely understorey herbs, although the family also includes epiphytes, shrubs
and sub-trees. The monophyly of the family has never really been questioned;
autapomorphies of the family like the asymmetric leaf, dry 3 winged fruit and
bifid style are common to most of the species, while a ring of collar cells below
the micropylar-hilar part of the seed is present in all species (Bouman & de
Lange, 1983). Hiiiebrandia is distinguished by being the only member of the
family to have a semi-inferior ovary, while Symbegonia is characterised by
including the only Asian species which have complete fusion of all tepals in the
female flowers into long tubes.
4.2
Taxonomic history
4.2.1 Begoniaceae:
The most recent comprehensive monograph of the
Begoniaceae was by Irmscher (1925); Smith et al. (1986) produced an
illustrated key to the species of Begoniaceae - subsequent taxonomic changes
and the publishing of many new species render this rather unwieldy work
outdated.
Although the order in which Begoniaceae is placed varies, the families it has
been considered to be allied to are usually consistent.
For example,
Begoniaceae has been placed in Passiflorales (Bentham & Hooker, 1862, with
Samydaceae Vent. [= Flacourtiaceae Rich.], Loasaceae Juss. ex DC,
Turneraceae Kunth ex DC, Passifloraceae Juss. ex DC, Cucurbitaceae Juss.
and Datiscaceae Bercht. & J.Presl ), in Cucurbitales (Hutchinson, 1959, with
57
Cucurbitaceae, Datiscaceae and Caricaceae Dumort.) and in the Violales (by
Richardson, 1993, who comments that Begoniaceae is an “homogeneous
assemblage of no obvious affinities
usually placed in the V iolales......
probably most closely related to Datiscaceae” (p. 114), and by Mabberly, 1998,
who also comments that Begoniaceae is considered to be allied to
Datiscaceae).
Begoniaceae is placed within the Cucurbitales by recent large-scale molecular
phylogenies e.g. Savolainen et al.’s rbcL phylogeny (2000), which includes it in
a clade with Anisophyllaceae Ridley., Datiscaceae, Cucurbitaceae,
Coriariaceae DC, Corynocarpaceae Engl, and Tetramelaceae (Warb.) Airy
Shaw. Datiscaceae has a sister group relationship with Begoniaceae in
phylogenies produced from rbcL sequence data (Chase et al., 1993; Swensen,
Mullin & Chase, 1994; Swensen, 1996; Swensen, Luthi & Rieseberg, 1998)
and 18S rDNA sequence data (Soltis et al., 1997, Swensen, Luthi & Rieseberg,
1998).
4.2.2 Begonia:
A recent subgeneric treatment classifies Begonia species
into 63 sections, each limited to one continent (Doorenbos, Sosef & de Wilde,
1998). There has been no published phylogeny of the genus (although
Doorenbos, Sosef & de Wilde (1998) produced a phenogram of sectional
similarities, based on some admittedly polyphyletic sections). The delimitation
of most of the sections of Begonia bate from 1855; Klotzsch created them as
genera in his monograph of the Begoniaceae; A. de Candolle (1859) reduced
most of these genera to sections within a more broadly defined Begonia.
However, the subsequent discovery of many intermediate species means that
several of the boundaries to these taxa are no longer distinct (Tebbitt, 1997).
Doorenbos, Sosef & de Wilde (1998) have produced a complete revision of the
sections of the genus, which also includes a complete list of currently accepted
species.
58
4.3
Taxonomie problems within Begonia
4.3.1 Homoplasy: One of the major problems with the genus Begonia is that,
while it is comparatively easy to assign specimens to the genus, working out
where they belong within it is extremely problematic. Identification to section is
sometimes possible, identification to species is virtually impossible without at
least a good indication of the area of geographic origin of the plant and some
prior knowledge of the plants. Furthermore, sectional delimitation is
inconsistent, for example the only characters shared by all members of section
Knesbeckia (Klotzsch) A.DC. are 3 locular fruit with bifid placentation
(Doorenbos, Sosef & de Wilde, 1998). These reproductive characters could be
considered quite reliable; however 3 locular fruit with bifid placentae are found
in 33 other sections of Begonia, 7 of which are African, 9 Asian and 17
American.
4.3.2 Genus size: Large genera are unwieldy and can be unpractical to
construct or use keys for. Many of the taxa currently recognised as sections in
Begonia were originally described as genera, and it may seem appealing to try
to reinstate some of these genera, to reduce the size of the genus back to
something more manageable.
a.
Morphological splits:
Dividing a large genus into several smaller
ones requires the identification of major phenetic discontinuities, so that the
resulting new genera are identifiable. However, if more divergent lineages
were moved out of Begonia, cutting along lines where there appears to be
most phenetic discontinuity, the result would be the removal of many of the
African species. Clear phenetic discontinuities between American and Asian
sections are not obvious. Africa is species-depauperate compared to Asia and
America, with only c. 150 species, so one would be left with a genus of c. 1250
species, still ranking among the larger vascular plant genera. Furthermore, the
African flora is relatively well studied and monographed and most of the
undiscovered species are liable to be found in regions like Sumatra, the
Philippines, New Guinea, Thailand, Viet Nam and Laos; it is more probable
that any morphological discontinuities between Asian sections will be filled in
as we discover and describe new species than that intermediates will be found
between the strikingly distinct morphologies of the African sections.
59
Doorenbos, Sosef and De Wilde (1998), in the most recent revision of Begonia,
have provided reliable placement of the estimated 1400 species into 63
preexisting sections, but have also highlighted the many problem areas within
the genus. A major difficulty in Begonia research has been establishing
whether species which have superficial similarities are closely or distantly
related. The taxonomy is confused by high levels of homoplasy in the
morphological characters traditionally used to delimit sections; consequently a
large proportion of these sections contain species which are not closely
related.
b.
Molecular splits:
Sequence divergence in ITS was reportedly very low
(Brouillet, pens. comm, to Tebbitt, 1995), indicating that Begonia is a genus in
which relatively rapid, recent spéciation has occurred (Tebbitt, 1997). Tebbitt
thus focused his research on cp-DNA, using restriction fragment length
polymorphisms (RFLPs) of nad4 exoni - nad4 exon2, psbC - trnS and trnC trnD for cladistic analysis of 25 taxa. Badcock (1998) sequenced into the trnC trnD intron (a non-transcribed non-coding region) from the tRNA genes,
obtaining between 835 (8. salaziensis (Gaud.) Warb.) and 1621 (8. rubella
Buch.-Ham ex D.Don) bases for 33 taxa. The data set contains a high number
of indels, many of which are parsimony-informative. However, sampling for
these phylogenies was concentrated on taxa from sections Sphenanthera
(Hassk.) Warb. (Tebbitt, 1997) and Knesbeckia ! Diploclinium (Lindl.) A.DC.
(Badcock, 1998); no large-scale phylogeny for the whole genus has been
constructed and no clear lines along which the genus could be split have been
isolated by these studies.
4.4
Why are there so many species of Begonia?
Begonia contains several very small sections, and a few very large ones. The
distribution of species per section (Figure 4.1) resembles the hollow curve
described previously (see Figure 1.1), and prompts similar questions about
taxonomy, such as whether the size of the genus Begonia reflects the
behaviour of a plant group or the behaviour of taxonomists. However,
attempting to answer such questions with the limited amount of phylogenetic
knowledge we have is meaningless given that authors accept that many of
60
these sections are not evolutionary units but artificial constructs.
Figure 4.1 :
The number of species per section for Begonia
(data from Doorenbos et al., 1998)
14
13
12
11
10
g
8
7
6
5
4
3
2
1
G
193
G
No. species
When addressing whether Begonia species richness is the product of recent
or ancient events, it is worth considering published estimates for the age of the
family. Wagstaff and Dawson (2000) use fossil evidence to infer a minimum
age of 55 My for a Begoniaceae / Datiscaceae clade in their rbcL phylogeny.
“The disparity in species-richness between families of the Cucurbitales
[Cucurbitaceae and Begoniaceae are species-rich, while the other families are
not] raises intriguing evolutionary questions” (p. 144): Has there been
extinction in some lineages but not in Cucurbitaceae and Begoniaceae? Has
the predominantly herbaceous nature of Begoniaceae and Cucurbitaceae
allowed radiation into diverse ecological niches? The age of these families
does not appear to relate to their species-richness, as, based on the fossil
record, the Cucurbitaceae are far older than the Tetramelaceae, Coriariaceae
and Corynocarpaceae, while Begoniaceae appear to be more recently derived.
Wagstaff and Dawson (2000) suggest that the disparity in species-richness
between these groups may be a result of “imposing ranks under a traditional
classification scheme” [thus artificial] and that a phylogenetic classification
61
assigning names to clades may better reflect patterns of diversification.
(However, this appears to rely on the number of nodes from the terminal taxa
down being the only consideration in rank assessment, without consideration
of branch lengths across the tree. Because they have sampled all 5
Corynocarpus Forster & Forster f. species for rbcL, and only 6 of the c. 1400
Begonia species, better sampling in Begonia would add in a vast number of
taxa on very short branches.)
4.5
Summary
Begonia is a remarkably species-rich genus and as such represents an useful
model for understanding the processes responsible for the generation of
biodiversity in the tropics. However, fundamental to any investigations seeking
to understand such processes is a reliable estimate of phylogenetic
relationship. Evolutionary hypotheses based on flawed estimates of
relationship will be misleading. Thus it is imperative to produce a phylogeny
for the genus before considering the evolutionary processes and patterns
within it.
62
4.6 Aims
The aims of this thesis are thus:
To produce and compare ITS and 2 6 8 phylogenies for Begonia.
To produce an ITS sectional-level phylogeny for Begoniaceae.
To investigate the effects of changing alignment methods and the
methods of analysis on tree topology.
To compare the ITS phylogeny with the existing data set for partial
sequence for the chloroplast trnC - trnD region (Badcock, 1998).
To investigate mophological correlations with ITS clades, and
morphological evolution in Begonia.
To investigate cytological evolution in Begonia.
To approach some understanding as to why Begonia is such a large
genus.
63
5.
Building a backbone
5.1
Introduction:
Obtaining Molecular-based Cladograms for Begoniaceae
Prior to evolutionary interpretation of molecular cladograms for Begonia, it is
necessary to evaluate the diversity, support and congruence of differing
topologies. Different topologies can stem from multiple most parsimonious
solutions from a single analysis to explain a given data set. In addition, using
different genes or parts of genes, different alignments and different search
algorithms, alternate topologies may also be found. In this chapter I evaluate
a range of cladograms obtained from Begoniaceae, to provide a framework for
interpreting the evolutionary history of the family in subsequent chapters.
My strategy has been to obtain partial 26S and ITS sequences for 38 species.
Initial results based on ITS alone presented alignment difficulties, particularly
among African species and with the outgroup. Thus, to provide an alternative
data set for the species which were difficult to align, the more slowly evolving
26S region was used. These two regions are physically proximal, maximising
the probability of common gene history. The species chosen for this two gene
approach were representative of the geographic range of the family, and
showed maximal ITS divergence. More intensive sampling using just ITS is
described in subsequent chapters.
5.2
Material and methods
5.2.1 Plant Material: The sources of plant material and vouchers used in this
analysis are listed in Table 5.1, with sectional placements from Doorenbos,
Sosef and de Wilde (1998). The choice of Datisca as outgroup was based on
a sister group relationship in phylogenies produced from rbcL sequence data
(Chase et al., 1993; Swensen, Mullin & Chase, 1994; Swensen, 1996;
Swensen, Luthi & Rieseberg, 1998), 18S rDNA sequence data (Soltis et al.,
1997; Swensen, Luthi & Rieseberg, 1998), and intuitive ideas about
morphology (Lindley, 1846; Lawrence, 1951; Dahlgren, 1980; Takhtajan, 1980;
Cronquist, 1981; Thorne, 1992; Bouman & de Lange, 1983; Boeswinkel,
1984). The monophyly of Begoniaceae was assumed due to the
65
synapomorphies of spirally arranged, asymmetric leaves and the ring of collar
cells below the micropylar-hilar part of the seed; also the Begonia species
sampled by previous molecular studies have been monophyletic with respect
to Datiscaceae and Cucurbitaceae (Swensen, Luthi & Rieseberg, 1998).
Table 5.1:
Taxa used in 26S and ITS analyses
SPECIES
SECTIONAL
PLACEMENT
GEOGRAPHIC DISTRIBUTION
SOURCE AND
ACCESSION No.
Begonia aequata
Peterm annia
Asia: Philippines (Luzon)
E 1997 2515
Begonia angularis
Pritzelia
America: Brazil (Rio de Janeiro, Minas Gerias)
E 1969 1797
Begonia ankaranensis
Quadrilobaria
Africa: Madagascar
GL 001 064 97
Begonia annobonensis
S exalaria
Africa: Cameroon, Principe, Sao Tom e, Pagalu
GL 007 059 98
Begonia balansana
Ignota
Asia: IndoChina
GL 002 152 95
Begonia capillipes
Tetraphila
Africa: Cameroon, Equatorial Guinea, Gabon
GL 004 079 97
Begonia convolvulacea
W ageneria
America: Brazil (Ceara, Bahia, Rio de Janeiro)
GL 001 093 79
Begonia crassirosths (=longifolia)
Sphenanthera
Asia: China
GL 007 079 97
Begonia dewildei
Scutobegonia
Africa: Gabon
GL 001 041 97
Begonia engleri
Rostrobegonia
Africa: Tanzania
E 1998 2762
Begonia fallax = B. malabarica
Ignota
Asia: India, Sri Lanka
GL 002 018 96
Begonia floccifera
R eichenheim ia
Asia: India
GL 030 099 89
Begonia francoisii
Quadrilobaria
Africa: Madagascar
GL 002 064 97
Begonia geranioides
Augustia
Africa: South Africa
GL 018 079 97
Begonia grandis var. holostyla
Diploclinium
Asia; China
E 1998 0035
Begonia holtonis
Ruizopavonia
America: Colombia, Ecuador
GL 011 129 84
Begonia incarnata
K nesbeckia
America: Mexico
GL 011 089 95
Begonia iucunda
Ignota
Africa: Congo, Dem. Rep. Congo
GL 022 079 97
Begonia lobata
Pritzelia
America: Brazil (Rio de Janeiro, Minas Gerias)
GL 020 167 95
Begonia luxurians
Scheidw eilaria
America: Brazil (Sao Paulo to Minas Gerais)
E 1968 5494
Begonia m adecassa
Nerviplacentaria
Africa: Madagascar
GL 003 064 97
Begonia masoniana
Coelocentrum
Asia: cult., Singapore
E 1998 0074
Begonia meyeri-johannis
M ezieria
Africa: East Africa
GL 002 041 97
Begonia molleri
Tetraphila
Africa: Sao Tome
GL 038 079 97
Begonia nossibea
Quadrilobaria
Africa: Madagascar
GL 007 064 97
Begonia obliqua
Begonia
America: Martinique
GL 005 105 91
Begonia palmata
Platycentrum
Asia: India, Nepal, Burma, China
E 1998 0059
Begonia poculifera
Squam ibegonia
Africa: Nigeria to Tanzania & Angola
E 1992 3143
Begonia roxburghii
Sphenanthera
Asia: India, Nepal, Burma
GL 004 093 79
Begonia salaziensis
M ezieria
Africa: Reunion, Mauritius
K 1986 412
Begonia scapigera
Loasibegonia
Africa: Nigeria, Cameroon, Gabon, Congo
GL 002 057 96
Begonia socotrana
Peltaugustia
Socotra
E 1989 1081
Begonia sp. 'macG'
?
America
GL 1969 6248
Begonia thomeana
Cristasemen
Africa: Sao Tome, Gabon
GL 054 079 97
Begonia violifolia
W eilbach ia
America: Mexico (Chiapas?)
GL 004 055 87
Datisca cannabina
N/A
Asia: S .W ., Him alayas
E 1984 1126
Datisca glomerata
N/A
America: USA, California
Susan Swensen
Symbegonia sanguinea
N/A
Asia: Papua New Guinea
GL 0 03 127 93
66
5.2.2 Molecular methods
A.
DNA extraction: DNA was extracted from fresh or silica gel-dried
leaves using an hexadecyl-trimethyl-ammonium bromide (CTAB) method
modified from Doyle and Doyle (1987), using one disc of fresh or silica dried
material, ground (using a plastic pestle, in the eppendorf tube) directly in 400
pi preheated (65° c) 2x CTAB with 2 pi 2-mercaptoethanol, a pinch of
polyvinylpolypyrrolidone (PVPP) and a pinch of acid-washed sand, and
incubated for c. 1 hr at 65°c in a water bath. Protein extraction was performed
with 500 pi 24:1 chloroform: isoamyl alcohol, gentle shaking, for c. 20 mins
then 10 mins centrifugation, 13,000 revs per minute (rpm); the supernatant
was removed and transferred to a clean eppendorf and this step was
repeated; the DNA was then precipitated from the supernatant by adding 2/3
volume freezer-cold isopropanol, and leaving overnight in a freezer. DNA was
pelleted by centrifugation (10 mins, 13,000 rpm) and left for at least 30 mins in
wash buffer (76% ethanol, 10 mM sodium acetate). The pellet was then dried
and dissolved in 50 pi tris-ethylenediaminetetraacetic acid (EDTA) (TE). See
also Kopperud and Einset, 1995, for a Begon/a-specific protocol.
DNA of Datisca glomerata was kindly supplied by Susan Swensen, Ithaca,
N.Y.; DNA for B. balansana was supplied by Mark Tebbitt, Brooklyn, N.Y.
B.
Sequence amplification and purification: For most taxa, ITS was
amplified using primers p4 (White et al., 1990) and p6 (Sluiman, pens, comm.,
1998). Where these did not result in a single clean amplification product,
other primers were used (see Table 5.2 for sequences of primers, and Figure
5.1 for their placement):
2g (Moeller & Cronk, 1997) and the reverse, 2g*.
p5 (White et al., 1990, modified by Moeller & Cronk, 1997, without the terminal ‘G ’ cited in their paper).
p61 (Oxelman in Oxelman & Linden, 1995).
17SE and 26SE (Sun et al., 1994).
Part of the 26S region was amplified using either primers p71 and p81
(Oxelman & Linden, 1995), or, where this was problematic, 2g* and p81.
Table 5.2: Primer sequences for ITS and 26S (5’ to 3’)
67
PRIMER
17SE(F)
p5 (F)
p6 (F)
2g* (F)
p71 (F)
2g (R)
p4 (R)
26SE (R)
p61 (R)
p81 (R)
SEQUENCE
ACGAATTCATGGTCCGGTGAAGTGTTCG
GGAAGGAGAAGTCGTAACAAG
GTAGGTGAACCTGCAGAAGGA
ACGTCTGCCTGGGTGTCAC
ACGAGTCGGGTTGTTTGGGAATG
GTGACACCCAGGCAGACGT
TCCTCCGCTTATTGATATGC
TAGAATTCCCCGGTTCGCTCGCCGTTAC
CATTCCCAAACAACCCGACT
CCCGCTCAGGCATAGTTCACCAT
Figure 5.1:
1 7S E
P5
Primer positions
p71
2g*
p6
jzlFct^
1«S
I
—
f
2g
p4
26S E
’ p61
p81
For B. morsei, where the DNA proved very problematic to amplify, ITS 1 and ITS
2 were amplified separately (p6 and 2g; 2g* and p4).
Polymerase chain reaction (PCR) was carried out in 50 |xl reactions, using
Biotaq DNA polymerase (0.2 ^il Taq, 5 pi 10x reaction buffer, 5 pi
deoxynucleoside triphosphates (dNTPs) at 2 mM, 2.5 pi MgCI^ at 50 mM, 1.5 pi
of each primer at 10 pM, 15-20 ng DNA, made up to 50 pi with water).
PCR products were electrophoresed in a 1.6% agarose gel, in 0.5 x Tris boric
acid EDTA (TBE) buffer with 2 pi ethidium bromide, and visualised on an ultra
violet light-box, to confirm that the PCR product was single banded.
Amplification products were purified using QIAquick PCR purification kits,
following protocols supplied by the manufacturer. Some double-banded
products were run out on agarose gels, cut out, and purified using QIAquick
Gel Extraction kits.
PCR amplification of ITS involved: a preliminary denaturing step, 94“ c for 3
minutes, (denaturing at 94“ c for 1 minute; annealing at 55“ c for 1 minute;
68
extension at 72°c for 1 minute 30 secs) for 28 - 30 cycles, a final extended
extension period of 72°c for 5 minutes, then a holding stage at 4°c, using a
Progene PCR machine.
PCR of 26S using p71 and p81 involved: a preliminary denaturing step, 95°c
for 4 minutes, then 30 cycles (denaturing at 95° c for 30 seconds; annealing at
57°c for 1 minute; extension at 72°c for 2 minutes), then a final extended
extension period of 72° c for 7 minutes, and a holding stage at 4°c, using a
Progene PCR machine. PCR of the 26S region using 2g* and p81 was
carried out using the ITS protocol.
A sequence for Datisca cannabina was obtained from Mark Tebbitt (Brooklyn,
N.Y.) and Susan Swensen (Ithaca, N.Y.); the sequence from Hillebrandia was
obtained from Susan Swensen (Ithaca, N.Y). Sequences for 8. dregei and its
varieties and 6. geranioides, B. socotrana, 6. samhahensis, B. floccifera and B.
dipetala were obtained from Mark Hughes, RBGE.
C.
Cloning reactions: Cloning was carried out for some ITS PCR
products, to check whether there were different copies present and because
heterozygosity for length mutations made some sequences unreadable from
consensus sequences. Ligation of the PCR product into the vector was
carried out using the protocol in the Promega pGEM-T Easy Vector kit, but
halving the reaction quantities. Reactions were spread onto ampicillin and
Luria-Bertani (LB) broth agar plates (with 20 ng/ml 5-bromo-4-chloro-3-indolylP-D-galactopyranoside (XGal) and 30 pi 0.1 M isopropyl-gthiogalactopyranoside (IPTG) for blue/white screening). Cells were cultured
overnight, 37°c, in flasks with 5 ml LB broth and 0.1 g/ml ampicillin. DNA was
isolated using QIAprep Spin kits and sequenced directly (3 pi product per 10 pi
sequence reaction, 2 pi sequencing mix).
D.
DNA sequencing: Sequencing was carried out using Amersham
Thermosequenase II dye terminator cycle sequencing kit (2 pi Thermo
Sequenase II reagent premix, 0.5 pi primer at 5 pM, 1-3 pi template, made up
to 5 pi with water).
69
PCR amplification involved 25 cycles of denaturing at 96°c for 10 secs,
annealing at 50° c for 5 secs, extension at 60° c for 4 minutes, then a 4°c
holding stage, using a Perkin Elmer 9600 PCR machine.
Sequence gels were run by staff at the Royal Botanic Garden, Edinburgh.
Sequences were edited and assembled using Sequence Navigator (Applied
Biosystems, Inc.) on a G4 Macintosh computer. All sequences will be
submitted to GenBank.
5.2.3 Alignment
a.
268:
The data were aligned by eye. Sites which included gaps in
more than 3 of the included species were removed from the data set prior to
analysis, because their precise placement was open to interpretation.
Excluded characters are 1-44, 68, 211-213, 335-337, 492, 499 and 587-595
from the matrix, see CD-ROM.
b.
ITS:
The data were aligned by eye; many sites were excluded
because the alignment was variable (same exclusion matrix as used in next
chapter). Excluded characters are 1-183, 188, 200, 204, 211-217, 223-225,
230-249, 255-256, 266, 274-329, 340-366, 378, 383-384, 406-407, 415, 419421, 426-428, 435-437, 444, 449-451, 460, 466-469, 475-483, 493-497, 503507, 513-514, 539, 571, 577, 603, 606, 615, 649, 686, 688, 693-856, 886-901,
930-931, 944, 957-966, 983-984, 992-993, 1013-1014, 1018, 1023, 10291035, 1041-1053, 1064-1093, 1110-1114, 1121-1122 and 1137-1154 from the
matrix, see CD-ROM.
5.2.4 Analysis:
Data matrix statistics (e.g. number of parsimony-
informative characters, uncorrected pairwise differences (total number of
differences/total number of available sites - Swofford et al., 1996)) were taken
from PAUP* 4.0b2a (Swofford, 2000); the skewedness statistic g1 was
estimated for a sample of 10,000 random trees, and the permutation tail
probability test (PTP) was performed on the ingroup to assess the degree of
cladistic covariation in the data set (Kitching et al., 1998) (MP heuristic search,
70
simple addition, saving no more than 100 MPTs for each replicate; 100 PTP
replicates).
Three different types of analysis (MP, ME and ML) were run on each of three
data sets, 26S, ITS and a combined 26S/ITS matrix. Maximum parsimony
methods search for solutions which minimise the amount of evolutionary
change required to explain the data, while maximum likelihood attempts to
estimate the actual amount of evolutionary change according to a (specified)
evolutionary model. Thus parsimony can underestimate ‘true’ change, due to
unseen events (e.g. superimposed changes), while likelihood models can
allow for such changes. Distance measures like minimum evolution can be
used where the data set is too large for maximum likelihood studies to be
feasible, although in simulation studies, likelihood methods have consistently
outperformed distance methods in choosing the correct tree (Swofford et al.,
1996).
5.2.4.1
Maximum parsimony (MP):
Heuristic analyses were
performed using maximum parsimony. No more than 100 MPTs were saved
for each step, with TBR swapping to completion, zero length branches
collapsed, for 1000 random addition replicates.
Bootstrapping was performed using the fast-heuristic search option, with
10,000 replicates. Bremer support was calculated using AutoDecay
(Eriksson, 1998) (10 random additions, TBR swapping).
5.2.4.2
Maximum likelihood (ML):
Using likelihood, the
explanation which makes the observed data the most likely (i.e. probable) is
preferred (Page & Holmes, 1998). An initial tree was calculated using the
HKY85 model (which allows unequal base frequencies and for transversions
(tv) and transitions (ts) to have different substitution rates) with gamma
distribution shape parameter (a) and ti/tv ratios estimated using ML, no
molecular clock assumed (discrete gamma approximation, 4 rate categories,
average rate approximated by mean). This tree was used to estimate ti/tv
rations and a and was then used as the starting tree for TBR swapping, using
the HKY85 model.
71
Low values for the gamma distribution shape parameter a result from an Lshaped distribution whereby most sites have little variation while a few sites
have very high rates of substitution, while when a > 1 the distribution is bell
shaped (i.e. there is a small range of rates) (Page & Holmes, 1998).
5.2.4.3
Minimum evolution (ME): For an unrooted metric tree for n
sequences, there are (2n-3) branches, each with their own length. The sum of
these branch lengths is the length of the tree, L; the minimum evolution tree is
that which minimises the value of L. Although this method is similar to
parsimony, length is computed from pairwise differences rather than from the
fit of characters to a tree (Page & Holmes, 1998). The LogDet/paralinear
distance measure (which recovers an additive distance between sequences
even when the base composition is variable - Page & Holmes, 1998) was
used; a starting tree was calculated using neighbour joining then swapped
with TBR. Zero length branches were not collapsed. (In additive distances,
the distance between any two taxa is equal to the sum of the branches joining
them - Swofford et al., 1996.)
5.3
Results
The data matrix of 263 sequences is presented in the Appendix, 14.5.
For each cladogram which is presented, the letters AF stand for Africa, S.AF,
for southern Africa, MAD for Madagascar, SOC for Socotra, AM, America and
AS, Asia.
5.3.1 268:
5.3.1.1
Data set:
The included data set comprises 439 constant
characters, 34 parsimony-uninformative characters and 58 parsimonyinformative characters.
Uncorrected pairwise distances (as given in PAUP 4*) are highest between
Datisca cannabina and B. dewildei (0.084); within the ingroup, the highest
values are between B. ankaranensis and B. crassirostris (0.065). The lowest
value between the outgroup and ingroup is between D. glomerata and B.
72
engleri (0.047); the lowest value within the ingroup is 0.000, between B.
molleri and B. capillipes and also between B. nossibea and B. francoisii. The
two species of Datisca have a distance of 0.011.
Mean base frequencies for the data matrix are as follows:
A = 0.214
C = 0.257
G = 0.352
T = 0.177
(GC = 0 .609)
The skewedness statistic gi is -0.395. The probability for the PTP test is
0.001.
5.3.1.2
MP:
216 trees of length 185 were retained. To test whether
there were more MPTs, these trees were used as starting trees on a second
heuristic search and were swapped to completion. No shorter trees were
found, nor any more equally parsimonious trees.
The consistency index is
0.61 (excluding uninformative characters, 0.52); retention index is 0.79. 12
clades had over 50% bootstrap support. 29 nodes were resolved in the strict
consensus tree. See Figure 5.2 for the strict consensus tree and one of the
phylograms.
The support values for internal branches are generally low; the best supported
clade consists of some African and Madagascan taxa. African taxa are
resolved as basal; a derived clade with 52% bootstrap support includes all the
Asian and American taxa as well as one Southern African species (B.
geranioides) and one Socotran species (B. socotrana). The branch lengths in
this derived clade are generally shorter than in the rest of the tree, with internal
branch-lengths often in the region of 1 to 3 changes.
73
Figure 5.2;
MP strict consensus of 18 MPTs and phylogram, 26S data set
r,
D. cannabina
j — D. cannabina
_m.
D. glomerata
1— D. glomerata
B. annobonensis
B. annobonensis
B. engleri
B. engleri
lo
B. poculifera
AF
B. capillipes
B. poculifera
I B. capillipes
I B. molleri
B. molleri
p- B. meyeri-johannis
B. meyeri-johannis
B. salaziensis
B. salaziensis
MAD
B. madecassa
B. madecassa
E
B. ankaranensis
B. ankaranensis
t
B. nossibea
B. nossibea
B. francoisii
B. francoisii
B. thomeana
B. thomeana
C
B. dewildei
B. scapigera
B. scapigera
B. iucunda
B. iucunda
S.AFi
B. dewildei
B. geranioides
B. geranioides
B. holtonis
B. holtonis
B. obliqua
B. obliqua
AM+AS
B. aequata
-C
B. aequata
r lf
B. masoniana
_ 1 change
S. sanguinea
B. masoniana
S. sanguinea
—
B. convolvulacea
B. convolvulacea
B. angularis
B. angularis
- B. luxurians
B. luxurians
4 “ B. sp., macG
B. sp., macG
B. lobata
— B. lobata
r B. incamata
B. incamata
— B. grandis holostyla
B. grandis holostyla
■” B. palmata
B. palmata
" B. balansana
B. crassirostris
B. crassirostris
B. balansana
__|
B. roxburghii
B. roxburghii
SOC
_
59 parsimony-informative
ctiaracters
ro- B. socotrana
— B. violifolia
Bootstrap support above lines;
Bremer support below lines
Tree length 193
Cl = 0.611
Cl ex uninformative = 0.519
RI = 0.794
— B. fallax
— B. floccifera
74
- B. socotrana
r B. violifolia
■ B. fallax
—
B. floccifera
5.3.1.3
ML:
The likelihood settings were as follows:
Assumed nucleotide frequencies are the mean base frequencies for the data
matrix; rates assumed to follow a gamma distribution with shape parameter a
= 0.0906; transition/transversion ratio = 2.943
(k
= 5.982); number of distinct
data patterns under this model = 129. -Ln likelihood of best tree found is
1856.375 (see Figure 5.3).
African taxa are resolved as basal, with Asian and American taxa in a derived
clade with S. geranioides and B. socotrana. The tree is congruent with those
derived by parsimony except for some of the placements of taxa within the
Asian/American clade. All the clades with bootstrap support in the MP trees
are found in the ML tree.
5.3.1.4
ME:
One tree was found, with tree-score 0.3667 (see Figure
5.4). There are many clades in common with the trees found by MP and ML,
with African taxa basal, but the placement of a few taxa is radically different. B.
iucunda, B. annobonensis and B. masoniana have all shifted across clades.
B. iucunda is not sister to the American/Asian clade, but is basal to an
African/Madagascan clade; B. annobonensis is not sister to the rest of
Begonia, but is included within an African/Madagascan clade, and B.
masoniana is not within the American/Asian clade but is in an African clade.
75
Figure 5,3:
Figure 5.4:
ML, 26S
ME, 26S
D. cannabina
C
C
D. glomerata
D. glomerata
B. engleri
B. annobonensis
—
B. engleri
B. iucunda
B. poculifera
AF
D. cannabina
l
B. poculifera
B. molleri
B. molleri
B. capillipes
B. capillipes
AF
— B. meyeri-johannis
B. annobonensis
B. meyeri-johannis
B. salaziensis
B. salaziensis
B. nossibea
k
MAD
r
B. nossibea
B. francoisii
k
MAD
B. madecassa
B. francoisii
B.
ankaranensis
B. thomeana
B. madecassa
B. ankaranensis
B. thomeana
B. dewildei
C
B. scapigera
1 -0 - B. masoniana
B. dewildei
B. iucunda
I B. aequata
B. scapigera
'--------- B.masoniana
B. geranioides
B. obliqua
B. angularis
B. holtonis
B. convolvulacea
r B. luxurians
B. aequata
s. sanguinea
B. sp.. macG
AM + AS
B. convolvulacea
B. lobata
- B. angularis
S. sanguinea
—
B. incamata
AM + AS
"" B. grandis holostyla
B. luxurians
B. palmata
B. lobata
“ B. crassirostris
B. socotrana
4— B. balansana
B. fallax
B. violifolia
B. roxburghii
B. socotrana
B. floccifera
S.AF
— B. incamata
A B. geranioides
\
|— B. obliqua
'—
B. grandis holostyla
B. holtonis
—
— B. violifolia
0.01 substitutions/site
Score of best tree(s)
found = 1856.37520
B. sp., macG
I—
0.005 changes
■ B. fallax
— B. floccifera
Score of best tree(s)
found = 0.36666
76
B. palmata
B. balansana
B. crassirostris
B. roxburghii
5.3.2 ITS sequence data:
5.3.2.1
Data matrix:
595 characters are excluded; the included data set comprises 223 constant
characters, 70 parsimony-uninformative characters and 214 parsimonyinformative characters.
Uncorrected pairwise differences range from 0.006 (8. nossibea to 8.
francoisii) to 0.279 (8. floccifera to 8. iucunda) within Begonia, and from 0.207
(8. grandis to Datisca) to 0.302 (8. engleri to Datisca) between the ingroup and
outgroup.
The mean base frequencies for the matrix are as follows:
A = 0.217
C = 0.275
G = 0.295
T = 0.213
(GC = 0.570)
The skewed ness statistic g1 is -0.694; the probability for the PTP test is 0.010.
5.3.2 2
MR:
3 most parsimonious trees were found, length 971.
These were used as starting trees for a second round of searches with no
restrictions on number of trees saved. No more or equally parsimonious trees
were found. The consistency index is 0.50 (0.46 excluding uninformative
characters); retention index is 0.63. 18 clades had over 50% bootstrap
support. 35 nodes were resolved in the strict consensus tree. The strict
consensus tree and one of the phylograms are presented in Figure 5.5.
African taxa are basal in Begonia, although the positions of 8. iucunda and a
8. annobonensis/B. engleri clade are the reverse of the 26S MP trees. Again,
American and Asian taxa are in a derived clade which also includes 8.
geranioides and 8. socotrana. This clade has generally shorter branch
lengths than the more basal part of the tree. Like in the 26S cladograms, there
is little bootstrap support for the internal branches; however, a clade of 5
Madagascan species has 100% bootstrap support, and a clade of 5 American
species has 98% support.
77
Figure 5.5:
Strict consensus of 3 MPTs and phylogram, ITS data set
d. glomerata
E
glomerata
c:
cannabina
B. iucunda
iucunda
— B. thomeana
thomeana
B. dewildei
dewildei
AF
c
scapigera
B. scapigera
B. poculifera
poculifera
B. capillipes
capillipes
£
molleri
B. molleri
B. meyeri-johannis
meyeri-johannis
madecassa
[— B. madecassa
salaziensis
r B. salaziensis
MAD
I— B. ankaranensis
ankaranensis
æ
D. cannabina
nossibea
B. nossibea
francoisii
B. francoisii
B. engleri
engieri
[
B. annobonensis
annobonensis
geranioides
"Âs^
B. geranioides
c
masoniana
- B. masoniana
— B. fallax
B. fallax
SOC
socotrana
floccifera
*—
B. floccifera
palmata
■ B. balansana
crassirostris
t
roxburghii
B. crassirostris
B. roxburghii
— B. grandis hoiostyla
grandis hoiostyla
I— B. aequata
aequata
100
B. socotrana
— B. paimata
balansana
AS
I
L s. sanguinea
sanguinea
B. incamata
incamata
B. holtonis
holtonis
B. obliqua
obliqua
AM
B. vioiifoiia
violifolia
B. convolvulacea
convolvulacea
I—
luxurians clone
sp., macG
Bootstrap support above
lines;
Bremer support below
line
10 changes
|- B. sp., macG
B. angularis
angularis
£ !•
B. luxurians clone
214 parsimony-informative
characters
lobata
Tree length 971
Cl = 0.501
Cl ex uninformative = 0.456
Rl = 0.627
78
B. lobata
5 3.2.3
ML:
Assumed nucleotide frequencies are the mean
frequencies for the data matrix; rates assumed to follow a gamma distribution
with shape parameter a = 0.2309; transition/transversion ratio = 2.062
(k =
4.233); number of distinct data patterns under this model = 442; -Ln likelihood
of the best tree found is 7756.352 (see Figure 5.6).
Most of the African species are in a clade sister to the rest of Begonia\ 6.
annobonensis and B. engleri are sister to the American/Asian clade. Clades
are broadly similar to those on the MP tree, although deeper level
relationships of the African taxa are different. As with the 26S cladograms, all
clades with bootstrap support in the MP analyses are present. American and
Asian taxa are each in monophyletic clades.
5 3.2.4
ME:
The tree found had a minimum evolution score = 1.98289 ■
see Figure 5.7. Internal branches are very short compared to the terminal
branch lengths. Again, many of the clades are similar to those recovered by
MP and ML, although their positions relative to each other vary; furthermore, B.
meyeri-johannis and B. thomeana have notably different positions in the ME
tree to the MP and ML trees.
79
Figure 5.6;
single ML tree, ITS
Figure 5.7;
single ME tree, ITS
D. cannabina
C
D. glomerata
D. glomerata
D. cannabina
B. thomeana
B. iucunda
B. iucunda
B. dewildei
B. dewildei
B. scapigera
B. scapigera
B. meyeri-johannis
B. poculifera
B. thomeana
B. capillipes
£
B. poculifera
B. molleri
[£ _ BB. capillipes
B. molleri
B. meyeri-johannis
— B. madecassa
AF
B. madecassa
B. salaziensis
MAD
AF
r~ B. salaziensis
MAD
i— B. ankaranensis
B. ankaranensis
q
B. nossibea
B. nossibea
B. francoisii
B. francoisii
B. engleri
------------------------- B. engleri
B. annobonensis
S.AF,
B. annotxxiensis
B. geranioides
B. holtonis
■ B. incamata
B. obliqua
■ B. violifolia
B. convolvulacea
B. holtonis
AM
— B. luxurians clone
LO
AM
B. obliqua
■ B. sp., macG
B. convolvulacea
B. angularis
£
|— B. sp., macG
B. luxurians clone
I—
B. incamata
B. angularis
B. violifolia
B. lobata
AF
— B. aequata
1_AS_
^ —
S. sanguinea
I
I
„
B. masoniana
S. sanguinea
B. fallax
JI j —SQC
o—
B. geranioides
■ B. aequata
- B. masoniana
AS^
B. lotaata
—
_
B. grandis hoiostyla
AS
B. socotrana
B. fallax
B. floccifera
SQC
B. socotrana
— B. grandis hoiostyla
B. floccifera
B. balansana
—
_
0.01
—
B. palmata
B. roxburghii
B. crassirostris
substitutions/site
B. roxburghii
-Ln likelihood = 7756.35145
B. crassirostris
B. palmata
— 0.01 changes
B. balansana
Minimum evolution score = 1.98289
80
5.3.3 Combined molecular analysis.
5.2.3.1
Data matrix: Values for types of character in the matrices are
additive (i.e. the sum of those for the 26S data set and for the ITS data set).
The mean base frequencies for the combined matrix are as follows:
A
C
G
T
=
=
=
=
0.216
0.266
0.324
0.194
The skewedness statistic g1 is -0.584; the probability for the PTP test is 0.010.
5.3.3.2
MP:
22 most parsimonious trees were found, of length 1298,
consistency index 0.50 (0.45 excluding uninformative characters) and retention
index 0.64. 23 clades had over 50% bootstrap support. 31 nodes were
resolved in the strict consensus tree. See Figure 5.8 for the strict consensus
tree and one of the phylograms.
The topology recovered is quite different from that recovered from the 268 data
set alone, but is similar to that recovered from the ITS data set, although the
positions of the African taxa 6. geranioides and B. meyeri-johannis have
changed, and the Asian and American taxa are both monophyletic in this
topology. Again, branch lengths within the Asian and American clade are
generally shorter than those in the more basal clades.
81
Figure 5.8:
26S and ITS combined, MP strict consensus of 22 MPTs and
phylogram
c
D. glomerata
urn.
D. glomerata
D. cannabina
D. cannabina
B. iucunda
B. iucunda
B. thomeana
B. thomeana
B. dewildei
B. dewildei
o-
—
B. scapigera
AF
B. meyeri-johannis
B. meyeri-johannis
—
B. poculifera
_SB_
B. poculifera
I— B. capillipes
B. capillipes
^
® *— B. molleri
MAD
B. scapigera
B. molleri
B. madecassa
B. madecassa
B. salaziensis
r B. salaziensis
— B. ankaranensis
B. ankaranensis
86
4
lo o l
B. nossibea
B. nossiljea
-f
B. francoisii
B. engleri
B. engleri
B. annobonensis
B. annobonensis
B. geranioides
B. geranioides
AM
rOH
B. francoisii
B. violifolia
B. violifolia
B. incamata
- B. incamata
B. holtonis
B. holtonis
B. obliqua
B. obliqua
B. convolvulacea
B. convolvulacea
I- B. sp., macG
B. luxurians clone
98
I—
B. sp., macG
C
B. angularis
B. angularis
B. lobata
B. bttata
r B. t)alansana
B. masoniana
B. grandis hoiostyla
— B. palmata
B. aequata
I—
B. crassirostris
S. sanguinea
1—
B. roxburghii
B. fallax
B. fallax
—
socotrana
B. palmata
JL
B. masoniana
— 10 changes
— B. grandis hoiostyla
B. balansana
parsimony-informative
characters = 291
B. crassirostris
y :
B. socotrana
— B. floccifera
B. floccifera
Bootstrap support
above lines;
Bremer support below
lines
B. luxurians clone
Tree length = 1298
Cl = 0.5031
Cl ex uninformative = 0.4529
Rl = 0.6378
B. roxburghii
82
B. aequata
S. sanguinea
5.3.3 3
ML:
Assumed nucleotide frequencies are the mean base
frequencies for the matrix; rates assumed to follow a gamma distribution with
shape parameter
a
= 0.2265; transition/transversion ratio = 2.138
(k
= 4.368);
number of distinct data patterns under this model = 433; -Ln likelihood of best
tree found is 7231.487 (see Figure 5.9 for tree).
The tree produced by ML for the combined data is quite different to that
produced by ML for the 26S data set, but is almost identical to that produced
from the ITS data set (the positions of B. incamata and B. violifolia are slightly
different). American and Asian taxa are monophyletic, with African taxa as
sister and basal.
5.3.3.4
ME:
One tree with minimum evolution score 1.22855 was
found (see Figure 5.10).
The tree differs from both the 26S and the ITS ME trees, for example in the
position of the S. annobonensis IB . engleri clade.
83
Figure 5.9:
ML tree, combined data
Figure 5.10: ME tree, combined data
c
D. glomerata
■ D. cannabina
D. cannabina
- B. engleri
B. thomeana
B. annobonensis
B. iucunda
B. thomeana
B. dewildei
--------------B. iucunda
B. scapigera
----------------- B. dewildei
B. poculifera
B. scapigera
B. capillipes
B. meyeri-johannis
B. molleri
—
B. meyeri-johannis
AF
B. capillipes
r B. salaziensis
r B. nossibea
“ B. madecassa
MAD
— B. ankaranensis
^ B. francoisii
B. nossibea
B. engleri
B. francoisii
- B. annobonensis
SAFr
AM
B. holtonis
B. geranioides
. B. obliqua
B. holtonis
c
— B. convolvulacea
B. obliqua
— B. sp., macG
B. incamata
|— B. luxurians
B. violifolia
^
B. convolvulacea
AM + AS|
- B. sp., macG
SOC
- B. socotrana
B. angularis
B. floccifera
B. lobata
- B. violifolia
— B. fallax
B. aequata
S.AF
—o —
sanguinea
B. aequata
B. fallax
C S. sanguinea
B. socotrana
SQC
- B. geranioides
— B. incamata
B. masoniana
AS
B. angularis
L B. lobata
— B. luxurians
s.
B. molleri
r B. salaziensis
r" B. ankaranensis
AF
B. poculifera
HI'
— B. madecassa
MAD
D. glomerata
- B. masoniana
B. floccifera
■B. grandis
— B. grandis
— B. palmata
— B. crassirostris
L- B. balansana
— B. roxburghii
— B. palmata
— B. crassirostris
•- B. balansana
—
— 0.01 substitutions/site
B. roxburghii
— 0.01 changes
Minimum evolution score = 1.22855
-Ln likelihood = 7231.48689
84
5.3.4 General results
For a summary of how much agreement (or disagreement) there is between
the three analytical methods for each of the three data sets, see the strict
consensus trees (of the trees produced using each analysis type) for each
data matrix. Figure 5.11. There are 11 nodes resolved in the 26S tree, 20 in
the ITS tree and 17 in the combined 26S-ITS tree. Therefore, the 268 data set
shows least similarity between MP, ML and ME, while the ITS data set shows
most (estimated by the amount of resolution in the strict consensus trees).
This is partly down to radical clade shifts, in the 26S analyses, by only a limited
number of taxa between the ME tree and the other two analyses (ML and MP).
Figure 5.11; Strict consensus of MP, ML and ME trees for 26S, ITS and
combined data sets
c. Combined 26S and ITS
b. ITS
a. 26S
j-
D. glomerata
^
D. cannabina
B. thomeana
B. iucunda
B. dewildei
B. scapigera
B. poculifera
B. capillipes
B. molleri
— B. meyeri-johannis
Lr
MAD
salaziensis
madecassa
ankaranensis
nossibea
francoisii
engleri
annobonensis
B.
“ “ B.
“ ~B.
I” B.
B.
B.
B.
incamata
violifolia
grandis
geranioides
holtonis
obliqua
masoniana
Lr
B. aequata
S. sanguinea
B. fallax
B. socotrana
B. floccifera
B. crassirostris
B.
B.
B.
—— B.
roxburghii
palmata
balansana
convolvulacea
------- B.
------- B.
------- B.
meyeri-johannis
thomeana
iucunda
dewildei
scapigera
poculifera
~
_r
*“
^
— B.
' B.
' B.
_j“ B.
^ B.
B.
B.
eg:
glomerata
cannabina
AF
^1
MAD I---------------1
r^i
capillipes
molleri
m adecassa
salaziensis
ankaranensis
nossibea
francoisii
engleri
eg;
MAD
-O
AF
eg;
annobonensis
incamata
violifolia
c :
O-
AM +
AS
c :
:B
■B
B
B
B
B
B. angularis
T B. luxurians
r B. sp., macG
B. lobata
grandis
geranioid
masoniana
holtonis
obliqua
aequata
sanguinea
fallax
socotrana
floccifera
crassirostris
roxburghii
palmata
balansana
convolvulacea
luxurians
sp., macG
angularis
lobata
B.
B.
B.
B.
■B.
------- B.
----B
B.
B.
■B.
eg;
'—
AM +
AS
s .
----------------- B.
s o C fO - B.
'— B.
—
■B.
B.
■B.
■B.
"B .
glomerata
cannabina
meyeri-johannis
thomeana
iucunda
dewildei
scapigera
poculifera
capillipes
molleri
m adecassa
salaziensis
ankaranensis
nossibea
francoisii
engleri
annobonensis
incamata
violifolia
grandis
geranioides
masoniana
holtonis
obliqua
aequata
sanguinea
fallax
socotrana
floccifera
crassirostris
roxburghii
palmata
balansana
convolvulacea
luxurians
sp., macG
angularis
lobata
The tree statistics for the maximum parsimony analyses of the three data sets
85
are presented below, in Table 5.3. From this it can be seen that, although tree
confidence measures are worse for the ITS and combined ITS and 26S data
sets, their bootstrap support is better than that of the 26S data set. Also, the
number of equally parsimonious trees are lower for the ITS and combined
data sets.
Table 5.3:
Data set
MP tree statistics
No.
inform.
chars
gi
PTP
No.
MPTs
Length
Cl
Cl ex
unlnf.
59
-0.3945
0.001
216
185
0.61
0.52
214
-0.694
0.01
3
971
0.5
273
-0.5837
0.01
22
1298
0.5
Rl
nodes
over
50%
nodes
strict
consen
0.79
12
29
0.46
0 .63
18
35
0.45
0 .6 4
123
31
268
ITS
combined
5.3.4 Molecular evolution in 268 and ITS data sets
The ITS data set has more positions which have more steps over a
phylogenetic tree than the 26S data set. 5 positions in ITS have 12 or more
steps (see Figure 5.12), while the maximum number of steps on the 26S tree
is 8 (see Figure 5.13). Within the ITS data set, the 5.8S region has a greatly
reduced number of changes per site than there are in both the ITS 1 and the
ITS 2 regions. The distinction between the D2 and D3 regions and the
conserved segments in the 26S data are less apparent.
Figure 5.12: ITS 1, 5.8S and ITS 2 for one MPT
CO
Q.
B
(/)
100
Position
200
3 00
4 00
700
5.8S
86
1000
1100
Figure 5.13: 26S change per site for one MPT
I
1
50
II
100
1 50
200
250
300
--------------------
Site
350
400
450
02
500
550
03
Both ITS and 26S are comparatively GC-rich (see Figure 5.14).
Figure 5.14:
26S
ITS
I 6000
I 5000
0
■
S3000
0
1
2000
E
1001
□
fL
A
C
G
57000
c6000
I 5000
^4000
•5 3000
6 2000
I 1000
Z
0
T
A
C
G
T
Transitions outnumber transversions for 26S; the balance is less clear for ITS,
which most notably has a higher number of changes from A to C than the 26S
data set has, and also less changes from T to C (see Figure 5.15).
Figure 5.15:
ITS
26S
To
A
A
C
C
•
#
G
A
I
#
(2^^^
C
From
G
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5.4
26S analyses and taxon sampling
5.4.1 Introduction: In order to investigate the effects of taxon sampling on
cladogram topology and support, and the relative support for different parts of
the tree within the different data sets, MP analyses were run using different
numbers of taxa from the 268 data set (D2 and D3) and from the ITS data set.
5.4.2 Material and methods:
For each analysis (see Table 5.4), records
were made of the number of parsimony informative characters in the data set,
the number of MPTs (exhaustive searches for analyses 1 - 8 ; branch and
bound for analyses 9 - 1 3 , heuristics (1000 random additions, TBR) for
analyses 14 and 15), MPT length. Cl, Rl, RC, g1 (exhaustive searches,
analyses 1 - 8 ; 10,000 random trees, analyses 9 - 15) , PTP excluding the
outgroup (1000 replicates; branch and bound for analyses 1 - 7 ; heuristics for
analyses 8 - 1 5 (10 random additions, TBR)), and the number of nodes with
over 50% bootstrap support (10,000 replicates fast addition).
Table 5.4:
Taxa included in different analyses
Analysis No.
1. (4 taxa)
Taxa (inclusive setsi
Datisca glomerata (O G )
G. annobonensis (A F)
G. iucunda (AF)
G. meyeri-johannis (AF)
G. thomeana (AF)
G. incarnata (AM )
G. geranioides (S .A F )
G. engleri (AF)
G. fallax (AS)
G. molleri (AF)
G. nossibea (M AD)
G. scapigera (AF)
G. convolvulacea
G. poculifera (AF)
G. salaziensis (AF)
G. aequata (A S )
G. roxburghii (AS)
G. luxurians (AM )
G. francoisii (M AD)
G. socotrana (SO C )
D. cannabina (O G )
ail species
2. (5 taxa)
3. (6 taxa)
4. (7 taxa)
5. (8 taxa)
6. (9 taxa)
7. (10 taxa)
8. (11 taxa)
9. (12 taxa)
10. (13 taxa)
11. (15 taxa)
12. (18 taxa)
13. (20 taxa)
14. (21 taxa)
15. (36 taxa)
(Key: AF = Africa; S.AF. = southern Africa; MAD = Madagascar; AM = America; AS = Asia;
SOC = Socotra.)
88
5.4.3 Results:
For the various tree statistics see Table 5.5 for 26S and
Table 5.6 for ITS.
Adding taxa makes little difference to the numbers of parsimony-uninformative
characters in the matrices, but the number of parsimony-informative
characters increases as taxa are added. Consistency indices fall as taxon
number increases, while the retention index and rescaled consistency indices
both rise. g1 values are not significant (i.e. values are positive) for the
analyses with less than 7 taxa. PTP values are insignificant (i.e. values are
less than 0.05) for the analyses with less than 9 taxa. There are more clades
which have bootstrap support in the ITS trees than there are in the 26S trees;
in general, the amount of support rises as the number of taxa rises.
Admittedly, selecting different taxa to include or exclude from any of these
analyses could have produced different results for any of these statistics; taxa
were selected mainly in order to examine the amount of support for
relationships between African taxa, which differ depending on the analytical
methods and data sets used.
Table 5.5:
Tree Statistics for different sized matrices, 26S
Analysis no. taxa no.
no.
pars.
inf.
chars
no.
pars.
uninf.
chars
no.
MPTs
tree
length
Cl
Cl ex
unlnf.
Rl
RC
91
PTP
clades
>50%
bootstr
ap
0
1
4
5
37
2
51
0.941
0.6 2 5
0.4 0 0
0.377
0.716
1.000
2
5
9
40
1
63
0.921
0.6 8 8
0.4 4 4
0 .409
0.409
0.866
0
3
6
12
42
1
74
0.892
0.6 8 0
0.4 2 9
0.382
0.324
0.952
0
4
7
19
36
7
78
0.8 5 9
0.711
0.5 4 2
0.465
-0.909
0.029
1
5
8
20
36
29
83
0.831
0.674
0.5 0 0
0.416
-1.075
0.073
1
6
9
22
34
8
88
0.807
0.6 6 7
0.5 4 0
0.436
-0.903
0.002
1
7
10
29
28
2
97
0.7 5 3
0.647
0.5 3 8
0.405
-0.849
0.001
2
8
11
32
28
11
104
0.731
0.6 2 7
0.5 6 9
0.416
-0.893
0.001
3
9
12
35
29
6
116
0.698
0.5 8 8
0.5 3 9
0.377
-0.805
0.001
3
10
13
36
30
6
122
0.689
0.5 7 8
0.5 6 8
0.391
-0.743
0.001
4
11
15
40
30
6
130
0.677
0.571
0.6 2 7
0.425
-0.710
0.001
6
12
18
40
36
6
141
0.681
0.5 5 9
0.6 8 8
0.468
-0.586
0.001
6
13
20
40
36
16
146
0.657
0.5 3 3
0 .7 0 8
0.465
-0.596
0.001
7
14
21
50
28
28
151
0.656
0.5 7 3
0.7 3 5
0.482
-0.696
0.001
8
15
38
59
34
18
193
0.611
0.5 1 9
0.7 9 4
0.485
-0.521
0.001
12
89
Table 5.6:
Tree statistics for different sized matrices, ITS
A nalysis
no.
no. taxa no.
pars.
inf.
chars
no.
pars.
uninf.
chars
no.
M P Ts
tree
length
Cl
Cl ex
uninf.
Rl
RC
gi
PTP
1
4
32
204
1
307
0.951
0.681
0.531
0 .5 0 5
-0.482
0.042
1
2
5
55
201
1
365
0.912
0.692
0.4 1 8
0.382
-1.007
0.078
2
3
6
81
187
1
424
0.863
0.676
0 .3 8 3
0.331
0.002
0.066
2
4
7
104
171
3
456
0.833
0.6 8 3
0.441
0 .368
-0.818
0.001
2
clades
>50%
bootstra
P
5
8
123
183
1
521
0.816
0.680
0.4 4 2
0 .360
-0.779
0.001
3
6
9
133
177
1
557
0.786
0.656
0.431
0 .339
-0.560
0.001
3
3
7
10
147
167
1
611
0.7 4 8
0.622
0.421
0 .315
-0.611
0.001
8
11
159
163
2
669
0.712
0.590
0.401
0 .285
-0.518
0.001
3
9
12
176
157
1
739
0.681
0.566
0.384
0.261
-0.582
0.001
4
10
13
186
155
1
792
0.667
0.5 5 5
0.397
0 .265
-0.546
0.001
5
11
15
201
147
1
821
0.6 5 5
0.5 5 8
0 .4 8 5
0 .318
-0.779
0.001
7
12
18
217
145
3
917
0.6 1 9
0.531
0.504
0.312
-0.601
0.001
6
13
20
224
138
6
967
0.5 9 5
0.511
0 .5 2 8
0.314
-0.676
0.001
7
14
21
256
111
1
989
0.5 9 0
0.527
0.581
0 .343
-1.248
0.001
9
15
38
291
103
22
1298
0.5 0 3
0.453
0 .6 3 8
0.321
-0.700
0.001
19
5.4.4 Discussion, taxon sampling:
5.4.4.1
Characters: The number of parsimony-uninformative characters
does not change greatly with different numbers of taxa (although it changes
more for ITS than for 26S), but the number of parsimony-informative characters
rises as taxa are added. Some autapomorphies become synapomorphies as
taxa are added (obviously it is not possible to turn a constant character into a
synapomorphy by adding one taxon to a matrix). Our matrices include a wide
range of the total taxonomic, geographic and thus, presumably, sequence,
divergence within Begonia. Adding taxa appears to be more likely to make
autapomorphies informative than to add more autapomorphies. Because
adding more taxa turns autapomorphies into synapomorphies, this suggests
that the information contents of the matrices are not saturated.
5.4.4.2
Indices:
Consistency index falls as taxon number increases;
this is a known affect of this statistic and is not necessarily related to the
information content of the matrices. Retention index and the rescaled
consistency index both rise as taxon number increase (although this is not a
linear increase for the ITS data set). Rl examines the actual homoplasy in a
data set as a fraction of the maximum possible homoplasy, effectively giving a
proportion of the similarities on a tree which are interpreted as synapomorphy
90
(Siebert, 1992). Thus it appears that as taxa are added, homoplasy levels
decrease. Bininda-Edmonds, Bryant and Russell (1998) suggest that, in
some reduced data sets, the removal of consistent parts of the cladogram
(from the more inclusive data set) causes RC and Rl to decline because,
relatively, the regions which remain are more homoplastic. Thus our values
for Rl may be lower for the smaller data sets, particularly for 26S, because the
parts of the matrix which have most cladistic structure are not present
therefore are not contributing. The American and Asian sequences, which are
less represented in these analyses than African sequences are, are
comparatively similar; because there are few substitutions between the
American and Asian taxa there may be a lower chance of multiple hits, and this
may relate to lower levels of homoplasy within American and Asian clades.
5.4.4.3
Skewedness:
The g i values are not significant for analyses
1, 2 and 3 (which includes Datisca, four African taxa and one American taxon),
indicating that there are many trees which are not significantly longer than the
MPT, and consequently, that the phylogenetic signal in these matrices (i.e.
between these taxa) is not strong.
5.4.4.4
Permutation tail probabilities:
PTP tests whether character
covariation within a matrix is greater than that expected given a random set of
characters, and can be defined as the proportion of all data sets which give
cladograms which are equal to or shorter than those produced by the
unpermuted data. A value of 0.05 is often chosen to imply significant cladistic
structure in the data (Kitching et al., 1998). PTP values for the ingroup are
insignificant for the groups with less than 7 taxa for 26S and ITS. It is possible
that only a few clades contain covarying characters and that these few clades
are responsible for the significant statistic values. The addition of 6.
geranioides between analyses 3 and 4, and of B. fallax between analyses 5
and 6, both caused big decreases in the PTP value, while adding B. engleri
between analyses 4 and 5 caused the value to rise. 8. geranioides and 8.
fallax both form a clade with 8. incamata] the implication of the data is that
many characters covary in this clade. The addition of 8. engleri, on the other
hand, decreases the covariance of the data.
91
Both g1 and PTP suggest that there is little cladistic structure in the matrices
used in analyses 1, 2 and 3. On this basis, it may be that our data are not
suitable for resolving the positions of B. annobonensis, B. iucunda, B. meyerijohannis, B. thomeana and 8. incarnata relative to each other and to the
outgroup, D. glomerata.
S.4.4.5
Bootstrap:
The number of nodes with over 50% bootstrap
support rise as the number of taxa added rise. However, in general the
supported nodes are not nodes already present in the less inclusive data
sets, but are new nodes created by the addition of closer relatives to the taxa in
the matrix. In a data set which includes less taxa, the reduced number of
terminals can alter support because the numbers of possible alternative
groupings of the taxa are decreased (and also, the number of characters per
node can increase). Therefore, bootstrap support for groups on smaller trees
can be relatively high even if there are also relatively high levels of homoplasy
in the data (Bininda-Edmonds, Bryant and Russell, 1998). Effectively this will
mean that a bootstrap value, x, in an analysis of five taxa offers less confidence
than the same value in an analysis of ten taxa.
92
5.5
General Discussion and conclusions
Of the nine topologies produced for the 38 taxa (MP, ML and ME analyses for
26S, ITS and combined sequence data sets) some conclusions can be
drawn. There is a general agreement that African taxa are basal within
Begonia, although precisely which African species are basal changes
according to the data set and the analysis method used. From looking at
reduced data sets, which include only some of these variably-placed taxa, it
seems that we do not have sufficient information to resolve these problems.
5.5.1 Taxonomy:
Most of the comments about the phylogeny of Begonia are
reserved for a later chapter. However, a couple of general points can be made
here.
Firstly, the placement of the Socotran endemic, B. socotrana (section
Peitaugustia) is worth comment. This is consistently associated with an
American and Asian clade (and most commonly, with the Indian species 8.
floccifera and 8. fallax), rather than with the African species of section AUgustia
(of which, 8. geranioides is the only one included in this analysis) with which it
has traditionally been associated (e.g. Warburg, 1894; Irmscher, 1925, 1961).
Secondly, it is clear that Begonia as a genus is paraphyletic without the
inclusion of the Asian taxon Symbegonia\ this taxon always resolves well
within the American/Asian clade.
5.5.2 Analysis methods - Which tree is truest?
Data sets:
The combined ITS and 26S matrix should be accepted as our
best approximation of a rDNA phylogeny for Begonia, because it is based on
the most information. The assumption that the ITS and 26S data sets are fully
congruent is no more problematic than the commonly made assumption that
ITS 1 and ITS 2, or ITS and 5.8S, can be treated together (and, depending on
the sites of the primers used, parts of the 26S gene are often appended to ITS
2 anyway). The combined data set produces a greater number of nodes with
over 50% bootstrap support, therefore confidence levels are greater than for
either of the constituent data sets.
93
Algorithms: Maximum parsimony and maximum likelihood produced broadly
similar topologies. Homoplasy (‘long branch attraction’) can be tested for by
comparing ML and MP cladograms; where the placement of long branches
differs between analysis methods, the ML tree is frequently accepted as more
reliable. For the 26S data set, all topological differences are within the
Asia/America clade, where branch lengths are extremely short, and most
differences are caused by lack of resolution in the parsimony tree.
For the ITS data set and the combined ITS-26S data set the position of B.
iucunda changes most radically, from sister to the rest of Begonia (MP) to
sister to 8. dewildei (section Scutobegonia) and 8. scapigera (section
Loasibegonia) in the ML treatment. The placement of 8. meyeri-johannis also
changes, from sister to a wider African clade in the MP analysis, to sister to the
mainly Madagascan clade in ML. Otherwise, the main differences lie in the
basal relationships (with almost all the African species monophyletic in the ML
trees, but paraphyletic in the MP trees). The data sets do not appear to offer
enough support to decisively resolve these relationships. (NB: for the sections
taxa are currently ascribed to, see the cladogram at the end of this chapter,
Figure 5.16.)
The ML analyses, for ITS and for the combined data set, offers the topology
most consistent with traditional Begonia taxonomy, by keeping the two species
from section Mezieria, 8. salaziensis and 8. meyeri-johannis, closest. Also,
although it is currently not placed in a section {Ignota, Sosef, 1994;
Doorenbos, Sosef & de Wilde, 1998), 8. iucunda has formerly been placed in
section Scutobegonia (Irmscher, 1925) and latterly in section Filicibegonia
(van den Berg, 1985; de Lange & Bouman, 1992), a section traditionally
thought to be closely related to sections Loasibegonia and Scutobegonia
(Sosef, 1994); in the ML tree it resolves as sister to Loasibegonia/
Scutobegonia. It is possible that the inconsistencies in the MP tree are
caused by homoplasy, and therefore the ML tree may be a better
representation of Begonia evolution - ITS has a lot of very variable characters
which must heighten the possibility of multiple hits.
The next chapter concerns the analysis of a far larger ITS data set. ML is not a
94
practical analysis method for more than c. 60 taxa (Soltis & Soltis, 2000), and
part of the point of including trees calculated using ME here was to see how
they compared to the ML analyses, and so, whether the technique could be
useful for the larger ITS data set as a comparison to MP. While ME produced
an identical topology to ML for the 26S data set, it produced a rather different
topology for the ITS data set (e.g. novel placements of the African 8. thomeana
(formerly in section Loasibegonia, now in a monotypic section, Cristasemen de Wilde, 1985) and the south African 8. geranioides (section Augustia)).
Again, for the combined data set, the tree produced by ME was inconsistent
with that produced by ML (e.g. the placement of the clade containing 8. engleri
and 8. annobonensis). In the light of such topological differences between the
ML and ME analyses, it was felt that there was little point in carrying out ME
analyses in conjunction with MP for the wider ITS analysis.
The ‘Truest’ tree
The tree presented in Figure 5.16 is the maximum likelihood tree for the
combined ITS and 26S data set; it is presented as a cladogram rather than a
phylogram in order to emphasis the branching order; current sectional
placements of the taxa have been marked on. This topology will be discussed
at greater length in a further chapter.
95
Figure 5.16: 26S and ITS phylogeny for 36 Begoniaceae taxa, produced using
ML (sectional placements as given in Doorenbos, Sosef and de
Wilde, 1998)
D. glomerata
D. cannabina
B. thomeana: Cristasemen
B. Iucunda; Ignota
B. dewildei; Scutobegonia
B. scapigera; Loasibegonia
B. poculifera; Squamlbegonia
B. capillipes; Tetraphlla
B. molleri; Tetraphlla
B. meyeri-johannis; Mezieria
B. madecassa; Nervlplacentarla
MADAGASCAR
B. salaziensis; Mezieria
B. ankaranensis; Quadrllobarla
AFRICA
B. nossibea; Quadrllobarla
B. francoisii; Quadrllobarla
B. engleri; Rostrobegonia
B. annobonensis; Sexalarla
B. geranioides; Augustia
B. holtonis; Rulzopavonia
B. obliqua; Begonia
AMERICA
r C U
B. Incarnata; Knesbeckla
B. violifolia; Wellbachia
B. convolvulacea; Wagenerla
B. sp.
B. luxurians; Scheldwellerla
B. angularis; Pritzella
B. lobata; Pritzella
B. aequata; Petermannia
S. sanguinea
ASIA
B. masoniana; Coelocentrum
L-O—
SOCOTRA
B. fallax; Ignota
B. socotrana; Peitaugustia
B. floccifera; Relchenhelmla
B. grandis; DIplocllnlum
B. crassirostris; Sphenanthera
B. roxburghii; Sphenanthera
B. palmata; Platycentrum
B. balansana; Ignota
96
5.6
Summary
Maximum parsimony (MP), maximum likelihood (ML) and minimum evolution
(ME) cladograms were produced for 35 species of Begonia, one species of
Symbegonia and two species of Datisca, for 26S, ITS and combined 26S-ITS
sequence data. While MP and ML both produced highly congruent trees for the
26S-only sequence data, ML produced a tree more in line with traditional
(morphological) Begonia classification for the ITS and combined 26S-ITS
sequence data. This may relate to homoplasy caused by multiple hits in the
more rapidly-evolving ITS region ‘misleading’ the parsimony algorithm.
Minimum evolution as implemented here was not felt to produce reliable
phylogenetic estimates for these data.
Although there is general agreement about the clades within Begonia, the
order of branching of these clades can vary dramatically. From parsimonybased analyses of subsets of taxa for ITS and for 26S it appears that neither
data set can conclusively resolve the question of what is most basal in
Begonia. Time constraints did not allow similar analyses to be run on the
combined 26S-ITS matrix; as it has more informative characters than either
26S or ITS alone, it may be more reliable. Certainly, Bremer support values for
the backbone of the combined analysis MP cladogram (Figure 5.8) are higher
than for either of the separate analyses (Figures 5.2, 5.5), suggesting that
some characters from each data set (26S and ITS) are supporting the
combined topology.
The main conclusion to be drawn from this chapter is that the best estimate
we have to date for the phylogeny of Begonia, on the basis of information from
the rDNA cistron for 36 species from the Begoniaceae, is the ML analysis of
the combined data set (Figures 5.8, 5.16).
97
6.
6.1
26S: The wider picture - adding GenBank taxa
Introduction
There are several published studies which make use of the 26S region, and
consequently, there are some 26S sequences available in GenBank. These
were used to investigate the utility of the part of 26S sequenced in
Begoniaceae within wider analyses of the angiosperms, and also to provide
further corroboration of the position of Datisca relative to Begonia (and so, its
utility as an outgroup for Begonia for ribosomal DNA sequence data). After all,
if the data set is highly homoplastic in the variable positions, it is possible for
Datisca to resolve within the Begoniaceae.
Due to the location of the primer site for p61 (and its reverse, p71) (Oxelman &
Linden, 1995), a short region near the beginning of the 26S region could not
be read. Aligning the incomplete sequences to complete sequences from
GenBank allowed the size and precise position of this gap to be estimated.
6.2
Material and methods
The Begonia 26S region which encompasses D1 to D3 was put into a BLAST
search to identify other similar sequences. Sequences from 26 genera in 17
angiosperm families (see Table 6.1) were downloaded. These were added to
a data matrix of 6 Begonia species and one species of Datisca.
Table 6.1;
GenBank sequences for 26S analysis
Taxon
Familv
GenBank accession no.
Acorus gramineus
Tragopogon dubius
Jeffersonia diphylla
Heliotropium curassavicum
Arabidopsis thaliana
Brassica napus
Sinapsis alba
Lobelia puberula
Humulus lupus
Ipomoea lacunosa
Jacquemontia tamnifolia
Eucryphia lucid a
Hamamelis virginiana
Oryza sativa
Polemonium reptans
Phlox divaricata
Hydrastis canadensis
A coraceae
A steraceae
Berberidaceae
Boraginaceae
Brasslcaceea
Brasslcaceae
Brasslcaceae
C am panulaceae
C an n a b a ce a e
Convolvulaceae
Convolvulaceae
C uoniaceae
Ham am elidaceae
P o a ce ae
Polem oniaceae
Polem oniaceae
Ranunculaceae
AF036490
A F036493
U 52604
A F148274
X52320
D 10840
X57137
A F148276
A F223066
A F146016
A F148499
A F036494
AF036495
M 11585
A F148282
AF148281
U 52636
98
Thalictrum dioicum
Citrus limon
Jepsonia parryi
Lithophragma trifoliatum
Mitella pentandra
Lycopersicon esculentum
Nolana humifuse
Physalis angulata
Drimys winteri
Begonia angularis
Begonia crassirostris
Begonia grandis
Begonia molleri
Begonia obliqua
Begonia palm ata
Datisca glomerata
R anunculaceae
R utaceae
Saxifragaceae
Saxifragaceae
Saxifragaceae
S oian aceae
S olan aceae
S oian aceae
W interaceae
B egoniaceae
B egoniaceae
B egoniaceae
B egoniaceae
B egoniaceae
B egoniaceae
D atiscaceae
U 52611
X05910
A F036497
A F 03 65 01
A F036502
X13557
A F148272
A F 14 82 71
A F 03 64 91
new sequence
new sequence
new sequence
new sequence
new sequence
new sequence
new sequence
Sequences were aligned in ClustalX (Thompson, Higgins & Gibson, 1997)
and then manually augmented in SeqPup (Gilbert, 1995); ambiguous sites
were excluded from the analyses. Data was analysed in PAUP* 4.0b2a
(Swofford, 2000) using 1000 fast addition bootstrap replicates to isolate well
supported clades.
6.3
Results
One of the results of this study was to identify the exact location of the end of
D1 in the Begonia sequence, as it appears to correspond with the primer site
for p61/p71. About 70 base pairs are unreadable in the Begonia and Datisca
sequences, about 40 at the 3’ end of the D1 region, and about 30 at the 5' end
of the second conserved region, 02 (segments identified using the
consensus motifs published by Kuzoff et al., 1998, p. 254). P71 (and therefore
its reverse, p61) sits exactly at the beginning of the second conserved region,
02.
The matrix (and the positions for the primer and for the variable regions
D1, D2 and D3) are given in the Appendix, 14.6.
From the bootstrap consensus tree (Figure 6.1), Begonia is monophyletic, with
100% bootstrap support, with Datisca its sister group (53% bootstrap support).
Within Begonia, the African species, B. molleri, is sister to the American and
Asian species (94% support). The Asian species resolve as monophyletic
with 89% support.
All angiosperm orders where more than one taxon was sampled
(Ranunculales, Saxifragales, Cucurbitales, Capparales, Ericales and
Solanales) are recovered by the bootstrap consensus tree, although the
99
position of these orders relative to each other is not resolved.
Figure 6.1:
Bootstrap consensus tree, 10000 fast replicates for 26S D1, D2,
D3 and linking regions (classification from Savolainen et al.,
2000 )
J3-
Drimys
Eumagnoliid
Oryza
Monocot
Acorus
Rosales
Humulus
Jeffersonia
_LL
I 79 I
Ranunculales
Hydrastis
Thalictrum
-
Eucryphia
Oxalidales
Citrus
Sapindales
Hamamelis
Jepsonia
.31.
100
Saxifragales
Rosid
Mitella
Lithophragma
Datisca
76
_ü_
Begonia molleri (AF)
Begonia obliqua (AM)
Cucurbitales
Begonia angularis (AM)
89
Begonia grandis (AS)
Begonia crassirostris (AS)
Begonia palmata (AS)
Arabidopsis
_m£L
Capparales
Brassica
Sinapsis
Asterales
Tragopogon
100
Phlox
Ericales
_
Polemonium
Lot)elia
Asterales
Heliotropium
69
Lamiales
Asterid
Ipomoea
Jacquemontia
74
58
Solanales
Physalis
Nolana
Bootstrap values
above branches
Lycopersicon
(Key: AF = Africa, Am = America, AS = Asia)
100
6.4
Discussion
The data support the monophyly of Begonia (see bootstrap consensus tree,
Figure 6.1) and because the Datisca sequences do not nest within Begonia
we can have additional confidence in the suitability of Datisca as an outgroup
for the 26S data set. Of the included taxa, Datisca appears closest to Begonia.
Although it is not necessary to root an analysis on the sister group, in cases
where there are alignment difficulties even within the ingroup (as is the case
for Begonia ITS), a close relationship between the ingroup and outgroup is
preferable, for practical reasons.
The relationships resolved within Begonia, with the African species B. molleri
basal and the Asian taxa as sister to the American species, are not
inconsistent with those recovered by the analyses which included more taxa
for 268 and ITS data (although shorter 26S sequences) in the previous
chapter.
The lack of resolution between dicot clades is probably due to the region of
26S used; the region of sequence includes D1, D2 and D3, which are
recommended for analysis within families (Kuzoff et al., 1998), while only short
stretches of core regions, more suitable for between-family reconstruction, are
included.
101
7.
Building the cladogram - ITS
7.1
Introduction
There is no published molecular phylogeny for the Begoniaceae; previous
authors (e.g. van den Berg, 1983, 1985 ; Legros & Doorenbos, 1969, 1971,
1973; Reitsma, 1984; Shui, Li & Huang, 1999; de Wilde & Arends, 1989) have
attempted to interpret morphological and cytological patterns in the absence of
any reliable genus-level phylogeny; some, like van den Berg (1985), de Wilde
and Arends (1989) and Shui, Li and Huang (1999) have been tempted into
hypothesising evolutionary directions based on supposition about what
construes a primitive character within the genus or species group they are
interested in. Schemske, Agren and le Corff (1996) resist this temptation, but
consider that “information on the phylogeny of Begonia would be very useful for
determining if the evolution of male and female floral traits is consistent with
the intersexual mimicry hypothesis" (p. 313).
In this chapter, a molecular phylogeny is produced in order that evolutionary
processes and patterns within the family may be discussed in its light in
subsequent chapters.
7.2
Material and methods
7.2.1 Plant Material: The sources of plant material and vouchers used in this
analysis are listed on the CD-ROM. In total I obtained ITS sequences from 163
individuals; 177 sequences were obtained, two from the outgroup and 175
from Begoniaceae. Sequences of Hillebrandia and Datisca cannabina
accession 2 were kindly donated by Susan Swensen (Ithaca, New York). All
three genera which are included in the Begoniaceae (Begonia, Hillebrandia
and Symbegonia) were included in the analysis. The choice of Datisca as
outgroup has been discussed in the previous chapter.
Identifications: Some of the taxa included in the analyses are unidentified.
Several of these taxa are from China; the new Flora of China account has not
been completed. Until it is, putting names onto species is highly problematic.
Other unidentified taxa either do not exactly match known species from the
region they were collected (e.g. the species collected in Bolivia, CAP 566), or
are thought to be new species (e.g. the species from the Philippines, RBGE
102
1997 2566, for which a description is in preparation), in a few cases,
morphologically interesting taxa were sampled using the names they were
being cultivated under in E and/or GL, and only later was it realised that they
were completely misidentified or mislabelled. Begonia species are very
problematic to identify; there are relatively few keys, and even fewer which work.
Given good collection details it can be possible to put names on plants; in the
case of apparent labelling errors, where there is no information about the
geographical origins of a taxon, it is virtually impossible. Of course, after the
taxa have been sequenced and a phylogeny produced, there is more chance of
naming the problem plant. Thus plants sequenced under the names ‘8.
macrocarpa’ (E and GL), an African species, are now known to each belong to
different clades of American species. Likewise, the supposedly Asian ‘B.
sychnanthera’ (GL) and '8. guttata’ (GL) are also mislabelled American plants.
One could argue that, given that there is no reliable way of knowing what these
plants are or where they originated, the sequences should be deleted from the
analysis. However, morphological data can be (and has been) gathered for
these taxa; deleting them would amount to not using all the available
information on the genus.
Unpublished names: 8. gabonensis is the name given to a new species by de
Wilde. It has not been published yet, but is given as a “provisional name” in de
Lange and Bouman (1992, p. 29).
7.2.2 Molecular methods
The methods were as described in Chapter 5.2.
7.2.3 Sequence alignment
7.2.3.1.
Automated alignment: Sixteen ClustalX (Thompson, Higgins &
Gibson, 1997) alignments were produced using a range of gap opening and
extension penalties (Table 7.1) (alignment one uses the default settings). The
alignments were imported into SeqPup (Gilbert, 1995) and converted into
Nexus format, then imported into MacClade 3.07 (Maddison & Maddison,
1992), where the edges of each alignment were checked and trimmed
consistently.
103
Table 7.1:
Automated Alignment Parameters:
Alignment
Number
1
2
3
4
5
6
7
Gap Opening
Penalty
15
15
30
30
6.66
6.66
45
Gap Extension
Penalty
6.67
15
6.67
15
6.66
Length of
Matrix
1012 i 910
952
878
1087
:8
13
14
15
16
10
25
20
25
10
6 .66
6.66
6.66
15
15
15
1022
1035
1000
894
893
901
9
10
11
45
3.33
3.33
20
15
: 6.66 i 15
6.66
3.33
928
! 9 05
1159
1413
: 859
Files were saved without interleaving and opened in PAUP* 4.0b2a (Swofford,
2000). The data matrices were then copied into Word and arranged so that the
taxa were in alphabetical order. Matrices were then copied back into the Nexus
files in PAUP*, and saved. Each matrix was copied and pasted into one large
Nexus file which was then interleaved to produce an elision data set (15848
characters long).
7.2.3.2.
Manual alignment: An initial alignment was done in ClustalX
(Thompson, Higgins & Gibson, 1997). This was transported into SeqPup 0.6f
(Gilbert, 1995) for manual augmentation. Conserved ITS 1 and ITS 2 regions
were identified from Hershkovitz, Zimmer and Hahn (1999) and Hershkovitz
and Zimmer (1996). Secondary structure was determined at 20° c using
MulFold (Zuker, 1989; Jaeger, Turner & Zuker, 1989a; Jaeger, Zuker & Turner,
1989b) and viewed in LoopDloop (Gilbert, 1995) (as described in chapter 8).
Secondary structure information was used to help clarify ambiguous regions of
alignment by identifying homologous regions (loops or stems) in ITS 2 (ITS 1
secondary structure proved too variable to be useful).
7.2.4 Phylogenetic analyses
Data matrices were analysed using the parsimony algorithm of the software
package PAUP* 4.0b2a (Swofford, 2000). Searches were conducted on the 16
automatic alignments produced by ClustalX (Thompson, Higgins & Gibson,
1997), on the elision matrix, and on the manually aligned matrix. When
searching on the automatic alignments and on the elision matrix, all data were
included. For the manual alignment, regions were identified where the
hypotheses of primary homology for bases were very tentative, and these
regions were excluded (culled) from the analysis. For purposes of
comparison, an analysis was also run with these regions included.
104
7.2.4.1
Automated alignments:
Individual analyses were run for each of
the 16 alignments, with 10 random addition replicates and no more than 10
trees of any length saved, swapping with TBR; the shortest trees from these
searches were then used as starting trees in a second search, TBR swapping
(MaxTrees set to 5100). Lengths and tree statistics from these analyses were
compared with those from the elision analysis topology. To save time,
bootstrap support measures were not obtained for these data sets, as the
relative support for clades was not thought relevant to the study and the trees
were not intended for discussing evolutionary scenarios (following Morrison &
Ellis,1997).
7.2.4.2
Elision alignments: An heuristic analysis of the elision data set
was carried out (1000 random addition replicates, TBR). Bootstrap support
was estimated using 10,000 fast addition replicates.
7.2.4.S
A
Manual alignment:
Unculied: For the manual alignment, variable characters were first
included and an analysis was run with 1000 random addition replicates, TBR,
saving no more than 10 trees per step. These were then used as starting
trees in a round of TBR swapping, MaxTrees set to 10,000. To check that there
were no equally parsimonious trees with very different topologies, a constrain
(the topology of the strict consensus of the MPTs) was imposed on a further
round of analyses. 1000 random additions were performed, TBR, saving only
trees which were not compatible with this topology. The shortest trees found
were one step longer than the MPTs from the unconstrained analyses.
Bootstrap support was estimated using 10,000 fast addition replicates.
B.
Culled: Variable positions were excluded from the matrix, and the
analysis was rerun (as above) with only two differences, that 10,000 random
addition replicates were performed in the first step of the analysis, and Bremer
support was estimated using AutoDecay (Erikkson, 1998) (10 random addition
replicates per constraint tree, TBR).
Excluded characters are the same as those given in the previous chapter (1183, 188, 200, 204, 211-217, 223-225, 230-249, 255-256, 266, 274-329, 340366, 378, 383-384, 406-407, 415, 419-421, 426-428, 435-437, 444, 449-451,
460, 466-469, 475-483, 493-497, 503-507, 513-514, 539, 571, 577, 603, 606,
615, 649, 686, 688, 693-856, 886-901, 930-931, 944, 957-966, 983-984, 992105
993, 1013-1014, 1018, 1023, 1029-1035, 1041-1053, 1064-1093, 1110-1114,
1121-1122 and 1137-1154, see CD-ROM).
T.2.4.4
Tree com parisons: Because the total number of MPTs for all 16
alignments is very high (43,433) and because the numbers of MPTs for
different alignments vary considerably (from six to 5100), which would
effectively weight some alignments over others, consensus methods were
used to compare the results of the analyses of the different alignments; thus
only one tree was compared per alignment.
A strict consensus was computed of trees produced from each of the 16
alignments. These 16 strict consensus trees were used to compute a further
strict consensus tree; this tree was unresolved except for a clade containing
the three Datisca sequences. A majority rule tree (50%) had considerably
more structure, and was used to look at areas of agreement between the
cladograms produced from the different alignments.
Majority rule trees (50%) were also calculated for each of the 16 alignments,
with other compatible groupings included. This was done in order to produce
trees with the maximum possible resolution, as using unresolved trees makes
some tree comparison statistics relatively meaningless. The symmetricdifference metric (or partition metric, PM)^ and the agreement-subtree metric
D /, as implemented by PAUP* 4.0 (Swofford, 2000), were calculated between
all pairs of trees.
A majority rule consensus of the fundamental elision trees was compared to
the majority rule tree for each of the 16 alignments, by using the symmetricdifference metric PM and D^.
The partition metric (PM ) can be defined as the minimum number of branch contractions and
decontractions needed to transform one of two trees into the other. It is analogous,
however, to a strict consensus tree in that the differential placement of just one taxon on two
pectinate trees can give the highest possible value of PM (the maximum value possible is 2N
- 6, where N = number of taxa) (Johnson & Soltis, 1998). PM was implemented in PAUP* 4.0
under the command T R E E D IS T M E T R IC = S Y M D IFF (Swofford, 2000).
" PAUP* 4.0 (Swofford, 2000) can be used to compute a ‘largest common pruned tree'
(LCPT) which summarises a number of input trees, using the A G R E E command. Two
distance measures can be computed, D iand D (TR E E D IS T M ETR IC = AGD1 or A G R ). Agree
D is the number of taxa pruned to form the LCPT weighted by the distance between the
taxa, while Agree Di is the minimum number of taxa which must be pruned to make two trees
identical (Johnson & Soltis, 1998).
106
The strict consensus trees for each of the 16 alignments were used to look at
the presence/absence of certain clades, the monophyly of certain geographical
regions and the position both of the outgroup and of Hillebrandia.
7.3
Results
7.3.1 Statistics: For statistics concerning the various data sets and
concerning the trees produced from their analysis, see Table 7.2.
Table 7.2:
Statistics for the various automated alignments and for the
elision, the manual, culled and the manual, unculled alignments.
Al. 1 : Al. 2
Al. 3
! Al. 4
Al. 5
Al. 6
Al. 7
: Al. 8
: Al. 9
Al. 10 Al. 11
Al. 12: Al. 13
Al. 14
Al. 15
Al. 16; Elision
; Man.. ; Man..
; Total ; O il
Opening ■
penalty
: 45
3.
3.3
20
10
25
20
25
6.7
«
: 6.7
3,3
6.7
6.7
: 6.7
15
15
928
905
: 859
: 1159
1413
1022
1035 ; 1000
894
893
901
! 15848
104
77
58
! 213
405
171
159
154
69
43
72
107
90
L
273
149
160
: 158
121
TOO
721
711
756
T .
702
716
i 688
704
15
: 15
30
: 30
6.7
6.7
6.7
15
6.7
! 15
6.7
15
952
: 878
1087
104
i 54
191
Extension ;
penalty
No.
ctiar.s
: 1012 : 910
No.
invariant ;
ctiar.s
: 120
78
No. pars.
uninf.
char.s
142
No. pars. ;
inform.
criar.s
ygl
720
116
182
708
993
522
; 2067
: 191
I 101
114
: 2321
; 137
92
715
; 11455
; 665
; 329
i 100
i 10000
No. trees :
: 5100 : 5100
360
5100
120
5100
128
5100
80
5100
140
1656 ; 6
5100
143
5100 : 6
: 9983 : 10325
11188
11205
9468
9594
12456
11769
9621
8615
10264
9634 i 10234
10206
11074
9741 ; 175227 ; 5979 ; 2844
: 0.099 : 0.103
0.084
0.098
0.104
0.114
0.075 : 0.094
0.1
0.118
0.091
0.105 : 0.093
0.103
0.099
0.113 i 0.087
i 0202 ; 0.205
Lengtti
Cl ex
uninf.
Rl
RC
invar./
total
chars
! 0.119 ! 0.086
0.109
0.062
0.176
0.112
0.085 I 0.068
0.184
0287
0.167
0.154 : 0.154
0.077
0.048
0.080 : 0.130
! 0.192 : 0.193
uninform/ :
total
chars
: o .l69 : 0.123
0.149
0.132
0.167
0.134
0.118 : 0.105
0.164
0.193
0.146
0.155 : 0.158
0.135
0.125
0.127 i 0.146
: 0.138 : 0.176
inform./
total
chars
0.742
0.806
0.657
0.754
0.797 : 0.828
0.652
0.520
0.687
0.692 : 0.688
0.787
0.826
0.794 : 0.723
: 0.670 : 0.630
!
; 0.712 ' 0.791
The number of characters in the different alignments range from 859
(alignment 8) to 1413 (alignment 10) (i.e. by 554 characters); the number of
invariant characters range from 43 (alignment 15) to 405 (alignment 10) (i.e. by
362 characters); the number of parsimony uninformative characters range from
90 (alignment 8) to 273 (alignment 10) (i.e. by 183 characters). However, the
number of parsimony-informative characters only range from 688 (alignment
13) to 756 (alignment 9) (a difference of 68 characters).
107
The percentage of invariant characters in each alignment ranges from 6.2%
(alignment 4) to 28.7% (alignment 10); uninformative characters range from
10.5% (alignment 8) to 16.9% (alignment 1) and informative characters range
from 52.0% (alignment 10) to 82.8% (alignment 7).
Characters - automated alignm ents: Changes in gap opening and gap
extension penalties have an effect on the proportion of different types of
characters in the matrices. Table 7.3 is a summary of the values from Table
7.2.
Table 7.3:
The Effect of Alignment on Characters
TOTAL C HARACTER
N U M B ER
CONSTANT
C H A R AC TER NUM B ER
PA RS IM O N Y U N INFO R M ATIVE
C H A R AC TER NUM BER
PA RSIM O N YIN FO RM ATIVE
C H A R AC TER NUM B ER
opening penalty
increasing, extension
penalty constant
usually increases
often increases
usually increases
no clear trend
extension penalty
increasing, opening
penalty constant
always increases
always increases
always increases
no clear trend
Because eight different gap opening penalties were used, while only three gap
extension penalties were used, the clear effect of increasing the gap extension
penalty when the gap opening penalty is constant may be lost if more
extension penalties are tested.
7.3.2. Trees: The tree statistics obtained from the elision topology and from
swapping each of the constituent data sets (automated alignments) are
presented in Table 7.2. One of the phylograms produced from analysis of the
elision data set is presented (Figure 7.1); clades which collapse in the strict
consensus tree are marked on. Also a majority rule tree of the strict
consensus trees for the 16 alignments is shown, as a summary of the areas of
most agreement between alignments (Figure 7.2); strict consensus trees and
phylograms are also shown for the culled (Figures 7.3, 7.4) and the unculled
(Figures 7.5, 7.6) manual alignments.
For all the cladograms presented, where geographical clades are marked on,
AF is Africa, S. AF is southern Africa, MAD is Madagascar, SOC is Socotra, AM
is America, and AS is Asia.
108
Figure 7.1;
Phyiogram from analysis of the ITS elision matrix
D. glomerata,
— D. cannabi
D. pannabina 2
H. sandwichensis
'B. annobonensis
B. engleri
r~ B. iohnstonii 1
B. iohnstonii 2
„ B. lucunda
B.boanen
madecassa
salaziensis
ipnaniabensis
^anKaranens
B. francoisii
B. nossibea
B. meyeri-johannis
^ liQO|
B. poculifera
B. loranthoides rhopalocarpa
molleri ..
^ ^ 941
mannii
I—
C _ B . capillipes
•a C T B. horticola
B. subscutata
R thnmpana , _
aaclfimfpiia
B. staudtii
^ . duncan-thomasii
rismatocarpa
scutifolia
B. potamophila
B. quadrialata
S.AF
B. rubella
B. sutheilandii
Bolivia
^
B. fissistvla„
^
.
B. cubensis
.___.
im
B. obliqua
B. minor
B. odorata
B. meridensis
B. fuchsioides
B, holtoniq
B. lamesoniana
B. guaduensis
B. sp., sych
B. maynensis
B. olbia
B. incamata
boliviençis
500 changes
. annabanna
Bootstrap values given above lines;
B. imperialis
Clades not present in strict consensus
" B. violifoli
B. edimonooi
indicated by thin lines
B. sp., gutt
lubbersij
. neracleifolia
B. sp., Ü172
B. involcrata AB
B. involucrata
B.sencopeura
B. manicata
B. peltata
B. theimei
B. gracilis g golananthera 1
B.integemma
B. soiananthera 2
B. wollnyi
B. herbacea
^ B. s^Trachelocarpus
b ! sp.,
■ ^ u ’lmifolia
B. acerifolia
I. valida ^
. sp., macE
—
B. egregia
B. angulans
"■ B. lobata
B. rufoseiicae
^ ^ ‘ècîiH^epala
B. listada
B. oxyphylla
B. oxyphylla AB
" luxuijans .
luxunans clone
'ilK à a læ
B. luxurians clone
109
B. geranioides
B. sonderana
B. dr^ei ‘partita’
*. (î^gei ‘homonyma’
B. grandis grandis
B. grandis holostyla
B. balansana
B. sp. nov. Yunnan
B. versicolor
^ ^i!^?fY'unnan 21
B. sp., Taiwan
B. formpsana
B. ravenii
J
B. sp., Yunnan 25
“Isa— B. sp. nov.. Philippine
B. sp., Sulawesi 254
A — & handelii
'
B. menyangensis
au— B. acetosella
— 1^ — B. longifolia
•— B. sp., Sulawesi 253
B. diadema
®r'ffaL=227
r—
Tau— B. annulata
'
B. roxburghii
B. hernsleyana
■ B. sp., Piatycentrum
B. sp., Yunnan 33
B. floccifera
sp., nam 2
B. beddomei
B. dipetala
B. Iatx)rdei
B. sp., Reichenheimia
■ B^goegoens.
B. samhahensis
B. socotrana
■ B. oxysperma
500 changes
Bootstrap values over 50% given above
lines;
Clades not present in strict consensus
indicated by thin lines
11455 parsimony-informative
characters
6. chloroneura
B.kingiana B.tayabensis
B. morsel ^ .
B. porten
B. masoniana
masortiana maculata .
masoniana maculata clone
B. masoniana maculata clone
B. masoniqna maculata done
B. masoniana maculata done
B. chlorosticta
I
B. isoptera
M l
s. sp., 121 c
11°^
B. amphioxis
“ ■ B. malachosticta
I
B. incisa
M l«Q
B. aequata
B. sp., cfbrevinmosa
B. sp., cfserratipetala
|.|8 ^ e ta la
S.sp.,136
Tree length = 175227
Cl = 0.1846
Cl ex uninformative = 0.1697
Rl = 0.4717
110
Figure 7.2:
Majority rule tree of the strict consensus trees from analyses of
the 16 automated alignments
D. glomerata
D. cannabina 1
3. cannabina 2
5. aequata
i;ip"?i®i824
B. balansana
. beddpmei
. brevinmosa
B. sp.,cf brevirimosa
B. sp., cfserratipetala
B. chlorosticta
. çrasgirostris
. deliciosa
B. diadema
g
g
B. fallax
B. floccifera
B. goegoens.
B. gracilis
B. grandis grandis
B. grandis holostyla
B. sp., gutt
B. hanoelii
B. hatacoa
B. hemsieyana .
H. sandwicnensis
B. incamata
B. incisa
B. isoptera
B. iucunda
B. kingiana
B. labordei
B. lubbersii
B. manicata
B. maynensis
B. menyangensis
B. meyeri-johannis
B. morsei
B. sp., nam 1
. sp., nam 2
. oibia
B. oxysperma
B. peltata
B. sp.. Philippine
B. sp., Piatycentrum
B. porteri
B. rajah
B. sp., Reichenheimia
B. rex
B. roxburghii
B. rubella
B. sericoneura
. seiratipetala _
. solananmera 1
B. sp. nov. Yunnan
B. sutherlandii
S. sp., 121 c
Ssanguinea
B. sp., Taiwan
B. theimei
B. thomeana
B. versicolor
B. wollnyi
B. sp., Yunnan 21
B. sp., Yunnan 25
. sp., Yunnan 26
. sp., Yunnan 33
B. acetosella
B. longifolia
B. amphioxis
B. malachosticta
B. boliviensis
B. dnnabarina
B. chloroneura
B. tayabensis
3. formogana
3. ravenii
B. heracleifolia
B. sp., U172
B. herbacea
B. sp., Trachelocarpus
B. imperialis
B. violifolia
B. integerrima
B. soiananthera 2
B. involucrata AB
B. involucrata
g
g
g
JU_
Æ.
_94_
_62_
_Lûû_
_aa_
_5S_
111
_62_
88
_Z5_
59
_Ü_
75
1-O
_5S_
AF
j2_
75
_&a_
S.AF
56
62
58
AS
94
MAD
_62_
_0__£5.
AF
88
,------------------------
---------------------59
53
69
_____ S2_____ 1-----------------
88
hO-
AF
66
_S2_
94
AM
66
_6a_
_ai
88
62
AM
75
112
B. sp. nov., Philippine
B. sp., Sulawesi 254
B. samhahensis
B. socotrana
B. longicarpa 1
B. longicarpa 2
B. sp., Sulawesi 252
B. sp., Sulawesi 253
S.sp., 121
S. sp., 136
B. palmata 227
B. palmata 74
B. palmata 75
B. annobonensis
B. engleri
B. iohnstonii 1
B. johnstonii 2
B. geranioides
B. dregei ‘partita’
B. sonderana
B. dregei
B. dregei ‘homonyma’
B. masoniana
B. masoniana maculata clone
B. masoniana maculata clone
B. masoniana maculata done
B. masoniana maculata done
B. masoniana maculata done
B. ankaranens
B.bogneri
B. madecassa
B. mananjabensis
B. salaziensis
B. francoisii
B. nossibea
B. aspleniifolia
B. staudtii
B. scapigera
B. duncan-thomasii
B. letouzeyl
B. dewildei
B. potamophila
B. prismatocaipa
B. quadrialata
B. scutifolia
B. longipetiolata
B. poculifera
B. loranthoides rhopalocarpa
B. capillipes
B. gabonensis
B. horticola
B. kisuluana
B. mannii
B. molleri
B. subscutata
B. sp., Bolivia
B. fissistyla
B. fuchsioides
B. holtonis
B. jamesoniana
B. meridensis
B. guaduensis
B. sp. sych
B. cubensis
3. obliqua
3. minor
B. odorata
B. angulans
B. echinosepala
B. egregia
B. listada
§! luxui^ns clone
B. luxurians clone
B. luxurians clone
B. luxurians clone
B. luxurians
B. sp.„macG
B. oxyphylla
B. 0)wphylla AB
B. rufoserica
B. acerifolia
B. convolvulacea
B. glabra
B. sp., 224
B. sp., macE
B. ulmlfolia
B. valida
Figure 7.3:
Strict consensus of 10,000 MPTs, culled manual ITS alignment
^ -# 4 =
AF
20
m
42
fil
3
74 1-------------------
4
D. glomerata
D. cannabina 1
D. cannabina 2
H. sandwichensis
B. annobonensis
B. engleri
B. johnstonii 1
B. johnstonii 2
B. lucunda
B. thomeana
B. aspleniifolia
B. staudtii
B. scapigera
B. duncan-thomasii
B. letouzeyi
B. dewildei
B. prismatocarpa
B. scutifolia
B. potamophila
B. quadrialata
B. meyeri-johannis
B. m adecassa
B. bogneri
B. salaziensis
B. ankaranens
B. mananjabensis
I. nossibea
. francoisii
B. longipetiolata
B. loranthoides rhopalocarpa
B. poculifera
B. mannii
B. molleri
B. kisuluana
l'.ÿüfôiîata
4
inn 81
12 6
[=
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
capillipes
gabonensis
sutherlandii
geranioides
sonderana
dregei partita"
dregei
dregei "homonyma"
sp.. gutt
lubbersii
edmondoi
integerrima
soiananthera 1
heracleifolia
sp., U172
involucrata
involucrata AB
violifolia
imperialis
sericoneura
peltata
theimei
manicata
maynensis
boliviensis
cinnabarina
incarnata
fissistyla
sp., Bolivia
odorata
minor
cubensis
obliqua
I: S
guaduensis
M"
113
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
meridensis
holtonis
fuchsioides
jam esoniana
olbia
gracilis
soiananthera 2
herbacea
sp., Trachelocarpus
wollnyi
ulmifolia
sp., 224
sp., macE
glabra
convolvulacea
acerifoli
valida
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
echinosepala
sp., macGL
oxyphylla
oxyphylla AB
rufoserica
angularis
lobata
luxurians
luxurians clone
luxurians clone
luxurians clone
luxurians clone
soc6 * 4 =
AS
Bootstrap support over
50% atxîve lines;
Bremer support below
lines
114
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
S.
B.
B.
B.
B.
B.
B.
B.
S.
S.
S.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
fallax
socotrana
sam hatiensis
porteri
morsei
masoniana
masoniana maculata
masoniana maculata
masoniana maculata
masoniana maculata
masoniana maculata
kingiana
amphioxis
malachosticta
chlorosticta
sp., 121 c
isoptera
serratipetala
sp., cf serratipetala
brevirimosa
sp., cf brevirimosa
aequata
incisa
sanguinea
sp., 136
sp., 121
sp.. Philippine
floccifera
sp., nam 1
sp., nam 2
grandis holostyla
grandis grandis
dipetala
beddomei
sp., Reichenheimia
rajah
goegoens.
oxysperma
sp., 1998 1824
chloroneura
tayabensis
labordei
rubella
sp., Yunnan 21
sp., Yunnan 25
versicolor
balansana
roxburghii
diadema
sp. nov., Yunnan
hatacoa
sp., Yunnan 26
deliciosa
sp., Sulawesi 254
sp. nov.. Philippine
longicarpa 1
longicarpa 2
rex
annulata
sp., Yunnan 33
sp., Taiwan
ravenii
formosana
sp., Piatycentrum
palmata 74
palmata 75
palmata 227
hem sieyana
handelii
menyangensis
acetosella
longifolia
crassirostris
sp., Sulawesi 252
sp., Sulawesi 253
clone
clone
clone
clone
clone
Figure 7.4:
Phyiogram for the culled manual ITS alignment;
one of 10,000 MPTs
D. glomerata
D. cannabina 1
D. cannabina 2
H. sandwichensis
B. annobonensis
B. engleri
B. ^hnstonii
Tnstonii 1
johnstonii 2
B. iucunda
-r
thom eang
aspleniifolia
j ----------------- B. staudtii
1----------1
------- B. scapigera
Ü— B. duncan-thomasii
B. letouzeyi
I
_B. dewildei
Ij—
B. prismatocarpa
T_|
B. scutifolia
" -T B. potamophila
B. quadrialata
AF
B. meyeri-johannis
B. m adecassa
,,
■ B. bogneri
H 1— B. salaziensis
■B. ankaranens
B. m ananjabensis
~ B. nossibea
B. francoisii
B. longipetiolata
— B. loranthoides rhopalocarpa
B. poculifera
B. molleri
B. mannii
.
MAD
B. subscutata
B. capillipes
B. gabonensis
—
B. sutherlandii
geranioides
sonderana
~ I
| B. sonde
dregei ‘partita’
'------ I r B.. drei
B. dregei
B. dregei homonyma
B. sp., gutt
^cP.dr
-S'tŒdoi
so^^Ti'tfiera 1
AM
- B. heracleifolia
B. sp., U172
r B involucrata
' B. involucrata AB
lmpel?a\?s
B. sericoneura
B. peltata
B. maynensis
B. boliviensis
B. cinnabarina
B. incarnata
5
changes
B. sp., Bolivia
I- B. odorata
I
B. minor
I I— B. cubensis
B. obliqua
[_B. sp., sych
B. guaduensis
B. meridensis
B. holtonis
B. fuchsioides
B. jam esonia.
B. olbia
B. gracilis
B. soiananthera 2
--------------------B. herbacea
B. sp., Trachelocarpus
B. wollnyi
-------- b
B.. Ull
ulmifolia
B. sp., 224
B. glabra
B. convolvulacea
B. sp., macE
B. acerifolia
B. valida
B. egregia
B. listada
B. echinosepala
r^i
B. oxyphylla AB
— B. rufoserica
B. angularis
B. lobata
B. luxurians clone
B. luxurians clone
B. luxurians clone
115
B. fallax
B. socotrana
B. samhahensis
B. porteri
B. morsei
B. masoniana
B. masoniana maculata clone
B. masoniana maculata clone
B. masoniana maculata clone
B. masoniana maculata clone
B. masoniana maculata clone
B. kingiana
B. amphioxis
B. malachosticta
B. chlorosticta
S. sp. 121 c
B. isoptera
B. aequata
B. incisa
— B. brevirimosa
— B. sp., cf brevirimosa
■ S. sanguinea
B. serratipetala
B. sj)., cf serratipetala
AS
-{"s. s& I2T
B. grandis holostyla
B. grandis grandis
B. sp., nam 2
B. floccifera
B. sp., nam 2
B. dipetala
B. beddomei
B. sp., Reichenheimia
B. rajah
B. goegoens.
B. sp.. Philippine
B
,338 1824
B. chloroneura
' B. tayabensis
B. labordei
—
5 changes
329 parsimony-informative
characters
Tree length = 2842
Cl = 0.2961
Cl ex uninformative = 0.2669
Rl = 0 .6 9 1 4
B. rubella
B. sp., Yunnan 21
— B. deliciosa
_ r B. sp., Yunnan 25
'------ B. hatacoa
I
B. sp., Piatycentrum
H
r B. palmata 74
‘ — \ B. palmata 75
• B. palmata 227
“ B. versicolor
- B. balansana
- B. sp. nov., Yunnan
■ B. sp., Yunnan 26
I 6. longicarpa 1
B. longicarpa 2
I------------- B. rex
T i — B. annulata
'— B. sp., Yunnan 33
B. sp., Taiwan
B. ravenii
B. formosana
B. roxburghii
B. diadema
B. sp., Sulawesi 254
B. sp. nov.. Philippine
“ B. hemsieyana
■ B. handelii
B. menyangensis
j - B. acetosella
P B. longifolia
| r - B. crassirostris
| _ r B. sp., Sulawesi 252
^
B. sp., Sulawesi 253
116
Figure 7.5:
Strict consensus of 100 MPTs, unculied manual ITS alignment
glomerata
cannabina 1
cannabina 2
sandwichensis
annobonensis
pT^lfonii 1
100
johnstonii 2
iucunda
aspleniifolia
staudtii
scapigera
duncan-thomasii
letouzeyi
dewildei
prismatocarpa
scutifolia
potamophila
quadrialata
meyeri-johannis
loranthoides rhopalocarpa
longipetiolata
poculifera
molleri
subscutata
gabonensis
capillipes
horticola
kisuluana
AF
_a2_
jTiannii
JOL
MAD
100
—
LZ3_
thomeana
salaziensis
m adecassa
bogneri
ankaranens
mananjabensis
nossibea
francoisii
socotrana
samhahensis
sutherlandii
geranioides
sonderana
dregei 'partita'
dregei
dregei ‘homonyma’
violifolia
imperialis
gracilis
sp., gutt.
lubbersii
edmondoi
sericoneura
a ,
manicata
heracleifolia
fi?voliicr^a
involucrata AB
incarnata
soiananthera 2
integerrima
soiananthera 1
herbacea
cinnabarina
fissistyla
sp., Bolivia
odorata
minor
cubensis
obliqua
meridensis
sp., sych
guaduensis
li» s "‘"-
fuchsioides
olbia
maynensis
wollnyi
ulmifolia
convolvulacea
sp., macE
acerifolia
valida
a
e c h in o s ^ a la
sp., macGL
Sîmi'i AB
rufoserica
angularis
lobata
luxurians
luxurians clone
luxurians clone
luxurians clone
luxurians clone
117
grandis holostyla
grandis grandis
rubella
labordei
sp., Yunnan 26
longicarpa 1
longicarpa 2
hatacoa
sp., Taiwan
ravenii
formosana
deliciosa
sp., Yunnan 33
sp., Yunnan 21
sp., Piatycentrum
palmata 74
palmata 75
palmata 227
sp., Yunnan 25
roxburghii
diadema
hemsieyana
annulata
rex
sp., Sulawesi 254
sp. nov., Philippine
versicolor
balansana
sp. nov. Yunnan
handelii
menyangensis
acetosella
longifolia
crassirostris
sp., Sulawesi 252
sp., Sulawesi 253
sp., nam 1
floccifera
fallax
sp., nam 2
dipetala
beddomei
sp., Reichenheimia
rajah
goegoens.
I? ;;» ®
oxysperma
chloroneura
tayabensis
kingiana
porteri
morsei
masoniana
masoniana maculata
masoniana maculata
masoniana maculata
masoniana maculata
masoniana maculata
isoptera
chlorosticta
sp., 121 clone
amphioxis
malachosticta
aequata
incisa
serratipetala
sp., cf serratipetala
sanguinea
brevirimosa
sp., cf brevirimosa
sp. 136
sp. 121
Bootstrap support
values over 50%
atxive lines
118
clone
clone
clone
clone
clone
Figure 7.6:
AF
10 changes
Phyiogram for unculied manual ITS alignment; one of 100 MPTs
D. glomerata
D. cannabina 1
D. cannabina 2
H. sandwichensis
I—
B. annobonensis
I
I
—
B. enjieri
f B. iohnstonii 1
B. johnstonii 2
B. iucunda
B. aspleniifolia
staudtii
scapigera
B_ durican-thomasii
' B. letouzeyi
I
B. dewildei
M l
B. prismatocarpa
M _ | — B. scutifolia
L r B. potamophila
...
. B. quadrialata
B. meyeri-johannis
B. loranthoides rhopalocarpa
B. longipetiolata
}. poculirera
nolleri
. subscutata
. gabonensis
B. capillipes
1-
B. mannii
B. thomeana
B. salaziensis
m adecassa
B. bogneri
B. ankaranens
B^m ananjabe
nossibea
francoisii
B. socotrana
B. samhahensis
rP- sutherlandii
rO~i I
ET geranioides
I B. sonderana
SAFHr%<lje|^;pdrtlta-
“ B. homonyma
” B. violifolia
B. imperialis
B. gracilis
m
B. edmondoi
B. sericoneura
B. peltata
B. theimei
B. manicata
_ r B. involucrata
B. i ^ C a W ‘='®‘^ A®
B. integerrima
^ -^ " B !% n a n th e ra 2
-------------------B. herbacea
B. b o l l , =
' Trachelocarpus
B. cinnabarina
fT” B. fissistyla
B. sp.,_Borivia
_ ï ’B7ôclbrâta
_J
B. minor
L_r B. cubensis
B. obliqua
B._rneridensis
-^ .^ g iia c iu en sis
B. jam esoniana
B. holtonis
B. fuchsioides
B. olbia
B. maynensis
B. wollnyi
B. ulmifolia
9%&ira^4
B. convolvulacea
B. valida
B. echinosepala
sp., rnacGL
oxyphylla
B. oxyphylla AB
“ B. rufoserica
B. luxurians
B. luxurians clone
B . luxurians clone
B. luxurians clone
B. luxurians clone
119
■ B. grandis holostyla
B. grandis grandis
B. rubella
‘--------- B. labordei
r B. sp., Yunnan 26
T — I B. longicarpa
B. longicarpa
— B. hatacoa
r B. sp., Taiwan
i j - B. ravenii
' B. formosana
“ B. deliciosa
B. sp., Yunnan 33
" B. sp., Yunnan 21
B. sp., Piatycentrum
r B. palmata 74
f B. palmata 75
' B. palmata 227
B. sp., Yunnan 25
—r B. sp., Sulawesi 254
B. sp.. Philippine
B. roxburghii
B. sp.noy. Yunnan
IT“ B. .versicolor
B. balansana
_ p B. annulata
B. rex
r~~ B. diadema
B. hem sieyana
handelii
m enyangensis
B. acetosella
B. longifolia
■ B. crassirostris
B. sp., Sulawesi 252
B. sp., Sulawesi 253
r B. sp., nam 1
Il
B. floccifera
^
B. fallax
q
iF ^
. . beddomei
B,
“
B. amphioxis
B. malachosticta
B. isoptera
B. aequata
B. incisa
B. brevirimosa
B. sp., cf brevirimosa
' B. serratipetala
B. sp., cf serratipetala
“ S. sanguinea
r S. sp. i3 6
^ S. sp. 121
B. sp., Reichenheimia
B. rajan
B. goegoens.
B. sp.. Philippine
— B. sp., 1998 1824
B. oxysperma
r B. chloroneura
*■ B. tayabensis
“ B. kingiana
B. porteri
B. morsei
B. masoniana
B. masoniana maculata clone
B. masoniana maculata clone
. masoniana maculata clone
B. masoniana maculata clone
B. masoniana maculata clone
10 changes
665 parsimony-informative
characters
Tree length 5979
Cl = 0.2927
Cl ex uninformative = 0.2711
Rl = 0.6910
120
7.3.2.I.
Topology:
clades which occur in trees produced by the majority
of alignments (see Figure 7.2, majority rule consensus tree) are as follows
(with bootstrap values given, firstly from the elision tree, secondly from the
culled manual ITS alignment):
1. ‘R ostrobegonia’: B. annobonensis. B. engleri, B. johnstonii (92% ; 66% ).
2. Augustia: B. geranioides, B. dregei ‘partita’, B. sonderana, B. dregei, B. dregei
homonyma (96% ; <50% ).
3. the S. masoniana clones (75% ; 72% ).
4. Madagascar: 6. ankaranensis, B. bogneri, B. m adecassa, B. mananjensis, B. salaziensis,
B. francoisii, B. nossibea (100% ; 100% ).
5. ‘Loasibegonia*: B. aspleniifolia. B. staudii, B. scapigera, B. duncan-thomasii, 6. letouzeyi,
B. dewildei. B. potamophila, B. prismatocarpa, B. quadrialata, B. scutifolia (98% ; 95% ).
6. ‘Tetraphila’: B. longipetiolata, B. poculifera. B. loranthoides ssp rhopalocarpa, B.
capillipes, B. gabonensis, B. horticola, B. kisuluana, B. mannii, B. molleri, B. subscutata
(100% ; 84% ).
7. American clade A {Begonia and Ruizopavonia): Bolivian B. sp., 8. fissistyla, B.
fuchsioides, B. holtonis, B. Jamesoniana, B. meridensis, 8. guaduensis, 8 . sp.
‘sychnanthera’, 8. cubensis, 8. obliqua, 8. minor, 8. odorata (100% ; 98% ).
8. Begonia: 8. cubensis, 8 . obliqua, 8. minor, 8. odorata (100% ; 98% ).
9. ‘P ritzeiia’: 8 . angularis, 8 . echinosepala, 8. e areaia. 8. listada, 8 . lobata, 8. luxurians
(and its clones), 8 . sp. ‘macrocarpa’ GL, 8. oxyphylla, 8. rufosericae, 8 . acerifolia, 8.
convolvulacea. 8. alabra. 8. sp. 224, 8. sp ‘macrocarpa’ E, 8. ulmifolia. 8. valida (100%;
83% ).
10. American clade B pro parte: 8. acerifolia, 8 . convolvulacea, 8 . glabra, 8. sp. 224, 8.
sp ‘macrocarpa’ E, 8. ulmifolia, 8. valida (100% ; 99% ).
Where section names are given in inverted commas, the vast majority of
species within the clade belong to that section (Doorenbos, Sosef & de Wilde,
1998), but the underlined species belong to related sections.
The strict consensus trees for the individual alignments were checked to see
which trees contained which of these clades. A few other features have also
been considered:
11. Hillebrandia has appeared as sister to Begonia in most of the analyses in
which it has been included, including the analyses of ITS which only use
conserved regions of sequence, Swensen, Luthi & Rieseberg (1998), Wagstaff
and Dawson (2000) and unpublished studies with trnL (Plana, 2000).
12. The placement of the outgroup on the trees has also been considered: in
many cases the ‘conventional’ tree of
[Datisca [Hillebrandia [Begonia]]]
121
has not been
obtained and so trees have been checked to see whether or not Datisca has
been resolved as sister to Hillebrandia or Begonia taxa. The elision tree gives
87% bootstrap support to a monophyletic Begonia, with Hillebrandia as sister.
13, 14. Lastly, in some preliminary analyses of manually aligned ITS data, the
African taxa have been paraphyletic including the American and Asian taxa as
follows:
Therefore trees were checked to see which
[Africa[Africa[Asia][America]]].
indicated monophyly of American and/or Asian taxa.
This information is all summarised in Table 7.4.
Table 7.4:
Topological features of the cladograms produced by different
alignments
Clade
Al. Al. Al. Al. Al. Al. Al. Al. Al. Al. Al. Al. Al. Al. Al. Al. Elision Manual Manual
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
Culled entire
1. 'Rostrobegonia'
+
2. Augustia
+
3. B. masoniana
+
4. Madagascar
+
+
5. ’Loasibegonia'
+
+
6. Tetraphila'
+
7. American clade A
+
8. Begonia
+
+
9. American clade B
+
10. American clade B pro parte +
11. Hillebrandia sister to
Begonia
12. Datisca sister to
Hillebrandia OR African taxa
13. American taxa
monophyletic
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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14. Asian taxa monophyletic
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Alignments 1 and 7 contain the greatest number of the described clades,
although in alignment 1 Hillebrandia does not appear as sister to Begonia.
122
The most consistently resolved clade is of the Madagascan species, which is
recovered from 15 out of 16 alignments. In only two out of 16 alignments are
the Asian taxa monophyletic. In several of the trees where the Asian taxa are
not monophyletic, this is because they have been rendered paraphyletic by
American taxa, not because taxa are scattered widely across the trees.
7.3.2.2.
Tree Distance Measures: The highest possible value for the
partition metric (PM) for these data is 2N - 6 = 2 x 177 - 6 = 348. Values for the
16 different Clustal alignments ranged from 212 (between the trees produced
from alignments 1 and 10, and alignments 5 and 12) to 314 (between
alignments 4 and 7). Values of
were lowest (97) between alignments 10
and 11, and highest (140) between alignments 8 and 13. Between the six
elision MPTs, PM ranged from two to six, and D,, from one to three. Between
the majority rule elision tree and each of the 16 majority rule alignment trees,
PM ranged from 176 (alignment 10) to 272 (alignment 4) and D^, from 85
(alignment 12) to 134 (alignment 4).
7.3.3 Compartmentalization
A.
Methods:
Well-supported clades were selected on the basis of strict
consensus trees from:
1. the 26S data set of 38 taxa
2. the 26S and ITS combined data set of 38 taxa
3. the elision ITS data set of 177 sequences
4. the individual automated alignments
5. the culled ITS data set of 177 sequences
6. the complete ITS data set of 177 sequences
Clades were selected which were monophyletic in all trees except those
produced from the automated alignments (which occasionally have widely
misplaced taxa in clades which otherwise agree with the other data sets and
data analyses) and the 26S alignment for taxa within the Asian - American
clade (because some clades here are based on only one or two characters,
with no bootstrap support, and differ from clades recovered by all other
treatments). Not all clades have bootstrap support in all data sets. The clades
which were isolated thus are:
123
1. ‘Loasibegonia’: B. aspleniifolia: B. staudtif, B. scapigera', B. duncan-thomasii', B.
letouzeyi', B. dewildei'. B. prismatocarpa', B. scutifolia', B. potamophila] B. quadrialata (total of
10 taxa).
2. ‘Tetraphiia’: B. loranthoides ssp rhopalocarpa] B. longipetiolata] B. poculifera: B. molleri]
B. subscutata] B. gabonensis] B. capillipes] B. horticola] B. kisuluana] B. mannii (total of 10
taxa).
3. Madagascar: B. bogneri] B. salaziensis] B. madecassa] B. mananjensis] B.
ankaranensis] 6. nossibea] B. francoisii (total of seven taxa).
4. Coelocentrum : B. ported] B morsei] 6. masoniana and the B. masoniana var. m aculata
clones (total of eight sequences).
5. ‘P eterm annia’: B. cholorosticta] B. amphioxis: B. malachosticta] B. isoptera] B. aequata]
6. incisa] B. serratipetala] B. cf. serratipetala] B. brevirimosa] B. cf. brevirimosa] Svm beaonia
sanauinea'. S. so. 136: S. so. 121 (two sequences) (total of 14 sequences).
6. ‘P iatycen tru m ’: Yunnan sp. 21; Yunnan sp. 25; Yunnan sp. 26; Yunnan sp. 33; 6.
versicolor, B. balansana: B. sp. nov. 20; 6. longicarpa (two individuals); 6. hatacoa] B. sp.,
Taiwan; 6. ravenii] B. formosana] B. deliciosa] Piatycentrum sp. 215; B. palmata (three
accessions); B. hemsieyana] B. roxburahif. B. diadema] B. annulata] B. rex; B. sp., Sulawesi
254; B. so. nov.; Philippines: B. handelii'. B. m envanaensis'. B. acetosella: B. lonaifolia: B.
crassirostris: B. sp, Sulawesi 252; 6. sp, Sulawesi 253 (total of 32 taxa).
7. ‘B egonia’: B. fissistvla: B. sp.. Bolivia: 6. odorata] B. minor, B. cubensis] B. obliqua] B.
sp. ‘sych’; B. guaduensis: B. meridensis: B. holtonis: B. fuchsioides: B. iamesoniana (total of
12 taxa).
8. ‘P ritzelia’: B. ulmifolia: B. sp. 224; B. alabra: B. convolvulacea: B. sp. ‘macE’; B. sp.
‘m acG’; B. acerifolia] B. valida] B. egregia] B. listada] B. echinosepala] 6 . rufosericae] B.
angularis] B. lobata] B. oxyphylla (two sequences); B. luxurians and its clones (total of 21
sequences).
For each clade, the region of the manual alignment which includes its taxa and
outgroups from within other well-defined clades (not from the closest taxa in
the larger phylogenies, because often the placement of these is uncertain over
several trees, and rooting each compartment clade on them may bias
subsequent reanalysis) were selected in MacClade 3.07 (Maddison &
Maddison, 1992, 1997) and saved as separate files.
The compartments were removed from the total alignment and realigned
manually in SeqPup 0.6f (Gilbert, 1995), before being exported to PAUP* 4.0
(Swofford, 2000). The form of parsimony analysis used depended on the size
of the data sets. For smaller compartment data sets, exhaustive (less that 12
taxa) or branch and bound (12 to 14 taxa) searches were run; heuristics were
used for compartment 6 (Piatycentrum) and compartment 8 (Pritzelia) (1000
random addition replicates, TBR). Values for g1 (10,000 random trees ) and
FTP (outgroup excluded) were also calculated. Searches were run with and
124
without ambiguous sites excluded. Bootstrap support was calculated using
10,000 replicates of fast addition; Bremer support values were calculated
using AutoDecay (Erikkson, 1998) (10 random addition replicates and TBR per
constraint tree).
For seven of the eight data sets, analyses were run both for the complete
alignments and for a culled subsection of the alignments (ambiguous
positions excluded). For compartment 6, the Piatycentrum data set, no culled
analyses were run, as no positions appeared ambiguous.
B.
Results:
In all analyses except that for compartment 1,
Loasibegonia, the topologies for both analyses (culled and unculled) were the
same. In all analyses except that for the section Begonia data set
(compartment 7) the topologies are also consistent with the cladogram
produced by analysis of the culled 177 taxon ITS matrix. In the first analysis of
compartment 5, the Petermannia data set, the cloned sequence of
Symbegonia sp. 121 does not cluster with the consensus sequence for
Symbegonia sp. 121. Removal of this cloned sequence {Petermannia
analysis 2) increases tree support and decreases the number of MPTs.
Although removing a taxon simply because one does not like the effect it has
on an analysis is hard to justify, the placement of this one cloned sequence, far
from the other Symbegonia species, may mean that it is a disfunctional
paralogue and perhaps best excluded.
Furthermore, looking at the 5.8S sequence of the Symbegonia clone, there are
eight point mutations (G to A, character 567; C to T, character 601 ; C to T,
character 640; A to T, character 642; C to T, character 646; 0 to T, character
654; C to T, character 661 and C to T, character 670). These add weight to the
hypothesis that the copy may be paralogous and can be safely excluded.
For a summary of tree statistics for these analyses, see Table 7.5. Individual
trees are presented subsequently under the headings for each compartment.
Where sectional placements are marked onto the trees, these are taken from
Doorenbos, Sosef and de Wilde (1998).
125
Table 7.5:
Tree statistics for compartment analyses
Comp. Clade
Loasibegonia
1 0 (1 2 )
Loasibegonia
culled
1 0 (1 2 )
Tetraphiia
1 0 (1 2 )
Tetraphila
culled
1 0 (1 2 )
M adagascar
7 (9 )
Madagascar
culled
7 (9 )
1
1
2
2
3
3
Uninform. Inform.
chars
chars
No.
trees
M PT
length
Cl
Cl ex
uninf.
Rl
gi
P IP
441
148
149
1
4 94
0.80
0 .69
0.66
-1.036
0.001
399
112
129
1
4 10
0.79
0.69
0.66
-1.082
0.001
513
161
83
1
371
0.84
0.67
0 .64
-0.779
0.01
444
110
73
1
2 82
0.82
0.66
0 .65
-0.797
0.01
534
150
77
2 89
0.90
0.75
0.71
-1.678
0.001
4 85
138
74
1
2 70
0.90
0.75
0 .72
-1.780
0.001
513
144
60
1
2 63
0.92
0.78
0.77
-1.254
0.01
478
110
46
1
195
0.92
0.79
0 .79
-1.144
0.01
554
164
81
36
357
0.82
0.62
0.64
-0.748
0.001
524
148
75
36
3 28
0.81
0.61
0 .64
-0.714
0.001
574
149
76
4
3 18
0.83
0.64
0.66
-0.814
0.001
543
132
72
4
292
0.82
0.64
0.66
-0.799
0.001
473
138
172
10
5 59
0 .70
0.58
0.67
-1.291
0.001
463
129
151
1
4 52
0 .83
0.75
0.79
-1.179
0.002
440
113
142
1
415
0.83
0.75
0.78
-1.076
0.002
4 26
140
159
2
521
0.78
0.67
0.81
-0.852
0.001
397
121
145
2
4 67
0.77
0.66
0 .82
-0.776
0.001
No. taxa Constant
(+ 0 G )
chars
Coelocentrum 8 (1 0 )
4
Coelocentrum
culled
8 (1 0 )
Peterm annia
1 4 (1 6 )
1 4 (1 6 )
5
Petermannia
culled
1 3 (1 5 )
5
Petermannia
2
1 3 (1 5 )
5
Petermannia
2 culled
Piatycentrum
32 (34)
Begonia
1 2 (1 5 )
Begonia
culled
1 2 (1 5 )
Pritzelia
21 (24)
Pritzelia
culled
21 (24)
4
5
6
7
7
8
8
7.3.3.1.
Compartment 1 :
Loasibegonia (Aifica)
The FTP probability is 0.001; g1 is -1.082. There were 259 characters
excluded, leaving 399 constant, 112 uninformative and 129 informative
characters. The furthest pairwise distances within Loasibegonia /
Scutobegonia are 0.130 (6. staudtii to 6. dewildei) and the closest are 0.013 (8.
potamophila to B. quadrialata)] the greatest distance between Filicibegonia
and Loasibegonia is 0.151 (8. aspleniifolia to 8. staudtii).
Analysis of the culled and unculled data sets both produced the same single
MPT (Figure 7.7).
126
Figure 7.7:
Phylogram of single MPT for culled 'Loasibegonia' data set:
B. loranthoides
---------------------------------------------------B. bogneri
O
FILICIBEGONIA
B. aspleniifolia
B. staudtii
52
100
• B. scapigera
24
100
12
B. duncan-thomasii
68
67
B. letouzeyi
LOASIBEGONIA
SCUTOBEGONIA
10 changes
51
B. dewildei
B. prismatocarpa
63
B. scutifolia
129 parsimony-informative characters
23.
—
Tree length 410
Cl = 0.7927
01 ex uninformative = 0.6931
Rl = 0.6586
B. potamophila
— B. quadrialata
Bootstrap values over 50% above lines;
Bremer support below lines
On the basis of this ITS phylogram (Figure 7.7), section Filicibegonia is sister
to section Loasibegonia, and section Loasibegonia is paraphyletic without the
inclusion of section Scutobegonia. The topology of the ingroup here is the
same as the elision, unculled manual and culled manual 177-sequence
analysis topologies for the same taxa (Figures 7.1, 7.3 and 7.5). (See
Appendix 14.4 for a comparison of this tree topology with a morphological
cladogram topology produced by Sosef, 1994.)
7.3 3.2.
Compartment 2:
Tetraphila (Africa)
The PTP probability is 0.010; g1 is -0.776. There were 249 characters
excluded, leaving 444 constant, 110 uninformative and 73 informative
characters. The maximum pairwise distance from ingroup to outgroup is 0.231
(B. longipetiolata to 8 . duncan-thomasii). Within the ingroup, the most
divergence is 0.103 (8 . man//to 8 . longipetiolata) and the least is 0.011 (8 .
gabonensis to 8 . capillipes).
127
Because the ingroup and outgroup were quite divergent, analyses were run
using each outgroup species separately. Both outgroups produced the same
topology (one MPT). Analyses were also run including all the matrix and
excluding variable positions. Both produced the same topology (one MPT)
(Figure 7.8). The tree from the culled matrix is presented here, as a more
conservative estimate.
Figure 7.8:
Phylogram of single MPT for Tetraphila matrix
B. duncan-thomasii
B. bogneri
B. longipetiolata
32.
B. loranthoides ssp rhopalocarpa
32
k >
32.
SQUAMIBEGONIA
B. poculifera
11
TETRAPHILA
B. molleri
73
B. mannii
B. kisuluana
10 changes
M
B. horticola
2
73 parsimony-informative characters
Tree length = 282
01 = 0.8156
01 ex uninformative = 0.6601
Rl = 0.6510
- B. subscutata
BA
B. capillipes
B. gabonensis
Bootstrap values over 50% above branches,
Bremer support below branches
On the basis of this ITS tree (Figure 7.8), section Tetraphila resolves into two
clades, one of which includes section Squamibegonia. The topology of the
ingroup has several differences to the elision and unculled manual 177128
sequence analysis topologies (Figures 7.1 and 7.5), but is consistent with the
topology from the culled manual 177-sequence analysis (Figure 7.3), although
this topology is more resolved.
7.3.3.3.
Compartment 3:
Madagascar
The PTP probability is 0.001; g1 (evaluated during the exhaustive search) is 1.753. The maximum pairwise distance from outgroup to ingroup is 0.210 (6 .
duncan-thomasii to B. nossibea)] within the ingroup, the maximum distance is
0.071 (B. ankaranensis to B. madecassa) and the minimum is 0.011 (B. •
nossibea to B. francoisii).
Using each outgroup separately and using the culled and unculled matrices
both found the same two MPTs (Figures 7.9 and 7.10).
Figure 7.9:
First phylogram (of two MPTs) for Madagascan matrix
-------------------------------------B. loranthoides
B. duncan-thomasii
B. madecassa
NERVIPLACENTRIA
in n
28
ERMINEA
B. bogneri
rO
B. salaziensis
MEZIERIA
B. ankaranens
10 changes
B. mananjabensis
Bootstrap values over 50% above
branches:
Bremer support below branches
4
QUADRIU OBARIA
-
100
B. nossibea
-
10
B. francoisii
129
Figure 7.10: Second Phylogram (of two MPTs) for Madagascan matrix
-------------------------------------- B. loranthoides
B. duncan-thomasii
" B. madecassa
B. salaziensis
10 changes
—
B. bogneri
— B. ankaranens
B. mananjabensis
74 parsimony-informative characters
Tree length 270
Cl = 0.8963
Cl ex uninformative = 0.7544
Rl = 0.7200
B. nossibea
B. francoisii
The trees differ by the position of B. bogneri and B. salaziensis, and the
Quadrilobaria clade is not fully resolved in the second tree. These ITS trees
suggest that section Quadrilobaria is monophyletic. Sampling does not allow
consideration of the monophyly of sections Nerviplacentaria or Erminea. The
monophyly of section Mezieria is not considered here, as it has been assumed
to be paraphyletic based on prior analyses (Figures 5.2, 5.3, 5.4, 5.5, 5.6, 5.7,
5.8, 5.9, 5.10, 7.1, 7.3 and 7.5).
The first phylogram is congruent with the culled manual 177-sequence
analysis (Figure 7.3), but is more resolved; it differs from the unculled manual
177-sequence analysis (Figure 7.5) in that the unculled alignment gives B.
salaziensis as basal. It also differs from the elision 177-sequence analysis
(Figure 7.1).
7.3 3.4.
Compartment 4:
Coelocentrum (Asia)
The PTP probability is 0.010; g1 (estimated from an exhaustive search) is 1.073. There were 272 characters excluded, leaving 478 constant, 110
uninformative and 46 informative characters. Pairwise distances range from
0.007 (between two clones of B. masoniana war. maculata) to 0.113 (6 .
masoniana var. masoniana to B. masoniana var. maculata). The largest
130
distance between the other species in section Coelocentrum and B.
masoniana is 0.106 (8 . ported to 8 . masoniana) and between 8 . ported and 8 .
morsei, the distance is 0.072. The maximum distance from the outgroup to the
ingroup is 0.171 (8 . masoniana to 8 . palmata).
Analysis of the unculled and of the culled data sets found a single MPT (Figure
7.11).
Figure 7.11 : Single MPT for Coelocentrum matrix
B.chlorosticta
B. palmata
B. ported
97
B. morsei
COELOCENTRUM
64
10 changes
23.
46 parsimony-informative characters
Tree length 195
01 = 0.9231
01 ex uninformative = 0.7857
Rl = 0.7857
Bootstrap values over 50% above branches;
Bremer support below branches
84
B. masoniana var.
masoniana
B. masoniana var.
maculata clone
______________ B. masoniana var.
maculata clone
__ B. masoniana var.
maculata clone
58
B. masoniana var.
52 maculata clone
B. masoniana var.
maculata clone
r-
Section Coelocentrum appears monophyletic. Within the section, all
sequences from 8 . masoniana resolve as monophyletic. The topology found is
the same as that from the unculled 177-sequence analysis (Figure 7.5); it is
congruent with, but less resolved that, the topology from the culled 177sequence analysis (Figure 7.3), and differs from the topology from the elision
177-sequence analysis (Figure 7.1).
When a locus which has been homogenised by concerted evolution is
compared across species, “all the paralogues within a species appear as
each others’ closest relatives in a gene tree” (Doyle & Gaut, 2000, p. 3). If the
131
different ITS sequences from clones of B. masoniana var. maculata represent
paralogous copies, their monophyly in this ITS gene tree is evidence for
concerted evolution in this species. However, it is also possible that the
different copies represent recent allelic variation rather than paralogues.
7.3.3.S.
Compartment 5:
Petermannia (Asia)
The PTP probability is 0.001; g1 is -0.799. There were 181 characters
excluded; of the remaining characters, 543 were constant, 132 were parsimony
uninformative and 72 were parsimony informative. The minimum pairwise
distance within Petermannia is 0.006, between B. brevirimosa and B. cf.
brevirimosa. The maximum distance is 0.081, between B. chlorosticta and B.
aequata. Between the ingroup and the outgroup, the maximum distance is
0.130 (6 . masoniana to B. aequata).
Four equally parsimonious trees were found. The strict consensus is shown
in Figure 7.12, and one of the MPTs in Figure 7.13:
Figure 7.12: Strict consensus of four MPTs, Petermannia matrix
B. masoniana
B. palmata
B. amphioxis
B. malachosticta
B. isoptera
100
11
B. chlorosticta
PETERMANNIA
iLL
B. incisa
B. aequata
33
B. serratipetala
B. cf serratipetala
22.
Bootstrap values over 50% above
branches,
Bremer support below branches
-Q SYMBEGONIA 8 . sanguinea
B. brevirimosa
32.
B. cf brevirimosa
8 . sp.,136
SYMBEGONIA
132
8 . sp .,121
Figure 7.13: Phylogram for Petermannia matrix, one of four MPTs
-------------------------------------------------------- B. masoniana
B. palmata
B. amphioxis
B. malachosticta
----------------------B. isoptera
----------------------------- B. chlorosticta
B. incisa
B. aequata
B. serratipetala
— B. cf serratipetala
I— B. brevirimosa
10 changes
I B. cf brevirimosa
- S. sanguinea
S. sp.,136
{ S. sp.,121
72 parsimony-informative characters
Tree length = 292
Cl = 0.8219
Cl ex uninformative = 0.6414
Rl = 0.6645
On the basis of this ITS data, Petermannia is clearly paraphyletic without the
inclusion of the genus Symbegonia.
The topology of the ingroup is consistent with, but more resolved than, those
from the culled and unculled 177-sequence analyses (Figures 7.3, 7.5); it
differs from the elision 177-sequence alignment topology (Figure 7.1).
7.3 3.6.
Compartment 6:
Platycentrum (Asia)
The PTP probability is 0.001; g1 is -1.291. The data set comprises 473
constant, 138 uninformative and 172 informative characters. There are few
indels in this data set and so the alignment is not ambiguous; consequently no
data are excluded. Pairwise distances between species ranged from 0.001 (6 .
longifolia to B. acetosella) to 0.095 (8 . roxburghii to 8 . palmata 74).
An heuristic search was run with 1000 random additions, TBR. 10 MPTs were
found (see Figures 7.14, 7.15).
133
Figure 7.14: Strict consensus of 10 MPTs for Platycentrum matrix
69
100
15
.100
8
PLATYCENTRUM
100
SPHENANTHERA
SPHENANTHERA r
O 77
1
63
99
99
Bootstrap values over
50% above lines,
Bremer support below
lines
100
25
68
o
SPHENANTHERA
88
100
11
33
134
74
B. chlorosticta
B. masoniana
B. balansana
B. versicolor
B. sp., Yunnan 26
B. sp. nov. Yunnan
B. longicarpa A
B. longicarpa B
B. sp., Yunnan 25
B. hatacoa
B. hemsleyana
B. sp., Yunnan 33
B. sp., Sulawesi 254
B. sp. nov., Philippine
B. roxburghii
B. diadema
B. deliciosa
B. sp., Yunnan 21
B. annulata
B. rex
B. sp., Taiwan
B. ravenii
B. formosana
B. sp., Platycentrum
B. palmata 74
B. palmata 75
B. palmata 227
B. handelii
B. menyangensis
B. acetosella
B. longifolia
B. crassirostris
B. sp., Sulawesi 252
B. sp., Sulawesi 253
Figure 7.15: Phylogram for Platycentrum matrix, one of 10 MPTs
------------------------------------------------------ B. chlorosticta
B. masoniana
B. balansana
— B. versicolor
B. sp., Yunnan 26
B. sp. nov. Yunnan
_________ I B. longicarpa A
' B. longicarpa B
B. sp., Yunnan 25
B. hatacoa
lOchanges
I B. sp., Sulawesi 254
^ B. sp.. Philippine
B. roxburghii
B. diadema
B. deliciosa
B. hemsleyana
B. sp., Yunnan 33
C
B. sp., Yunnan 21
B. annulata
B. rex
B. sp., Taiwan
B. ravenii
B. formosana
B. sp., Platycentrum.
r B. palmata 74
B. palmata 75
B. palmata 227
B. handelii
B. menyangensis
B. acetosella
B. longifolia
B. crassirostris
-B . sp., Sulawesi 252
B. sp., Sulawesi 253
172 parsimony-informative characters
Tree length = 559
Cl = 0.6995
Cl ex uninformative = 0.5842
Rl = 0.6706
The phylogram (Figure 7.15) shows internai branches short relative to the
terminal branches. Section Platycentrum, on the basis of ITS data, is
paraphyletic without the inclusion of section Sphenanthera. The position of
section Sphenanthera within section Platycentrum is not resolved here, with
135
Sphenanthera appearing poiyphyletic in several of the MPTs.
The topology of the ingroup is inconsistent with those from the elision and
unculled manual 177-sequence analysis topologies (Figures 7.1, 7.5). It is
largely congruent with, but more resolved than, the topology from the culled
manual 177-sequence analysis (Figure 7.3); it differs by the placements of B.
sp., Yunnan 21 and B. sp., Yunnan 33.
7.3 3.7.
Compartment 7:
'Begonia' (America)
The PTP probability for this matrix is 0.002; g1 is -1.087. There were 179
characters excluded, leaving 440 constant, 113 uninformative and 142
informative characters. Pairwise distances between taxa range from 0.011 (S.
obliqua to 6 . cubensis) to 0.128 (S. minor \o B. guaduensis). The widest
distance to the outgroup is 0.258 (6 . guaduensis to B. egregia).
Both the culled data set and the unculled data set found the same topology
(Figure 7.16. The branch-lengths shown here are from the culled data set.
136
Figure 7.16: Single MPT for ‘Begonia’ matrix
B. egregia
B. chlorosticta
93
----------- B. palmata
B. meridensis
57
— B. sp., sych
100
79
22
B. guaduensis
CM RUIZOPAVONIA
4
B. Jamesonia.
LEPSIA
B. holtonis
100
^
26
B. fuchsioides
LEPSIA
— B. fissistyla
rCH HYDRISTYLES
4 ^ B. sp., Bolivia
94
10 changes
142 parsimony-informative characters
55
Tree length = 415
Cl = 0.8265
Cl ex uninformative = 0.7491
Rl = 0.7791
Bootstrap values over 50% above
lines;
Bremer support below lines
100
k>
^
99
12
BEGONIA
r B. odorata
99
B. minor
— B. cubensis
B. obliqua
This phylogram resolves sections Hydristyles and Begonia as monophyletic,
while sections Ruizopavonia and Lepsia are not well differentiated.
The topology of the ingroup here differs from the topologies produced by the
elision, culled and unculled manual 177-sequence analyses (Figures 7.1, 7.3,
7.5). However, the inconsistency is not due to the placement of a few taxa, but
to the rooting of the trees. Given that the wider analyses include closer
relatives of the ingroup taxa here, it is likely that they provide a more accurate
representation of evolution within this clade.
7.3.S.8.
Compartment 8:
'Pritzelia' (America)
The PTP probability is 0.001; g1 is -0.776. There were 201 characters
excluded, leaving 397 constant, 121 uninformative and 145 informative
characters. Pairwise distances range from 0.000 between two of the B.
137
luxurians clones and between B. valida and S. acerifolia, to 0.202, between B.
egregia and 6 . sp. 224.
The same two MPTs were found from analysis of the culled and unculled data
matrices (see Figures 7.17, 7.18). Data given here are from the analysis of the
culled data set.
Figure 7.17: Strict consensus of two MPTs for Pritzelia matrix
sp., sych
DONALD A
86
3
WAGENERIA
P RITZELA
Bootstrap values over
50% above lines,
Bremer support below
lines
SCHEIDWEILERIA 1
palmata
chlorosticta
ulmifolia
sp., 224
glabra
convolvulacea
sp., macE
acerifolia
valida
egregia
listada
echinosepala
sp., macG
rufoserica
angularis
lobata
oxyphylla
oxyphylla AB
luxurians
luxurians clone
luxurians clone
luxurians clone
luxurians clone
138
Figure 7.18: Phylogram for Pritzelia matrix, one of two MPTs
10 changes
145 parsimony-informative characters
Tree length = 467
Cl = 0.7666
01 ex uninformative = 0.6583
Rl = 0.8165
B. sp., sych
B. palmata
— B. chlorosticta
B. ulmifolia
B. sp., 224
B. glabra
r{ B. convolvulacea
r B. sp., macE
B. acerifolia
H B. valida
------------- B. egregia
B. listada
— B. echinosepala
— B. sp., macG
- B. rufoserica
B. oxyphylla
- I B. oxyphylla
r- B. angularis
”T B.
I lobata
— B. luxurians
- B. luxurians clone
— B. luxurians clone
B. luxurians clone
B. luxurians clone
The two MPTs differ in the placement of B. oxyphylla, and the B. angularis/B.
lobata clades. Section Pritzelia is paraphyletic in the basis of this ITS
phylogeny, including the sections Donaldia, Wageneria and Scheidweilaria.
The topology of the ingroup is congruent with, but more resolved than, the
topologies of the same taxa in the culled and unculled manual 177-sequence
analyses (Figures 7.3, 7.5); it differs from the topology produced from the
elision 177-sequence analysis (Figure 7.1).
As with the clones of B. masoniana in the analysis of compartment 4
(Coelocentrum), the clones of B. luxurians are monophyletic, indicating
concerted evolution (Doyle & Gaut, 2000) (if they are paralogs).
139
Comparisons with previous topologies - summary: The compartment
analyses have the benefit of more alignable data sets than the 177-taxon
analyses, as they represent clades from within those wider analyses.
Therefore estimates of character homology, and therefore the resulting
topologies, are more reliable. Furthermore, less data needs to be excluded
due to uncertainly. Thus we can use these topologies as a guide to how well
the larger analyses performed. Table 7.6 summarises these comparisons.
From this it can be seen that the method which was least reliable was elision,
while that which performed best was the culled manual alignment.
Table 7.6:
Summary of comparisons between compartment analysis
topology and 177-sequence analysis topologies for different
alignments
COMPARTMENT
ELISION
UNCULLED
same
CULLED
1. Loasibegonia
same
same
2. Tetraphila
differs
differs
congruent, more resolved
3. Madagascar
differs
differs
congruent, more resolved
4. Coelocentrum
differs
same
congruent, more resolved
5. Petermannia
differs
congruent, more resolved
congruent, more resolved
6. Platycentrum
differs
differs
differs (2 taxa interchange)
7. Begonia
differs
differs
differs - root
8. Pritzelia
differs
congruent, more resolved
congruent, more resolved
7.3.3 9
The remaining taxa
a.
Introduction
Yeates (1995) points out that the character states which best represent a
supra-specific taxon (by keeping it at the same position in a cladogram that the
clade it was derived from took) are those of its common ancestor. If there is no
homoplasy in a data matrix, replacing a monophyletic group by a terminal taxon
using either the exemplar method or an hypothetical ancestor will not alter the
inferred relationships (Bininda-Edmonds, Bryant & Russell, 1998). However, if
some members of a clade have homoplasies with taxa outside the clade,
using them as exemplar taxa can lead to incorrect phylogenetic reconstructions
(through ‘branch attraction' problems). Using an hypothetical ancestor
reduces this problem with homoplasy because apomorphies of some clade
members (which can be homoplasies with other clades) are ignored (BinindaEdmonds, Bryant & Russell, 1998).
140
Three different procedures for obtaining compartmentalised trees were initially
considered:
1. A constraint tree was constructed, including the topology of each of the
compartment analyses, with all other taxa in a basal polytomy; this was used to
direct phylogenetic analyses of the polytomous taxa. However, this did not
reduce analysis times because the search algorithm in PAUP* 4.0 (Swofford,
2000) still considered trees based on any topology; PAUP then rejected trees
which did not fit the constraint. This offers no perceivable advantage in terms
of data analysis time.
2.
An alternate method was tried, wherein the states on the branch leading to
each compartment were reconstructed (using the ‘describe trees’ command in
PAUP* 4.0 (Swofford, 2000), ACCTRAN) and added to the data matrix as
hypothetical ancestors. Hovever, subsequent reanalysis of the compartment
this was tested on {‘Platycentrum’), including the hypothetisised ancestor as a
taxon, did not place the ancestor in a basal position, and also grossly inflated
the number of equally parsimonious trees for the data set. Furthermore, the
ancestral states could have been affected not only by whether ACCTRAN or
DELTRAN were used but also by the topology of the tree chosen (where there
were more than one MPT for a data set) and by the choice of ancestor. Given
these concerns, and coupled with the fact that an hypothesised ancestor is
neither real nor testable, this method was then rejected.
3. Exemplar taxa can be used instead of hypothetical ancestors. Using
exemplar taxa as place-holders also has disadvantages; the branch lengths
may be far longer than they would be if an hypothetical ancestor was used. For
example, in Figure 7.19, the distance to the hypothetical ancestor is only W to X,
while that to the nearest exemplar taxon is W to Y. Thus long-branch attraction
is more likely to cause problems in analyses which use exemplar taxa. A
further consideration is whether it may be better to use taxon Z, which occupies
a basal position relative to taxon Y, or taxon Y, which is on a shorter branch
than taxon Z.
141
Figure 7.19: Choosing exemplar taxa
b.
Material and methods: It was decided to select the exemplar taxa from
each of the compartments, on the basis of a combination of factors - firstly,
some taxa have missing data and were immediately rejected. Secondly, taxa
on shorter branches were selected. Where there were more than one taxon
with comparable branch lengths, the more basal taxon was chosen. Finally,
some taxa cause more alignment difficulties than others, and were less liable
to be chosen.
Further to excluding non-exemplar taxa from the compartment analyses for the
reanalysis of the ITS matrix, multiple accessions or sequences were removed.
The remaining data set contained 66 taxa. The matrix was imported into
SeqPup 0.6f (Gilbert, 1995) and manually realigned. Variable positions and
highly ‘gappy’ sites were then culled.
Maximum parsimony analysis was run using 1000 random addition replicates,
TBR, saving no more than 10 equally parsimonious trees for each replicate
(MaxTrees set at 5000). The saved trees were then used as the starting trees
in a second round of searching, with TBR and swapping to completion, saving
all most parsimonious trees. Bremer support was calculated using AutoDecay
(Erikkson, 1998) (10 random addition replicates per constraint tree, TBR);
Bootstrapping was performed using the fast addition’ option in PAUP* 4.0
(Swofford, 2000) with 10,000 replicates; PTP (1000 replicates, simple addition,
TBR, outgroup excluded) and g1 (10,000 random trees) were also calculated in
PAUP* 4.0 (Swofford, 2000).
The strict consensus tree of the MPTs was saved and used as a topological
constraint for a further round of analyses, 10,000 random addition sequences,
TBR, keeping trees not compatible with the constraint tree, in order to test
whether there were any equally parsimonious topologies which differed from
142
the strict consensus tree.
Taxa which were not resolved in the strict consensus of MPTs were identified,
and the PTP values between some of these unresolved taxa were calculated
using a branch and bound algorithm.
0.
Results and Discussion: There are 555 characters excluded; of the 564
included characters, 133 are constant, 115 are uninformative and 316 are
parsimony-informative across the entire data set of 66 taxa. The g1 value for
the matrix is -0.816; PTP (excluding the outgroup and Hillebrandia) is 0.001.
There were 554 MPTs found, length 2186, which were used to construct the
topological constraint tree. Rerunning the analysis with the constraint tree in
place found 8525 trees of length 2187 (i.e. one step longer than the MPTs).
The strict consensus of these less parsimonious trees had very little
resolution. Twenty-one clades have over 50% bootstrap support. The
consistency index is 0.37 (0.33 excluding uninformative characters); the
retention index is 0.45.
PTP values for partitions of the matrix (unrooted, so no outgroup excluded;
branch and bound search; 1000 replicates) are as follows:
1. B. iucunda, B. molleri, B. m adecassa, B. meyeri-Johannis (unresolved on parsimony tree):
1.000 (insignificant).
2. B. balansana, B. sp., Reichenheim ia, B. rubella, B. labordei, B. sutherlandii, B.
geranloides (unresolved): 0.704 (insignificant).
3. B. beddomei, B. sonderana, B. oxysperma, B. thelmei (unresolved):
0.059 (insignificant).
4. B. floccifera, B. sp. ‘nam ’, B. dipetala, B. beddom ei (resolved): 0.031 (significant).
5. B. theimei, B. meridensis, B. incarnata, B. olbia, B. gracilis, B. maynensis, B. sericoneura,
B. peltata, B. manicata (unresolved): 0.001 (significant).
6. B. oxysperma, B. sp., Philippine, B. sp. 1998 1824, B. chloroneura, B. tayabensis
(resolved): 0.001 (significant).
7. B. violifolia, B. imperialis, B. edmondoi, B. lubbersii, B. sp. ‘guttata’ (resolved): 0.001
(significant).
This indicates that there is significant character covariance (taken as indicative
of cladistic structure) in at least one part of this data set which is not resolved in
the strict consensus of MPTs (partition 5); however, other unresolved taxa show
no character covariance and so, as there is no cladistic structure to the data,
any attempts to obtain further resolution between them would be superfluous
(partitions 1, 2 and 3). Partition 4 was resolved in the strict consensus tree;
143
there is however only a relatively low level of character covariance between the
taxa and so the reconstructed topology must have relatively low confidence.
More reassuringly, partitions 6 and 7, which are resolved in the strict
consensus trees, have significant character covariance.
In order to compare the amount of information provided by this analysis (which
only included exemplar taxa from well-structured clades) with the total analysis,
the taxa which were not included in this analysis were pruned from the strict
consensus of 10,000 MPTs for the culled manual ITS alignment (Figure 7.3),
and the topologies were compared. Figure 7.20 is the strict consensus tree for
the exemplar-included (compartment-removed) ITS data set. Figure 7.21 is the
pruned strict consensus for the culled ITS analysis. Both trees have bootstrap
and Bremer support values on the branches (obviously, for the pruned tree,
these have been taken from the complete 177-sequence analysis). Taxa
which are highlighted in bold are those which have been selected as
exemplars. There is more resolution in the pruned tree. Both support
monophyly for America, but only the pruned tree supports monophyly for Asia (if
Socotra is included).
Tree comparison statistics for the two trees are
= 47, PM = 40 (31.7% of
maximum possible PM value 126). The strict consensus tree for the
compartment-removed data set has 33 resolved nodes, while the pruned
consensus tree for the 177-sequence analysis has 56 resolved nodes.
Some clades are shared by both trees, but there is also some conflict, e.g. in
the position of 8 . morsei. Many of the exemplar taxa are in more resolved
positions on the pruned tree, suggesting that presence of other related taxa in
the analysis affected their placement.
It seems therefore that the best resolution is produced by the 177-sequence
analysis, and compartmentalization has little to offer in analyses of this data
set. Tree support measures are not greatly increased in the reduced-taxon
analysis. In fact, given that most of the compartment analyses are congruent
with the culled 177-sequence analysis topology, and that the culled 177sequence analysis offers higher resolution across the spine of the tree than
analysis of a smaller data set, it seems that the best estimate of Begonia
phylogeny is the culled ITS tree.
144
Figure 7.20: Strict consensus of 554 MPTs, compartment-removed ITS data
set
57
3
100
94
92
AF
77
1
98
S.AF
100
9
73
1
83
AS
-52.
100
97
1
jm .
100
Matrix has 316 pars, inform, characters.
Bootstrap values over 50% above lines,
Bremer support below lines
1
100
1
95
145
1
D.
D.
H.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
glomerate
cannabina
sandwlchensis
m a d ec as sa
meyerl-johannis
m olleri
Iucunda
thom eana
a sp le n iifo lia
annobonensis
johnstonii
englerl
b alan san a
rubella
labordei
sp., Reich.
sutherlandii
geranloides
grandis holostyla
grandis grandis
rajah
goegoensis
floccifera
sp.
dipetala
beddomei
sonderana
partita
dregei
homonyma
fallax
socotrana
samhahensis
kingiana
m alach o sticta
m orsei
oxysperma
sp., Philippine
19981824
chloroneura
tayabensis
theimei
m erid en sis
incarnata
olbia
gracilis
maynensis
sericoneura
peltata
manicata
integerrima
solananthera
herbacea
sp., Trach.
ulm ifolia
wollnyi
boliviensis
cinnabarina
involucrata
heracleifolia
sp., U 172
violifolia
imperialis
lubbersii
sp. ‘guttata’
edmondoi
Figure 7.21: Pruned strict consensus of 10,000 MPTs, culled ITS data set
_ai
66
10
AF
o -
_51
D. glomerate
D. cannabina
H. sandwichensis
B. annobonensis
B. johnstonii
B. engleri
B. iucunda
B. thomeana
B. aspleniifolia
B.
100
meyeri-johannis
B. m adecassa
B. molleri
42
soc^io
B.
B.
B.
fallax
socotrana
samhahensis
B. morsei
B.
kingiana
B. m alachosticta
B.
B.
B.
B.
B.
B.
B.
B.
84
3
85
floccifera
sp., Philippine
sp.
grandis holostyla
grandis grandis
dipetala
beddomei
labordei
B. balansana
57
100
S.AF
o-
100
12
81
91
92
AMr O
100
98
20
10
Æ.
63
100
B. rubella
B. sp., Reich.
B. rajah
B. goegoens.
B. oxysperma
B. 19^901824
B. chloroneura
B. tayabensis
B. sutherlandii
B. geranloides
B. sonderana
B. ‘partita’
B. dregei
B. homonyma
B. sp. ‘guttata’
B. lubbersii
B. edmondoi
B. integerrima
B. solananthera
B. involucrata
B. heracleifolia
B. sp., U 172
B. violifolia
B. imperialis
B. sericoneura
■ B. peltata
■ B. theimei
• B. manicata
■ B. maynensis
■ B. boliviensis
• B. cinnabarina
B. meridensis
56
Matrix has 270 pars, inform, characters
Bootstrap values over 50% above lines,
Bremer support below lines
■B. incarnata
■B. herbacea
■B. sp., Trach.
- B. ulmifolia
■B. wollnyi
• B. olbia
• B. gracilis
146
d.
The Jigsaw Tree
Figure 7.22: ITS phylogeny of Begoniaceae (culled ITS sequence analysis,
altered to reflect compartment topology)
D.
D.
H.
B.
B.
B.
glomerata
cannabina
sandwichensis
annobonensis
engleri
johnstonii
B. iucunda
B. thomeana
B. aspleniifolia
B. staudtii
B. scapigera
B. duncan-thomasii
B. letouzeyi
B. dewildei
B. prismatocarpa
B. scutifolia
B. potamophila
B. quadrialata
. meyeri-johannis
. m adecassa
B. bogneri
B. salaziensis
B. ankaranens
B. mananjabensis
e
francoisii
lori?n?l?oi3es^rhopaloca rpa
poculifera
molleri
mannii
kisuluana
horticola
subscutata
capillipes
gabonensis
sutherlandii
geranioides
sonderana
dregei partita'
dregei
dregei ‘homonyma’
sp.. gutt.
lubbersii
edmondoi
integerrima
solananthera
heracleifolia
sp., U172
involucrata
B. violifolia
B. imperialis
B. sericoneura
B. peltata
B. theimei
. manicata.
. maynensis
B. boliviensis
B. cinnabarina
B. incarnata
B. fissistyla
B. sp., Bolivia
B. odorata
B. minor
B. cubensis
B. obliqua
I ISÆls
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
meridensis
holtonis
fuchsioides
jam esoniana
olbia
gracilis
herbacea
sp., Trachelocarpus
wollnyi
ulmifolia
sp., 224
glabra
convolvulacea
sp.. macE
acerifoli
valida
i;Œ
i
B. echinosepala
B. sp., macGL
B.
B.
B.
B.
B.
147
oxyphylla
rufoserica
angularis
lobata
luxurians
SOC i - H
ii
AS
-CE
B. fallax
B. socotrana
B. samhahensis
B. porteri
B. morsei
B. masoniana
B. masoniana maculata
B. kingiana
B. amphioxis
B. malachosticta
B. chlorosticta
B. isoptera
B. incisa
B. aequata
B. serratipetala
B. sp., cf serratipetala
B. brevirimosa
B. sp., cf brevirimosa
S. sanguinea
S. sp., 136
S. sp., 121
B. sp.. Philippine
B. floccifera
B. sp., nam
B. grandis holostyla
B. grandis grandis
B. dipetala
B. beddomei
B. sp., Reichenheimia
B. rajah
B. goegoens.
B. oxysperma
B. sp., 1998 1824
B. chloroneura
B. tayabensis
B. labordei
B. rubella
B. balansana
B. versicolor
B. sp., Yunnan 26
B. sp. nov., Yunnan
B. longicarpa 1
B. longicarpa 2
B. sp., Yunnan 25
B. hatacoa
B. sp., Yunnan 33
B. sp., Sulawesi 254
B. sp. nov., Philippine
B. roxburghii
B. deliciosa
B. diadema
B. rex
B. annulata
B. sp., Yunnan 21
B. sp., Taiwan
B. ravenii
B. formosana
B. sp., Platycentrum
B. palmata 74
B. hemsleyana
B. handelii
B. menyangensis
B. acetoselTa
B. longifolia
B. crassirostris
B. sp., Sulawesi 252
B. sp., Sulawesi 253
The backbone from the 177 sequence analysis of variable-position culled ITS
sequence data was taken; multiple sequences from the same individual were
pruned from it for purposes of clarity. The topology was then altered to reflect
the increased resolution within clades from the individual compartment
analyses. Although this may mean that the topology shown (Figure 7.22, The
Jigsaw Tree) is not necessarily a most parsimonious solution for the culled
ITS data set, this does not mean that it cannot be our best estimate of
phylogeny because, although there are alignment difficulties over the entire
data set, the individual compartments (which largely represent within-clade
variation) are less ambiguous: firstly, it was possible to tidy up the individual
alignments, giving more reliable estimates of homology within them, and
148
secondly, positions which were excluded from the larger analyses due to being
highly variable in some part of the data set could be included in these smaller
analyses, meaning that more characters are being used in the compartments.
In addition, given the smaller size of these compartment data sets, the search
algorithms used are more likely to find globally rather than locally optimal trees
(within each compartment).
7.4
Corroborating information from ITS sequences
- Gap data:
The alignment of sequence data, by its nature, induces gaps into the
alignment. Gaps, like point mutations, are phylogenetic events and can
therefore offer information about evolutionary history. However, where
potentially homologous gaps in different taxa are slightly different lengths,
coding them as characters becomes complex. Simmons and Ochoterena
(2000) only treat gaps with identical 5’ and 3’ termini as homologous, because
if these are not identical, “at least one indel event must be postulated to turn
one gap into another” (p. 371). They propose a simple coding method whereby
all gaps with different 5’ and/or 3' ends are coded as separate presence/
absence characters; completely overlapping gaps are coded as inapplicable.
McDade et al. (2000) discuss the use of indels in ITS sequence alignments as
presence/absence characters. Gap characters have been found informative for
ITS by several authors, including Jeandroz, Roy and Bousqet (1997) and
Manos (1997). However, McDade et al. did not use an indel matrix because
they had serious difficulties in aligning ITS across the Acanthaceae. From their
aligned matrix they consider that “some [indels] may be informative in more
narrowly circumscribed studies where alignments, and thus identification of
indels, would be unambiguous” (p. 115).
However, even when gaps have not been coded as part of the matrix and used
in the analysis of data, they can still be used to support (or possibly
undermine) clades in the form of mapped characters. Prather and Jansen
(1998), for example, mapped indel events onto an ITS phylogeny of Cobaea
Cav. They found a high degree of congruence between the evidence from point
mutations (the phylogeny) and information provided by indels (the mapped
characters). Out of the 14 phylogenetically informative indels from their ITS
matrix, only one was homoplastic.
149
The situation within the Begoniaceae is similar, in that the high levels of
divergence across the family render gaps extremely problematic to code.
However, there are some gaps within the matrix which appear to have strong
phylogenetic signal, for example a 38 base pair gap near the end of the ITS 2
region is shared by nine American taxa. These taxa are resolved into a clade
on the basis of ITS point mutations; therefore while the use of the gap as a
character is not necessary to obtain this clade, it can help reinforce our faith in
it. Similarly, there is a gap shared by all the Madagascan species at the start of
the ITS 2 region.
Looking at the ITS alignment produced for this thesis (see CD-ROM), very few
gaps are clear-cut; although it would be possible to deal with them in the
manner Simmons and Ochoterena (2000) suggest, this would be time
consuming for relatively little reward. Instead eight gaps without ragged edges
were isolated by eye and coded as presence/absence. Gaps which are very
similar but have slightly different 3' and/or 5’ ends are named 'A' and B' (see
Table 7.7).
Table 7.7
Unambiguous gaps in ITS manual alignment
GAP
POSITION
TAXA
N1
172-180 G
S.
duncan-thomasii, B. staudtii, B. letouzeyi, B. potamophila
(uncertain taxa: B. scutifolia] B. quadrialata)
N2A
275-319 G
S. longipetiolata, B. poculifera, B. loranthoides ssp rhopalocarpa
N2B
275-324 G
6. kisuluana, B. capillipes, B. mannii,
N3
311-332 G
B. duncan-thomasii, B. letouzeyi
N4
354-359
B. kisuluana, B. capillipes, B. mannii,
B. molleri, B. horticola,
B. gabonensis, B. subscutata
S
B. molleri, B. horticola,
B. gabonensis, B. subscutata, B. longipetiolata,
B. loranthoides ssp rhopalocarpa, B. poculifera
N5
693-695 G
N6A
1042-1100 G
N6B
1061-1098 G
B.ankaranensis, B. m adecassa, B. m ananjabensis, B. salaziensis,
B. nossibea, B. francoisii, B. bogneri
B. listada, B. echinosepala, B. rufosericae, B. sp. macG, B. oxyphylla,
B. luxurians
B. glabra, B. convolvulacea, B. ulmifolia, B. acerifolia, B. sp. macE, B. valida,
B. angularis, B. egregia, B. lobata
(G = all the taxa cited share a gap; 8 = all the taxa cited share sequence)
The gaps coded in Table 7.7 were mapped across the ‘Jigsaw’ ITS phylogeny
(Figure 7.22) (see Figure 7.23).
150
Figure 7.23: ITS phylogeny (the Jigsaw Tree) for African and American taxa,
with coded ITS gaps mapped on
glomerata
cannabina
sandwichensis
annobonensis
engleri
johnstonii
iucunda
thomeana
aspleniifolia
staudtii
scapigera
duncan-thomasii
letouzeyi
dewildei
prismatocarpa
scutifolia
potamophila
quadrialata
meyeri-johannis
m adecassa
bogneri
salaziensis
ankaranens
m ananjabensis
nossibea
francoisii
or^n?lioKies^rhopalocarpa
poculifera
molleri
mannii
kisuluana
horticola
subscutata
capillipes
gabonensis
sutherlandii
geranioides
sonderana
dregei ‘partita’
dregei
dregei homonyma
sp.. gutt
lubbersii
edmondoi
integerrima
solananthera
heracleifolia
sp., U172
S.AF
involucrata
violifolia
imperialis
sericoneura
peltata
theimei
manicata.
maynensis
boliviensis
cinnabarina
incarnata
fissistyla
sp., Bolivia
odorata
minor
cubensis
obliqua
gu'écfJensis
meridensis
holtonis
fuchsioides
jam esoniana
olbia
gracilis
herbacea
sp., Trachelocarpus
wollnyi
ulmifolia
IPabr
convolvulacea
N1 to N6 are ITS
indels - see text
for details
sp., macE
acerifoli
valida
à
echinosepala
sp., macGL
oxyphylla
rufoserica
angularis
lobata
luxurians
to Asian clade - no
indels coded; so clade
not shown
151
Gaps N2A, N2B, N3, N4 and N5 fit this topology perfectly. Gap N1 shows some
homoplasy on this topology; gaps N6 A also shows homoplasy (although this
may be due to a problem with coding - if gaps N6 A and N6 B were homologous
there would be no homoplasy). It certainly seems as if these ITS indels are in
general agreement with the ITS point mutation data; clades in Africa and one
clade in America ÇPritzelia’) are supported by them.
7.5
General discussion and conclusions
- Testing different alignments
The majority rule tree produced from automated alignment 4 is the most
markedly different from those produced from other alignments and from the
elision data set. It disperses several morphologically robust-seeming
sections into clades which have no apparent geographic or morphological
basis. The tree statistics for this data set (see Table 7.2) are by no means the
worst for any data set - the consistency index is one of the lower values, but the
retention index is among the higher end of the range, and the rescaled
consistency index appears somewhere around the middle. Thus confidence
measures themselves would not necessarily lead to the rejection of this
hypothesis. The gap and extension penalties used in different alignments
ranged from gap penalties of 3.3 to 45, and extension penalties of 3.3 to 15;
alignment 4 is at neither end of these ranges, with a gap penalty of 30 and an
extension penalty of 15. Extremes of the penalties range are represented in
alignments 10 (3.3/3.3) and 8 (45/15). For alignment 8 , the consistency index
is low but the retention index is high; alignment 10 has a high consistency
index and rescaled consistency index although a relatively low retention index.
Two things are worth noting here, firstly that values for these statistics are
renowned to be negatively correlated with the number of characters and of taxa
(Siebert, 1992) (the numbers of taxa are constant in each alignment; the
difference in number of informative characters i.e. characters involved in the
algorithms, particularly with autapomorphies excluded, is not nearly as large
as the difference in the total number of characters). Secondly, the direct
opposition of these numbers is not unexpected because with low penalties for
creating and extending gaps, the bases will have been aligned in a way which
maximises sequence similarity; thus there will be many characters which have
(only) one or two states; where the penalties are higher and insertion of gaps
152
is discouraged, there are likely to be more multistate characters and so more
potential for multiple state changes over a cladogram.
One surprising result of looking at different alignments is that, although the
total numbers of characters in the data sets vary greatly (as discussed), the
numbers of invariant characters vary from 43 (in alignment 15, although the
value is also low for alignment 8 , with 58 characters) to 405 (alignment 10)
(range 362), the total numbers of parsimony informative characters only vary
from 688 (alignments 13) to 756 (alignment 9) (therefore by only 68 characters)
and do not show the inverse correlation with the gap opening and extension
penalties that the other character numbers do. This means that the real size of
each data set is similar, which increases the comparability of the tree statistics
among the 16 alignments.
As the gap opening and extension penalties relax, the numbers of characters
of all sorts increase, but the numbers of parsimony-informative characters fall
in proportion to other sorts of characters. When the gap opening and
extension penalties are higher, however, the numbers of multistate characters
increase (as more data are shoe-horned into a smaller space) and thus the
numbers of characters which are informative can also increase relative to other
sorts of characters.
Although these methods can in many ways be considered purely data
manipulation (even where a range of statistics are applied, to chose between
solutions, it is difficult to be confident of the information provided by
ambiguously aligned regions - and choices based on ranges of statistics have
been shown for these Begoniaceae alignments to produce unconventional
topologies) an awareness of the effects of altering alignments gives an
indication of the amount of support for certain clades; I can see no reason not
to feel more confident of clades which can withstand such data manipulation.
One important point is the difficulty and importance of rooting; due to the
divergence between outgroup and ingroup, the OG/IG relationship is highly
sensitive to alignment and can dramatically alter the evolutionary hypothesis.
There is a weight of evidence for a sister group relationship between the
outgroup and African taxa (26S sequences, trnL (Plana, unpublished data,
2001), unambiguously aligned ITS regions, the elision data and Badcock's
153
(1998) trnC-trnD intron data); in some alignments, however, this is not the
favoured hypothesis. The position of Hillebrandia in many alignments is more
reliable (according to conventional hypotheses) as a root; however rooting on
Hillebrandia is not advisable if one is interested in testing its position within
Begoniaceae. The sister group relationship between Hillebrandia and
Begonia is geographically unusual in that it necessitates acceptance of an
Hawaii/Africa disjunction; Hawaii has always been isolated from the
continental land-masses and has been populated through long-distance
dispersal events (Kim et al., 1998). Africa has never been proximal to Hawaii
(and is currently c. 15,000 km away), which makes it a surprising place to find
Begonia's closest relative.
A remarkably shorter search time for swapping the elision data set to
completion when compared to TBR swapping of the individual alignments
appears to be due to the decreased probability of hitting islands of equally
parsimonious trees as the amount of data increases (although comparisons
of starting and final tree lengths were not made; it is possible that shorter
distances between these lengths could be responsible for shorter analysis
times - see Savolainen et al., 2000). Instead the search descends rapidly to
some local minimum. With fewer character differences in the individual
automated alignment data sets, many trees can share the same length
(MaxTrees was hit in eight out of 16 searches). Island structure of the elision
data set was revealed by running 1000 random addition replicates. No island
contained more than 24 trees, while most contained less than 10. The lengths
of equally parsimonious trees found on different islands ranged by 138 steps,
from 175227 to 175464.
Of course, the difference between the elision and the individual alignment data
sets is more subtle than ‘character differences', as these different data sets do
not represent different character sets. Instead the elision represents a special
form of character weighting. Successive weighting of characters, for example
by their rescaled consistency index, can also be used to analyse data where
large numbers of equally parsimonious trees are found by analyses using
Fitch analysis. Successive weighting favours characters which perform
consistently over an hypothesis (cladogram); elision (weighting by alignability)
is not dependent on an initial parsimony stage (although will be influenced by
the distance measure used in CLUSTAL for alignment generation).
154
There is no a priori reason to accept or dismiss one set of trees on the basis of
similarity or difference from another set of trees (such as the elision trees)
although a more parsimonious interpretation of data would seek congruence
with other data sets. Comparisons with the elision tree are more complex, in
that elision does not represent another data set but a manipulation of the sets
under study; however, in that it weights conserved regions, it should be more
robust than the individual automated alignments.
The position of the root is critical for the interpretation of evolutionary events
within Begonia] several alignments give unconventional rooting. However
these (badly) rooted trees may more accurately reconstruct relationships within
the'ingroup; a major problem with ITS sequence data in Begonia is the
difference in levels of sequence divergence between different clades.
Parameters which perform badly across wide sequence divergences may well
reconstruct more accurately the relationships within (and between closely
related) clades.
The different alignments contain two classes of characters which could be
loosely described as ‘homoplasy’. Some of the observed homoplasy is due to
taxa sharing derived characters which are not due to common ancestry but to
convergence (e.g. multiple hits); this sort of homoplasy is relevant, for instance,
if we are interested in mutation rates, and may be locally informative
phylogenetically. However, the other class of homoplasy is due to nonsense
characters (‘hybrids’ of true characters, created by data misalignment) and has
nothing to say about evolution. There is no way to separate these except
through careful culling of our data. However, in these analyses the consistency
index is actually lower for the culled tree than for the unculled tree - the removal
of 336 parsimony-informative characters caused a fall in consistency index
(uninformative characters excluded) from 0.271 to 0.267.
Despite the arguments of some of the more transformed cladists (such as
Wenzel & Siddall, 1999) that the exclusion of data is undesirable regardless of
the presumed levels of homoplasy, it is apparent that because differences in
alignment do not create straightforward homoplasy but ‘nonsense’ characters,
the exclusion of data which align ambiguously across the taxa being
considered is the most reliable option. However, elision, although including
155
‘nonsense’ characters, should downweight these characters to an extent
where they do not have a huge influence on the overall topology.
Compartmentalization (Mishler, 1994) as an alternative method of using all (or
almost all) the data offers the benefit of avoiding any use of ‘nonsense’
characters but still obtaining the fine resolution that is more likely to be
obtained from more variable regions of sequence; in practice, however, it is
time-consuming and has offered little overall advantage in terms of support
and resolution with this data set.
Manual alignment is more sensitive (than using an algorithm which has set
parameters) to the real situation wherein parts of a sequence have diverged
more or less than other parts. The conserved regions will reconstruct higher
order phylogeny, while the less conserved regions can reconstruct the
hierarchy of closely related taxa, and so the probability of indel events in
different parts of the sequence will vary. Another reason to support manual
over automated alignment is that different mutational events (e.g. duplication,
inversion, repetitive DNA) all require different alignment decisions.
The manual alignment, even with the misaligned parts of sequence included
(“unculled”), although providing less parsimony-informative characters than
any of the automated alignments, has better consistency, retention and
rescaled consistency index values, suggesting that there are fewer
homoplastic characters in the matrix. Thus if one accepts the alignment which
optimises values for the consistency, retention and rescaled consistency
indices, the manual alignment outperforms the automated alignments.
The three data sets considered here (elision, manual, unculled and manual,
culled) give basically similar tree shapes (see Figure 7.24), with less speciesrich clades on longer branches at the base of the trees. The overall tree
shapes are unbalanced, and many of the clades on the trees are also
unbalanced. The unculled, manual alignment gives the most unbalanced
topology, this is due to African taxa resolving as highly paraphyletic; analyses of
the culled manual alignment and the elision alignment resolve many of the
African species within one clade. The African taxa suffer most alignment
ambiguity, with blocks of sequence alignable within but not between clades.
This artifact of alignment is most probably responsible for the patterns
156
observed here, with the differences between clades overriding their shared
characters in the unculled manual alignment.
Figure 7.24: Tree shape (phylograms) for manual (culled and unculled) and
elision data sets
culled manual alignment
unculled manual alignment
elision alignment
Pa
4
L
-
5 changes
10 changes
500 changes
frfe
%
[fe:
%
^5
marks the ingroup (Begonia)
157
7.6 Summary
Different alignment methods (automated, elision and manual) were tested
using an ITS sequence matrix. Further, different ways of analysing large data
sets were tested, by heuristic parsimony analysis of the manually aligned 177sequence matrix, followed by compartmentalization of that matrix. Analyses
were run for eight compartments isolated from the total matrix; these were
used to test the performance, in parsimony analyses, of the elision and
manual alignments from the beginning of the chapter. The manual alignment
for ITS, with ambiguous regions of sequence excluded, performed best (i.e.
produced topologies most similar to those produced in the compartment
analyses). Three ways of dealing with the taxa which were not included in the
compartments were also tested (constraint trees, hypothetical ancestors and
exemplar taxa). Of these, using exemplar taxa was preferred, although
analysis of the complete 177-sequence matrix gave better results. A topology
was constructed using the 177-sequence manual alignment, culled of
ambiguous regions, and adjusted to reflect the topologies of the compartment
analyses (and was nicknamed the ‘Jigsaw’ tree. Figure 7.22). Finally, some of
the indel events in the ITS matrix were coded and mapped across this ‘Jigsaw’
topology. The indel data were shown to be phylogenetically informative in this
case, and reinforced some of the clades identified using nucleotide
substitutions. The ‘Jigsaw’ topology will be used in further chapters, to
discuss evolution in the Begoniaceae.
158
8.
Secondary structure
8.1
Introduction
8.1.1 Length of ITS regions: Baldwin at al. (1995) reported that all flowering
plants examined had less than 300 base pairs in both ITS 1 and ITS 2. The
longest regions they report are in Malvaceae, which has up to 298 base pairs
for ITS 1, and Cucurbitaceae, up to 252 bases for ITS 2. ITS 1 is usually 200 300 bases long; ITS 2 is usually 180 - 240 bases and 5.8S, 163 - 165 bases
(Hershkovitz, Zimmer & Hahn, 1999).
There are also a few reported lengths for taxa in the Cucurbitales (i.e. taxa
phylogenetically close to Begonia according to recent classifications, such as
Savolainen et al., 2000). In Corynocarpus ITS 1 varies between 234 - 258
bases, while ITS 2 is shorter, between 197 and 220 bases. The 5.8S region
is 165 bases (Wagstaff & Dawson, 2000). Jobst, King and Hemleben (1998)
found that the ITS 1 spacer varies from 186 to 233 bases in Cucurbitaceae,
while ITS 2 varies from 224 to 263 bases.
8.1.2 Secondary structure: Hershkovitz and Zimmer (1996) produced
secondary structures for ITS 2 for nine angiosperm genera. All but one
consist of a central loop with four radiating stems (three stems in
Arabidopsis). Mai and Coleman (1997), who reconstructed similar structures
for angiosperms and algae, describe ITS 2 as a “self-contained folding
complex, usually consisting of four distinct hairpin loops” (p. 262). They found
a lot of sequence conservation near the bases of each of the four stems, and
note that the considerable length variation found in ITS 2 does not impede the
formation of thèse four conserved structures.
Mai and Coleman (1997) found that the first stem (which I will call ‘A’) can be
highly variable in length and sequence; the second ('B') shows extensive
nucleotide covariation; the third (‘C’) is generally the longest region, and also
shows the highest degree of structural conservation; the fourth (D) is the most
variable region within their study (see Figure 8.1 for schematic representation
of ITS 2 secondary structure).
159
Figure 8.1:
Schematic summary diagram of ITS 2 secondary structure
Stem lengths in the angiosperm s: Stem A is between 31 {Sinapsis) and 55
{Cucurbita) bases long; B, from 16 (Arabidopsis) to 39 (Vida)-, C, from 84
(Oryza) to 108 (Canella) and the fourth stem is absent in Arabidopsis, up to 34
bases in Cucurbita (values from Hershkovitz & Zimmer, 1996; Mai & Coleman,
1997).
8.2
Material and methods
The lengths of ITS 1 and ITS 2, and of the 5.8S region between them, were
estimated using the start and end points from Hershkovitz and Zimmer (1996).
Secondary structure reconstruction was undertaken for a selection of
sequences (sequences were obtained as described previously). One of the
reasons for reconstructing secondary structure in Begonia was to assist with
difficulties in manual alignment of sequences across the genus. Taxa were
selected from an initial manual alignment, focusing on taxa which were
problematic to align, and where possible, more than one taxon from groups of
similar sequences were selected in order to check that similar structures
were obtained. Taxa with the fewest ambiguous base calls were preferred.
Secondary structure was determined using MulFold (Zuker, 1989; Jaeger,
Turner & Zuker, 1989a; Jaeger, Zuker & Turner, 1989b). Foldings were done
at 20°c, saving up to 15 folds within a 10% range from the optimal free energy
160
value. The folds were viewed in LoopDloop (Gilbert, 1995) and compared to
ITS 2 secondary structures published by Hershkovitz and Zimmer (1996) and
by Mai and Coleman (1997). Foldings were also made to determine the
secondary structure of ITS 1, but this was abandoned as a common pattern
could not be determined from the range of structural variants found. No parts
of 18S, 5.8S or 26S were included in the foldings, partly to follow Hershkovitz
and Zimmer (1996), also because including up to 50 bases from each of the
flanking coding regions would have made many of the sequences over 300
base pairs long (creating analytically difficulties in MulFold), and also because
trial folds made with parts of the coding regions included were less
comparable with the secondary structures found by previous authors
(Hershkovitz & Zimmer, 1996; Mai & Coleman, 1997). Sequences were not
constrained in any way.
8.3 Results
The length of ITS 2 is very variable in Begonia, ranging by 149 bases, from 212
in 8. angularis to 360 in 8. masoniana var. maculata (see Table 8.1); in
several species it is over 300 base pairs, which is unusually long for the
angiosperms (see Baldwin et al., 1995). ITS 1 is less variable. It ranges from
223 in 8. thomeana to over 270 in 8. prismatocarpa^, a difference of over 47
base pairs. The 5.8S region, on the other hand, is largely invariant at 144
base pairs.
®part of the start of ITS 1 is missing for B. prismatocarpa and for S. salaziensis, so exact
values cannot be given
161
Table 8.1 :
The length of ITS 1, 5.8S and ITS 2 for representative taxa
TAXON
D. cannabina
D. glomerata
B. molleri
B. gabonensis
B. nossibea
B. salaziensis
B. bogneri
B. thomeana
B. iucunda
B. engleri
B. madecassa
B. duncan-thomasii
B. prismatocarpa
B. aspleniifolia
B. socotrana
B. samhahensis
8. dregei
B. sonderana
B. annobonensis
B. hemsleyana
B. palmata
8. masoniana
8. kingiana
8. tayabensis
8. aequata
Symbegonia
B. cubensis
B. fissistyla
8. oxyphylla
B. valida
8. angularis
ITS 1
257
263
231
232
247
>232
249
223
251
258
248
240
>270
244
258
268
257
258
258
250
254
260
256
260
262
258
244
255
268
256
257
5 .8 S
159
157
146
146
144
144
144
144
144
144
144
144
144
144
144
144
144
144
144
144
144
144
144
134
144
144
144
144
144
144
144
ITS
222
222
267
269
304
304
240
306
293
?
273
298
306
298
317
330
274
275
225
306
306
360
308
317
300
301
296
295
267
281
212
Secondary structure was reconstructed for 21 taxa (see Table 8.2 for taxon
names; accession details etc. are given elsewhere). Examples of the
secondary structure of Datisca glomerata (the outgroup) (Figure 8.2), B.
nossibea (Figure 8.3) and B. gabonensis (Figure 8.4) (African) 6. socotrana
(Figure 8.5) (Socotra) B. hemsleyana (Figure 8.6), B. aequata (Figure 8.7), B.
masoniana (Figure 8.8) and Symbegonia sp. (Figure 8.9) (Asian) and S.
fissistyla (Figure 8.10) and B. oxyphylla (Figure 8.11) (American) are given.
162
Figure 8.2:
Datisca glomerata ITS 2 secondary structure (free energy -102.8)
^G-C
C - G
A - T
^
A - T
G - C
C - G T t
T * G T
A - T
C - G
T - A
G # T A
• gV ,
" G T „ r
kc C - G
. C - G
'C/ %
Vn^
Figure 8.3:
T c. v < -% .
GpT
(
B. nossibea ITS 2 secondary structure (free energy -103.9)
t1°
A_T.
V* C.
q
%?
163
Figure 8.4:
8. gabonensis ITS 2 secondary structure (free energy -145.5)
A - t CA
8:8
8:8°gt
G -C ,
c _ g t
c° 7 t„
G Af
C _G
°T
G „
I
Figure 8.5:
8. socotrana ITS 2 secondary structure (free energy -175.3)
8= 8
g=S*%
gI cA*
8=8
I*
...
Cg\
•Jv.V
164
'% /
Figure 8.6:
B. hemsleyana ITS 2 secondary structure (free energy -140.0)
c - G C ° Aj,
T -A
^
A —T
m
G #TAc
C -G
'«A
,
,C “.
^t c ’c
■?o'
- " : ° r c o \ 'o T A
'y ”
aA
-s ...
T YcAc
T ".
C° \ C
T C
Figure 8.7:
B. aequata secondary structure (free energy -119.5)
tA
#
Ac
/ C
n ’ '. 'O A
' ^ C " \ . A _
T c-
J"
xTGTcf
""I
C
t'
165
. C ' A
Tc(
Figure 8.8:
B. masoniana ITS 2 secondary structure (3’ end eut short)
(free energy -130.1)
C,
Cq.
T
C°
r , m
\>rTÀ^
Figure 8.9:
T°°v'^v
c
G
'c
V='r-CCC
r
Symbegonia sp. 136, ITS 2 secondary structure (free energy
131.8)
,#5
..%')
%.
*A O
g
C c
166
Figure 8.10: B. fissistyla ITS 2 secondary structure (free energy -120.3)
Figure 8.11: B. oxyphylla ITS 2 secondary structure (free energy -115.8)
c^c
'.'G
%
=V=A\V>°=“‘ ’'\«
167
Structures with four to five stems were obtained for most of the taxa analysed.
All taxa share a highly conserved second (B) and third (C) stem; most of the
variability is in the first stem (A). The reconstruction of the fourth stem was
often ambiguous (with a fifth stem sometimes present); therefore the lengths
of the fourth stem are not considered here.
From Table 8.2, it can be seen that, of the three stems considered, stem B is
almost always invariant at 32 bases; stem C is slightly more variable, between
88 and 91 bases in Begonia (83 to 84 in Datisca), and stem A is the most
highly variable, between 42 (8. angularis) and 148 (8. masoniana) bases long.
Table 8.2:
Lengths of the first, second and third stems from secondary
structure reconstructions of ITS 2
TAXON
C. melo ®
D. cannabina
D. glomerata
B. molleri
B. gabonensis
B. nossibea
B. salaziensis
B. bogneri
B. iucunda
B. prismatocarpa
B. socotrana
B. dregei
B. sonderana
6. hemsleyana
B. palmata
B. masoniana
B. aequata
S. sp 136
B. fissistyla
B. oxyphylla
B. valida
B. angularis
A
55
52
52
82
76
107
107
?
103
?
123
83
84
115
115
148
108
111
1 05
1 05
108
42
B
32
32
32
32
32
32
32
32
32
32
32
32
32
32
32
38
32
32
31
32
32
32
Ç
90
83
84
88
91
90
88
90
90
90
90
90
90
90
90
?
90
90
89
91
90
91
®Values for Cucurbita melo are based on the secondary structure depicted by Hershkovitz
and Zimmer (1996, p. 2864).
168
8.4
Discussion
The highly conserved structure of stem B may suggest some sort of functional
constraint; stem C also has some highly conserved secondary structure
including a loop quite near to the top of the 3’ side of the stem, and often a
second loop nearer to the base of the stem on the same side (see Figure
8.12) (although the first loop is not evident in the reconstruction shown for 6.
nossibea, Figure 8.3).
Figure 8.12: Schematic diagram of Stem C showing conserved secondary
structure
K Second
r loop
5'
3'
B. angularis (not shown) has distinctly shorter ITS 2 than other Begonia
species sampled; this appears to be due to deletion of the end of stem A;
there is also a deletion around the region of the fourth stem. B. oxyphylla,
which also has a short ITS 2, has lost bases from the region where the 4th
stems occurs (see Figure 8.11). The very long ITS 2 sequences found in B.
socotrana (Figure 8.5) and B. masoniana (Figure 8.8) are mainly caused by
the extended length of stem A. The most ambiguities in the sequence
alignments for ITS 2 are around the region of stem A (see chapter 7); although
similar taxa have similar sequences in this region, disparate taxa have very
low levels of sequence similarity.
The sequence for Begonia masoniana was obtained from a clone of B.
masoniana var. maculata, due to difficulties in obtaining readable sequence
from consensus PCR of Begonia masoniana or B. masoniana var. maculata.
The difference in the second ITS 2 stem (B), which is 34 bases rather than the
32 bases it is in the rest of the Begonia species examined, suggests that we
could have amplified a non-functional paralogue. There are also a few
mutations in the 5.8S sequence for other cloned B. masoniana var. maculata
(which also have 34-base-long B stems) One clone has a one base pair
169
deletion at character 555; one has a T to C mutation at character 578, and
another has a T to C mutation at character 591. However, not only do the
sequenced clones nest together (and with the parts of consensus sequence
which could be read) in parsimony analyses (see chapter 7, Figures 7.1, 7.3,
7.5), but B. masoniana also resolves with the consectional B. porteri and B.
morsei, which were not cloned (i.e. the sequences give the ‘expected’
topology, and no obviously atypical relationships are inferred). Unfortunately
neither B. porteri nor B. morsei gave complete sequences; ITS 1 for 6. morsei
is 255 bases, while ITS 2 is over 287 bases (the first 15 or more bases are
missing); 8. porteri was less complete. Due to these problems with
incomplete sequences, it was not possible to reconstruct secondary structure
for these other species.
Further studies involving cloned ITS Begonia sequences, particularly for
section Coelocentrum, are needed to see whether some sequences exist
which form secondary structures more within the range shown by other
Begonia species (and so, whether it is likely that we have recovered some
paralogous and potentially non-functional members of a gene family).
170
9.
trnC to trnD\ separate and combined
analyses with ITS
9.1
Introduction
The ITS region has been discussed in earlier chapters. The non-coding,
non-transcribed region trnC - trnD is located in the large single-copy region
of the chloroplast. It varies in length from c. 3000 to 4000 bases in
Begonia] it is AT rich, with a large number of simple sequence repeats
(Badcock, 1998). Badcock did not sequence the entire region, but obtained
sequence data inwards from universal primers located in the tRNA genes
(sequencing in from the trnC region at the 5’ end, and the trnD region at the
3' end).
Because of differences in inheritance, phylogenies reconstructed from
nuclear and chloroplast regions can vary, particularly where there have
been evolutionary reticulations. Using DNA data from two genomes (e.g.
McDade et al., 2000 - ITS and trnL-trnF, Acanthaceae) potentially allows the
tracking of these different evolutionary histories, with biparental inheritance
of nuclear DNA and predominantly uniparental inheritance of chloroplast
DNA (in most angiosperms).
9.2
Material and Methods
The trnC - trnD matrix was taken from Badcock (1998); ITS sequences were
taken from a larger matrix compiled for this thesis (chapter 7). Voucher
details are the same as in previous chapters (and are on the CD-ROM). A
list of the taxa included in this study is presented in Table 9.1.
Although the trnC - trnD data has already been analysed by Badcock (1998),
analyses were rerun with 8. oacacana A.DC. excluded, as it did not prove
possible to amplify the ITS region for this taxon. Badcock (1998) found
Datisca species amplified poorly for trnC - trnD] therefore she used a
consensus sequence for the two species. There was no problem getting
sequence for ITS for Datisca] D. cannabina was used in place of a
consensus sequence in the ITS analyses.
170
Badcock (1998) provides an indel matrix for trnC - trnD, which she included
in her analyses and found to be phylogenetically informative. However,
there is not an indel matrix for the ITS data set, due to the ragged nature of
many of the indels; because the purpose of this chapter is to compare
phylogeny reconstruction from trnC - trnD and ITS, the gap matrix for trnC trnD was consequently not used. However, several unambiguous gaps
from the trnC - trnD matrix were coded and mapped across MPTs produced
from MP analysis of both the trnC - trnD and the ITS data sets to see
whether there is any conflict in their signal.
9.2.1 Taxa included In this study
Table 9.1:
Summary of taxa included in molecular analyses.
S P E C IE S
SEC TIO NA L
P LA C E M E N T
G EO GR APH IC DISTRIBUTION
SO U R C E A N D
A C C E SS IO N No
B. acerifolia H.B.K.
K nesbeckia
America; Ecuador
GL 001 057 96
B. acutifolia Jaq.
Begonia
America: W est Indies
G L 0 0 2 1147 66
B. convolvulacea (Klotzsch) A DC.
W ageneria
America: Brazil
GL 001 093 79
B. dipetala Graham
Haagia
Asia: S. India & Sri Lanka
GL 003 018 96
B. dregei Otto & Dietrich
Augustia
Africa: S. Africa
GL 004 026 94
B. dregei Otto & D. non 'partita'
Augustia
Africa: S. Africa
GL 002 036 89
B. floccifera Bedd.
Reichenheim ia
Asia: S. India & Sumatra
GL 030 099 89
B. goegoensis N.E.Br.
R eichenheim ia
Asia: Sumatra
GL O il 125 57
B. gracilis Humb., Bonpl. & Kunth
Quadriperigonia
America: Mexico
Z. Badcock no. 9
GL 004 085 80
B. grandis Dryand. ssp grandis
Diploclinium
Asia: China
B. grandis Dryand. ssp holostyla
Diploclinium
Asia: China
E 1998 0035
B. heracleifolia Schltdl. & Cham.
Gireoudia
America: Mexico
G L 00 1 126 83
B. incarnata Link & Otto
K nesbeckia
America: Mexico
G L 01 1 089 95
B. malachosticta Sands
Peterm annia
Asia: Malesia, Sabah
G L 0 1 0 117 94
B. mannii Hook.f.
Tetraphila
Africa: Nigeria, Eq. Guinea, Cameroon
GL 008 067 80
B. masoniana Irmsch.
Coelocentrum
A sia
GL 001 007 56
B. maynensis A DC.
K nesbeckia
America: Peru, Ecuador
G L 0 0 1 107 92
B. obliqua L.
Begonia
America: Martinique
GL 005 105 91
B. olbia Kerch.
K nesbeckia
America: Brazil
GL 002117 94
B. palmata D.Don
Platycentrum
Asia: China
E 1998 0048
B. peltata Otto & Dietrich
K nesbeckia
America: Mexico, Central America
GL 308 000 XX
B. rajah Ridl.
Reichenheim ia
Asia: M alaya
GL 003 081 96
B. ravenii C .I.Peng & Y.K.Chen
Diploclinium
Asia: Taiwan
E 1993 3938
B. roxburghii A.DC.
Sphenanthera
Asia: N.E. India to Burma
GL 004 093 79
B. rubella Buch.-Ham. ex D.Don
Diploclinium
Asia: Nepal
GL 005 094 94
B. salaziensis (G aud.) W arb.
M ezieria
Africa: Reunion, Mauritius
K 1986 412
B. sutherlandii Hook.f.
Augustia
Africa: S.Africa & Tanzania
E 1971 1552
B. tayabensis Merr.
Reichenheim ia
Asia: Philippines
GL 006 035 89
B. ulmifolia Willd.
Donaldia
America: V enezuela
GL 014 125 57
B. wollnyi Herzog
K nesbeckia
America: Brazil, Bolivia
GL 003 057 96
Datisca cannabina L.
Asia: S .W . Asia to Himalaya
E 1969 4093
Datisca glomerata (PresI) Baill.
America: California, USA
S.Swensen 767
Symbegonia sanguinea Warb.
Asia: New Guinea
G L 0 0 3 127 93
171
9.2.2 Analyses
MP analyses were run on three data sets: trnC - trnD (from Badcock, 1998);
the corresponding species for ITS; the two regions combined. ME and ML
analyses were run only on the trnC - trnD data set.
To look at cladistic structure within the data matrices, PTP was estimated
with the outgroup {Datisca) excluded (although the outgroup in this case is
only one taxon so should not influence character covariance), 1000 PTP
replicates, 10 random addition replicates, TBR, steepest descent, five trees
saved per step. G1 was estimated using 10,000 random trees.
Uncorrected pairwise distances and the base composition of the matrix
were obtained from PAUP* 4.0b2a (Swofford, 2000).
a.
MP (Maximum parsimony): MP searches were performed with 1000
random addition sequence replicates, using TBR, saving no more than 10
MPT at any step. The trees from the initial search were input as starting
trees for a further heuristic search, with TBR, and no limit on the number of
MPTs saved.
Bootstrap support was estimated with 1000 replicates, heuristic search, 10
replicates random addition per bootstrap replicate, no more than 10 trees
of any length held, TBR, steepest descent. Bremer support was estimated
using AutoDecay (Eriksson, 1998), with 10 random addition replicates per
constraint tree, TBR.
b.
ML (Maximum likelihood): Likelihood was only used for the trnC -
trnD data set, because of time limitations. The tree was constructed using
the methodology described in Chapter 5, Section S.2.4.2.
c.
ME (Minimum evolution): Again, ME was only used for the trnC - trnD
data set, as a comparison to the trees produced by MP and ML. The tree
was constructed using the methodology described in Chapter 5, Section
5.2.4.3.
172
9.3
Results
All the trees presented have geography marked onto the clades. AF =
Africa, S.AF. = southern Africa, AM = America and AS = Asia.
9.3.1 trnC - trnD:
a.
Data matrix: There were 324 characters excluded; 1569 constant,
369 parsimony-uninformative, and 188 parsimony informative characters
were included. Excluded characters are 348-362, 497, 748-901, 11661172, 1330-1332, 1424-1436, 1786-1792, 1971, 2021-2035, 2117 and
2344-2450 from the matrix in Badcock (1998).
The PTP probability is 0.002; the skewed ness statistic g1 is -1.364.
Uncorrected pairwise distances vary from 0.000 between B. dregei and B.
dregei 'partita' (conspecifically), 0.011 between B. acerifolia and B.
convolvulacea, to 0.087, between B. mannii and 8. convolvulacea within the
ingroup, and 0.203 between the outgroup and ingroup (Datisca and 8.
acerifolia).
The mean base frequencies for taxa are:
A = 0.340
c = 0.141
G = 0.159
T = 0.360
(GC = 0.301).
b.
Trees
i.
MP: There were 186 MPTs found, length 807 steps, with a
consistency index of 0.82 (0.63 excluding uninformative characters);
retention index 0.68. Seventeen clades have over 50% bootstrap support,
while there are 18 resolved nodes in the strict consensus tree. See Figure
9.1 for the strict consensus and for a phylogram.
From the topology presented in Figure 9.1, African taxa are basal in
Begonia, with 8. salaziensis as sister to an American/Asian clade. Most of
the taxa are unresolved in the strict consensus, although one clade of six
Asian taxa has 81% bootstrap support, and one of four American taxa has
173
97% bootstrap support.
Despite different exclusion sets and the removal of one taxon, the topology
is consistent with Badcock’s (1998) substitutions-only analysis (her Figure
3.4), although her analysis is slightly more resolved, with an American
clade of B. wollnyi, B. maynensis, B. peltata, B. heracleifolia, B. acutifolia, B.
gracilis, B. incarnata and B. oacacana sister to B. sutherlandii and B. dregei.
Badcock’s analysis with substitutions and coded indels (Figure 3.6 in
Badcock, 1998) is again consistent with this strict consensus, but is
considerably more resolved.
Figure 9.1
trnC - trnD, MP strict consensus of 186 MPTs and phylogram
Datisca
B.
B.
B.
B.
B.
B.
oAF
meyeri-johannis
mannii
salaziensis
olbia
ulmifolia
acerifolia
AF
B. convolvulacea
B. dipetala
B.
B.
B.
B.
floccifera
gracilis
heracleifolia
incarnata
B. malachosticta
B. masoniana
B. obliqua
B.
S.
B.
B.
67
o-
78
2
AM + A S
72
I
100
81
Bootstrap support
over 50% above
lines,
Bremer support
below lines
11
B.
peltata
sanguinea
maynensis
wollnyi
sutherlandii
dregei
dregei ‘partita’
tayabensis
B.
B.
B.
B.
goegoensis
rajah
grandis cf
grandis
rubella
Datisca
B. meyeri-johannis
B. mannii
B. salaziensis
B. olbia
B. ulmifolia
B. acerifolia
B. convolvulacea
p B. dipetala
B. grandis cf
B. grandis
I
B. rubella
^
B. ravenii
^ B . palmata
L B. roxburghii
I— B. floccifera
B. masoniana
AS — S. sanguinea
p B. malachosticta
| r - B. tayabensis
^ j - B. goegoensis
. J -B . rajah
V - B. sutherlandii
^ B. dregei
' B. dregei ‘partita’
j - B. heracleifolia
T B. peltata
j — B. gracilis
AM I
B. obliqua
j - B. incarnata
10
^ j — B. maynensis
changes
'— B. wollnyi
B. ravenii
B. palmata
B. roxburghii
174
ii.
Maximum Likelihood: The assumed nucleotide frequencies are the
mean base frequencies for the data set. Gamma distribution shape
parameter a
=
0.6895; the transition/transversion ratio is 0.699,
k
=
1.667.
There are 942 distinct patterns under the model.
All the clades which were resolved by MP are in the ML tree (Figure 9.2 a);
both methods put B. meyeri-johannis as sister to the rest of Begonia.
Neither Africa, America or Asia are monophyletic.
Figure 9.2:
a.
trnC - trnD, ML and ME trees.
ML
b.
AF
ME
Datisca
Datisca
— B. meyeri-johannis
B. wollnyi
AM
8. mannii
B. salaziensis
masoniana
I—? B. floccifera
B. olbia
>— % sutherlandii
S.AF^
. B. meyeri-johannis
B. ulmifolia
B. acerifolia
B. convolvulacea
B. mannii
B. salaziensis
B. olbia
[ - B. dipetala
■o[Âiÿi
r B. grandis cf
B. ulmifolia
B. acerifolia
— B. grandis
—
-Ln likelihood =
7365.48479
0.01 changes
B. rubella
. ravenii
0.01
substitution
s/site
B. palmata
B. roxburghii
I B. dregei
B. dregei "partita"
Minimum
evolution score
= 0.72990
B. incarnata
B. maynensis
' B. floccifera
B. masoniana
C
AM
—
S. sanguinea
B. heracleifolia
B. tayabensis
B. obliqua
|— B. dipetala
| _ p B. goegoensis
B. rajah
I
B. sutherlandii
S.AF ^ B. dregei
—
—
B. maynensis
AS
B. wollnyi
' B. obliqua
B. gracilis
—
B. malachosticta
S. sanguinea
B. tayabensis
* B. dregei ‘partita’
AM
B. gracilis
rr r B.
B.pe
peltata
AS — B. malachosticta
I
B. convolvulacea
S.AF
B. goegoensis
B. rajah
I- B. grandis cf
t-
L - B. grandis
r — B. rubella
—I r B. palmata
^ B. ravenii
- B. incarnata
r,
B. heracleifolia
1- B. roxburghii
B. peltata
175
iii.
Minimum evolution: one tree was found, with minimum evolution
score = 0.72990 (see Figure 9.2 b).
ME, while recovering several clades in common with MP and ML, produces
very different basal relationships, with B. wollnyi (American), B. masoniana
and B. floccifera (Asian) and B. sutherlandii (Southern African) basal to the
rest of Begonia. The African taxa which are basal in MP and ML (B. meyerijohannis and B. salaziensis, section Mezieria, and B. mannii, section
Tetraphila) resolve as sister to an American clade in this tree.
9.3.2 ITS
a.
Data: There were 632 characters excluded; 247 constant, 92
parsimony-uninformative and 183 parsimony-informative characters were
included. Excluded characters are 1-183, 188, 200, 204, 211-217, 223-225,
230-249, 255-256, 266, 274-329, 340-366, 378, 383-384, 406-407, 415,
419-421, 426-428, 435-437, 444, 449-451, 460, 466-469, 475-483, 493497, 503-507, 513-514, 539, 571, 577, 603, 606, 615, 649, 686, 688, 693856, 886-901, 930-931, 944, 957-966, 983-984, 992-993, 1013-1014, 1018,
1023, 1029-1035, 1041-1053, 1064-1093, 1110-1114, 1121-1122 and
1137-1154 from the ITS matrix, see CD-ROM, i.e. the same exclusion set
as in Chapters 5 and 7.
The PTP probability is 0.001; the skewedness statistic g1 is -0.993.
Un corrected pairwise distances range from 0.008 (B. convolvulacea and B.
acerifolia) (within-species values are slightly higher, 0.010 (B. dregei and B.
dregei ‘partita’) and 0.019 (B. grandis ssp grandis and B. grandis ssp
holostyla)) to 0.224 between B. fioccifera and B. salaziensis. Pairwise
distances between the outgroup and ingroup range from 0.237 (D.
cannabina and B. mannii) to 0.317 (D. cannabina and B. floccifera).
M ean base frequencies for taxa are:
A = 0.209
C = 0.271
G = 0.306
T = 0.214
(GC = 0.577)
176
b.
Trees: Sixteen MPTs were found, of length 862, consistency index
0.53 (0.45 excluding uninformative characters); retention index 0.46. Eleven
clades have over 50% bootstrap support, while there are 21 resolved nodes
in the strict consensus tree.
On the basis of this topology (Figure 9.3), African taxa are basal in Begonia,
with 8. saiaziensis sister to a largely unresolved clade which includes
American and Asian taxa, as well as the southern African taxa B.
sutherlandii and B. dregei. However, from the phylogram, it can be seen
that internal branches are generally short, particularly within the
Asian/American clade.
There are some areas of conflict between the trnC - trnD strict consensus
tree and this ITS strict consensus. The positions of B. mannii and B.
meyeri-johannis are reversed; other changes are the position of B.
maynensis and B. wollnyi (which are within a B. olbial B. ulmifolial B.
convolvulacea! B. acerifolia clade for ITS, but unresolved for trnC - trnD) and
the separate positions of B. sutherlandii and B. dregei (which have 77%
bootstrap support as a clade in the trnC - trnD analysis).
177
Figure 9.3;
ITS, Strict consensus of 16 MPTs and phylogram.
D. cannabina
- D. cannabina
B. mannii
k>
AF
1 S.AF‘
4
AS
95
6
100
S.AF
74
AMiO
Bootstrap support
over 50% above lines,
Bremer support below
lines
B. mannii
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
meyeri-johannis
salaziensis
AF
masoniana
dipetaia
grandis holostyla
grandis
rubella
sutherlandii
tayabensis
floccifera
rajah
B.
S.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
goegoensis
sanguinea
malachosticta
dregei ‘partita’
dregei
roxburghii
palmata
ravenii
obliqua
incarnata
gracilis
heracleifolia
peltata
olbia
B.
B.
B.
B.
B.
maynensis
wollnyi
ulmifolia
convolvulacea
acerifolia
B. meyeri-johannis
B. salaziensis
B. obliqua
r C B. incarnata
B. gracilis
AM
t
— B. heracleifolia
- B. peltata
B. olbia
B. maynensis
B. wollnyi
B. ulmifolia
B. convolvulacea
B. acerifolia
B. grandis holostyla
B.• S
grandis
S. sanguinea
L - B. malachosticta
I— B. dipetaia
B. masoniana
B. dregei ' partita’
AS
^ B. dregei
|— B. palmata
“ I— B. roxburghii
'— B. ravenii
I
B. rubella
•-0 — B. sutherlandii
10 changes
S A ^ B tayabensis
3
B. floccifera
»■
B. rajah
T — B. goegoensis
178
9.3.3 Combined trnC - trnD and ITS analyses
a.
Data: There were 292 characters excluded; of the remaining 2672
included characters: 1816 characters are constant (1569 from trnC - trnD
and 247 from ITS), 461 variable characters are parsimony-uninformative
(369 from trnC - trnD and 92 from ITS) and 371 are parsimony-informative
(188 from trnC - trnD and 183 from ITS).
Mean base frequencies for taxa are:
A = 0.303
C = 0.178
G = 0.200
T = 0.319
The PTP probability is 0.001; the skewedness statistic g1 is -1.434.
b.
Trees:
Four MPTs were found, of length 1699, consistency
index 0.65 (0.50 excluding uninformative characters) and retention index
0.52. Fourteen clades had bootstrap support of over 50%, and 22 nodes
are resolved in the strict consensus tree.
Like the individual trnC - trnD and ITS analyses, this topology (Figure 9.4)
shows African taxa basal to a largely unresolved Asian and American clade,
which is sister to 6. salaziensis. Within this largely unresolved clade,
however, several smaller clades are resolved (one of southern African taxa,
64% bootstrap support; one of Asian taxa, no bootstrap support; and two of
American taxa, one lacking support and one with 72% bootstrap support).
179
Combined trnC - trnD and ITS
Figure 9.4:
Strict consensus of 4 MPTs and phylogram.
AF
52
10
94
M
S.AF'
AS
AM
4Â1100I
iTi
jm.
4
AM
Bootstrap support over 50% above lines,
Bremer support below
Datisca
B. mannii
B. meyeri-johannis
B. salaziensis
B. masoniana
B. tayabensis
B. floccifera
B. dipetaia
B. rajah
B. goegoensis
S. sanguinea
B. malachosticta
sutherlandii
dregei ‘partita’
B. dregei
B. olbia
B. ulmifolia
B. convolvulacea
B. acerifolia
B. grandis holostyla
B. grandis
B. rubella
B. ravenii
B. roxburghii
B. palmata
B. wollnyi
B. maynensis
B. obliqua
B. incarnata
B. gracilis
B. heracleifolia
B. peltata
Datisca
B. mannii
B. meyeri-johannis
B. salaziensis
B. olbia
B. ulmifolia
B. convolvulacea
B. acerifoli
B. wollnyi
B. maynensis
I----------------B. obliqua
f“T— B. incarnata
u
B. gracilis
[j
B. heracleifolia
I— B. peltata
B. grandis holostyla
B. grandis
B. rubella
B. ravenii
B. roxburghii
B. palmata
B. dipetaia
B. masoniana
B. sutherlandii
B. dregei partita'
B. dregei
B. floccifera
B. rajah
B. goegoensis
B. tayabensis
S. sanguinea
B. malachosticta
— 10 changes
9.3.4 General Comments: The statistics for the MP trees produced from
the three different data sets are summarised in Table 9.2
Table 9.2:
Data set
Summary: statistics for MP analyses, three different data sets
No.
inform.
chars
gi
PTP
No. MPTs length
Cl
Cl ex
Rl
unlnform.
nodes
Nodes >
strict
50%
consens. bootstrap
188
-1.364
0.002
186
807
0.82
0.63
0 .68
18
17
183
-0.993
0.001
16
862
0.53
0.45
0 .46
21
11
371
-1.434
0.001
4
1699
0.65
0.5
0.52
22
14
trnC - trnD
ITS
combined
Although the trnC - trnD analysis has the most clades with bootstrap
support and higher consistency and retention indices, the ITS analysis has
less MPTs and (perhaps in consequence) more nodes resolved in the strict
consensus of those MPTs.
180
9.3.5 Gaps
Although Badcock (1998) included a detailed matrix of gaps in trnC - trnD,
this has been greatly simplified here. Only informative indels with identical
sequence at the 5’ and 3’ ends have been coded (Table 9.3):
Table 9.3
Unambiguous gaps in the trnC - trnD alignment
SITE
TAXA
01
349-357 8
Datisca] B. m eyeri-johannis, B. salaziensis, B. mannii
C2
436-450 S
B. palm ata, B. ravenii, B. roxburghii (Inapplicable in 6. incarnata)
C3
616-617 S
B. obliqua, B. acerifolia
C4
1341-1847 G
B. acerifolia, B. convolvulacea, B. ulmifolia
C5
1411-1423 S
B. goegoensis, B. malachosticta, B. m asoniana, B. ravenii,
INDEL
B. tayabensis, Sym begonia (inapplicable in S. acerifolia,
B. convolvulacea, B. ulmifolia, B. meyeri-johannis)
C6
2137-2143 G
B. acerifolia, B. convolvulacea (inapplicable in B. dregei,
B. dregei ‘partita’, B. goegoensis, B. masoniana, B. m eyeri-johannis,
B. olbia, B. palm ata, B. rajah, B. salaziensis, B. sutherlandii, B. wollnyi)
These indels were then mapped onto the MP strict consensus trees for
trnC - trnD (Figure 9.1) and for ITS (Figure 9.3), and are presented here as
Figure 9.5.
181
Figure 9.5:
trnC - trnD indels mapped onto trnC - trnD and ITS strict
consensus trees
ITS
trnC - trnD
oAF
Q
— H-
e
AM + AS
S.AF
Datisca
D. cannabina
B.
B.
B.
B.
meyeri-johannis
mannii
salaziensis
k>
AF
olbia
B. mannii
B.
B.
B.
B.
ulmifolia
acerifolia
convolvulacea
dipetaia
B.
B.
B.
B.
floccifera
gracilis
heracleifolia
incarnata
B.
B.
B.
B.
malachosticta
masoniana
obliqua
peltata
S.
B.
B.
B.
B.
B.
sanguinea
maynensis
wollnyi
sutherlandii
dregei
dregei partita'
B.
B.
B.
I— B.
— B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
I— B.
B.
^ B.
e
C
AS
^ B. floccifera
j — B. rajah
B. goegoensis
S. sanguinea
B. malachosticta
C
#
j — B. dregei ‘partita’
B. dregei
B. roxburghii
palmata
ravenii
B. obliqua
B. incarnata
B. gracilis
B. heracleifolia
B. peltata
S.AF
#
tayabensis
goegoensis
rajah
grandis cf
grandis
rubella
ravenii
palmata
roxburghii
meyeri-johannis
salaziensis
masoniana
dipetaia
grandis holostyla
grandis
rubella
sutherlandii
tayabensis
AM
%
B. olbia
B. maynensis
B. wollnyi
B. ulmifolia
B. convolvulacea
B. acerifolia
Indel congruence: Indels 1, 2, 4 and 6 map onto both trees without
homoplasy. Indels 3 and 5 are homoplastic on both the ITS and the trnC trnD topologies. Part of the difficulty is the lack of resolution (a
consequence of mapping onto a consensus tree rather than one of the
individual MPTs). However, indel 3 would require two (i.e. its maximum
number of) changes even were the backbones of these trees fully resolved.
Indel 5 requires a minimum of one loss (B. rajah) and one independent
gain (8. ravenii) in the trnC - trnD topology, and at least one more change in
the ITS topology (to account for 8. floccifera).
182
9.3.6 Molecular Evolution:
Figure. 9.6
trnC - trnD: Number of steps per position for one MPT
(grey shading on the x-axis represents positions excluded
from the analysis).
iiljiiiAMwiJjJLliiiW jlJ JL
Unlli
100
2 00
3 00
4 00
500
1600
1700
1800
6 00
700
8 00
^00
1000
2000
2100
2200
2300
1100
iu
1200
Site
to °1 3 0 0
1900
Site
Figure 9.7:
ITS: Number of steps per position for one MPT
(grey shading on the x axis represents positions excluded
from the analysis).
1c
8
6
4
I!
1 00
200
300
Jj|
400
lll.lL J
500
J
600
700
800
900
1000
1100
S ite
The ITS matrix (Figure 9.7) includes characters which have more steps (11)
then the trnC - trnD matrix (Figure 9.6) (which has a maximum of 7 steps).
There are many more positions in trnC - trnD which have one step on the
tree (i.e. fit perfectly or are uninformative) than there are in the ITS matrix.
While the trnC - trnD data set is considerably longer (more than twice the
length of ITS) it has fewer changes per variable site; less data from trnC trnD was excluded due to alignment ambiguities.
183
Figure 9.8:
Base composition of the different matrices
ITS
trnC - trnD
4000
§ 10000
*fe5 5000
E
A
3000
td
c
G
Bases
2000
1000
0
A
T
C G
Bases
T
As was noted by Badcock (1998), and can be seen in Figure 9.8, trnC - trnD
is appreciably AT rich. ITS has a less skewed base composition, although
it is GC rich.
Figure 9.9:
Proportions of transitions and transversions in the different
matrices, measured over one MPT.
ITS
trnC - trnD
To
OO O
no
o
From
O OO
#
Transitions
®
0 o o
o
o
o
O
o O o
o
Transversions
As can be seen in Figure 9.9, trnC - trnD has a larger proportion of
transversions to transitions than ITS has.
184
9.4
Discussion
All the topologies agree that African taxa (B. mannii, B. meyeri-johannis and
B. salaziensis) are paraphyletic, including a monophyletic clade of Asian,
American and southern African taxa.
Gaps which were coded from the trnC - trnD matrix mapped onto the trees
with varying degrees of homoplasy. The four gaps which mapped on
without homoplasy mapped equally well onto ITS and trnC - trnD
topologies, while the two gaps which were homoplasious on one topology
were also homoplasious on the other. Regarding the two homoplasious
gaps, gap C3 is very short, only two base pairs shared by two American
taxa; gap C5 is 12 base pairs shared by six Asian taxa.
Although analysis of the combined data set produces topologies with better
tree statistics than analysis of the ITS data set does, and with more
resolved nodes than the strict consensus from analysis of the trnC - trnD
data set, it is uncertain whether both regions, from different genomes, track
the same history. The question of reticulation in Begonia evolution will be
dealt with in more detail in a further chapter.
185
9.5: Summary
Sequence data from the chloroplast region trnC - trnD, the nuclear
ribosomal ITS region and a matrix consisting of both regions combined, for
32 taxa (one Datisca, one Symbegonia and 30 Begonia taxa), were
analysed using MP. The trnC - trnD region was also analysed using ML
and ME.
The trnC - trnD topology obtained using ML is fully congruent with the strict
consensus tree produced using MP. However, ME produced some highly
unconventional groupings; as implemented here it appears unsuitable for
this data set.
MP analyses of both ITS and trnC - trnD support African taxa as basal in
Begonia] however, trnC - trnD supports polyphyly/paraphyly of American
taxa. The positions of these taxa are not resolved in the ITS tree produced
here (although monophyly of American taxa is supported by earlier ITS
analyses - see Figure 5.5, Figure 7.3). Partly because the consensus trees
from all data sets are not very well resolved, there is no real evidence for
conflict between the signal in these regions.
Mapping six indels from the trnC - trnD data matrix across both the trnC trnD and the ITS MP strict consensus trees, four fit both topologies perfectly
while two were homoplasious on both topologies; again, both regions
appear to be showing similar signal.
186
10. Morphology
10.1 Introduction
One of the major problems facing systematists who are dealing with Begonia
is that many of the morphological changes within the genus are continuous most notably, shape and size do not give the sort of discrete characters useful
for delimiting higher taxa. Begonia leaves, for example, occur in many shapes
and sizes, and these seem to bear no relation to the evolutionary history of the
group - strap-like leaves are found in the Madagascan B. bogneri and the
American B. herbacea\ compound dissected leaves are found in B.
hemsleyana (Yunnan, China) and the American 8. luxurians. Despite the leaf
similarities, close relationships of these species have never been suggested the floral morphology would not warrant it.
Arends (1992, pp. 82-85) observes that the number of styles on some
Tetraphila species can vary within the same collection locality, and even within
the same inflorescence (8. longipetiolata). Similarly, the plant 8. cf. rubella in
cultivation at RBGE produces inflorescences with both two and three locular
fruits. These are the sort of characters traditionally highly weighted in Begonia
classification, but frequent state reversals within the genus, in the light of such
plasticity, cannot be ruled out.
High homoplasy levels have led to suggestions that phylogeny reconstruction
using morphology is not viable for plant taxa (Cronk, pers. comm., 2000).
Selection pressures for certain morphological features can result in the
recurrent evolution of similar morphologies in independent lineages. Given the
potential for non-hierarchical patterns of character distribution (e.g. where
environment influences phenotype and where mosaic evolution occurs) and
problems with character delimitation (e.g. for shapes or numerical ranges)
molecular data has come to be perceived as better for phylogenetic purposes.
However, morphological characters are of interest for a number of reasons:
1.
phylogeny reconstruction (where sequence data are unavailable,
e.g. for fossil taxa);
2.
as clade markers for another data set;
3.
to trace character evolution over a tree produced largely from another
data set, e.g. molecular, e.g. to test hypotheses of homology.
188
If the purpose of the morphological data gathering is not to reconstruct
phylogeny, then the homology of characters is of less importance. Things like
leaf shape are unlikely to be quantifiable into homologous character states
across a family, but may still be interesting to trace across a phylogeny. Some
clades may have a predisposition to some shapes. Many ‘problem’
characters, such as stomatal density, leaf shape and habit, tie in with ecology.
Other problem characters include those with overlapping ranges - like flower
number per inflorescence, or anther number per flower. Although these may
be deconstructable into characters which could show trends across a
phylogeny, it is difficult to see how ranges of numbers can be homologes.
10.1.1 Previous morphological studies: The phylogenetic utility of
morphological characters in Begonia has been discussed in Badcock (1998)
and in Tebbitt (1997). Badcock coded 70 unordered morphological characters
for 86 species. She suggested that there were several equally probably
evolutionary hypotheses for the data set, thus it was ‘difficult to draw many
strong conclusions about the evolution of Begonia'. However, she found the
results useful within sections and between closely related sections.
Tebbitt (1997) coded 40 morphological and anatomical characters for 56
species, which include a detailed study of anther endothecial wall patterns
(expanded and published by Tebbitt & Mclver, 1999). Low consistency indices,
retention indices and resolution in the trees he obtained led him to conclude
that there was a large amount of homoplasy, there were few synapomorphies
supporting clades, and there was a degree of character conflict within his data.
Doorenbos, Sosef and de Wilde (1998) also examined morphological evolution
within Begonia, using 63 characters, and all 63 sections of Begonia as
terminal units. They used this data to produce a phenetic classification of
sections (noting that cladistics would not be applicable as some of the
sections were paraphyletic or polyphyletic, although one could also question
the applicability of phonetics in this situation).
They describe the fit of
characters to their phonogram as “poor”. They were surprised to find that
African and Asian sections are dispersed across their tree, while American
sections are relatively clustered.
189
Sosef (1994) conducted a cladistic morphological analysis to assess the
monophyly of the African sections Loasibegonia and Scutobegonia. He chose
characters according to two constraints, that they were (preferably) not
polymorphic within species, and that both character states occur within more
than a single species. Sosef identified 132 characters: 76
macromorphological, 32 from leaf anatomy, 17 from ovary and style anatomy
and 7 from seed micromorphology, for 43 taxa. Sosef rejected the most
parsimonious cladogram for his data in favour of a less parsimonious tree,
which he felt to be closer to the ‘truth’. From this tree, Sosef (1994) was able to
support the monophyly of sections Loasibegonia and Scutobegonia.
Morphology is also discussed by Arends (1992), with particular reference to
species in the African section Tetraphila A. DC.
The rest of Section 10.1 gives a brief overview of some of the morphological
diversity within the genus Begonia.
10.1.2 Vegetative morphology
10.1.2.1
Perenniating organs: Many Begonia species are rhizomatous,
e.g. B. masoniana, B. violifolia, B. letouzeyi. Most rhizomatous Begonia
species are acaulescent, although upright stems can form from rhizomes,
particularly when the plant is in flower (e.g. B. josephii). Another class of
Begonia is described in horticultural circles as ‘cane’; species possess upright
stems which can grow to over one metre. This group includes plants like B.
maculata Raddi and 8. longifolia. Some more woody species, like Begonia
luxurians, can grow to several metres tall. Woody stems are found in several
Old and New World Begonia species; the wood anatomy is similar to that of
Datisca (Carlquist, 1985).
Some Begonia are tuberous, like 8. boliviensis and 8. grandis. Not all tubers
are homologous: 8. grandis has stem tubers, swollen storage roots and
axillary tubercles, while American species like 8. boliviensis have root tubers
(Badcock, 1998). 8. socotrana possesses bulbils, which are produced from
axile stem nodes (Irmscher, 1925). The difference between bulbils and
tubercles is that in bulbils, the storage organs are reduced leaves, while in
tubercils, the stem is the storage organ, and has rudimentary leaves around it.
Bulbils and tubers are typically found in species which occur in seasonally
190
water-limited environments, where the fleshy above-ground parts of the plants
die back annually. Another adaptation to this sort of environment is
deciduousness, which can occur in some of the thick-stemmed taxa like B.
dregei and B. wollnyi.
B. dregei and related species have a caudex, which is a swollen woody stem
base. This may be an adaptation to fire. The caudex only forms on individuals
grown from seed, not on plants propagated by cuttings (and so will not be seen
on all individuals held in Botanic Garden collections), and is probably derived
from the hypocotyl (Hughes, pers. comm., 2000).
10.1.2.2
Stipules: Stipules provide ‘characters of considerable diagnostic
value to the taxonomist’ (Foster & Gifford, 1959, p. 447). Begoniaceae leaves
are always stipulate (Doorenbos, Sosef & de Wilde, 1998). These are attached
to the node, free from the base of the petiole, and are always formed before the
leaves are produced (Arends, 1992). Minute white hair-like stipules are also
present at the base of young leaves of Datisca cannabina, although Chant (in
Heywood, 1978) states that the leaves of Datiscaceae are without stipules.
Burt-Utley describes Begonia stipules as ‘caducous’ or ‘fugacious’ depending
on whether they fall before a new leaf starts expanding or as the leaf is
maturing (Burt-Utley, 1985, p. 14). Each of a pair of stipules may be slightly
asymmetric, with both members of the pair mirror images. There are distinct
differences between the inner and outer stipules in some species, e.g. B.
imperialis.
The stipules of some species have hairs on the outer surface, e.g. B. palmata',
other taxa have glabrous stipules, e.g. B. glabra. In some taxa, the margins of
the stipules are dentate to finely fringed, e.g. B. sutherlandii, while in most
species, they are entire (e.g. B. palmata).
Some species possess a very distinct rib along the back of the stipule, like a
keel, while others have little more than a slight thickening over the main vein.
Within stipule pairs in sect. Gireoudia, one member has the keel excurrent
apically, while in the other it is excurrent subapically, and any indumentum
tends to only be found on the lamina of the outer member of the stipule pair
(Burt-Utley, 1985).
191
Several taxa have a tooth which projects from the back of the main nerve near
the tip of the stipule. This spur may be an extension of the keel; however, in
many taxa the spur is found even where a keel is not apparent.
“[T]he major role of most stipules seems to be the protection of young
developing leaves” (Foster & Gifford, 1959). In 8. jamesoniana the young
stipules are about one cell thick over most of their surface. Enclosed inside the
stipules, the environment seems very damp. After the enfolded leaf has
emerged, the stipules soon change from green to brown, losing all moisture
from their cells and becoming papery. It is possible that keeping the growing
leaf from drying out is one function of the stipules; furthermore, hairy or strongly
keeled stipules may offer greater protection from browsers.
10.1.2.3
Leaves: The leaves of Begonia are occasionally cauline, e.g. 8.
herbacea (Figure 10.19 e) but usually petiolate. In some species there is a
ring of hairs or trichomes at the top of the petiole, e.g. the African species, 8.
johnstonii (Figure 10.18 b), the Asian species 8. tayabensis (Figure 10.18 e)
and the American species 8. manicata. The homology of these is hard to
ascertain, as the hairs may be of different colours, and in some taxa the bases
of clusters of hairs are fused together, forming scales. Furthermore, such
rings may have an adaptational advantage in reducing access to the lamina to
non-flying insects and have arisen several times independently.
Peltate leaves are found in many sections of Begonia, in plants which are not in
any other way similar, e.g. 8. peltata (American), 8. tayabensis (Asian; Figure
10.18 e) and 8. socotrana (Socotran). However, some individuals of 8.
socotrana form non-peltate leaves on flowering stems (pers. obs., 2000; pers.
comm., Hughes, 2000). In some taxa, like those mentioned, the point of
insertion of the petiole is more or less central to the lamina; many species in
section Loasibegonia have highly asymmetric insertion.
There are several reasons why it may be advantageous to be peltate, including:
1.
a peltate leaf needs less lignification to support its weight;
2.
a peltate leaf should provide the most efficient nerve arrangement to
transport water and nutrients (Burt-Utley, 1985);
3.
with the functional separation of the petiole and the lamina, leaf (lamina)
192
orientation is not directly dependent on petiole orientation (pers. comm.,
Cronk, 2000);
4.
the lamina may form a water-catching cup (pers. comm., Cronk, 2000);
5.
a peltate leaf may make more efficient use of its leaf meristems, as
expansion can occur at equal rates all round the edge of the leaf rather
than being mainly limited to the tip (pers. comm., Cronk, 2000).
Only the third point, leaf orientation, applies to the leaf arrangement of some
species in sections Loasibegonia and Scutobegonia (e.g. B. letouzeyi), where
the point of petiolar insertion is very close to the leaf margin. It may be possible
to compare the habit of some of these taxa, e.g. B. dewildei (section
Scutobegonia) with 8. herbacea, which is non-peltate but has similar overall
leaf-shape.
Another possibility is that there is no advantage conferred to plants in these two
sections from being peltate, but it is more difficult to switch back from peltate to
basifixed.
The lamina is usually asymmetric at the base (e.g. 8. lyman-smithii. Figure
10.18 c), although it can be difficult to see the asymmetry in species like 8.
bogneri, which has long, strappy leaves, and in some peltate species which
have circular (e.g. 8. socotrana) or pointed (e.g. 8. tayabensis. Figure 10.18 e)
laminas. Other peltate species, e.g. 8. sericoneura (Figure 10.18 d), may show
an asymmetric lamina ‘base’, despite the point of petiolar insertion being
elsewhere.
Most Begonia species have simple leaves, although in some species they are
highly dissected, like 8. aspleniifolia (Figure 10.18 a) in Africa, and 8. incisa in
Asia. Other species have truly compound leaves, like 8. luxurians and 8.
theimei in America, and 8. hemsleyana in Asia.
The lamina can either be flat, e.g. in species in section Tetraphila, or be bullate
(raised into many cones on the upper surface, visible as pits on the leaf
underside), like the leaves of 8. masoniana or 8. imperialis.
a.
Leaf colour: Burt-Utley (1985) does not consider leaf patternation to be
taxonomically useful within section Gireoudia; she has seen populations with
193
maculate and plain leaved forms growing together, and also suggests that the
expression of maculation is environmentally determined. Likewise, plants of B.
palmata which had plain green leaves when collected from shady under-forest
sites in Yunnan developed coloured leaf patterns in cultivation at the Royal
Botanic Garden, Edinburgh and Glasgow Botanic Garden. However, some
patterning, e.g. that on the leaves of B. brevirimosa, B. serratipetala and B. cf.
brevirimosa (all in section Petermannia), may be homologous, as the leaves
are similar in texture, colour and maculation. Leaf pattern is consistent across
several accessions of 6. serratipetala.
b.
Leaf venation: Leaves may have palmate (see Figure 10.18 b),
palmate/pinnate, or pinnate venation (see Figure 10.19.3 c). Further, the texture
of the veins can differ greatly, from raised interconnected networks to barely
visible, vanishing veins. There are almost always hairs along the veins on the
leaf underside.
c.
Stomata: Stomata are found either singly (e.g. section Coelocentrum) or
in groups (e.g. section Lepsia). Stomatal density and group size have been
found to vary with environmental factors in Begonia (Hoover, 1986) and so are
not reliable for phylogeny reconstruction.
10.1.2.4
Hairs: Begonia species have glandular and non-glandular hairs,
which, on close inspection, can be found on almost every organ of almost every
species. Long branching hairs (which give an overall impression of
‘fuzziness’) are found on certain American species e.g. B. egregia. Stellate
trichomes are found on many African species, particularly within section
Tetraphila, like B. mannii.
Burt-Utley (1985) found trichome morphology and density useful for species
delimitation in section Gireoudia. She recognised two basic classes of
trichomes - glandular (or capitulate, uniserate) and multiseriate (including villi
and ‘whiplash’ trichomes) (although “in some species these trichomes [villi]
often become uniseriate distally” (Burt-Utley, 1985, p. 13)). Burt-Utley (1985)
suggests that, given the wide distribution of villi within Begonia, they (villi) may
represent the primitive condition from which lacerate scales and whiplash
trichomes arose. She suggests that scales, which are found in a number of
sections, arose repeatedly. Shui, Li and Huang (1999) examined the hairs on
46 species from the Chinese province of Yunnan. They found that epidermal
194
and hair characters are useful at the specific and varietal levels, but not in
distinguishing sections.
Hair presence or absence can be striking on different organs - e.g. some taxa
have very hairy leaves (e.g. B. versicolor), while the leaves of others are
glabrous (e.g. B. glabra). However, glandular trichomes are frequently present
on both surfaces of the leaf primordium but are not found on mature leaves
(McLellan, 1990). Thus presence or absence of hairs is not a simple
character, and its determination may require electronmicrograph studies of very
young leaves.
10.1.3
Sexual characters
10.1.3.1
Sexual separation and inflorescence architecture: Begonia
show a wide range of inflorescence structure and of sexual separation.
Flowers are (almost always) monoecious^ plants, dioecious (e.g. B.
menyangensis, B. roxburghii, Figure 10.19.2 d), protandrous (e.g. B.
chloroneura, B. oxyphylla) or (rarely) protogynous (e.g. 6. brevirimosa).
Inflorescences are rarely unisexual (e.g. B. herbacea. Figure 10.19.1 e) or,
more usually, bisexual. Inflorescences are rarely racemes (e.g. section
Petermannia, Symbegonia - see Figure 10.19.2 c), but usually cymes (e.g. B.
diadema. Figure 10.19.2 a; 6. luxurians); a few species have monochasial
rather than dichasial branching, e.g. in section Loasibegonia, where species
frequently have one female and two male flowers per inflorescence. Bisexual
inflorescences may have two female flowers and one male in each terminal
dichasium, or all the female flowers may be found at the base of the
inflorescence (e.g. B. brevirimosa) or otherwise separate from the males.
Inflorescence architecture is discussed in depth by Goulet, Barabe and
Brouillet (1994).
^ One taxon in cultivation at RGBE (6. sp. nov., Philippine) has, for the last 3 years, produced
functional female flowers with a few anthers and male flowers with 3 fully developed stigmas
(but no ovary). This sort of abberation can be brought on by cultivation, e.g. in 6.
samhahensis.
195
While the actual numbers of male and female flowers per bisexual
inflorescence are often similar, their temporal distribution is not. In
protandrous inflorescences (e.g. B. oxyphylla), the male flower at the basal
branching point is the first to mature; there is then a progression of male
flowers maturing at branching points progressively distal to the base. The
female flowers are last to open, and may not do so until all the males in the
inflorescence have dropped. An individual plant may contain several
inflorescences at various stages of maturity. It is often the case that the plant is
functionally male for several weeks before any females are mature;
furthermore, nearing the end of its flowering period, the plant may retain only
female flowers. It is not uncommon to find individuals which look superficially
dioecious. This will tend to promote outcrossing.
Having a deciduous (male) flower central to each dichotomy within a dichasial
inflorescence makes some sense for resource allocation in large
inflorescences, as the male is unlikely to be a major sink for resources after
anthesis; a female after fruit set could compete with the rest of the
inflorescence. Often in very large inflorescences, e.g. B. oxyphylla, B. luxurians,
the (terminal) females do not develop until most (or all) of the male flowers
have fallen.
10.1.3.2
Inflorescence size: The number of flowers per inflorescence
range from one (e.g. the female inflorescence for B. herbacea) to over 1000
(e.g. B. luxurians).
Even where the basic structure is dichasial (as is most
commonly the case), inflorescences may have symmetrical (e.g. B. luxurians;
B. diadema, Figure 10.19.2 a) or asymmetrical (e.g. B. heracleifolia, Figure
10.19.1 b; B. theimei. Figure 10.19.1 a) branching (see Figure 10.1).
196
Figure 10.1: Symmetric and asymmetric inflorescence structure
A rough estimate of the number of flowers in dichotomous inflorescences can
be obtained from the number of dichotomies (branching points), as follows:
Table 10.1:
Number of flowers in different sized inflorescences
No. branching
points
No. male
flow ers
No. fem ale
flow ers
Total no.
flowers
1
2
3
4
5
6
7
8
9
10
1
3
7
15
31
63
127
2
4
8
16
32
64
128
256
512
1024
3
7
15
31
63
127
255
511
1023
2047
255
511
1023
Naturally, the numbers of male and female flowers rely on a ‘typical’
inflorescence structure where males are central in dichasia. In some taxa, the
basal few branching points lack this central flower (e.g. B. luxurians). This has
only been seen in taxa with large inflorescences (over four branching points),
and will slightly reduce the actual numbers of male flowers in these
inflorescences. Further, often not all the female flowers develop.
197
10.1.3.3
Bracts: In some taxa the basal pair of bracts are large and
enclose the entire immature inflorescence (e.g. B. poculifera] B. ampla, Figure
10.20 g), while in other species the bracts are not obvious (e.g. B. oxyloba
Welw. ex Hook.f.). Bracts are often deciduous (although are reportedly
persistent even on the fruit of species from section Squamibegonia, e.g. 6.
poculifera), and shapes, sizes and colours vary between species. Bract size
and shape also changes between different nodes on an inflorescence (BurtUtley, 1985) thus complicating the use of any bract characters cladistically. It
may be unreasonable to assume homology between bracts from different
species based on position without a very clear understanding of inflorescence
branching patterns. Bract colour can also vary within species (commonly green
to deep pink) and Burt-Utley (1985, p. 21) has found “more intense coloration
often developing in bracts on inflorescences in exposed locations”.
10.1.3.4
Bracteoles: The staminate flowers in section Gireoudia are
ebracteolate, and in over half the species in the section, the female flowers are
also ebracteolate (Burt-Utley, 1985). However, other Gireoudia species have
rudimentary or minute bracteoles on occasional flowers. Because the female
flowers are terminal and solitary, these bracteoles may be homologous to the
bracts which enclose the dichasium (i.e. indicative of an unformed dichasium).
Where there are pairs of well developed bracteoles at the base of the ovary,
these may be inserted directly below the ovary (e.g. B. convolvulacea, B.
peltata), or at some distance down the pedicel.
Variations in shape appear to
have little taxonomic significance (Burt-Utley, 1985), but the presence or
absence of bracteoles “can be useful in distinguishing among morphologically
otherwise similar taxa and in evaluating putative hybrids” (Burt-Utley, 1985, p.
22). Similar bracteoles occur, either in pairs or in threes, on many other taxa of
Begonia, including 8. annobonensis and 8. cubensis (two bracteoles) and 8.
fissistyla (three bracteoles).
See Figure 10.2 for the difference between bracts and bracteoles; both can be
seen on the inflorescence of 8. hercleifolia in Figure 10.19.1 b.
Figure 10.2: Bracts and bracteoles
M
Bracteoles
Bracts
198
10.1.3.5
a.
Flowers
Tepal colour: Flower colour in Begonia is most commonly white (e.g. B.
involucrata, Figure 10.19.1 c) and/or pink (e.g. B. socotrana, Figure 10.19.3 a)
(many species possess both forms, e.g. B. grandis). Yellow flowers are
predominantly found in African taxa (e.g. 8. letouzeyi. Figure 10.20 d), while red
{Symbegonia sanguinea. Figure 10.19.2 c; 8. fuchsioides) and orange (8.
oxysperma, 8. boliviensis) are found in some Asian and American taxa
(respectively). Most taxa have only one colour in the flower, but some African
(e.g. 8. ampla. Figure 10.20 f; 8. aspleniifolia) and American (e.g. 8.
solananthera) species have pink markings on otherwise white or yellow tepals.
These markings can be asymmetric, appearing strongest on the lower tepal.
In section Platycentrum, it is not uncommon for the outer and inner whorls of
tepals (particularly in the male flower) to be different colours (e.g. the
unidentified 8. species. Figure 10.19.2 b).
Tepal colour is reported to vary between white to dark pink, in the section
Gireoudia, according to species, population and light levels (i.e. genetic and
environmental factors) (Burt-Utley, 1985).
b.
Stigma and anther colour: Yellow colour and strong ultraviolet
absorption in stigmas and anthers was found in all insect-pollinated Begonia
species examined by Schemske, Agren and le Corff (1996). They suggest that
this implies mimicry of the anthers by the stigmas (‘similarity of
nonhomologous organs’). They go on to say: “[b]ecause a phylogeny of
Begonia is not available, we do not know if characters such as stigma colour
and uv absorption in female flowers represent the ancestral condition, or have
evolved to increase the resemblance of female to male flowers” (Schemske,
Agren & le Corff, 1996, p. 313).
c.
Tepals: The commonest tepal numbers for male flowers are two (e.g. 8.
brevirimosa] 8. letouzeyi, Figure 10.20 d; B. ampla. Figure 10.20 f, g; 8.
herbacea) and four (e.g. 8. luxurians] 8. handelii, Figure 10.20 b; 8.
loranthoides. Figure 10.20 e; 8. socotrana. Figure 10.19.3 e). I have not seen
plants with other numbers, although they are reported in the literature. In fourtepalled flowers, two tepals are usually smaller. The four tepals of fourtepalled flowers are usually arranged with two planes of symmetry, although
occasionally the smaller pair point downwards, giving bilateral symmetry (see
199
Figure 10.4; see also Figure 10.20 e, B. loranthoides).
Figure 10.3: tepal symmetry planes in male flowers
Female tepal number is more variable: two (e.g. B. oxyloba, B. prismatocarpa),
three (e.g. 8. amphioxis, 8, fallax, 8. masoniana, 8. herbacea. Figure 10.21 g),
four (e.g. 8. molleri. Figure 10.21 f), five (e.g. 8. brevirimosa. Figure 10.21 b; 8.
listada; 8. palmata), six (e.g. 8. socotrana. Figure 10.19.3 a; 8. crassirostris) and
occasionally more. Three-tepalled flowers may have strong bilateral symmetry,
with two larger tepals arranged opposite each other, and one smaller tepal at
90° to them (e.g. 8. masoniana) - see Figure 10.4.
Figure 10.4: Tepal arrangement in 8. masoniana female flowers
Several authors have distinguished two whorls of tepals in the male flower into
sepals and petals (e.g. de Candolle, 1859, 1864; Irmscher, 1925). Endress
(1994) described the difference between sepals and petals being that sepals
have broad bases with three vascular traces, and petals have narrow bases
with just one vascular trace. All Begonia species are thought to have two
sepals in the male flower (Badcock, 1998), therefore flowers with two tepals
lack petals. It has proved less easy to distinguish the tepals of the female
flower in such a way. Barabe (1980) looked at the vascularisation of the tepals
in pistillate flowers of 8. handelii, and found that the flower has two whorls of
perianth parts, differentiated into calyx and corolla. However, this differentiation
of petals and sepals in the female flower has not been widely followed, given
perhaps the greater variation in tepal number in the female.
Tepal fusion is uncommon in Begonia, although it characterises Symbegonia.
The male flowers of the species grown by Glasgow Botanic Garden have two
tepals which are fused to a degree - in S. sanguinea they are fused along most
200
of their edge (this can be seen in Figure 10.19.2 c), while in the Symbegonia
species accessioned 004 137 91 (GL) they are fused very shortly. B.
brevirimosa similarly has two shortly fused tepals in the male flower. The
female flowers in Symbegonia have five tepals fused into a long tube, with only
the tips free (and pointed). This affords some evidence that the five tepals in
the female Symbegonia flowers all represent the same organ (i.e. petals or
sepals), because they are able to fuse; male flowers with tepal fusion all have
two tepals, which may represent either sepals or petals (and are generally
interpreted as sepals).
Female flowers of species in section Squamibegonia, e.g. B. ampla, B.
poculifera, have a perianth tube between the top of the ovary and the tepals.
Some other species of Begonia show some tepal fusion - B. chloroneura, for
example, has partial fusion of two of the five tepals of the female flower (or,
alternatively, four tepals, one deeply divided).
This is also seen in S.
tayabensis. 6. brevirimosa often produces flowers with tepal fusion in the
female flowers, e.g. Figure 10.21 b.
d.
Scent: Some Begonia species possess perceptibly scented flowers
(e.g. flowers of B. menyangensis, B. handelii, B. roxburghii, B. hatacoa and S.
diadema are sweet-scented; S. herbacea flowers are slightly almond-scented).
0.
Size: Male and female flowers are often superficially similar, at least
being approximately of equal sizes. However in a few taxa the female is many
times larger than the male (e.g. B. chlorosticta', B. incisa’, B. maynensis. Figure
10.19.1 d). While the actual tepal sizes may not be hugely different (both have
two male and five female tepals; male tepal length is c. 7 mm and female tepal,
c. 10 mm in 8. incisa and c. 6 mm and c. 14 mm in 8. cholorosticta) the
females have very large and showy ovaries with obvious, coloured wings.
f.
Male flowers
I.
Androecium: The androecium of the male flowers can be very
varied. All the stamens can be free (e.g. 8. handelii. Figure 10.20 b), or the
filaments can be fused to varying degrees into a column. This fusion can be
along most of the filament length of all the stamens, creating a long, prominent
column (e.g. 8. palmata, 8. grandis), or just among the central stamens with
201
anthers leaving the column at different heights (e.g. B. annulata, B. fallax). The
anthers in these sorts of androecia are usually actinomorphic, forming a dome
and facing all directions. The fusion of filaments can also be zygomorphic, to
only one side of the androecium, creating an effect which has been compared
to a hand of bananas (e.g. B. letouzeyi, Figure 10.20 d; B. ampla, Figure 10.20
f). The anthers in androecia which have this sort of fusion usually all face the
same direction (the upper tepal), although occasionally half may face the
upper, and half the lower, tepal. In a few taxa, all the anthers dehisce inwards,
e.g. B. subscutata, section Tetraphila. See Figure 10.5 for an illustration of
anther arrangements.
Figure 10.5: Anther arrangement
FR E E
FU SED AT
CENTRE
ON A
ALL
COLUMN FACING
ONE WAY
FACING
TW O
W AYS
FACING
IN S ID E
The anthers themselves may dehisce laterally, or the slits can open down the
front of the anther. The anther may be longer than (e.g. B. cubensis, B.
dietrichiana Irmsch.) or shorter than (e.g. B. holtonis, B. ulmifolia) the filament.
All anthers may be the same length in one androecium, or they may vary. The
connective can be the same length as the anthers or can be extended into a
rounded tip (e.g. B. wollnyi) or a point (e.g. B. menyangensis) beyond them.
The top of the connective may form a hood (e.g. B, letouzeyi). There are reports
of dehiscence via pores rather than slits in some taxa, although the difference
between a short slit and a pore may be marginal.
The numbers of stamens per flower varies from about five (e.g. B. herbacea) to
well over 100 (e.g. B. palmata\ B. sp., Yunnan 25, Figure 10.20 a). Lower
anther number may be associated with increasing reliability of pollinators. The
flowers of B. herbacea are quite strongly scented, in monosexual
inflorescences on short pedicels - the inflorescence is hidden in the leaves.
This may tie in with a specific pollinator. In other cases, stamen number may
relate inversely to the number of flowers on an individual plant, with lower
individual anther numbers per flower in species with bigger inflorescences.
The stamen colour is usually yellow (occasionally orange in some taxa, e.g. B.
202
wollnyi)] however species of Symbegonia in cultivation in Glasgow have white
filaments and red anthers.
ii.
Bud and sepal shape: There are distinct differences in the
shapes of male flower buds between taxa in Begonia. Many species have flat
buds (e.g. B. invoiucrata, Figure 10.19.1 c; B. maynensis, Figure 10.19.1 d),
while others have more or less spherical buds (e.g. S. roxburghii, Figure
10.19.2 d). These differences do not correlate exactly with the size of the
androecium; although no taxa with a small number of stamens have spherical
buds, not all taxa with many stamens do either. I do not know of any taxa with
two tepals in the male flower which have spherical buds.
Sepal shape is reported (Burt-Utley, 1985) as varying not just on different
flowers on an individual, but also over time - with differences before and during
anthesis. Thus this is not a reliable character for phylogenetic analyses
without some detailed quantification of variability.
g.
Female flow er
I.
Styles: Style number varies, occasionally two (e.g. B. goegoensis)
or four (e.g. B. molleri, Figure 10.21 f), but most commonly three (e.g. B.
convolvulacea, Figure 10.21 h; B. chlorosticta, Figure 10.21 d). The styles may
be free (e.g. 8. convolvulacea, Figure 10.21 h) or fused to a varying degree (e.g.
B. boisiana. Figure 10.21 e). They are usually bifid (e.g. B. convolvulacea,
Figure 10.21 h), but may be entire (e.g. B. gabonensis] B. mannii, Figure
10.19.3 c), kidney-shaped (e.g. 6 . letouzeyi) or three- or four-fid (e.g. 6 .
fissistyla). Stigmatic papillae usually occur in a spiralling band, but can be
confined to the tips of the styles (e.g. B. quadrialata, B. gabonensis) or more
widely across the surface (e.g. B. annobonensis, B. fissistyla).
Style colour is usually yellow, although may tend towards green or orange in
some taxa.
ii.
Ovary: The female flowers always have an inferior ovary (except in
Hillebrandia, where the ovary is semi-inferior). Within the ovary, the most
common state is three locules (e.g. 8. malachosticta), although there are
species with one (e.g. 8. masoniana), two (B. goegoensis, B. annulata, B.
kingiana, B. imperialis) and four (e.g. 8. handelii, 8. letouzeyi, 8. molleri)
203
locules. Species with one locule have parietal placentation. The placentation
in the other species is either axile (e.g. B. palmata) or septal (e.g. 8.
gabonensis). Septal placentation may occur when the multilocular condition is
caused by the inward growth and fusion (or partial fusion) of parietal placentae,
and so is really homologous with the parietal condition (Reitsma, 1984). It can
be difficult to determine. See Figure 10.6 for an illustration of placentation
types.
Figure 10.6: Placentation types
Parietal
Septal
Axile
The placentae may be unbranched (e.g. 8. kingiana) or bifid (e.g. 8.
malachosticta, 8. masoniana), or less commonly many-fid. In the case of bifid
placentae, ovules may be present on all surfaces or may be absent from the
two facing surfaces within each locule (e.g. 8. solananthera, 8. lubbersii).
Placentae may be green or white, and can be more or less fleshy (e.g. 8.
princeps A.DC. has quite fleshy placentae). In some species the ovules may
sometimes appear pink (e.g. 8. dewilder, although this is not consistent in the
same individuals over time); ovules are normally white.
In some two-locular species, there has almost certainly been a secondary loss
of one locule from an ancestral condition with three locules. Occasionally
individual ovaries can be found within a tiny locule in the position where the
third locule would ordinarily be. One fruit of 8. annulata was found which had
such a locule, with a small placenta and a few ovules. This aberrant fruit also
had two normal styles and one highly reduced (aberrant) third style.
The ovary may have a number of wings running along it, from the style to the
pedicel. Most Begonia species have three wings (e.g. 8. johnstonii, Figure
10.22 a; 8. maynensis. Figure 10.19.1 d; 8. herbacea. Figure 10.21 g), although
there are species with more, or where the wings are reduced or absent (e.g. 8.
gabonensis and 8. oxyloba are wingless (Figure 10.22 b); 8. prismatocarpa
and 8. loranthoides have ribs (Figure 10.19.3 b)). The wings can be equal in
size (e.g. 8. dregei, 8. brevirimosa, 8. dietrichiana), or (more commonly) the
upper wing is distinctly larger (e.g. 8. glabra; the unidentified species with
204
American Begonia Society (ABS) no. U205, Figure 10.22 d). In some species
this larger wing is on the underside of the mature fruit; the pedicel is curved so
that the whole fruit is bent back on itself (e.g. B. palmata; B. hatacoa, Figure
10.22 c). The wings, when present, may be the same colour as the rest of the
ovary (e.g. S. solananthera, B. dipetala - wings and body white; B. boisiana wings and body pink. Figure 10.21 e) or may be a different colour (e.g. B.
manicata - pink wings, green body; S. valida - white wings, green body).
Species in the epiphytic section Trachelocarpus (e.g. B. herbacea) have a very
distinctive fruit shape, with a long beak (or throat, as the section name
suggests) between the top of the locules and the tepals (see Figure 10.21 g).
This appears to have a similar function to the pedicel in other taxa, as the
pedicel in these species is very short and the fruit sits more or less on the
rhizome. The long beak lifts the tepals and stigmas out from among the
leaves.
iii.
Fruit: The fruit, when matured, is most commonly dry and papery
(e.g. B. Johnstonii, Figure 10.22 a; B. glabra), although in some taxa it is fleshy.
Fleshy fruit are more frequent in wingless taxa (e.g. B. oxyloba. Figure 10.22 b;
B. gabonensis), although some fleshy fruits have wings or ribs (e.g. B. sp. nov.,
Philippine; B. bogneri). The style (and less commonly, the tepals (e.g. B.
tomentosa Schott)) can remain on the mature fruit (e.g. 8. annobonensis, 8.
socotrana, 8. ulmifolia), or can be deciduous (e.g. 8. brevirimosa, 8.
chlorosticta). Fruits may be indéhiscent (which often correlates with
fleshiness) or form short splits near the pedicel, or right along the edges of the
wings (e.g. 8. palmata, 8. brevirimosa). Fruits dehiscing through the wings
have been reported in the literature. The fruit may be erect (e.g. 8. herbacea),
pendant (e.g. 8. chlorosticta) or recurved (e.g. 8. palmata).
205
10.2 Material and methods
10.2.1 Plant material: Taxa in this analysis are the same as those included in
the ITS analysis; accession and voucher details are the same, and can be
found on the CD-ROM.
10.2.2 Non-DNA character coding: Characters which refer to shape were
avoided as far as possible, due to complications with scoring indiscrete
characters. Because this matrix was intended to compliment an ITS DNA
matrix, wherein the sampled taxa are individuals not species, a similar
approach was taken with morphology: only the individual plant from which DNA
was extracted was scored for the selected characters. This avoids any
problems with plant identification which could occur were characters to be
taken from literature, and of species delimitation which may complicate scoring
characters from herbarium sheets. However, this approach does generate
rather more ‘missing data', and is particularly problematic where plants are
dioecious or have not been known to flower in cultivation. For some taxa,
herbarium sheets of the same accession were made at the time of collection
(or after introduction to cultivation) and could be used to obtain floral characters
for plants which did not flower within the time-frame of this study (6. aequata,
Wilkie et al. 1997 2515, E; B. formosana, ETE 24, E; 6. oxysperma, Wilkie et al.
29142, E; B. rufo-sericae, C l 1195, E; B. serratipetala, Reeves 588, E; 8. sp.
‘exotica’. Reeves 142, E; 8. sp., Sulawesi 252, Argent et al., 00116, E; 8. sp.,
Sulawesi 253, Argent et al., 00151, E; 8. sp., Sulawesi 254, Argent et al., 00152,
E - see Appendix 14.5 for further details). The problem is less retractable for
dioecious plants; in the case of 8. handelii, male and female plants were
collected at the same location in Yunnan; for 8. menyangensis, although there
is only a male plant in cultivation in Glasgow, there is field information for
female plants from the same locality. For both these taxa it was decided to
relax criteria and score characters from both sexes.
See Table 10.2 for a list of the non-DNA characters.
206
Table 10.2:
Summary of non-DNA characters and their states
VEGETATIVE CHARACTERS
1. Stem tuljers
0: absent
1: present
2. Root tubers
0: absent
1: present
3. Bulbils
0: absent
1: present
4. Tubercils
0: atjsent
1: present
5. Caudex
0: atjsent
1: present
6. Leaf shape
0: simple
1: compound
7. Peltateness
0: basifixed
1: peltate
8. Leaf maculation
0: colour same all over
1: with patterning
9. Petiole transverse section
0: circular
1: crescent
2: square
10. Trichome ring at top of petiole
0: absent
1: present
11. Stipule persistence
0: persistent
1: caducous
12. Stipule pair
0: txjth the same
1: different
13. Stipule keeling
0; indistinct
1: strongly keeled
14. Stipule spur
0: imperceptible
1: distinctly spurred
15. Stipule edge
0: entire
1: fringed
16. Stipule back
0: glabrous
1: hairy
17. Fuzzy"hairs'
0: absent
1: present
18. Stellate hairs®
0: absent
1: present
207
SEXUAL CHARACTERS - INFLORESCENCE
19. Lifestyle
0; perennial
1: monocarpic
20. Infloresœnce position
0: axile
1: terminal
21. Inflorescences per axil
O:one
1: more
22. Sexual separation
0: dioecious
1: monoecious
23 Inflorescence type
0: cyme
1: raceme
24. Inflorescence branching at base
0: dichasial
1: monochasial
25. Inflorescence symmetry
0: symmetric
1: asymmetric
26. Dichasial inflorescence; basal dichotomies
0: with central flower
1: without central flower
27. Flower number per inflorescence
0: less than 70
1:over 100
28. Sexual separation
0: male and female in same inflorescence, interspersed
1: male and female in same inflorescence, female basal
2: male and female on separate inflorescences
29. Flower sizes
0: similar in male and female
1: distinctly larger female than male
30. Flower colour (most prevalent)
0: white or pink
1 ; yellow
2: red
3: orange
30: Flower pattern
0: tepals all one colour
1: both tepals with similar red veins or patches
2: red veins or patches only on one tepal
32. Scent
0: imperceptible
1: strong
33. Perianth tukie
0: at>sent
1: present
SEXUAL CHARACTERS - MALE FLOWER
34. Male tepal number
0:2 tepals
1:4 tepals
2: absent
35. Male flower symmetry
0: radial symmetry of tepals
1: bilateral symmetry of tepals
36. Male tepal fusion
0: free
1: partly fused
208
37. Male tepal hairiness
0; glabrous
1: with hairs
38: Male tepal edge
0: entire
1: lobed
39. Male bud shape
0:flat
1:spherical
40. Androecium
0: anthers face all directions
1: anthers face upper and lower tepals
2: anthers face upper tepal
41. Stamen number
0: less than 10
1:10 or more
42. Stamen colour
0: yellow
1: orange
2: red
43. Anther dehiscence
0: via slits
1: via pores
44. Stamen fusion
0:free
1: fused only in the centre
2: fused only at one side
3: on a column (all fused)
45. Anther connective extension
0: not extended
1: extended
46. Anther connective hooding
0: nottxxxJed
1:hooded
SEXUAL CHARACTERS - FEMALE FLOWER
47. Female tepal number
0:2 tepals
1:3 tepals
2:4 tepals
3:5 tepals
4:6 tepals
7: absent
48. Female tepal fusion
0:free
1: two tepals partly fused
2: all tepals partly fused
49. Female tepal hairiness
0: glabrous
1: hairy
50. Female tepal edge
0: entire
1: lobed or serrate
51. Style number
0:2 styles
1:3 styles
2:4 st^es
3: (5-) 6 (-7) styles
52. Style colour
0: yellow
1: greenish
2: white
3: pink
4: red
209
53. Style fusion
0:free
1: fused
54. Style branching
0: unbranched
1: kidney-shaped
2; bifid
3 :3-fid - 4-fid
55. Style persistence on fruit
0: persistent
1: caducous
56. Ovary position
0; inferior
1; semi-inferior
57. Locule number
0:1 locular
1:2locular
2: 3 locular
3:4 locular
4: (5-) 6 (-7) locular
58. Placentation
0: parietal
1: septal
2. axile
59. Placentation
0: one-fid
1: bifid, with ovules on inner and outer surfaces of placentae
2: bifid, with ovules only on outer surfaces of placentae
60. Fruit wing number
0: absent
1:2 wings
2:3 wings
3:4 wings
4: c. 6 wings (coronate)
5:1 wing
61. Fruit wing symmetry
0: equal to subequal
1: one distinctly larger
62. Fruit dry or fleshy
0: dry
1: fleshy
63. Fruit orientation
0: upright
1: pendant to nodding
2: recurved
64: Fruit hair
0: glabrous
1: with hairs
65: Beaked ftuit
0: absent
1: present
66: Dehiscence
0: not between styles
1: between styles
67. Bracteole subtending ovary
0: absent
1:2 bracteoles
2:3 bracteoles
The data matrix for these non-DNA characters is included on the CD-ROM.
210
10.2.3 Cladistic Analyses
Several characters were missing for many taxa. For example, the differences
between the outer and inner stipules in some taxa were not observed until
most species had been scored. This character is not easily observed from
herbarium material, and it was not possible to revisit all the living plants to add
in this data. Several other characters were felt to be obviously homoplastic, e.g.
hairiness on the backs of stipules. However, a priori exclusion of data on such
grounds involves the assumption that taxa which share this character are
unrelated; this should be a deduction from the analysis, not an assumption of
it.
10.2.3.1
Data sets:
The taxa in the morphological matrix were sorted into
the same order as the taxa in the ITS matrix; duplicate sequences (e.g. clones,
different primers) were removed and the two matrices were combined by
interleaving.
Thus there are three data sets to be analysed in this chapter:
1.
The non-DNA matrix
2.
The corresponding ITS matrix
3.
The combined non-DNA and ITS matrix.
10.2.3.2
Analyses:
Analyses were run using PAUP* 4.0 (Swofford,
2000). For each matrix, g1 was estimated using 10,000 random trees. PTP
was estimated with the outgroup (the two Datisca species) excluded, with 100
replicates, simple addition, saving no more than five trees per step. An
heuristic search was run, 1000 random additions, saving no more than five
trees at each step, steepest descent, TBR swapping. MaxTrees was set to
1000. The strict consensus topology from the resulting trees was input as a
constraint file, and a further heuristic search with 1000 random additions, TBR,
saving only five trees at any step, was performed to see if any other equally
parsimonious topologies were supported. Bootstrapping was performed with
the fast heuristic option in PAUP, 5000 replicates. Bremer support was
estimated using AutoDecay (Erikkson, 1998) (10 random addition replicates,
TBR, steepest descent, maximum of five trees held per step).
211
10.3
Results
10.3.1.
Non-DNA data set: The skewedness statistic g 1 is -0.1799. PTP
probability is 0.010. One thousand MPTs were found, of length 499. Searching
with topological constraints found a shortest tree length of 501.
There was little resolution in the strict consensus tree; a majority rule tree is
presented (Figure 10.7). Nodes are annotated with the percentage of trees
they appear in and Bremer support values on the relevant clades. A phylogram
is also presented (Figure 10.8).
There are 33 nodes in the strict consensus tree; five nodes have over 50%
bootstrap support. Clades with bootstrap support over 50% are listed below:
55%,
64%,
61%,
74%,
97%,
B. grandis ssp. grandis and B. grandis ssp. hoiostyla;
S. letouzeyi and B. quadrialata;
6. masoniana and B. masoniana van maculata;
S. samhahensis and S. socotrana;
D. cannabina and D. glomerata.
The consistency index is 0.21 (0.20 excluding uninformative characters) and
the retention index is 0.65.
212
Figure 10.7: Majority rule cladogram from 1000 MPTs, non-DNA data set
10014
213
sp., Sulawesi 252
sp., Sulawesi 253
crassirostris
bogneri
sp. nov., Philippine
guaduensis
longifolia
meyeri-johannis
olbia
sandwichensis
morsei
odorata
sp., sych
sp., Platycentrum
hatacoa
sp., Yunnan 33
deliciosa
diadema
palmata 74
palmata 75
versicolor
Yunnan 25
annulata
formosana
rex
hemsleyana
imperialis
violifolia
balansana
capillipes
longipetiolata
mannii
rhopalocarpa
kisuluana
gabonensis
salaziensis
handelii
menyangensis
roxburghii
molleri
poculifera
subscutata
longicarpa
echinosepala
luxurians
oxyphylla
rufosericae
peltata
ulmifolia
listada
masoniana
masoniana maculata
labordei
fallax
horticola
solananthera
fuchsioides
sp., macE
valida
convolvulacea
sp. nov.,Yunnan
sp., gutt
madecassa
samhahensis
socotrana
annotxxiensis
cutiensis
engleri
johnstonii
jamesoniana
angularis
glabra
holtonis
minor
meridensis
I— B, sp., Sulawesi 254
'— B. incisa
B. aequata
B. brevirimosa
121
sanguinea
S. sp., 136
B. cf. brevirimosa
B. isoptera
B. malachosticta
B. amphioxis
B. serratipetala
B. cf. serratipetala
B. chlorosticta
B. maynensis
B. sp., Reichenheimia
B. goegoensis
B. kingiana
B. floccifera
B. sp., Bolivia
B. herbacea
B. sp., Trachelocarpus
B. boliviensis
B. cinnabarlna
B. oxyspemna
B. rubella
B. sp., macGL
B. gracilis
B. grandis grandis
B. grandis holostyla
B. acerifolia
B. francoisii
B. incamata
B. lubbersii
B. rajah
B. sp., 1998 1824
sp.. Philippine
porter!
B. sp., Taiwan
B. sp., U172
B. heracleifolia
B. theimei
B. manicata
B. invoiucrata
B. asplenlifolia
B. letouzeyi
B. quadrialata
B. scutifolia
B. prismatocarpa
B. staudtii
B. scapigera
B. dewildei
B. duncan-thomasii
B. potamophila
B. thomeana
B. iucunda
B. dipetala
B. beddomei
B. fissistyla
B. egregia
B. obliqua
B. sericoneura
B. lobata
B. sp., Yunnan 26
B. diloroneura
B. tayabensis
B. integerrima
B. sutheriandii
B. wollnyi
B. mananjabensis
B. sp., Yunnan 21
B. aœtosella
B. dregei
B. dregei homonyma
B. dregei 'partita'
B. sp., nam
B. sonderana
- B. geranioides
- B. edmondoi
- B. nossibea
- B. ravenii
- B. ankaranens
“ D. glomerata
- D. cannabina
Bremer support values
over 50% above
branches;
percentage cladograms
below branches
96
214
Figure 10.8: Phylogram of one of 1000 MPTs, non-DNA characters
I
B. sp., Sulawesi 252
j B. sp., Sulawesi 253
— B. crassirostris
' B. bogneri
sp. nov., Philippine
J B. guaduensis
B. longifolia
B. meyeri-johannis
— 1 change
I B. olbia
H. sandwichensis
B. morsei
B. sp.. sych
B. sp., Platycentrum
B. hatacoa
B. sp.. Yunnan 33
B. deliciosa
B. diadema
IB . palmata 48
—I ' B. palmata 59
B. versicolor
B. sp., Yunnan 25
I B. annulata
—I
B. formosana
'--------------- B. rex
' B. hemsleyana
B. imperialis
B. violifolia
-------------- B. balansana
B. capillipes
_ p “ B. longipetiolata
B. mannii
B. rhopalocarpa
B. kisuluana
B. gabonensis
B. salaziensis
j — B. he
handelii
|BB.. m
menyangensis
B. roxburghii
' B. molleri
-f— B. poculifera
B. subscutata
B. longicarpa
— B. echinosepala
B. luxurians
B. oxyphylla
|—M b
B.. rufose
rufosericae
B. p
peltata
H
B.
B. ulmifolia
B. listada
B. masoniana
B. masoniana maculata
B. labordei
' B. fallax
B. horticola
B. solananthera
B. fuchsioides
B. sp., macE
B. valida
B. convolvulacea
B. sp. nov., Yunnan 20
B. sp., gutt
B. madecassa
B. samhahensis
B. socotrana
B. annobonensis
B. cubensis
— B. engleri
B. johnstonii
B. jam esoniana
— B. angularis
B. glabra
— B. holtonis
— B. minor
B. meridensis
B. odorata
cc
-I
215
£
B. sp.. Sulawesi 254
— B. incisa
B. aequata
B. brevirimosa
|— S sp.. 121
I
'
S. sanguinea
S. sp., 136
' B. cf. brevirimosa
B. isoptera
— B. malachosticta
“ B. amphioxis
B. serratipetala
B. cf. serratipetala
— B. chlorosticta
B. maynensis
B. sp., Reichenheimia
B. goegoensis
B. kingiana
B. floccifera
B. sp., Bolivia
j ^ . herbacea
B. sp., Trachelocarpus
B. boliviensis
B. cinnabarina
B. oxysperma
B. rubella
B. sp., macG
B. gracilis
B. grandis grandis
' B. grandis holostyla
I B. acerifolia
”1 ” B. francoisii
' B. incamata
' B. lubbersii
4;
B. rajah
B. sp., 1998 1824
B. sp.. Philippine
B. porteri
B. sp., Taiwan
B. sp., U172
' B. heracleifolia
' B. theimei
B. manicata
B. invoiucrata
B. aspleniifolia
B. letouzeyi
quadrialata
B. scutifolia
B. prismatocarpa
B. staudtii
“I '
B. scapi
scapigera
B. dewildei
B. duncan-thomasii
B. potamophila
B. thomeana
B. iucunda
B. dipetala
B. beddomei
rl
B. fissistyla
' B. egregia
*B . obliqua
B. sericoneura
■ B.
D lobata
If
iB . sp., Yunnan 26
\~~~ B. chloroneura
B. tayabensis
B. integerrima
B. sutheriandii
B. wollnyi
B. mananjabensis
B. sp., Yunnan 21
B. acetosella
— 1 change
B. dregei
B. dregei homonyma
B. dregei 'partita'
B. sp., nam
B. sonderana
— B. geranioides
B. edmondoi
B. nossibea
B. ravenii
B. ankaranens
I
D. cannabina
D. glomerata
LF
216
B
.:
There are no clear correlations between this tree and the ITS trees. The clear
geographical structuring apparent in analyses of ITS data is lost here. A few
clades survive - the Loasibegonia group of species appear to be held together
by several morphological characters, and Petermannia/Symbegonia also hold
together. In other clades, it is possible to guess which characters are
responsible for the unconventional groupings - there is a clade which includes
some fleshy-fruited African species from section Tetraphila and some fleshy
fruited Asian species. Elsewhere there is a clade of orange-flowered taxa (8.
boliviensis, 8. cinnabarina and 8. oxysperma). In general, however, this tree
makes little sense in the light either of previous taxonomic treatments or of
geographical distributions, or in the light of the ITS, 268 and trnC - trnD
cladograms discussed previously.
Using majority rule to summarise a group of alternative topologies is one thing;
using it as an estimator of phylogeny would be very different, and not justifiable
under a criterion of parsimony. There will be other equally parsimonious
topologies which are not congruent with this topology. Given that the strict
consensus tree for these data is highly unresolved (N.B. the 100% branches
on the majority rule tree do not all appear in the strict consensus of 1000 MPTs;
presumably a grouping found in 999, i.e. 99.9% of the trees, is rounded up to
100%) there is little that can be said about Begonia evolution based on this
analysis.
10.3.2.
ITS sequence data analysis:
There were 122 constant, 92 uninformative, and 311 informative characters
included. The skewedness statistic g1 for this data set is -0.453.
One thousand MPTs were found, of length 2702. Searching with topological
constraints found trees of length 2703. The consistency index is 0.30; with
uninformative characters excluded it is 0.27. Retention index is 0.68. The strict
consensus tree is presented as Figure 10.9; one of the MPTs is presented as
a phylogram. Figure 10.10. There are 108 nodes in the strict consensus tree;
71 nodes have over 50% bootstrap support.
217
Figure 10.9: Strict consensus of 1000 MPTs, ITS data set
B. sp., Sulawesi 252
B. sp., Sulawesi 253
B. crassirostris
B. acetosella
B. longifolia
B. handelii
B. menyangensis
B. hemsleyana
I
B. sp., Sulawesi 254
B. sp. nov.. Philippine
1-—
B. sp., Taiwan
I_22_|
B. formosana
3 ‘
B. ravenii
I
B. sp., Platycentrum
1 100 I
B. palmata 48
19
B. palmata 59
B. sp., Yunnan 20
B. sp., Yunnan 26
B. balansana
B. longicarpa
• B. versicolor
B. sp., Yunnan 25
B. sp., Yunnan 33
B. annulata
B. rex
B. deliciosa
B. diadema
B. hatacoa
B. roxburghii
B. sp., Yunnan 21
B. rubella
B. labordei
B. sp.. 1998 1824
B. chloroneura
B. tayabensis
B. oxysperma
B. sp.. Philippine
I
B. sp., Reichenheimia
159 I
B. goegoensis
6 *
B. rajah
r
B. beddomei
'--------- B. dipetala
'
B. floccifera
I
B. grandis grandis
B. grandis holostyla
B. sp., nam
B. aequata
B. brevirimosa
B. cf. brevirimosa
B. incisa
B. serratipetala
B. cf. serratipetala
S. sp., 121
S. sp., 136
S. sanguinea
B. isoptera
B. amphioxis
B. malachosticta
B. chlorosticta
B. kingiana
B. masoniana
B. masoniana maculata
B. morsei
B. porteri
Æ.
3
84
218
sp., sych
guaduensis
fuchsioides
holtonis
jam esoniana
meridensis
cubensis
obliqua
minor
odorata
sp., Bolivia
fissistyla
incarnata
sp., macE
acerifolia
valida
convolvulacea
glabra
ulmifolia
sp., macG
angularis
lobata
rufosericae
luxurians
oxyphylla
echinosepala
listada
Bootstrap support
values over 50%
above lines;
Bremer support
below lines
cinnabarina
gracilis
herbacea
sp., Trachelocarpus
maynensis
olbia
wollnyi
sp., U172
heracleifolia
invoiucrata
edmondoi
sp., gutt
lubbersii
imperialis
violifolia
integerrima
solananthera
manicata
75
65
.100
18
4
5
99 1-------9 ^
sericoneura
dregei
dregei homonyma
dregei 'partita'
sonderana
geranioides
sutheriandii
fallax
samhahensis
socotrana
ankaranens
francoisii
nossibea
mananjabensis
salaziensis
bogneri
madecassa
capillipes
kisuluana
subscutata
mannii
molleri
longipetiolata
poculifera
rhopalocarpa
meyeri-johannis
aspleniifolia
dewildei
potamophila
quadrialata
scutifolia
prismatocarpa
duncan-thomasii
letouzeyi
a r"
thomeana
iucunda
annobonensis
engleri
johnstonii
sandwichensis
cannabina
glomerata
219
Figure 10.10;
Phylogram, ITS data set, one of 1000 MPTs
J ” B. sp., Sulawesi 252
l - P - B . sp., Sulawesi 253
B. crassirostris
^ B. acetosella
B. longifolia
r~ B. handelii
*"B. menyangensis
B. hemsleyana
B. sp., Sulawesi 254
B. sp. nov.. Philippine
B. diadema
B. roxburghii
B. sp., Taiwan
— 5 changes
. formosana
B. ravenii
B. sp., Yunnan 33
B. annulata
— B. rex
J “ B. sp., Yunnan 25
B. hatacoa
J
B. sp., Platycentrum
1
r B. palmata 48
B. palmata 59
J" B. sp.. Yunnan 20
'
B. longicarpa
•B . sp., Yunnan 26
— B. versicolor
B. balansana
^ B. deliciosa
— B. sp., Yunnan 21
B. rubella
B. labordei
B. sp., 1998 1824
r B. chloroneura
B. tayabensis
B. oxysperma
B. sp.. Philippine
B. sp., Reichenheimia
B. goegoensis
B. rajah
B. beddomei
B. dipetala
B. floccifera
B. sp., nam
B. grandis grandis
' B. grandis holostyla
— B. aequata
^ B. brevirimosa
B. cf. brevirimosa
r B. serratipetala
I r s . sp., 121
M S. sp., 136
' B. cf. serratipetala
S. sanguinea
B. incisa
B. isoptera
AS
B. amphioxis
B. malachosticta
B. chlorosticta
B. kingiana
B. masoniana
B. masoniana maculata
B. morsei
B. porteri
B. fallax
' B. samhahensis
B. socotrana
e
E
O
soc^
220
_r B. sp., sych
'— B. guaduensis
B. fuchsioides
J q — B. holtonis
1 ^
B. jam esoniana
B. meridensis
B. cubensis
B. obliqua
B. minor
B. odorata
B. sp., Bolivia
B. fissistyla
B. incarnata
• B. sp., macE
B. convolvulacea
B. glabra
B. acerifolia
B. valida
B. ulmifolia
— B. sp., macG
^
B. angularis
B. lobata
r — B. rufosericae
- I — B. luxurians
*■ B. oxyphylla
B. echinosepala
B. listada
- B. egregia
' B. herbacea
— B. sp., Trachelocarpus
' B. wollnyi
r B . boliviensis
^ B. cinnabarina
B. maynensis
B. gracilis
B. olbia
_[— B. integerrima
B. solananthera
I
B. sp., U 172
B. heracleifolia
B. invoiucrata
B. imperialis
B. violifolia
B. manicata
B. theimei
B. peltata
— 5 changes
B. sericoneura
4]
AM
O
S.AF
B. edmondoi
B. lubbersii
B. sp., gutt
B. dregei
B. dregei homonyma
B. dregei 'partita'
sonderana
B. geranioides
B. sutheriandii
B. ankaranens
B. mananjabensis
B. francoisii
B. nossibea
B. salaziensis
B. bogneri
B. madecassa
r B . capillipes
B. gabonensis
— B. horticola
B. kisuluana
‘” B. subscutata
B. molleri
B. mannii
B. longipetiolata
B. poculifera
B. rhopalocarpa
B. meyeri-johannis
B. aspleniifolia
---------------B. dewildei
B. potamophila
B. quadrialata
B. scutifolia
B. prismatocarpa
B. duncan-thomasii
B. letouzeyi
B. scapigera
B. staudtii
B. thomeana
B. iucunda
B. annobonensis
B. engleri
B. johnstonii
' H. sandwichensis
— D. cannabina
D. glomerata
221
10.3.3.
The combined ITS/non-DNA analysis:
Of a total of 1224 characters, 632 are excluded (the ITS exclusion set from
previous chapters); 123 constant, 95 uninformative and 374 parsimony
informative characters are included.
The skewedness statistic g1 is -0.4778.
One thousand MPTs of length 3365 were found; searching with topological
constraints found a shortest length of 3367.
Consistency index is 0.27 (0.24 with uninformative characters excluded);
retention index is 0.65. There are 131 nodes in the strict consensus tree; 67
nodes have over 50% bootstrap support.
The strict consensus tree is presented as Figure 10.11, and one of the 1000
MPTs is presented as Figure 10.12.
222
Strict consensus of 1000 MPTs,
Figure 10.11:
combined non-DNA and ITS
sp., Sulawesi 252
sp., Sulawesi 253
crassirostris
acetosella
longifolia
handelii
menyangensis
sp., Sulawesi 254
sp. nov., Philippine
sp., Taiwan
formosana
ravenii
Bootstrap values
over 50% atrave
lines;
Bremer support
below lines
sp., Platycentrum
palmata 48
palmata 59
sp., Yunnan 25
hatacoa
sp., Yunnan 33
annulata
deliciosa
diadema
roxburghii
hemsleyana
rex
sp., Yunnan 20
balansana
longicarpa
sp., Yunnan 26
versicolor
sp., Yunnan 21
rubella
labordei
sp., 1998 1824
chloroneura
tayabensis
oxysperma
sp., Philippine
floccifera
sp., Reichenheimia
goegoensis
rajah
kingiana
aequata
of. serratipetala
sp. 121
sp. 136
sanguinea
of. brevirimosa
serratipetala
isoptera
AS
■O
1
chlorosticta
amphioxis
malachosticta
grandis grandis
grandis holostyla
beddomei
dipetala
sp., nam
fallax
masoniana
masoniana maculata
223
j
B. sp.. sych
B. guaduensis
B. fuchsioides
B. holtonis
B. jam esoniana
B. meridensis
B. cubensis
B. obliqua
B. minor
B. odorata
B. sp., Bolivia
B. fissistyla
B. sp., macE
B. acerifolia
B. valida
B. glabra
B. convolvulacea
B. ulmifolia
B. sp., macG
B. angularis
B. lobata
B. luxurians
B. oxyphylla
B. rufosericae
B. echinosepala
B. listada
B. egregia
B. herbacea
B. sp., Trachelocarpus
B. wollnyi
B. sp., U 172
B. heracleifolia
B. invoiucrata
B. imperialis
B. violifolia
B. boliviensis
B. cinnabarina
B. gracilis
B. maynensis
B. olbia
B. incarnata
B. integerrima
B. solananthera
B. manicata
B. theimei
B. peltata
B. sericoneura
B. edmondoi
B. lubbersii
B. sp., gutt
B. dregei
B. dregei homonyma
B. dregei 'partita'
B. sonderana
B. geranioides
B. sutheriandii
B. samhahensis
B. socotrana
B. ankaranens
B. francoisii
B. nossibea
B. mananjabensis
B. salaziensis
B. bogneri
B. m adecassa
B. capillipes
B. gabonensis
B. kisuluana
B. horticola
B. mannii
B. subscutata
B. molleri
B. longipetiolata
B. poculifera
B. rhopalocarpa
B. meyeri-johannis
B. aspleniifolia
B. dewildei
B. potamophila
B. quadrialata
B. scutifolia
B. prismatocarpa
B. duncan-thomasii
letouzeyi
scapigera
B. staudtii
B. thomeana
B. iucunda
B. annobonensis
B. engleri
B. johnstonii
H. sandwichensis
D. cannabina
D. glomerata
E
*
4
\
I
'
—
5
87 I
J
I
I
’
224
Phylogram, one of 1000 MPTs,
Figure 10.12:
combined non-DNA and ITS
B. sp., Sulawesi 252
B. sp., Sulawesi 253
B. crassirostris
| j B. acetosella
B. longifolia
[ ~ B. handelii
B. menyangensis
I
B. sp., Sulawesi 254
^ B. sp. nov., Philippine
I
B. sp., Taiwan
B. formosana
— B. ravenii
B. sp., Yunnan 25
B. hatacoa
B. sp., Yunnan 33
B. annulata
— B. rex
B. deliciosa
B. diadema
B. roxburghii
B. hemsleyana
J
B. sp., Platycentrum
1 r B. palmata 48
B. palmata 59
J — B. sp. nov, Yunnan 20
i j ' — B. balansana
—I
B. longicarpa
r B. sp., Yunnan 26
B. versicolor
— B. sp., Yunnan 21
B. rubella
' B. labordei
- B. sp, 1998 1824
f~ B. chloroneura
B. tayabensis
■B. oxysperma
B. sp., Philippine
B. floccifera
B. sp., Reichenheimia
B. goegoensis
B. rajah
B. kingiana
B. aequata
B. incisa
i— B. brevirimosa
I I B. cf. serratipetala
H _ r S sp., 136
i p - s. sp., 121
S. sanguinea
B. cf. brevirimosa
B. serratipetala
B. isoptera
B. chlorosticta
B. amphioxis
B. malachosticta
B. grandis grandis
B. grandis holostyla
B. beddomei
B. dipetala
B. sp., nam
B. fallax
B. masoniana
B. masoniana maculata
B. morsei
B. porteri
|—
10 changes
AS.
225
f B. sp., sych
'— B. guaduensis
B. fuchsioides
B. jam esoniana
B. holtonis
B. meridensis
,
I
B. cubensis
_ _ J
^ B. obliqua
I
[ ~ B. minor
B. odorata
I— B. sp., Bolivia
— B. fissistyla
incarnata
B. sp., macE
B. acerifolia
valida
I
B.. gla
glabra
Yr B
1
B. convolvulacea
'
B. ulmifolia
B. sp., macG
,— T ” B. angularis
J B. lobata
I
B. luxurians
L-P- B. oxyphylla
B. rufosericae
” B. echinosepala
' B. listada
------------- B. egregia
B. herbacea
— B. sp., Trachelocarpus
“ ■ B. wollnyi
boliviensis
cinnabarina
B. maynensis
B. gracilis
B. olbia
rW :
4:
- B . SP..U172
AM
B. heracleifolia
B. invoiucrata
B. imperialis
B. violifolia
B. manicata
" B. theimei
B. peltata
B. sericoneura
J — B. integerrima
'— B. solananthera
B. edmondoi
B. lubbersii
____
10 changes
B. sp., gutt
B. dregei
B. dregei homonyma
B. dregei 'partita'
sonderana
“ B. geranioides
B. sutheriandii
— B. samhahensis
' B. socotrana
B. ankaranens
B. francoisii
B. nossibea
B. mananjabensis
B. salaziensis
B. madecassa
B. bogneri
I
—
B. capillipes
B. mannii
B. subscutata
B. gabonensis
B. kisuluana
B. horticola
B. molleri
B. longipetiolata
B. poculifera
B. rhopalocarpa
B. meyeri-johannis
B. aspleniifolia
B. dewildei
B. potamophila
B. quadrialata
B. scutifolia
B. prismatocarpa
B. duncan-thomasii
B. letouzeyi
B. scapigera
B. staudtii
B. thomeana
B. iucunda
annobonensis
B. engleri
B. johnstonii
H. sandwichensis
D. cannabina
D. glomerata
lO
SAP
SOC
t e
“L|
AF
226
10.3.4 Tree comparisons:
See Table 10.3 for a summary of the statistics for the different analyses. From
this, it can be seen that the ITS data set performs better than the other two
(non-DNA and combined) in terms of consistency and retention indices and in
the bootstrap support for nodes, although more nodes are resolved in the strict
consensus tree of the combined data analysis. The combined analysis MPT
length is 164 steps longer than the total lengths of the non-DNA and ITS MPTs.
Table 10.3:
Data and tree statistics for the non-DNA, ITS and combined
analyses.
DATA SET
MORPH
ITS
COM BINED
INF.
C HARS
gi
No. MPTs
LENGTH
63
-0.180
1000
499
311
-0.453
1000
2702
0.30
0.27
0.68
108
71
374
-0.478
1000
3365
0.27
0.24
0.65
131
67
Cl
0.21
Cl ex
UNINF.
Rl
0.20
0.65
No.
NO DES
50% a s
33
5
NO D ES >
The majority rule tree for the non-DNA data was compared with the strict
consensus tree for the ITS data. The partition metric is 233 (maximum value is
312, i.e. 74.7% of the maximum); agree D^ is 130. The agreement subtree tree
for the majority-rule non-DNA tree and the strict consensus tree for ITS is as
follows (size 29/159, i.e. with 130 taxa pruned) (Figure 10.13):
227
Figure 10.13:
Agreement subtree tree,
non-DNA and ITS analyses
B. sp., Reichenheimia
B. goegoensis; Reichenheimia
B. grandis grandis; Diploclinium
B. grandis holostyla; Diploclinium
B. cf. brevirimosa; Petermannia
s. sp., 121; Symbegonia
s. sp., 136; Symbegonia
B. isoptera; Petermannia
B. amphioxis; Ignota
B. meridensis; Ruizopavonia
B. cubensis; Begonia
B. minor; Begonia
B. luxurians; Scheidweileria
B. oxyphylla; Pritzelia
B. echinosepala; Pritzelia
B. listada; Pritzelia
B. olbia; Knesbeckia
B. dregei; Augustia
B. dregei homonyma; Augustia
B. dregei 'partita'; Augustia
S. AF
B. sonderana; Rostrobegonia
B. geranioides; Augustia
B. dewildei; Scutobegonia
B. quadrialata; Loasibegonia
B. scutifolia; Loasibegonia
B. prismatocarpa; Loasibegonia
B. duncan-thomasii; Loasibegonia
AF
B. thomeana; Cristasemen
B. iucunda; Ignota
It is obvious, on the basis of this tree (Figure 10.13), that while there are areas
of agreement between the non-DNA and ITS data sets, there is also a lot of
conflict (with 130 taxa in different places). Indeed, tracing morphological
characters, across non-DNA, combined and ITS trees, shows one of the major
problems with the non-DNA characters chosen in this study. Many of the
characters which offer good support for some clades are homoplastic in
others. Furthermore, many of the characters which are characteristic of clades
228
suffer reversals and state changes within those clades. The ‘best’ characters
in terms of fit are those, like character 65, beaked fruit (see Table 10.4), which
only occur in a few closely related species; unfortunately these are not
informative about the deeper level relationships across Begonia.
10.3.5 Character performance: For a breakdown of how different non-DNA
characters performed when analysed in combination with the ITS data set, see
Table 10.4.
Table 10.4:
Statistics for individual morphological characters, over a tree
produced by analysis of the combined ITS - non-DNA data set.
Min
Character
1 (Tubers - stem)
2 (Tubers - root)
3 (Bulbils)
4 (Tubercils)
5 (Caudex)
6 (Leaf shape)
7 (Peltateness)
8 (Leaf colour)
9 (Petiole TS)
10 (Trichôme ring)
11 (Stipule persistence)
12 (Stipule pair)
13 (Stipule keel)
14 (Stipule spur)
15 (Stipule edge)
16 (Stipule back)
17 (Fuzzy hair)
18 (Stellate hair)
19 (Lifestyle)
20 (Inflor. position)
21 (lnflor./axil)
22 (Sexual separation)
23 (Inflor. type)
24 (Cyme type)
25 (Inflor. symm.)
26 (Inflor. basal dichotomy)
27 (Flowers/inflor.)
28 (Sexual separation)
29 (Flower size)
30 (Flower colour)
31 (Flower pattern)
32 (Scent)
33 (Perianth tube)
34 (Male tepal no.)
35 (Male flower symm.)
36 (Male tepal fusion)
37 (Male tepal hair)
38 (Male tepal edge)
40 (Androecium)
41 (Stamen no.)
42 (Stamen colour)
44 (Stamen fusion)
45 (Anther connective ext.)
46 (Anther connective hood)
47 (Female tepal no.)
48 (Female tepal fusion)
49 (Female tepal hair)
50 (Female tepal edge)
51 (Style no.)
52 (Style colour)
53 (Style fusion)
Range
5tçp5
1
1
1
1
1
1
1
1
2
2
1
1
2
1
1
1
1
1
1
1
1
1
1
1
1
1
1
2
1
3
2
1
1
3
1
1
1
1
3
1
2
3
1
1
6
2
1
1
4
4
1
1
1
1
1
1
1
1
1
2
2
1
1
2
1
1
1
1
1
1
1
1
1
1
1
1
1
1
2
1
3
2
1
1
3
1
1
1
1
3
1
2
3
1
1
6
2
1
1
4
4
1
Tree
$teps
4
4
1
1
1
4
10
16
27
10
19
6
9
20
11
31
7
2
1
5
2
3
5
1
7
7
5
10
5
8
13
7
1
16
.
13
1
24
2
10
9
2
36
18
18
28
4
18
5
11
6
25
Max
5tÇP9
5
5
2
2
3
5
18
25
52
13
25
8
11
29
20
61
9
11
1
6
2
5
16
9
10
13
8
21
8
15
19
11
1
45
23
3
41
2
22
9
4
70
46
23
60
7
32
5
29
8
42
229
Cl
0250
0250
1.000
1.000
1.000
0250
0.100
0.062
0.074
0200
0.053
0.167
0222
0.050
0.091
0.032
0.143
0.500
1.000
0200
0.500
0.333
0200
1.000
0.143
0.143
0200
0200
0200
0.375
0.154
0.143
1.000
0.188
0.077
1.000
0.042
0.500
0.300
0.111
1.000
0.083
0.056
0.056
0.214
0.500
0.056
0200
0.364
0.667
0.040
Rl
0250
0250
1.000
1.000
1.000
0250
0.471
0.375
0.500
0273
0250
0286
0222
0.321
0.474
0.500
0250
0.900
0/0
0200
0.000
0.500
0.733
1.000
0.333
0.500
0.429
0.579
0.429
0.583
0.353
0.400
(VO
0.690
0.455
1.000
0.425
0.000
0.632
0.000
1.000
0.507
0.622
0227
0.593
0.600
0.452
0.000
0.720
0.500
0.415
RQ
0.062
0.062
1.000
1.000
1.000
0.062
0.047
0.023
0.037
0.055
0.013
0.048
0.049
0.016
0.043
0.016
0.036
0.450
(VO
0.040
0.000
0.167
0.147
1.000
0.048
0.071
0.086
0.116
0.086
0219
0.054
0.057
(VO
0.129
0.035
1.000
0.018
0.000
0.189
0.000
1.000
0.042
0.035
0.013
0.127
0.300
0.025
0.000
0262
0.333
0.017
HI
0.750
0.750
0.000
0.000
0.000
0.750
0.900
0.938
0.926
0.800
0.947
0.833
0.778
0.950
0.909
0.968
0.857
0.500
0.000
0.800
0.500
0.667
0.800
0.000
0.857
0.857
0.800
0.800
0.800
0.625
0.846
0.857
0.000
0.812
0.923
0.000
0.958
0.500
0.700
0.889
0.000
0.917
0.944
0.944
0.786
0.500
0.944
0.800
0.636
0.333
0.960
(H U
0.500
0.500
1.000
1.000
1.000
0.500
0.250
0.167
0.107
0273
0.143
0.375
0.300
0.136
0231
0.091
0.333
0.750
1.000
0.429
0.750
0.600
0.429
1.000
0.333
0.333
0.429
0273
0.429
0.375
0214
0.333
1.000
0.188
0200
1.000
0.115
0.750
0.300
0273
1.000
0.083
0.150
0.150
0.120
0.600
0.150
0.429
0.300
0.600
0.111
54 (Style branching)
55 (Style persistence)
56 (Ovary position)
57 (Locule no.)
58 (Placentation type)
59 (Placentation no.)
60 (Fruit wing no.)
61 (Fruit wing symm.)
62 (Fruit dry/fleshy)
63 (Fruit orientation)
64 (Fruit hair)
65 (Fruit beaking)
66 (Dehiscence)
67 (Bracteole)
3
1
1
4
2
2
4
1
1
2
1
1
1
2
3
1
1
4
2
2
4
1
1
2
1
1
1
2
16
6
1
14
8
16
9
17
6
6
24
1
1
13
25
10
1
36
14
37
25
43
19
16
44
2
3
21
0.188
0.167
1.000
0286
0250
0.125
0.444
0.059
0.167
0.333
0.042
1.000
1.000
0.154
0.435
0.444
Q/D
0.688
0.500
0.600
0.773
0.619
0.722
0.714
0.465
1.000
1.000
0.421
0.082
0.074
010
0.196
0.125
0.075
0.343
0.036
0.120
0238
0.019
1.000
1.000
0.065
0.812
0.833
0.000
0.714
0.750
0.875
0.556
0.941
0.833
0.667
0.958
0.000
0.000
0.846
0.188
0.375
1.000
0231
0.333
0.176
0.375
0.158
0.375
0.429
0.115
1.000
1.000
0214
10.3.6 Character evolution, some case studies: A few selected characters
have been reconstructed across one of the MPTs from the combined ITS - nonDNA data matrix. (Reconstructions from MacClade, ACCTRAN optimisation).
A. Leaf characters: Figure 10.14 shows characters 6 (leaf: compound or
simple), 7 (leaf peltateness) and 10 (trichome ring at top of petiole).
Out of a maximum of five possible steps, character 6 (leaf compound/simple)
takes four steps on this tree (one between the outgroup and ingroup) (ci 0.25; ri
0.25). It seems that compound leaves have arisen several times
independently within Begoniaceae.
Leaf peltateness is a ‘better’ character, at least in terms of retention; out of 18
possible steps it takes 10 (ci 0.10; ri 0.47). Peltateness is a good character for
the Loasibegonia!Scutobegonia clade (8. staudtii to B. potamophila), with only
one reversal (B. prismatocarpa) and for the Peltaugustia clade (B. socotrana
and B. samhahensis). It may also be useful in section Reichenheimia (B. sp.,
Reichenheimia to B. goegoensis): on this tree it resolves as belonging to the
ancestor for the section, with a reversal in B. rajah.
The presence or absence of a trichome ring is very homoplastic - out of 13
possible steps it takes 10 (ci 0.20; ri 0.27), although it does group B.
annobonensis, B. engleri and B. Johnstonii.
230
Leaf characters, ACCTRAN optimisation
Figure 10.14:
C H . 6:
S simple leaf
X compound leaf
CH. 7; □
■
CH. 1 0 : 0
Basifixed
Peltate
without ring at top of petiole
o
with ring of hairs
•
with raised ridge
r—
I
.formosana
.ravenii
.sp., Taiwan
.sp., Yunnan 25
.hatacoa
.sp., Yunnan 33
.annulata
.rex
.deliciosa
.diadem a
.roxburghii
.hem sleyana
.palm ata48
.palm ata59
sp., Piatycentrum
.sp., Sulawesi 252
sp., Sulawesi 253
.crassirostris
.acetosella
.longifolia
.handelii
B .m enyangensis
B.sp., Sulawesi 254
B.sp. nov., Philippine
B.sp., Yunnan 20
B .balansana
B.longicarpa
B.sp., Yunnan 26
B.versicolor
B.sp., Yunnan 21
B.rubella
B.labordei
B.chloroneura
B .tayabensis
B.sp., 19981824
B.oxysperm a
B.sp., Philippine
B.flocclfera
i; g ,e g o e n s is
PLATYC.
DIPLOCL.
?
PLATYC.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
SPHENAN.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
?
?
SPHENAN.
SPHENAN.
SPHENAN.
SPHENAN.
SPHENAN.
?
SPHENAN.
PLATYC.
IGNOTA
PLATYC.
PLATYC.
PLATYC.
PLATYC.
DIPLOCL.
DIPLOCL.
DIPLOCL.
DIPLOCL.
DIPLOCL.
B ARYAN D.
DIPLOCL.
R EIC HEN .
R E IC HEN .
R E IC HEN .
R E IC HEN .
R IDLEY.
S Y M B EG .
S Y M B EG .
S Y M B EG .
PE TE R M .
PE TE R M .
PE TE R M .
PE TE R M .
B.sp., Reichenheim ia
kingiana
sp., 121
sp., 136
■sanguinea
cf. serratipetala
brevirimosa
cf. brevirimosa
serratipetala
aequata
incisa
P E TER M .
isoptera
P E TER M .
chlorosticta
IGNOTA
am phioxis
P E TER M .
m alachosticta
DIPLOCL.
grandis grandis
grandis holostyla
DIPLOCL.
PLATYC.
beddom ei
HAAGIA
dipetala
?
sp., nam
IGNOTA
fallax
.m asoniana
COELOC.
m asoniana maculata COELOC.
COELOC.
COELOC.
231
angularis
lobata
luxurians
oxyphylla
rufosericae
sp., macG
echinosepala
listada
egregia
acerifolia
valida
sp., M acE
glabra
convolvulacea
ulmifolia
herbacea
sp., Trachelocarpus
wollnyi
boliviensis
cinnabarina
m aynensis
gracilis
.olbia
.fuchsioides
. jam esoniana
.holtonis
.m eridensis
.sp., sych
.guaduensis
.cubensis
.obliqua
minor
odorata
sp., Bolivia
.fissistyla
■incarnata
. sp., ABS U 172
.heracleifolia
.involucre ta
.im perialis
.violifolia
.m anicata
.theim ei
.peltata
.sericoneura
.integerrima
solananthera
.edmondoi
lubbersii
sp., 'guttata'
dregei
dregei homonyma
•dregei 'partita'
. sonderana
.geranioides
suthertandii
.sam hahensis
.socotrana
.m annii
.subscutata
c apillipes
.gabonensis
.Risuluana
.horticola
.molleri
.poculifera
.loranthoides rhop.
.longipetiolata
.francoisii
.nossibea
.m ananjabensis
.ankaranens
.s a la zie n s is
.m adecassa
.bogneri
.m eyeri-johannis
potamophila
.quadrialata
.scutifolia
.prismatocarpa
■dewildei
.duncan-thomasii
.letouzeyi
. scapigera
.staudtii
.aspleniifolia
thom eana
iucunda
.engleri
.johnstonii
.annobonensis
.sandw ichensis
.cannabina
.glomerata
232
S C H E ID W .
P R ITZELIA
P R ITZELIA
PR ITZELIA
P R ITZELIA
P R ITZELIA
TETRACH.
?
W A G EN ER .
W A G EN ER .
D ONALDIA
TRACHEL.
TRACHEL.
K N ES B E C K .
BARYA
E U PETA L.
K N E SB EC K .
QU A DR IPER .
K N ES B E C K .
L E P S IA
L E P S IA
RUIZOPAV.
RUIZOPAV.
?
RUIZOPAV.
BEGONIA
BEGONIA
BEGONIA
^E G O NIA
H YDRIST.
K N E SB EC K .
G IREO UDIA
G IREO UD IA
G IREO UDIA
G IREO UD IA
GIREO UDIA
G IREO UD IA
G IREO UDIA
SOLANANT.
SOLANANT.
G AERTIA
G AERTIA
?
AUG USTIA
A UG USTIA
AUG USTIA
ROSTROB.
A UG USTIA
A UG USTIA
PELTAUG.
PELTAUG.
TETRAPHIL.
TETRA PH IL.
TETRAPHIL.
îilK fflll::
TETRA PH IL.
TETRAPHIL.
SQUAMIB.
TETRAPHIL.
TETRA PH IL.
QUADRILO.
QUADRILO.
QUADRILO.
QUADRILO.
M E ZIER IA
N ERV IPLA C .
ER M IN EA
M E ZIE R IA
LOASIBEG.
LOASIBEG.
LOASIBEG.
LOASIBEG.
SCUTOBEG.
LOASIBEG.
LOASIBEG.
LOASIBEG.
LOASIBEG.
FILICIBEG.
C R IS TA S E M .
IGNOTA
ROSTROB.
ROSTROB.
S E X A LA R IA
HILLEBR.
D ATISCA
DATISC A
B.
Tepal characters: Figure 10.15 shows characters 34 (male tepal
number) and 47 (female tepal number).
Male tepal number takes 16 steps out of a possible 45 (ci 0.19; ri 0.69).
Although there is homoplasy in this character, it tends to be reliable in grouping
clades, e.g. the 'Petermannia' clade (8. malachosticta - Symbegonia) has two
tepals (i.e. lacks petals). Female tepal number takes 28 out of a total of 60
possible steps (ci 0.21; ri 0.59). Again, tepal number tends to be reliable
between groups.
Figure 10.15:
Male and female tepal number, ACCTRAN optimisation
.formosana
.ravenii
.sp., Taiwan
sp., Yunnan 25
.hatacoa
sp., Yunnan 33
.annulata
rex
.deliciosa
.diadem a
.roxburghii
.hem sleyana
.palm ata48
.palm ata59
sp., Piatycentrum
sp., Sulawesi 2 52
sp., Sulawesi 253
crassirostris
.acetosella
longifolia
.handelii
m enyangensis
O tepals absent
MALE
® 10 tepals
4 tepals
2 tepals
D
tepals absent
3 10 tepals
2 tepals
FEMALE g 3 tepals
3 4 tepals
3 5 tepals
E 6 tepals
PLATYC.
DIPLOCL.
?
PLATYC.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
SPH ENA N .
PLATYC.
PLATYC.
PLATYC.
PLATYC.
?
?
SPH ENA N .
S PH ENA N .
S PH ENA N .
S PH ENA N .
S PH ENA N .
S P H ENA N
sp., Yunnan 20
PLATYC.
IGNOTA
balansana
longicarpa
PLATYC.
PLATYC.
sp., Yunnan 26
PLATYC.
versicolor
sp., Yunnan 21
PLATYC.
DIPLOCL.
rubella
DIPLOCL.
labordei
DIPLOCL.
chloroneura
DIPLOCL.
tayabensis
DIPLOCL.
sp., 19981824
oxysperm a
B AR YA ND .
sp., Philippine
DIPLOCL.
R EIC HEN .
floccifera
R EIC HEN .
goegoensis
rajah
R EIC HEN .
sp., Reichenheim ia R EIC H E N .
RID LEY.
kingiana
S YM B E G .
sp., 121
S YM B E G .
sp., 136
sanguinea
S YM B E G .
P E TER M .
cf. serratipetala
brevirimosa
P E TE R M .
cf. brevirimosa
serratipetala
aequata
P E TE R M .
P E TER M .
incisa
P E TE R M .
isoptera
P ETE R M .
chlorosticta
IGNOTA
amphioxis
P E TE R M .
m alachosticta
DIPLOCL.
grandis grandis
grandis holostyla
DIPLOCL.
PLATYC.
beddomei
HAAGIA
dipetala
?
sp., nam
IGNOTA
fallax
COELOC.
m asoniana
m asoniana m aculataCOELOC.
233
B .angularis
B.lobata
luxurians
oxyphylla
rufosericae
sp., macG
echinosepala
listada
egregia
acerifolia
v alida
sp., M acE
glabra
convolvulacea
ulmifolia
herbacea
sp., Trachelocarpus
wollnyi
boliviensis
cinnabarina
m aynensis
gracilis
olbia
fuchsioides
jam esoniana
holtonis
m eridensis
sp., sych
.guaduensis
.cubensis
.obliqua
minor
.odorata
sp., Bolivia
.fissistyla
.incarnata
. sp., ABS U172
.heracleifolia
.involucrata
.imperialis
.violifolia
.m anicata
.theimei
.peltata
.sericoneura
.integerrima
.solananthera
.edmondoi
.lubbersii
sp., 'guttata'
.dregei
.dregei homonyma
.dregei 'partita'
. sonderana
.geranioides
.sutherlandii
.sam hahensis
.socotrana
.m annii
.subscutata
.capillipes
.gabonensis
.Kisuluana
.horticola
.molleri
.poculifera
.loranthoides rhop.
.longipetiolata
.francoisii
.nossibea
.m ananjabensis
.ankaranens
.s a laziensis
.m adecassa
.bogneri
.m eyeri-johannis
.potamophila
.quadrialata
.scutifolia
.prismatocarpa
.dewildei
.duncan-thomasii
.letouzeyi
. scapigera
.staudtii
.aspleniifolia
.thom eana
.iucunda
.engleri
.johnstonii
.annobonensis
.sandwichensis
.cannabina
.glomerata
234
SC HE IDW .
PR ITZELIA
PR ITZELIA
P R ITZELIA
PR ITZELIA
PR ITZELIA
TETRACH.
mmm?
WAGENER.
WAGENER.
DONALDIA
TRACHEL.
TRACHEL.
KNESBECK.
BARYA
EU PE TA L.
K N ES B E C K .
Q U A DR IPER .
KNESBECK.
LE P S IA
L E P S IA
R UIZOPAV.
R UIZO PA V.
?
R UIZOPAV.
BEGONIA
B EGONIA
BEGONIA
^ E G O N IA
H YD R IS T.
KNESBECK.
G IREO UD IA
G IREO UD IA
GIREO UD IA
:|.
G IREO UD IA
G IREO UD IA
G IREO UD IA
GIREO UD IA
SOLANANT.
SOLANANT.
G AERTIA
GA ER TIA
?
A U G U S TIA
A UG USTIA
A U G U S TIA
ROSTROB.
A UG USTIA
A UG USTIA
PELTAUG.
PELTAUG.
TE TR A P H IL
TE T R A P H IL
TE TR A P H IL
TE TR A P H IL
TE TR A P H IL
TE TR A P H IL
TETRA PH IL
SQUAM IB.
T E T R A P H IL
TE TRA PH IL.
QUADRILO.
QUADRILO.
QUADRILO.
QUADRILO.
M E Z IE R IA
N ER V IP LA C .
E R M IN EA
M E ZIE R IA
LOASIBEG.
LOASIBEG.
LOASIBEG.
LOASIBEG.
SCUTOBEG.
LOASIBEG.
LOASIBEG.
LOASIBEG.
LOASIBEG.
FILICIBEG.
C R IS TA S E M .
IGNOTA
ROSTROB.
ROSTROB.
S E X A LA R IA
HILLEBR.
D ATISC A
D ATISC A
C.
Ovary characters: Figure 10.16 shows characters 51 (style number),
57 (locule number) and 59 (placentation number).
Figure 10.16:
Ovary characters, ACCTRAN optimisation
CH. 51
Q
n
CH. 57
styles 2
locules 1
styles 3
locules 2
locu es 3
styles 4
locules 4
La styles 5
locules 5
locules 6
styles 6
CH. 59
<0
Placenta single
Placenta bind, ovules
both sides
%
Placenta bifid, ovules
one side
235
B.formosana
.ravenii
.sp., Taiwan
sp., Yunnan 25
.hatacoa
sp., Yunnan 33
.annulata
.rex
.deliciosa
diadem a
roxburghii
hem sleyana
.palmata48
palm ata59
sp., Piatycentrum
sp., Sulawesi 252
sp., Sulawesi 253
crassirostris
acetosella
longifolia
handelii
m enyangensis
sp., Sulawesi 254
sp. nov., Philippine
sp., Yunnan 20
balansana
longicarpa
sp., Yunnan 26
versicolor
,sp., Yunnan 21
rubella
labordei
chloroneura
tayabensis
sp., 19981824
oxysperma
sp., Philippine
floccifera
goegoensis
rajah
sp., Reichenheimia
kingiana
sp., 121
sp., 136
sanguinea
cf. serratipetala
brevirimosa
,cf. brevirimosa
serratipetala
aequata
.incisa
isoptera
chlorosticta
amphioxis
m alachosticta
grandis grandis
grandis holostyla
beddomei
dipetala
sp., nam
fallax
m asoniana
masoniana maculata
PLATYC.
DIPLOCL.
?
PLATYC.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
SPH ENA N .
PLATYC.
PLATYC.
PLATYC.
PLATYC.
?
?
SPH ENA N .
SPH ENA N .
SPH ENA N .
SPH ENA N .
SPHENAN.
?
SPH ENA N .
PLATYC.
IGNOTA
PLATYC.
PLATYC.
PLATYC.
PLATYC.
DIPLOCL.
DIPLOCL.
DIPLOCL.
DIPLOCL.
DIPLOCL.
BARYAND.
DIPLOCL.
R EIC HE N .
R EIC HE N .
R E IC H E N .
REIC HEN .
R ID LEY.
S Y M B EG .
S Y M B EG .
S Y M B EG .
P E TER M .
P E TER M .
P E TER M .
P E TER M .
PE TE R M .
P E TER M .
IGNOTA
PE TE R M .
DIPLOCL.
DIPLOCL.
PLATYC.
HAAGIA
?
IGNOTA
COELOC.
COELOC.
COELOC.
COELOC.
B.angularis
B.lobata
SC H E ID W .
B.luxurians
PR ITZELIA
B.oxyphylla
P
R ITZE LIA
B.rufosericae
PR ITZELIA
B.sp., macG
PR ITZELIA
B .echinosepala
PR ITZE LIA
B .listada
B.egregia
TETRACH.
B.acerifolia
B .valida
?
B.sp., M acE
B .glabra
WAGENER.
W A G EN ER .
B .convolvulacea
DONALDIA
♦ •B .u lm ifo lia
B .herbacea
TRACHEL.
B.sp., TrachelocarpusTRACHEL.
B .wolinyi
K N E SB EC K
BARYA
B.boliviensis
B.cinnabarina
EU P E TA L.
B .m aynensis
KNESBECK.
j — B .gracilis
Q UADRIPER.
^ — B .olbia
K N ES B E C K .
B.fuchsioides
LE P S IA
B. jam esoniana
L E P S IA
B.holtonis
RUIZOPAV.
B.m eridensis
RUIZOPAV.
B.sp., sych
?
B.guaduensis
RUIZOPAV.
B .cubensis
BEGONIA
B.obliqua
BEGONIA
B .minor
BEGONIA
B.odorata
^E G O N IA
I— B.sp., Bolivia
H YDR IST.
I
B .fissistyla
KNESBECK.
B.incarnata
GIREO UDIA
B. sp., ABS U 172
B .heracleifolia
GIREO UD IA
GIREO UDIA
B.involucrata
B .im perialis
E.I
IILBÂCH'.
B.violifolia
GIREO UDIA
B .m anicata
GIREO UD IA
B .theim ei
GIREO UDIA
B.peltata
B.sericoneura
GIREO UD IA
I— B.integerrima
SOLANANT.
SOLANANT.
'— B.solananthera
B.edm ondoi
G AERTIA
B.lubbersii
GAERTIA
?
B.sp., 'guttata'
AUG USTIA
B.dregei
B.dregei homonyma A UG USTIA
A UG USTIA
B.dregei 'partita'
B. sonderana
ROSTROB.
j — B.geranioides
A UG USTIA
A UG USTIA
‘— B.sutherlandii
r —B .sam hahensis
PELTAUG.
' — B.socotrana
PELTAUG.
I— B .m annii
TETRAPHIL.
1— B.subscutata
TETRAPHIL.
G1— B .cap illipes
TETRA PH IL.
TETRAPHIL.
TETRAPHIL.
B.horticola
TETRAPHIL.
B.m olleri
TETRAPHIL.
B.poculifera
SQUAM IB.
B.loranthoides rhop. TETRAPHIL.
B.longipetiolata
TETRA PH IL.
B.francoisii
QUADRILO.
QUADRILO.
B.nossibea
B.m ananjabensis
QUADRILO.
B.ankaranens
QUADRILO.
B .s ala zie n s is
M E ZIER IA
B .m ad ecassa
N E R V IPLA C .
B.bogneri
ER M IN EA
— B .m eyeri-johannis
M E ZIE R IA
LOASIBEG.
B.potam ophila
LOASIBEG.
B.quadrialata
B .scutifolia
LOASIBEG.
B.prism atocarpa
LOASIBEG.
SCUTOBEG.
B.dew ildei
LOASIBEG.
B.duncan-thom asii
LOASIBEG.
B .letouzeyi
B. scapigera
LOASIBEG.
LOASIBEG.
B.staudtii
B .aspleniifolia
FILICIBEG.
C R IS TA S E M .
B.thom eana
-------------B .iucunda
IGNOTA
I—
B.engleri
ROSTROB.
ROSTROB.
_ r " i — B.johnstonii
*
B .annobonensis
S E X A LA R IA
-© [s H — H. sandwichensis
HILLEBR.
I— D .cannabina
D ATISCA
*— D.glom erata
D ATISCA
m m uk
r®-
-Q-
-O ® -
236
style number takes 11 out of a possible 29 steps (cl 0.36; ri 0.72) and locule
number takes 14 out of 36 possible steps (ci 0.29; ri 0.69). These two
characters are quite strongly correlated; most taxa have the same numbers of
locules as styles. However, there are some discrepancies, e.g. species from
section Coelocentrum (8. morsei, B. porteri and 8. masoniana) have one locule
and three styles; those from section Weilbachia (8. imperialis, 8. violifolia)
have two locules and three styles.
The number of placentae takes 16 out of 37 possible steps (ci 0.13; ri 0.60).
The change from two placental branches to one appears to have occurred
independently in several lineages including FilicibegonialLoasibegonial
Scutobegonia (8. aspleniifolia - 8. potamophila), Peltaugustia (8. socotrana
and 8. samhahensis), Augustia (8. sutherlandii - 8. dregei) and Reichenheimia
(8. sp., Reichenheimia - 8. goegoensis).
10.4 Micromorphology - congruence with other data sets
10.4.1 Introduction
One way to test novel phylogenetic hypotheses is to compare them to other
information, which has not been used in their generation. A commonly used
example is the mapping of chromosome counts across a cladogram to see
whether particular numbers support any of the clades (see Chapter 11).
Botanical literature offers a wealth of morphological and micromorphological
characters; although these are not always initially discussed in a phylogenetic
context, once we have a phylogeny it is possible to map these characters
across it, to see whether they are useful in delimiting groupings or not (and
whether some of the clades reconstructed by the cladogram need
reconsidered in the light of the new information).
There are several papers concerned with micromorphological characters of
Begonia, including detailed trichome structure (Bona & Alquini, 1995; Shui, Li &
Huang, 1999), stem anatomy (Garlquist, 1985; Lee, 1974), anther endothecial
cells (Tebbitt & Maclver, 1999), stigmatic papillae (Panda & de Wilde, 1995),
seed (Bouman & de Lange, 1982, 1983; Keraudren-Aymonin, 1983; de Lange,
1988; de Lange & Bouman, 1986, 1992, 1999; Seitner, 1972) and pollen (van
237
den Berg, 1983, 1985). The characters concerned have not been coded and
included in the non-DNA analysis, largely due to time factors, but also because
the authors of these studies have been working with different taxa; this would
violate the ‘all data from the same individual’ rule followed in this study.
In the light of the ITS cladograms produced here, however, previous
conclusions about some of these micromorphological characters can be
reexamined.
10.4.2
The Data Sets
10.4.2.1
Anther endothecial cells: The endothecium is a subepidermal
layer of the anther, and usually possesses lignified or cellulose thickenings
(Tebbitt & Maclver, 1999). Tebbitt and Maclver (1999) found six classes of
endothecial patterns within the 173 species of Begoniaceae they looked at;
those relevant to this study are U-shaped, perforate base plate, tympanate
base plate, and endothecial thickening absent. They could find no correlation
between the endothecial pattern and anther morphology or dehiscence (Tebbitt
& Maclver, 1999).
10.4.2.2
Stigmatic papillae: Panda and de Wilde (1995) looked in detail at
the stigmatic papillae of 65 species of Begonia, and at whether the styles are
dry or wet. They found that all species of Begoniaceae (from the genera
Begonia and Symbegonia; Hillebrandia was not available) have unicellular
stigmatic papillae, and suggest that this reinforces the monophyly of the group.
10.4.2.3
Seed: The seed in Begoniaceae is characterised by the presence
of specialised testa cells known as collar cells. These are longitudinally
stretched cells which form a transverse ring around one end of the seed, and
have not been found in any other angiosperm family. On germination, the walls
between the seed lid and the collar cells split along the middle lamellae, and
the walls between the collar cells split (Bouman & de Lange, 1983).
Hillebrandia seed have a rather irregular border between the collar cells and
the seed lid. Datisca seeds are broadly similar to those of Begoniaceae, and
also germinate by a seed lid which tears off along the middle of the lamellae,
but they have no collar cells (Bouman & de Lange, 1983). Begonia seeds are
almost always ellipsoid, and normally straight, although curved seeds are
found in the American sections Solananthera and Begonia (Bouman & de
238
Lange, 1983). They usually measure between 300 |im and 600 pim long (de
Lange & Bouman, 1999).
Most of the species in the genus Begonia are anemochorous. De Lange and
Bouman (1999) suggest three adaptations to wind dispersal:
1.
increased surface area to volume ratio
2.
decreased mass, e.g. with air filled testa cells
3.
promoted laminar airflow (microturbulance) due to surface roughness.
Species with special adaptations to wind dispersal are mostly climbers and/or
epiphytes, e.g. sections Wageneria and Solananthera. Rain is also utilised as
a disperser. The African sections Filicibegonia, Loasibegonia and
Scutobegonia have indéhiscent fruits which rot, and the seeds are thought to
be carried in rain-wash. The Asian section Piatycentrum has fruits which are
adapted to rain ballistics; the two shorter wings of the recurved fruits form a cup
to catch raindrops. Within the fleshy-fruited African sections Baccabegonia,
Mezieria, Squamibegonia and Tetraphila, the seed are relatively large, and
may possess arils (de Lange, 1988). These differences in fruit and seed
structure appear to relate directly to habitat and dispersal.
African Begonia show the “greatest diversity in type of seed dispersal,
especially in view of the relatively small number of species” (approximately 140
out of the global total of c. 1400 species) (de Lange & Bouman, 1992). They
include the largest and smallest Begonia seeds (8. ebolowensis Engler, mean
length 2240 |xm; 8. iucunda, mean length 220 ^im) (de Lange & Bouman,
1999).
10.4.2.4
Pollen: Van den Berg (1983) conducted a study on the pollen
types of the three genera of the Begoniaceae. He recognised three types,
'Hillebrandia-type' (resembling some Begonia-type pollen), 'Symbegonia-type'
(in an “isolated position compared to the other types within the family”, p. 59,
although in an “extremely derived position”, p. 64) and 'Begonia-type' (based on
8. oxyloba, 8. johnstonii, 8. quadrialata and 8. ampla, although he felt that
there may be more types within the genus). Van den Berg went on to look at
the pollen of African Begonia (1985). He split the genus into several pollen
types.
239
10.4.2
Results
10.4.3.1
Anther endothecial cells: From the list below (from Tebbitt &
Maclver, 1999), of endothecial thickening-type for the species included in the
ITS analysis, it can be seen that most species have U-shaped thickenings; the
exceptions are the American section Solananthera, the Asian section
Petermannia (which clearly should include B. amphioxis) and the related
genus, Symbegonia, and the isolated Socotran section Peltaugustia. The
other two species which have perforate-tympanate base plates (marked with *)
also have U-shaped plates.
Absent:
Sym begonia: S. sanguinea, S. sp.
Perforate-tympanate:
Peltaugustia: B. socotrana-,
B. loranthoides ssp. rhopalocarpa*, B. prism atocarpa*
Perforate:
Peterm annia: B. brevirimosa, B. chlorosticta,8. incisa,
8. isoptera,
8. malachosticta, 8. serratipetala-, Ignota: 8. amphioxis-,
Solananthera: 8. intergerrima, 8. solananthera
U-shaped
H. sandwichensis-, Africa: 8. prism atocarpa*, 8.
staudtii, 8. m eyeri-
johannis, 8. salaziensis, 8. dregei, 8. geranioides, B. sutherlandii,
8. Johnstonii, 8. sonderana, 8. annobonensis, B. mannii, 8. molleri,
8. squamulosa, B. loranthoides ssp rhopalocarpa*-,
America: 8. obliqua, 8. ulmifolia, 8. involucrata, 8. manicata, B. theimei,
8. fissistyla, 8. foliosa, 8. angularis, 8. lobata, 8. rufosericae, 8. gracilis,
B. holtonis, 8. luxurians, 8. egregia, 8. herbacea, 8. convolvulacea,
8. glabra-,
Asia: 8. m asoniana, 8. grandis, 8. tayabensis, 8. dipetala, 8. annulata,
8. deliciosa, B. diadem a, B. hatacoa, 8. hem sleyana, 8. versicolor,
B. floccifera, 8. goegoensis, 8. kingiana, 8, acetosella, 8. handelii,
8.
10.4.3.2
longifolia, 8. roxburghii.
Stigmatic papillae: Within the genus Begonia there appears to be
no phylogenetic pattern to the distribution of the five categories of stigmatic
papillae type Panda and de Wilde (1995) recognised; they do not match
traditional taxonomy, geographic distribution, or the 268, ITS and trnC - trnD
phylogenies presented here, with the exceptions of types IV (clavate, only in
section Weilbachia) and V (lageniform, only in section Solananthera).
10.4.3.4
Seed: De Lange and Bouman (1992) subdivided the species they
examined into categories based on seed micromorphology. They found three
major groups, which included ten smaller classes, each of which included
several types. The species included in this thesis fall into these categories:
240
1. ‘A u gustia’ type
B. dregei, B. homonyma
B. geranioides
B. annobonensis, B. johnstonii
B. sonderana
B. sutherlandii
B. engleri
2. ‘Peltaugustia’ type
B. socotrana
3. ‘C ristasem en’ type
B. thom eana
4. ‘Filicibegonia’ type
B. aspleniifolia
B. iucunda
5. ‘Scutobegonia!Loasibegonia’
B. potam ophila, B. scutifolia
B. hirsutula
B. quadrialata, B. prism atocarpa, B. scapigera, B. staudtii
6.
‘M ezieria’ type
B. salaziensis
B. meyeri-johannis
8. ‘Squam ibegonia’ type
9. ‘ Tetraphila’ type
B. poculifera
B. mannii, B. horticola, B. subscutata, B. molleri
B. loranthoides ssp rhopalocarpa
B. capillipes
B. gabonensis
B. squamulosa, B. kisuluana, B. longipetiolata
10.
Madagascar
B. bogneri
B. nossibea
B. ankaranensis, B. francoisii, B. m adecassa,
B. m ananjabensis
The major sectional groupings in Africa, according to de Lange and Bouman
(1992), are:
A
Mezieria, Baccabegonia, Squamibegonia, Tetraphila
B.
Augustia, Sexalaria, Rostrobegonia
C.
Filicibegonia, Scutobegonia, Loasibegonia
Within America (de Lange & Bouman, 1999), where there are c. 600
recognised species of Begonia, there is rather less quantifiable diversity in
seed structure. A few sections show “a special seed structure characteristic at
the sectional level” (p. 24). All these sections have restricted geographical
distributions. They are:
Brazilian:
Trachelocarpus (B. herbacea)
Solananthera (6. solananthera, B. Integerrim a)
Scheidweileria (8. luxurians)
W ageneria (8. glabra, 8. convolvulacea)
Trendelbergia
241
Andean;
Casparya
Gobenia
Hydristyles
Rossmannia
Warburgina
Central Am., Mexico, Caribbean:
Urniforma
Species names where given are those which were examined by de Lange &
Bouman, 1992, which are included in the ITS analysis.
10.4.3.4 Pollen: Pollen types (van den Berg, 1985) of relevance to the species
examined in this thesis are:
1.
comorensis-\ype
B.
3.
thom eana-iype
B.
5.
em/n/7-type
B.
6.
komorensis-type
B.
7.
cavallyensis-\ype
B.
8.
squamulosa-type
B.
10.
poculifera-iype
B.
12.
annobonensis-Xype
B.
13.
dregei-Xype
B.
B.
14.
filicifolia-Xype
15.
quadrialata-Xype
B.
B.
B.
Within Madagascar, van den Berg found no distinct groups of pollen types.
10.4.3.5
Mapping the characters
In order to trace how well the characters described above fit the ITS phylogeny
of Begoniaceae, the topology collated in Chapter 7 as the ‘Jigsaw’ tree (Figure
7.22) was taken and endothecial cell types and seed types were mapped
across it (see Figure 10.17). Pollen type was not mapped because most of the
characters are uninformative; also, van den Berg has only looked at African
species and so his groups are only relevant to a subsection of the ITS tree.
Stigmatic papillae were not mapped because it was patently clear that the
classes Panda and de Wilde described were homoplastic.
242
Figure 10.17;
ITS phylogeny, with endothecial cell types
and seed types
DATISC A
DATISC A
HILLEBR.
S EX A LA R IA
ROSTROB.
ROSTROB.
IGNOTA
iu cu n d a (S )
thom eana (S)
C R IS TA S E M .
aspleniifolia (S)
FILICIBEG.
staudtii ( S ,^
LOASIBEG.
scapigera (S)
LOASIBEG.
duncan-thomasii
LOASIBEG.
letouzeyi
LOASIBEG.
dewildei
__________
SCUTOBEG.
prism atocarpa (S,E) LOASIBEG.
scutifolia (S)
LOASIBEG.
potam ophila (S)
LOASIBEG.
quadrialata (S)
LOASIBEG.
glomerata
cannabina
sandw ichensis (E)
annobonensis (S,E)
engleri (S)
johnstonii (S,E)
f fiS ÏS 'c 'fc W '® ’U e r « p l a c .
bogneri (S)
ER M IN EA
s alaziensis (S.E)
M E ZIE R IA
ankaranens \S)
OUADRILO.
m ananjabensis (S) OUADRILO.
OUADRILO.
.
OUADRILO.
îiîgîfHll:
TETFtAPHIL.
SOUAMIB.
TETRAPHIL.
TETRAPHIL.
TETRAPHIL.
TETRAPHIL.
TETRAPHIL.
Is ïz H ëpK ^
m annii (S,E)
kisuluana (S)
horticola (S)
subscutata (S)
capillipes (S)
gabonensis (S)
sutherlandii (S,E)
AUG USTIA
geranioides (S,E)
sonderana (S.E)
dregei ‘partita
A UG USTIA
AUG USTIA
dregei (S,E)
dregei hom onym a(S)A UG USTIA
sp.. gutt
?
lubbersii
GAERTIA
edm ondoi (S)
GAERTIA
integerrim a (S ,EL
SOLANANT.
b: solananthera (S,E) SOLANANT.
heracleifolia (s )
GIREO UDIA
B.' sp., U172
GIREOUDIA
involucrata (E,S)
GIREOUDIA
violifolia
W EILB AC H .
im perialis (S)
W EILB AC H .
s erico neura (S)
GIREO UDIA
peltata (S)
GIREO UDIA
theim ei (E,S)
GIREO UD IA
m anicata.(E)
G IREO UDIA
m aynensis (S)
K NE SB EC K .
boliviensis (S)
BARYA
cinnabarina (S)
E U PETA L.
K NE SB EC K .
incarnata
H YDR IST.
fissistyla (E)
?
sp., Bolivia
B EGONIA
odorata (S)
B EGONIA
minor
cubensis (S)
BEGONIA
ob liqua (E,S)
B EGONIA
?
gu'é^Rlensis
RUIZOPAV.
meridensis
RUIZOPAV.
holtonis (E,S)
RUIZOPAV.
fuchsioides (S)
L E P S IA
jam e so n ia n a (E,S) l e P S IA
olbia (S)
K NE S B E C K .
g racilis (E,S)
O UADRIPER.
herbacea (S,E )
TRACHEL.
sp., Trachelocarpus TRACHEL
woiinyi (S)
K NE S B E C K .
ulm ifolia (E)
DONALDIA
sp. 2 24
9
sp., macE
acerifolia
valida
e greg ia (E ,S )
listada
echinosepala
sp., macGL
oxyphylla (S)
rufoserica (E,S)
angularis (E )
lobata (E,S)
8 1 3 B luxurians (S,E)
243
9
K NE S B E C K .
PR ITZELIA
TETRACH.
PRITZELIA
PRITZELIA
PRITZELIA
PRITZELIA
PRITZELIA
PRITZELIA
PRITZELIA
SC HEIDW .
SOC fs2|Epti
AS
%
B. fallax
B. socotrana (S.E)
B. sam hahensis
B. porteri
B. morsei
B. m asoniana (E)
B. m asoniana maculata
B. kingiana (E)
B. am phioxis (E)
B. m alachosticta (E)
B. chlorosticta (E)
B. isoptera (E)
B. incisa (E)
B. aequata
B. serratipetala (E)
B. sp., cf serratipetala
B. brevirim osa (E)
B. sp., cf brevirimosa
S. sanguinea (E)
S. sp., 136 (E )
S. sp., 121 (E )
B. sp., Philippine
B. floccifera (E)
B. sp., nam
B. grandis holostyla
B. grandis grandis (E)
IGNOTA
PELTAUG.
PELTAUG.
COELOC.
COELOC.
COELOC.
COELOC.
R IDLEY.
IGNOTA
PETE R M .
P E TE R M .
P E TE R M .
P E TE R M .
P E TE R M .
P E TE R M .
P E TE R M .
P E TER M .
P E TE R M .
SYMBEG.
SYMBEG.
SYMBEG.
DIPLOCL.
R EIC HEN .
?
DIPLOCL.
DIPLOCL.
I'ttS iP
E denotes endothecial
cell types:
a = absent
u = U-shaped
p = perforate
pt= perforate-tympanate
S denotes seed characters:
1 = Augustia type
2 = Peltaugustia type
3 = Cristasemen type
4 = Filicibegonia type
5 = Scuto/Loasibegonia type
6 = Mezieria type
8 = Squamiljegonia type
9 = Tetraphila type
10= Madagascar
11= Trachelocarpus
12= Solananthera
13= Wageneria
C=
B. ,p ^ Reichenheim ia
R || C H | N .
B. goegoensis (E)
B. oxysperma
B. sp., 1998 1824
B. chloroneura
B. tayabensis (E)
B. labordei
B. rubella
B. balansana
B. v ers ic o lo r (E)
B. sp., Yunnan 26
R EIC HEN .
BARYAND.
DIPLOCL.
DIPLOCL.
DIPLOCL.
DIPLOCL.
DIPLOCL.
IGNOTA
PLATYC.
PLATYC.
B.
B.
B.
B.
B.
B.
B.
B.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
?
SPH ENA N .
sp. nov., Yunnan
longicarpa 1
longicarpa 2
sp., Yunnan 25
hatacoa (E)
sp., Yunnan 33
sp., Sulawesi 254
sp. nov.. Philippine
B. diadem a (E)
B. rex
B. annulata (E)
B. sp., Yunnan 21
B. sp., Taiwan
B. ravenii
B. formosana
B. sp., Piatycentrum
B. palmata 74
B. hem sleyana (E)
B. handelii (E)
B. menyangensis
B. acetosella (E)
B. longifolia (E)
B. crassirostris
B. sp., Sulawesi 252
B. sp., Sulawesi 253
PLATYC.
PLATYC.
PLATYC.
PLATYC.
?
DIPLOCL.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
SPH ENA N .
SPH ENA N .
SPH ENA N .
SPH ENA N .
SPHENAN.
?
?
Species in this phylogeny which were mentioned in the micromorphology papers are highlighted
in bold. Those in Tebbitt & Mclver (1999) have an ‘E’ after the species name; those mentioned
in de Lange & Bouman (1992, 1999) have an ‘S’.
10.4.4
Discussion:
10.4.4.1
Anther endothecial cells: It appears that U-shaped plates are
phylogenetically basal in the Begoniaceae, being shared by Hillebrandia and
by all African taxa examined. There have been changes in endothecial cell
types in three independent lineages - that leading to section Petermannia/
Symbegonia, that leading to section Solananthera, and that leading to section
Peltaugustia. Perforate cell plates have evolved more than once, so this is not
a character without homoplasy, but it certainly reinforces the (already very
244
clearly defined) lineages of Petermannia, Solananthera and Peltaugustia.
10.4.4.2
Seed: The seed micromorphology of Asian species has not yet
been comprehensively surveyed, although Symbegonia seed were examined
by Bouman and de Lange (1983); they are very small, and mostly consist of
collar cells, with a general morphology which agrees “fully with the general
seed characters of the genus Begonia” (p. 78). Seitner (1972) also included
some Asian species in his observations, and De Lange and Bouman (1999)
have looked at the seed of some Diploclinium and some Sphenanthera
species; all appear to belong to the "ordinary Begonia seed type” (de Lange &
Bouman, 1999, p. 26).
From the data here, most of the seed types fit the cladogram (and conventional
Begonia groupings) well. In America, where most seed of most species is
apparently fairly uniform, the sections Soiananthera and Trachelocarpus are
picked out. These sections are highly distinct and already well characterised
by many characters. The far less distinct sections Scheidweileria and
Wageneria, both of which appear within section Pritzelia, are also picked out.
Species in section Wageneria are among the most widely distributed American
Begonia; the section is found throughout Central and South America (although
absent on the Guianas) (Doorenbos, Sosef & de Wilde, 1998). Perhaps their
seed are particularly well adapted to dispersal.
The homoplastic seed types are 'Filicibegonia-type' and ‘Mez/er/a-type’,
although if ‘Cristasemen-\ype' and 'ScutolLoasibegonia-Xype' were
modifications of ‘Filicibegonia-type’, then there would be no inconsistency.
'Mezieria-type' is found in B. meyeri-johannis and B. salaziensis. This
suggests that it may be premature to split this section on the results of ITS
analysis, as there is data which suggests that it may be monophyletic after all
(or alternatively de Lange and Bouman may have, in the absence of major
differences, assigned a common seed type based on the existing taxonomies).
10.4.4.3
Pollen: Van den Berg (1985) put his pollen types into an
evolutionary context; he found that sections Mezieria, Baccabegonia,
Cristasemen and Filicibegonia have the most primitive size, shape and
endoaperture; Madagascan species also have a “relatively low evolutionary
level” (p. 82). From these basic types, “the developments have taken place in a
number of directions, sometimes diverging, sometimes converging” (p. 67).
245
10.5 Discussion
Within the limited time-frame of this project, molecular analyses give an
evolutionary scenario which appears more congruent with gross morphology
(and with previous sectional treatments) than a straight cladistic analysis
based on non-DNA characters alone. The problems with the characters which
hold together some of the clades in the non-DNA analysis are obvious, and
they have also proved problematic in previous studies.
Tebbitt (1997) produced morphological cladograms which split the section he
was studying, section Sphenanthera, into at least three clades. Several of the
taxa resolved as sister to the African sections Tetraphila and Mezieria (others
resolved within the Asian sections Petermannia and Piatycentrum). Species
from sections Tetraphila, Mezieria and Sphenanthera all have fleshy,
indéhiscent, frequently wingless fruits, and although Tebbitt is not explicit about
which characters change on each clade, it is likely that fleshiness and related
characters (fruit shape and dehiscence) may be responsible for this pattern.
Badcock (1998) obtained a similar fleshy-fruited clade from her morphological
analyses, which included species from Asia (S. roxburghii), America (8.
oacacana) and Africa (8. salaziensis, B. poculifera, 8. meyeri-johannis and 8,
mannii). Whether the fruit is dry or fleshy is strongly correlated with the mode of
seed dispersal, as fleshy fruits are associated with zoochory and dry fruits, with
wind dispersal. In a genus the size of Begonia, it does not seem improbable
that unrelated species have evolved similar adaptations to seed dispersal, and
therefore that a clade based on this character may well be the result of
convergence or parallel adaptation. Similar groupings occur in the non-DNA
cladogram which I have produced, with a clade of fleshy-fruited African and
Asian species. Clearly, reassessing the homology of this character may reveal
different types of fleshiness, although such anatomical work was not
conducted as part of this analysis.
Morphological character evolution makes more sense when reconstructed over
a combined analysis of non-DNA and ITS sequence data (Figures 10.11,
10.12). Although there is homoplasy in almost all characters, they are still
useful for grouping clades within the genus. This locally informative nature of
morphological characters has been documented in other plant groups, e.g.
Pennington, 1995, in Andira Juss. (Fabaceae).
246
The presence or absence of a trichome ring at the top of the petiole (see Figure
10.14) has been used to distinguish between sections Augustia (absence: 6.
sutherlandii - B. dregei) and Rostrobegonia (presence: B. engleri, B. Johnstonii
and B. sonderana are included here) (Irmscher, 1961; Doorenbos, Sosef & de
Wilde, 1998). One exception to this group is B. sonderana, which although
traditionally placed in section Rostrobegonia on the basis of unbranched
placenta, is resolved in molecular and combined analyses in Augustia. In this
respect it is noteworthy that B. sonderana is one of only two Rostrobegonia
species quoted by Doorenbos, Sosef and de Wilde as being “without a tuft of
hairs” (p. 176); the presence of a tuft of hairs is congruent with its phylogenetic
placement in Augustia. The sharing of Augustia characters (the tuft of hairs)
and Rostrobegonia characters (bifid placentae) lends some support to the
comment from Doorenbos, Sosef and de Wilde that Rostrobegonia is “closely
related to sect. Augustia and possibly identical with it” (p. 178). However, in the
molecular and combined analyses these sections are well separated. (It is
interesting that the character which misleads in this case is that of placental
branch number, which has “always played an important role in the
classification of Begonia” (Doorenbos, Sosef & de Wilde, 1998, p. 28).)
Within sections Loasibegonia and Scutobegonia the character state
‘peltateness’ is variable (see Figure 10.14), in that it occurs both with the point
of insertion in the centre of the leaf in some taxa, and with a highly asymmetric
point of insertion in others. There does not appear to be any clear trend to this,
as the species with the least asymmetric insertion, B. scapigera, is well within
the clade.
Given the anatomical division of Begonia tepals into petals and sepals, it is
interesting to see that, for the male flower, almost every change on the tree is
caused by the loss of two tepals (Figure 10.15). Only on one occasion (8.
peltata) is there a subsequent reversal back to four. If this result holds up to
further scrutiny, it would be desirable to look at the vascularisation of the tepals
in 8. peltata, in case they are all sepals or all petals rather than that one organ
has been lost and then regained.
Female tepal numbers are far more variable, and may show increases and
decreases within clades. This may correlate with a more complex relationship
between petal and sepal number in the female, than the male, flower.
247
The number of locules in Begonia appear to correlate quite strongly, but not
absolutely, with the number of styles. Loss of one locule and one style (from
three to two) is a good defining character for Piatycentrum (B. sp., Piatycentrum
- B. formosana) (on this topology. Figure 10.16).
Placental branch number, like locus number, has, as mentioned previously,
been considered important in Begonia evolution. Most Begonia species have
two branches, with ovules on both sides of them. However, there have been 11
independent cases of the loss of one of these branches over this topology
(Figure 10.16) (as well as subsequent reversals back to two branches).
Therefore, it is not a suitable character for Begonia classification if used in
isolation, but rather, must be considered along with a suite of other characters.
Perhaps disappointingly, none of the characters considered here will, in
isolation, split Begonia into distinct morphological chunks - and too high an
emphasis on any one character will almost certainly lead to polyphyly (or
paraphyly). Although it will be possible to reclassify the genus in such a way
that monophyly is upheld, this is unlikely to be achieved using clear-cut
morphological apomorphies, but instead, with suites of (sometimes
overlapping) morphological characters.
248
10.6 Summary
The morphological characters found in Begonia species have been discussed,
and a non-DNA data matrix constructed. This matrix has been analysed (MP)
alone and in combination with an ITS sequence matrix. The ITS matrix was
also analysed, in order that comparisons between tree statistics could be
drawn, and areas of agreement with the non-DNA topology could be
established. The combined ITS - non-DNA analysis was used to look at how
well the individual morphological characters fit the tree, and a few leaf, tepal
and ovary characters were reconstructed across the ITS - non-DNA analysis
topology.
Cladistic analysis of molecular data have produced evolutionary scenarios
which are more congruent with gross morphology (and prior sectional
treatments) than analyses based on non-DNA characters.
Micromorphological data sets published by previous authors were examined to
see how well the data fits the ITS phylogeny produced in a previous chapter.
Seed and anther endothecial cell characters are generally congruent with the
molecular phylogenies.
249
Figure 10.18
Begonia Leaves - Colour plate
B. aspleniifolia Hook.f. ex A.DC.
sect. Filicibegonia
GL 001 097 97
B. Johnstonii Oliv. ex. Hook.f.
sect. Rostrobegonia
E 1999 0653
B. lyman-smithii Burt-Utley & Utley 8. sericoneura Liebm,
sect. Gireoudia
sect. Gireoudia
GL 003 155 94
GL 009 124 82
8. tayabensis Menr.
sect. Reichenheimia
GL 006 035 89
250
Figure 10.19:
10.19.1
Begonia inflorescences - Colour plate
American species
*
B. theimei C.DC ex J.D. Sm.,
sect. Gireoudia
GL 002 093 79
B. heracleifolia Cham. &
Schlecht., sect. Gireoudia
GL001 126 83
8. involucrata Liebm., sect. Gireoudia
GL004 100 57
%
8. maynensis A.DC.,
sect. Knesbeckia
GL001 107 92
8. herbacea Veil.,
sect. Trachelocarpus
E 1973 1857
251
10.19.2
Asian species
B. diadema Linden ex Rodigas
sect. Platycentrum
GL001 117 97
B. sp., sect. Platycentrum]
GL 004 033 96
Symbegonia sanguinea Warb.
GL003 127 93
B. roxburghii A.DC.,
sect. Sphenenthera
GL 001 068 98
10.19.3
African species
S. loranthoides Hook.f. ssp
rhopalocarpa (Warb.) J.J. deWilde
sect. Tetraphila] GL 030 079 97
B. socotrana Hook.f.,
sect. Peltaugustia]
E 1999 0424
B
B. mannii Hook., sect. Tetraphila
GL 008 067 80
252
Figure 10.20
Male Begonia flowers - colour plate
B. sp., Yunnan no. 25
sect. Platycentrum
E 1998 0061
B. handelii Irmsch.
sect. Sphenanthera
E 1998 0050
S. boisiana Gagenp.
sect. Ignota
GL 002 033 96
e
B. letouzeyi Sosef
sect. Loasibegonia
GL 027 079 97
B. loranthoides Hook.f.
sect. Tetraphila
GL 002 087 84
B. ampla Hook.f.
sect. Squamibegonia
E 1999 0258
B. ampla Hook.f.
sect. Squamibegonia
E 1999 0258
253
Figure 10.21
Female Begonia flowers - colour plate
a
b
S. sanguinea Warb.
GL 003 127 93
B. brevirimosa Irmsch.,
sect. Petermannia] E 1982 1108
8. sp., Yunnan no. 25
sect. Platycentrum
E 1998 0061
8. chlorosticta M.J.S.Sands
sect. Petermannia
E 001 167 94
□
8. boisiana Gagnep.
sect. Ignota
GL 002 033 96
8. mo//er/Warb., sect. Tetraphila
GL 036 079 97
8. herbacea Veil,
sect. Trachelocarpus
E 1973 1857
Figure 10.22
8. convolvulacea (Klotzsch) A.
DC. sect. Wageneria
E 1979 1884
Begonia Fruits - colour plate
b
8. johnstonii Oliv. ex Hook.f.
sect. Rostrobegonia
E 1999 0653
8. oxyloba Welw. ex Hook.f.
sect. Mezieria
E 1998 2761
8. hatacoa Buch.-Ham. ex
D.Don sect. Platycentrum
GL001 029 97
8. sp., ABS U205
GL
254
11. Cytology and Phylogeny In Begonia
11.1 Introduction
Cytogenetics can offer phylogenetic information at several different levels,
from genome size, through morphology (shape, size, number and
behaviour of chromosomes during meiosis and mitosis) to the structural
organisation of genetic information along the lengths of individual
chromosomes (Sessions, 1996).
11.1.1 Karyotype: There have been very few attempts to karyotype Begonia
chromosomes. According to Arends (1985) the chromosomes of African
species are generally (sub)metacentric, with trends towards increasing
asymmetry in some sections (and because Arends associates
primitiveness with symmetry, he regards the less symmetric sections,
particularly section Squamibegonia, as more advanced). Arends (1970)
found that the somatic chromosomes of ‘Elatior’ Begonia hybrids (6.
socotrana x tuberous Begonia hybrids (probably from crosses between
Bolivian and Peruvian species)) could be separated into longer and shorter
chromosomes. The longer chromosomes have been inherited from the
tuberous Begonia hybrids used in the original crosses, and the shorter
ones came from the male parent, B. socotrana. In general, though, the
small size of Begonia chromosomes has led to most authors being
concerned simply with counts. For instance, Legros and Doorenbos
(1971), who had produced chromosome counts from 190 species of
Begonia at this time, found that the only species where they could
recognise individual chromosomes is B. nepalensis (A.DC.) Warb (B.
gigantea Wall.), from section Monopteron (A.DC.) Warb.
11.1.2 Numbers: Several studies have examined chromosome counts for
Begonia. This is in part because of the huge amateur interest in Begonia
cultivars; the chromosome numbers are of interest to growers concerned
with the crossability of different species and cultivars. “Crosses between
species [of Begonia] of similar chromosome numbers are usually
successful while those between groups of dissimilar numbers if
successful are usually sterile” (McGregor, 1969, p. 230).
255
Legro and Doorenbos have been the most prolific counters of Begonia
chromosomes (1969, 1971, 1973). They give counts for over 220 species;
they found 22 different chromosome numbers, which range from 16 (in B.
nepalensis) to 156 (B. acutifolia Jacq., section Begonia). Apparently “[t]his
complicated situation is considerably clarified if the species are arranged
into sections. Most sections were found to be characterised by one basic
chromosome number, from which the other numbers within the section (if
any) have been derived by polyploidy” (p. 167, 1973).
However, none of these studies place Begonia chromosome numbers
(and Begonia sections) into a formal phylogenetic context. Although
Doorenbos, Sosef and de Wilde (1998) briefly discuss chromosome
numbers under each sectional heading in their revision of Begonia
sections, this is of limited value given that at the time no phylogeny of
Begonia was available and thus the sections may not represent
monophyletic units; furthermore, no picture of the direction of evolutionary
change can be drawn.
11.2 Methods
My literature review for chromosome counts in the Begoniaceae revealed
604 published counts. These represent 255 species, in 47 sections.
There are also a number of counts for hybrids and/or cultivars of
horticultural interest. The taxonomy of the species has been revised
according to Doorenbos, Sosef and de Wilde (1998), and all the counts are
presented on the accompanying CD-ROM.
The ITS ‘jigsaw’ tree (Chapter 7, Figure 7.22) has been used as a
framework for consideration of chromosome numbers; existing counts for
species in the tree have been annotated onto the figure (Figure 11.1). For
tree and node support indices, refer back to Figure 7.3.
Where there are several differing counts for one taxon, the more recent
counts (Legro and Doorenbos, 1969, 1971, 1973) have been preferred,
because these were felt to be more reliable. Some of the earliest counts
256
predate the squash technique (as described in Jong, 1997), and were
made by sectioning the cells. This could easily lead to errors. For
instance, the work of Heitz (1927) was disregarded by Legro and
Doorenbos (1969), due to “the high incidence of incorrect results” (p. 193).
However, all Begonia chromosome counts (including suspect ones) are
included in a table (14.10) presented on the CD-ROM in the interests of
completeness.
Legro and Doorenbos (1969, 1971, 1973) use the symbol
presence of “stainable fragments
to indicate the
about a third [the size] of the smallest
chromosomes” (1969, p. 193); this has been followed in the reports of their
counts on the accompanying CD-ROM.
A further potential source of error is identification of material, both in the
molecular and cytological studies. In the current molecular studies,
voucher specimens have been deposited at E. In the course of this study it
was not possible to check voucher specimens for chromosome counts
(indeed, many are not supported by vouchers) and this represents a
weakness in any evaluation of chromosome number evolution in Begonia.
11.3 Results
See Figure 11.1, which represents the ‘jigsaw’ topology for ITS sequence
data analysis from Chapter 7 (Figure 7.22), with chromosome numbers
from the table on the CD-ROM annotated on. There are also seven arrows,
which mark nodes which appear to be characterised by a particular
chromosome number.
12 clades have been annotated. Of these, one to four are African, five to
nine are American and ten to twelve are Asian. These will form the basis
for discussion about trends in chromosome numbers.
257
Figure 11.1: Chromosome counts across an ITS phylogeny
D.
D.
H.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
glomerata
cannabina
sandwichensis
annobonensis
engleri
johnstonii
iucunda
thomeana
aspleniifolia
staudtii
scapigera
duncan-thomasii
letouzeyi
dewildei
prismatocarpa
scutifolia
potamophila
quadrialata
meyeri-johannis
m adecassa
bogneri
salaziensis.
ankaranensis
mananjabensis
nossibea
francoisii
longipetioiata
. lor. rhopalocarpa
. poculifera
molleri
B. mannii
kisuluana
horticola
. subscutata
capillipes
gabonensis
sutherlandii
geranioides
sonderana
dregei partita'
dregei
dregei ‘homonyme’
if
AF
■38
38
rÇ i
■38
M
i
edmondoi
g K C r.
r -É
28
heracleifolia
sp., U172
B involucrata
28
28
■28
■28
B.
B.
B.
-[^ 2 8
B:
violifolia
imperialis
sericoneura
oeltata
Iheimei
manicata
maynensis
bo iviensis
cinnabarina
28/56 R
r ië h
sp., Bolivia
odorata
minor
cubensis
obliqua
sp., sych
guaduensis
meridensis
holtonis
fuchsioides
jam esoniana
olbia
gracilis
herbacea
sp., Trachelocarpus
B wolinyi
ulmifolia
sp., 224
ri::
H
28
38?
convolvulacea
sp.. macE
acerifoli
B valida
à
echinosepala
sp., macGL
oxyphylla
lobata
luxurians
258
D ATISC A
D ATISC A
HILLEBR.
S E X A LA R IA
ROSTROB.
ROSTROB.
IGNOTA
C R IS TA S E M .
FILICIBEG.
LOASIBEG.
LOASIBEG.
LOASIBEG.
LOASIBEG.
SCUTOBEG.
LOASIBEG.
LOASIBEG.
LOASIBEG.
LOASIBEG.
M E ZIE R IA
N ER V IP LA C .
ER M IN E A
M E ZIE R IA
QUADRILO.
QUADRILO.
QUADRILO.
QUADRILO.
TETRA PH IL.
TETRAPHIL.
SQUAM IB.
TETRA PH IL.
TETRA PH IL.
TETRA PH IL.
A U G U S TIA
A UG USTIA
ROSTROB.
A UG USTIA
A UG USTIA
A UG USTIA
?
GAERTIA
GAERTIA
SOLANANT.
SOLANANT.
GIREO UD IA
GIREO UD IA
GIREO UD IA
W E ILB A C H .
W E ILB A C H .
GIREO UD IA
GIREO UD IA
GIREO UD IA
GIREO UD IA
KNESBECK.
BARYA
EU P E TA L.
KNESBECK.
H YDR IST.
BEGONIA
BEGONIA
BEGONIA
BEGONIA
?
R UIZOPAV.
RUIZO PA V.
RUIZO PA V.
L E P S IA
L E P S IA
KNESBECK.
QU A DR IPER .
TR ACHEL.
TR ACHEL.
KNESBECK.
DONALDIA
?
W A G EN ER .
WAGENER.
K N ES B E C K .
P R ITZELIA
TETRACH.
P R ITZELIA
P R ITZELIA
P R ITZELIA
P R ITZE LIA
P R ITZE LIA
P R ITZELIA
P R ITZE LIA
S C H E ID W .
1ÏÔ1"
30
HZ"
IGNOTA
fallax
PELTAUG.
socotrana
PELTAUG.
samhahensis
porteri
COELOC.
morsel
COELOC.
COELOC.
masoniana
masoniana maculataCOELOC.
R ID LEY.
B. kingiana
IGNOTA
B. amphioxis
P E TE R M .
B. malachosticta
B. chlorosticta
P E TE R M .
B. isoptera
P E TE R M .
P E TE R M .
B. incisa
B. aequata
P E TE R M .
serratipetala
P E TE R M .
sp., cf serratipetala P E TE R M .
P E TE R M .
brevirimosa
sp., cf brevirimosa P E TE R M .
SY M B E G .
sanguinea
sp., 136
sp., 121
sp., Philippine
DIPLOCL.
R E IC H EN .
floccifera
?
sp., nam
grandis holostyla
DIPLOCL.
grandis grandis
DIPLOCL.
dipetala
beddomei
sp., Reichenheimia
râjàh
R EIC H E N .
goegoensis
R E IC H EN .
oxysperma
BAR YA ND .
sp., 1998 1824
DIPLOCL.
chloroneura
DIPLOCL.
tayabensis
DIPLOCL.
labordei
DIPLOCL.
rubella
DIPLOCL.
. balansana
IGNOTA
versicolor
PLATYC.
sp., Yunnan 26
PLATYC.
sp. nov., Yunnan
PLATYC.
longicarpa 1
PLATYC.
longicarpa 2
PLATYC.
sp., Yunnan 25
PLATYC.
hatacoa
PLATYC.
. sp., Yunnan 33
PLATYC.
sp., Sulawesi 254 ?
sp. nov., Philippine SP H ENA N .
roxburghii
deliciosa
diadema
PLATYC.
rex
PLATYC.
PLATYC.
annulate
sp., Yunnan 21
PLATYC.
sp., Taiwan
?
DIPLOCL.
ravenii
formosana
PLATYC.
sp., Platycentrum
PLATYC.
palmata 74
PLATYC.
. hemsleyana
PLATYC.
. handelii
SP H ENA N .
. menyangensis
SPH ENA N .
. acetosella
SP H ENA N .
. longifolia
SP H ENA N .
. crassirostris
SP H ENA N .
. sp., Sulawesi 252 ?
. sp., Sulawesi 253 7
I
■C26 B:
■Cig i-
-L
I
I denotes a clade marker
259
11.4 Discussion
Plotting preexisting chromosome numbers onto a tree like this is a highly
frustrating exercise. Patterns begin to emerge but either something does
not quite fit, or a count for a crucial taxon is missing. Given that almost all
the taxa used in this analysis are in cultivation in Scotland, reaffirming
counts and filling in gaps is a possibility, and, given also that patterns are
emerging, this is something which should be looked at in the future.
11.4.1 Africa
African species on this phylogeny have chromosome counts of 22 (one
species), 26 (six species), 32 (one species), 34 (one species), 38 (eight
species) and 52 (one species).
Clade 1 : The counts in this clade are 22 and 26 (the lowest numbers from
this continent) (see Figure 11.2). Section Rostrobegonia, to which the
species with the counts of 26 belong, also includes species with counts of
28 (which have not been included in this ITS phylogeny); however, the
section is possibly polyphyletic (one species from it resolves in clade 4)
and so the placement of the species with 2n = 28 cannot be estimated.
Figure 11.2: Clade 1 (Africa)
22 B. annobonensis S E X A LA R IA
26 B. engleri
ROSTROB.
26 B. johnstonii
ROSTROB.
Clade 2: The numbers in the clade are varied (see Figure 11.3); three of the
counts fit the polyploid series described in Legro and Doorenbos (1969) of
2x = 26, 3x = 38 (loss of one from 39" ), 4x = 52; however, counts of 32 and
34 do not fit this series. Obviously if there are clear patterns in this clade,
more sampling is needed to reveal them.
" The loss a chromosome usually leads to inviability in diploids; however, higher
polyploids have a buffering effect, and aneuploids can survive (Heslop-Harrison, 1953).
260
Figure 11.3: Clade 2 (Africa)
38
-0
34
32
26
52
B. iucunda
IGNOTA
B. thomeana
C R IS TA S E M .
B. aspleniifolia
PILICIBEG.
B. staudtii
LOASIBEG.
B. scapigera
LOASIBEG.
B. duncan-thomasii LOASIBEG.
B. letouzeyi
LOASIBEG.
B. dewildei
B. prismatocarpa
B. scutifolia
LOASIBEG.
B. potamophila
LOASIBEG.
B. quadrialata
LOASIBEG.
Clade 3: This clade is apparently characterised by 2n = 38 (see Figure
11.4); however, there are tetraploids reported in some species from section
Tetraphila (which were not sampled here) (Arends, 1992). Counts are
needed for 8. meyeri-johannis and 8. salaziensis] the only species from
section Mezieria which has been counted is 8. seychellensis, which has 2n
= 26 (Legro & Doorenbos, 1973); it may be that the situation in the clade
containing the Madagascan and Mezieria species is more complex than is
suggested here.
Figure 11.4: Clade 3 (Africa)
meyeri-johannis
m adecassa
bogneri
salaziensis
ankaranensis
mananjabensis
nossibea
38?
B. francoisii
36/38 B. longipetioiata
lor. rhopalocarpa
poculifera
mollerj.
mannii
kisuluana
horticola
subscutata
capillipes
gabonensis
ner
I^ p l a c .
QUADRILO.
QUADRILO.
QUADRILO.
t
°eW
h^ .
TETRAPHIL.
SQUAM IB.
TETRAPHIL.
TETRA PH IL.
TETRA PH IL.
TETRA PH IL.
TETRA PH IL.
TETRA PH IL.
TE TRA PH IL.
Clade 4: This clade consists of southern African species, which have
resolved as basal to all the America species. This clade is apparently
characterised by 2n = 26 (se Figure 11.5). Previous authors have
considered the 2n = 26 species in Clade 1 to be inseparable from the
species in Clade 4 - Doorenbos, Sosef & de Wilde, 1998. These taxa are
well separated in this ITS phylogeny.
N.B. There is a mistake in Doorenbos, Sosef and de Wilde (1998, p. 68):
“2n = 56 (8. dregei, B. homonyma, 8. princeaef SHOULD read 2n = 26
(pers. comm., Doorenbos, 1999).
261
Figure 11.5: Clade 4 (southern African)
i
26 B. sutherlandii
B. geranioides
B. sonderana
A U G USTIA
AUG USTIA
ROSTROB.
26 B. dregei ‘homonyma’ A UG USTIA
11.4.2 America:
American species on this phylogeny have chromosome counts of 26 (one
species), 28 (13 species), 30 (one species), 52 (two species), 54 (one
species), 56 (12 species), 60? (one species), 78 (one species), 84? (one
species) and 104 (one species).
The chromosome number 2n = 28 occurs in several clades representing a
broad geographical area. It is the lowest widespread number, and may be
basal in America. The tetraploid 2n = 56 appears to have arisen several
times; occasionally it characterises clades; at other times it appears along
with the diploid number within species (and the morphology is not
apparently distinguishable).
Clades 5 & 6: There are two numbers recorded from these clades, 2n = 56
(in clade 5 and part of clade 6) and 2n = 28 (see Figure 11.6). Six species
from section Gaerdtia (clade 5) have been counted with 2n = 56 (of which,
two are included in this phylogeny), while the one other species in section
Solananthera (B. radicans Veil.) also has 2n = 56. The rest of this clade
represents sections Gireoudia and Weilbachia (36 species from these
sections have been counted, and all have 2n = 28; eight of these species
are represented here). The 2n = 56 taxa probably represent tetraploids
based on 2n = 28.
262
Figure 11.6: Clades 5 and 6 (America)
56
28
28
8
5°
28
28
28
B. lubbersii
B. edmondoi
GAERTIA
GAERTIA
I:
B.
B.
B.
œ
S I r .
heracleifolia
sp., U172
involucrata
G IREO UDIA
GIREO UDIA
GIREO UDIA
B.
B.
B.
B.
B.
B.
violifolia
imperialis
sericoneura
peltata
theimei
manicata
W E ILB A C H .
W EILB A C H .
G IREO UDIA
G IREO UDIA
G IREO UDIA
G IREO UDIA
the rest of America
Clade 7: Counts exist for two of the taxa in this clade (see Figure 11.7).
Although only B. cinnabarina from section Eupetalum is represented here,
chromosome counts exist for seven species from the section; two of then
have 2n = 26, the other five, like B. boliviensis (section Barya), have 2n = 28.
Figure 11.7: Clade 7 (America)
__ B. maynensis K N ES B E C K .
28 B. boliviensis BARYA
26 B. cinnabarina E U PETA L.
Clade 8: This clade is highly heterogeneous, with a mixture of numbers
between 2n = 28 and 2n = 104 (both of which have been recorded within a
single species, 6. guaduensis) (see Figure 11.8). Section Begonia is
included in this clade, with counts of 2n = 52 and 2n = 78. Legro and
Doorenbos (1969) speculated that high and varied chromosome counts
within this section may reflect the long amount of time many of the species
within it have been in cultivation, and the possibility of hybridisation since
cultivation. Counts from recently wild-collected material would enable this
to be tested. Alternatively, this may represent a predisposition towards
polyploidy within this clade.
Figure 11.8: Clade 8 (America)
—
2 8/5 6
B.
52
78
52
B.
B.
B.
B.
B.
fisslTtyla
o5ora® ^''‘®
minor
cubensis
obliqua
H Y D R ^ t "*^'
BEGONIA
BEGONIA
BEGONIA
BEGONIA
28/104 § g& A c^n sIs RUIZOPAV.
B. meridensis RUIZOPAV.
60?
84?
263
I: tts S d e s
B. jam esonianaLE PS IA
Clade 9: This large clade is partially unresolved; most species have 2n =
56 (see Figure 11.9). Legros and Doorenbos commented in 1969 that the
scandent/ trailing species in section Pritzelia are always 2n = 38, while the
shrubby species are always 2n = 56. There is certainly some sort of pattern
within this clade, but the clear-cut morphological correlation has been lost.
The shrubby B. ulmifolia (section Donaldia), with 2n = 30, is sister to a
clade which includes scandent species from section Wageneria (8. glabra
and 8. convolvulacea) and shrubby species from section Pritzelia (8.
valida), which have 2n = 38. Sister to 8. ulmifolia and the 2n = 38 clade is a
clade which appears characterised by 2n = 56 (although one taxon shows
2n = 54). Species in this clade are largely shrubs; 8. luxurians (section
Scheidweileria) and 8. oxyphylla (section Pritzelia) can grow several
metres tall. However, 8. listada is a delicate rhizomatous species
(Karegeannes, 1981). Chromosome and ITS evidence do certainly
suggest that some form of division of this clade is needed. The origin of
the number of 2n = 38 is a bit of a mystery; Legro and Doorenbos (1969)
speculate that this is part of a series 2x = 26, 3x = 38, 4x = 52; there is little
evidence for this in this phylogeny with no other counts from this series
recorded; instead the clade is predominantly based around the 28 - 56
series.
Figure 11.9: Clade 9 (America)
I— 56
^ 28/56
r - 56
*—
38?
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
olbia .
gracilis
herbacea
sp.. Trachelocarpus
wolinyi
ulmifolia
sp., 224
glabra
convolvulacea
sp., macE
acerifoli
valida
i:Œ
B. echinosepala
B. sp., macGL
B.
.
.
B.
B.
oxyphylla
rufoserica
angularis
lobata
luxurians
§
264
KNESBECK.
Q U A DR IPER .
TR ACHEL.
TRACHEL.
KNESBECK.
DONALDIA
?
W A G EN ER .
W AGENER.
?
KNESBECK.
P R ITZE LIA
TETRA C H.
P R ITZE LIA
P R ITZE LIA
PR ITZELIA
PR ITZELIA
P R ITZE LIA
P R ITZE LIA
P R ITZE LIA
S C H E ID W .
H E RB
HERB
HERB
H E RB
H ERB - SHRUB
SH RU B
HERB
S C AN D E N T
S C AN D E N T
S HRUB
S H RU B
S H RU B
S H RU B
H E RB
H ERB - SHRUB
H E RB
TALL SH RUB
S H RU B
H ERB - SHRUB
H ERB - SHRUB
TALL SH RUB
11.4.3 Asia:
Asian species on this phylogeny have chromosome counts of 22 (eight
species), 26 (two species), 28 (three species, including one from Socotra),
30 (four species), 32 (two species), 34 (one species) and 44 (two species).
Clade 10: The clade is shown in Figure 11.10. This is not exactly an ‘Asian’
clade per se; this clade, sister to all other Asian species, includes one
Indian and two Socotran species (the geographic affinity of Socotra could
be argued to be either Asian or African). 2n = 28, the count for B. socotrana,
is the most frequent count on this phylogeny and therefore does not allow
us any speculation about one of the more isolated and unusual taxa
(section Peltaugustia) in Begonia.
Figure 11.10:
Clade 10 (Asia I Socotra)
3Q
I
B. fallax
IGNOTA
b p 2 8 B. socotrana
PELTAUG.
Q ^
B. sam hahensis PELTAUG.
Clade 11: It is hard to say anything meaningful based on so few counts
(see Figure 11.11). The pattern appears clear, but whether it would hold up
to the addition of any more data is impossible to say. Legro and
Doorenbos (1971) speculate that the count of 2n = 44 in section
Petermannia represents a triploid of 2n = 30 (45, with one chromosome
lost), not a tetraploid of species with 2n = 22. This phylogeny tends to
support that view, particularly as all the Asian species with 2n = 22 are
confined to Clade 12. There may be a geographic correlation in section
Petermannia, with 2n = 30 found in western species and 2n = 44 only in
New Guinea (Legro & Doorenbos, 1969); however, only eight taxa out of c.
200 have been counted for this section (including two from New Guinea
with 2n = 30); it is too soon to generalise. It would however be very
interesting to have counts for the Symbegonia species.
265
Figure 11.11:
Clade 11 (Asia)
g: a
8811:88:
30
r-[
B. masoniana
COELOC.
B. masoniana maculataCOELOC.
B. kingiana
R ID LEY .
B. amphioxis
IGNOTA
B. malachosticta
P E TE R M .
B. chlorosticta
P E TE R M .
30
—
44
B. isoptera
P E TE R M .
B. incisa
P E TE R M .
B. aequata
P E TE R M .
B. serratipetala
P E TE R M .
B. sp., cf serratipetala P E TE R M .
B. brevirimosa
P E TE R M .
B. sp., cf brevirimosa P E TE R M .
S. sanguinea
SY M B É G .
S. sp., 136
SY M B E G .
S. sp., 121
SY M B E G .
44
Clade 12: At the base of clade 12 there is a large polytomy (see Figure
11.12); there is a variety of chromosome numbers within this, and few
indications of trends. The resolved part of this clade appears to be
characterised by 2n = 22; there is some premium on obtaining counts for B.
rubella and S. labordei, both from section Diploclinium. Diploclinium is a
large and polyphyletic section which is “a show-case of the difficulties one
meets when trying to delimit sections” (Doorenbos, Sosef & de Wilde,
1998, p. 93); species assigned to it have chromosome numbers 2n = 22,
26, 28, 32, 36, 38 and 44. 6 . picta, which is morphologically similar to 8 .
rubella and 8. labordei, has been counted and, tantalisingly, has 2n = 22.
Section Platycentrum, to which most of the species in the resolved clade
belong, has had 2n = 22 counted for 15 species (seven of which are
represented in this ITS phylogeny) (and also a few counts of 2n = 44);
Section Sphenanthera, which is included within section Platycentrum, has
had two counts, one (8. roxburghii, sampled here) of 2n = 22; the other, for
8. robusta, is 2n = 88.
266
Clade 12 (Asia)
Figure 11.12:
B. sp., Philippine
• 28-32 B. floccifera
B. sp., nam
B. grandis holostyla
26
B. grandis grandis
'3 0
B. dipetala
' 26
B. beddomei
B. sp., Reichenheimia
'3 0
B. rajah
'3 4
B. goegoensis
?
B. oxysperma
B. sp., (9 9 8 1824
B. chloroneura
B. tayabensis
B. labordei
B. rubella
B. balansana
' 22
B. versicolor
B. sp., Yunnan 26
B. sp. nov., Yunnan
B. longicarpa 1
B. longicarpa 2
B. sp., Yunnan 25
■22/32 B. hatacoa
B. sp., Yunnan 33
B. sp., Sulawesi 254
• „
B. sp. nov.. Philippine
■22
B. roxburghii
- 22
B. deliciosa
-2 2
B. diadema
■ 22
B. rex
B. annulata
B. sp., Yunnan 21
B. sp., Taiwan
B. ravenii
B. formosana
B. sp., Platycentrum
- 22
B. palmata 74
■22
B. hemsleyana
B. handelii
B. menyangensis
B. acetosella
B. longifolia
B. crassirostris
B. sp., Sulawesi 252
B. sp., Sulawesi 253
DIPLOCL.
R E IC HEN .
?
DIPLOCL.
DIPLOCL.
HAAGEA
PLATYC.
R E IC HEN .
REIC HEN .
REIC HEN .
BARYAND.
DIPLOCL.
DIPLOCL.
DIPLOCL.
DIPLOCL.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
?
SPHENAN.
SPH ENA N .
fm i:
PLATYC.
?
DIPLOCL.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
SPHENAN.
SPHENAN.
SPHENAN.
SPHENAN.
RHENAN.
?
11.4.4 Summary of cytological patterns
Table 11.1
Chromosome trends: Summary of CD-ROM Table.
No. species No.
counted (out individual
of total)
counts
No. different Range of
Chrom. no.s numbers
AFRICA
36 spp (out
ofc. 140)
27 numbers
20-76
(i.e. 56)
AMERICA
160 spp (out 260 counts
ofc. 600)
28 numbers
24-156
(i.e. 132)
ASIA
59 spp(out
of c. 645)
22 numbers
16-88
(i.e. 72)
98 counts
116 counts
Looking at Table 11.1, it seems that the most cytological diversity in
Begonia is in America, at least in terms of range of numbers (although it is
possible that more sampling in Asia, where less than 10% of species have
been counted as opposed to c. 27% in America, may reveal a wider range
267
of numbers there). Africa, where c. 26% of species have been counted, has
the smallest range of chromosome numbers, and Asia has the lowest
number of different counts.
This is interesting, because Africa has the greatest amount of ITS
sequence divergence, while ITS sequences from America and Asia are far
less divergent, and molecular evidence (the ITS phylogeny) suggests that
the African lineages are older than the Asian and American lineages.
Some general trends in chromosome number are apparent - for example,
the prevalence of 2n = 22 in the Asian Platycentrum clade (within clade 12).
It also appears that polyploidy has occurred several times. The polyploid
2n = 56, for example, characterises part of the American Pritzelia clade
(clade 9), but has also arisen on other occasions, for example, within clade
7 (in 8. incarnata) and in clades 5 and 6. Transitions up an euploid series
are far easier than transitions down a series, thus in cases like clade 6,
which have 2n = 28 and 2n = 56, 28 is probably the basal number. Thus
numbers of chromosomes are frequently homoplastic in Begonia.
The occurence of what have been suggested to be triploids (e.g. 2n = 3x =
44 in clade 11 ; 2n = 3x = 38 in clades 2 and 3) does not correlate with
sterility. For example, B. brevirimosa (2n = 44) and 8. ampla (2n = 38; not
sampled for ITS, but consectional with 8. poculifera in clade 3) certainly set
plentiful seed in cultivation at E. If the polyploid series suggested by Legro
and Doorenbos (1969) are right, it could be that these are higher polyploids
and therefore the basic number for Begonia is lower than any of the
numbers which have been found. More evidence that the basic number is
low and that nearly all species are polyploid lies in the aneupolid series
which have been reported in Begonia (e.g. counts of 20, 21, 22, 23, 24, 25,
26 in Africa). The species in clade 1, with 2n = 22 and 2n = 26, set copious
seed.
268
11.4.5 Hybridisation in Begonia
There are clearly many different chromosome numbers within Begonia.
Although the source of this variety is not clear based on this study, there are
a few probable causes: polyploidy, aneuploidy and hybridisation.
Peng and Chen (1991) investigated the endemic Taiwanese species, B.
buimontana Yamam. (2n = 30). The male flowers of this species always
drop before anthesis^^, and pollen is nearly completely aborted. Meiosis in
the species is also abnormal, with “some sticky, often disoriented bivalents
and at least 11 univalents; multivalents are often present” (p. 997). Peng
and Chen suspected that this plant is of hybrid origin, from a cross between
B. palmata (2n = 22; section Platycentrum) and 8. taiwaniana (2n = 38;
section Diploclinium). They made artificial crosses between the putative
parents, and obtained F Is which resemble 8. buimontana, drop their male
flowers prematurely, and have a somatic chromosome number 2n = 30 (i.e.
a novel number).
Peng and Chen think that 8. buimontana is represented only by FI hybrids
in the wild, because the populations are very uniform morphologically, and
because the experimentally derived hybrids are very similar to wild plants.
A few wild origin plants have been found which have set seed, but although
some of the seed (“probably derived from back crosses with the putative
parental species” - p. 998) was germinated in a greenhouse, it died at the
cotyledon stage. They put the maintenance of these hybrids, once
established, down to the perennial habit, and suggest that expansion of the
distribution of this hybrid can be achieved by recurrent natural
hybridisations.
The character of male flower opening or dropping (as rang alarm bells for Peng &
Chen, 1991) must be investigated in the plant’s natural habitat. B. listada in cultivation
at the Royal Botanic Garden, Edinburgh and Glasgow Botanic Garden (pers. obs.), and
at the Royal Botanic Garden, Kew (pers. comm.. Sands, 2000) drops its male flowers
before they open. However, descriptions of the species (Smith & W asshausen, 1981;
Karegeannes, 1981) are with open male flowers. Thus the problem may lie in its growing
conditions under glass. Legro and Doorenbos (1971) counted 6. listada as 2n = (76),
although Doorenbos (pers. comm., 1999) gives a new count of 2n = 56, which is the
most common chromosome number in section Pritzeiia (it is found in 31 species out of 41
which have been counted).
269
Although this hybrid does appear to be largely sterile, the fact that it was first
described in 1933 and could still be found in the wild over 50 years later,
distributed through three counties in Taiwan, suggests that either the
original plants have a relatively long lifespan and have spread clonally, or
that the B. palmata - B. taiwaniana cross has occurred repeatedly (or rare
sexual events may be sufficient to maintain populations). Either way, the
longer the (largely) sterile plant can survive in the wild, the greater the
chance of polyploidy conferring it a degree of fertility, or of introgression with
one or other of the parents. Had this plant been fully fertile, an hybrid origin
would not necessarily have been investigated; thus how many of what act
as good Begonia species are the results of reticulations rather than
divergent spéciation it is not possible to say.
There is also a record of a natural Begonia hybrid in Malaysia, between B.
decora Stapf and 8. venusta Ridl., both from section Platycentrum (Teo &
Kiew, 1999). Six hybrid populations have been identified using
morphological characters; within them, some individuals are
morphologically more similar to one parent, and some more similar to the
other. The pollen germination of the hybrid plant is c. 97%, and seed
germination is 98%. Teo and Kiew conclude that the fertile hybrids backcross with the parents to produce hybrid swarms; there appear to be no
genetic barriers between the morphologically distinct species 8. decora
and 8. venusta.
Assuming these hypotheses of hybridisation are correct (some molecular
studies may be informative), caution must be used in the interpretation of
cladograms based on species of Begonia. Where data have a strong
geographic structure, as is the case in the Begonia ITS analyses, this may
either reflect the real evolutionary history of the genus, or a series of
reticulations between plants which grow together. Comparisons between
chloroplast and nuclear phylogenies can be instrumental in untangling
these questions (Rieseberg & Soltis, 1991).
That one of the recorded wild hybrids (Peng & Chen, 1991) is a cross
between species from two sections somewhat negates any argument that
270
reticulations are most likely between closely related species so will not
affect overall topology. Further, the cross is between species with different
chromosome numbers. Hybridisation may thus confound phylogenetic
inference, especially if just a single region is used.
How badly reticulation events affect other species within Begonia depends
somewhat on how common or rare such events are in nature. Different
species are commonly found growing in similar habitats; Begonia flowers
do not appear to be adapted to specific pollinators (except a few probable
shifts from the common condition of insect pollination, to bird pollination, in
the Andes and in New Guinea), and different species often have very similar
flower structure; many Begonia species are cross-fertile; so the main
barrier to hybridisation may be some form of temporal separation. Most
Begonia do not produce nectar, so pollen is thought to be the only reward.
Therefore sophisticated temporal separations based on the timing of
nectar-release would not be a consideration. Of course, there may be
many other ways plants maintain their identities, and it remains that there
are little empirical data unambiguously documenting hybridisation in
natural populations of Begonia.
11.5 Summary
604 chromosome counts, representing 239 species, have been gathered
and are presented on the accompanying CD-ROM. Counts for species
which are represented in the ITS phylogeny have been mapped onto the
phylogeny; this phylogeny has then been used to look for trends in
chromosome number in Begonia lineages.
Most of the cytological diversity in Begonia appears to be in America, which
has the largest range of chromosome numbers. There are some trends
within clades, for example the prevel a nee of 2n = 22 in the Platycentrum
clade; there is also some homoplasy, with the same number generated
several times, for example, 2n = 56 in clades 5 and 6, 7 and 9.
271
12. Evolution, Biogeography and the
Begoniaceae
12.1 Introduction
The production of cladograms for a group is only the start of an
interpretative process; converting a cladogram to a phylogeny may involve
little more than accepting it as a picture of the evolutionary pattern within a
group; alternatively, some less parsimonious or optimal solution may be
accepted (hopefully with some sort of justification), as is the case in Sosef
(1994). In previous chapters I have considered cladograms produced from
nuclear and chloroplast sequence data (26S, ITS and trnC-trnD) and from
morphology. I have also considered the available cytological information for
the family. From these data sets it should be possible to say something
about evolution and biogeography within the Begoniaceae.
Before discussing the evolution and biogeography of Begonia, it is worth
briefly reviewing some major events in Earth’s history over the last c. 150
million years, to place into context the environment in which the genus has
evolved.
12.2 Geology through time
For dates of the geological time periods discussed, see Table 12.1.
Table 12.1
Geological Time Scale
ERA
PERIOD
(Hallam, 1994)
PERIOD
(Bennett, 1997)
EPOCH
AGE (Ma)
Cenozoic
Neogene
Quaternary
Holocene
Pleistocene
Pliocene
Miocene
Oligocene
Eocene
Palaeocene
0.01
1.64
5.2
23.3
35.4
56.5
65
145.6
208.0
Tertiary
Palaeogene
Mesozoic
Cretaceous
Jurassic
272
12.2.1 CRETACEOUS: The Gondwanan continent consisted largely of the
land masses currently known as South America, India, Africa, Madagascar,
Australia, New Zealand and Antarctica. On the eastern side of what is now
Africa, Madagascar and then India were joined. Madagascar / India began
to separate from mainland Africa during the early Cretaceous (Hallam,
1994). Madagascar reached the position it now occupies (relative to Africa)
about 105 Ma. Sea also began to open up on the western side, between
South Africa and Argentina, about 130 Ma (Scotese, Gahagen & Larsen,
1988); all the connections between Africa and South America were severed
during the Late Cretaceous, about 95 to 80 Ma (Parrish, 1993).
12.2.2 PALEOGENE: There have been suggestions, based on freshwater
frog and snake distributions (Hallam, 1994, p. 148-151), that some form of
land bridge occurred between the Rio Grande Rise (South America) and
the Walvis Ridge (southern Africa) in the south, and/or the Ceara (South
America) and Sierra Leone Rise (Africa) to the north, during the late
Cretaceous to early Palaeocene (c. 65 Ma). The Walvis Ridge is thought to
have been completely submerged by the end of the Eocene (Parrish, 1993),
while the Rio Grande Rise may have been submerged by the late
Oligocene (Thiede, 1977); a Palaeogene sweepstakes route^^ is thought
more plausible than a continuous land corridor, “not just because of
geological considerations but also the strong endemism of African and
South American mammals” (Hallam, 1994, p. 165).
During the Mesozoic, temperate forests extended as far as the polar
regions, and there was a wide tropical-subtropical zone; the mid-Eocene
flora in western Europe was predominantly tropical. Global cooling
occurred across the Eocene - Oligocene boundary; this was probably
associated with the development, in the early Oligocene, of a circumAntarctic oceanic circulation system, and led to the development of
glaciation and ice-sheet formation (Hallam, 1994).
“Chance crossings or migrations across a water barrier or other major biogeographic
obstacle by rafting or other means of transport" (Lincoln, Boxhall & Clark, 1982, p. 240).
273
India separated completely from Madagascar-Africa a little before 90 Ma
(Veevers, Powell & Johnson, 1980); it carried on it many African plant
species. The descendants of these species dispersed into SE Asia after
the collision of the Indian plate with Asia in the mid Eocene. This pattern
can be traced in several palm taxa (Merely, 1998). The collision of India
and Asian caused the thickening of the Tibetan crust between the mid
Eocene and early Miocene; the Tibetan plateau reached its present
elevation c. 8 Ma (Windley, 1995).
After falling considerably at the end of the Cretaceous, sea levels rose in
the Palaeocene and the Eocene. However, another large fall in sea level
occurred in the mid Oligocene, when levels could have dropped by up to
100 m (Hallam, 1992).
Although most of the Mozambique Channel is over 2000 m deeep, there is
evidence of a land bridge between Africa and Madagascar between the mid
Eocene and lower Miocene (c. 45 - 26 Ma) (McCall, 1997).
The major global fall in sea level in the mid Oligocene exposed large areas
of Sundaland and Sunda shelf; there was probably more dry land than at
any subsequent time until the end of the Cenozoic. Around 25 Ma the north
Australian margin came into contact with Sulawesi and the Halmahera arc,
possibly creating a discontinuous land connection across the Philippines
into Sulawesi (Hall, 1998).
12.2.3 NEOGENE: In the early Miocene Africa collided with Eurasia. It is
thought that there was also a major increase in aridity 20 to 30 Ma, causing
a reduction in the amount of surface water (and consequently, extinctions in
aquatic vertebrates in the western United States - Hutchinson, 1982). By
the mid to late Miocene, the cooling of the global climate caused southern
Africa to undergo aridification; closed forest was fragmented, and replaced
by woodland and savanna.
There is evidence that tropical Africa was cooler and drier in the Pleistocene
than it is today (Bonnefille, Roeland & Guiot, 1990); this may have
274
influenced the area occupied by rain forest species during these times
(Sosef, 1994). Réfugia sites for species during periods of glaciation have
been postulated for a number of regions around the globe (for detailed
reviews on European phylogeography, see Hewitt, 1996, and Ferris, King &
Hewitt, 1999; for the Amazon region, see the paper by Haffer, 1969, based
on bird distributions); in tropical Africa, refuges have been proposed in
several regions including Cape Three Points, Ghana; the coast of Sierra
Leone / Liberia; Cameroon I Gabon; and eastern Zaire (Sosef, 1994).
North and South America were isolated until late in the Neogene (Hallam,
1994); the Panama Isthmus became emergent early in the Pliocene,
allowing relatively free migration between the continents.
A large area of land may have been exposed between Australia and
Sulawesi by the late Miocene / early Pliocene (Hall, 1998). Although many
of the islands of eastern Indonesia are thought to be very young (e.g.
Seram, Irian Jaya, eastern Sulawesi), the island chains of the Philippines
and Halmahera probably had emergent land with tropical plant cover
through most of the Tertiary (Hallam, 1994).
Intermittent dry periods are recorded during the Neogene in the Sunda
region of Asia (these are reflected by maxima of Gramineae pollen) (Morley,
1998). Such significant climatic fluctuations, as polar ice-caps expanded
and retreated, were a feature of the Holocene; during these periods sea
levels rose and fell globally; land links were formed and lost, e.g. across
the northwest European shelf, the Bering Strait, and the Sunda shelf
(Indonesia/Malaysia) (Hallam, 1994).
South Sulawesi (to the east of Wallace’s line) today shows geological
affinity with the Sunda plate and floristic affinity to the Eocene floras of India,
Java and SE Kalimantan. The New Guinea flora, to the west of Wallace’s
line, is speculated to be a product of the mingling of East Malesian,
Sundanian and Australian floras in the Miocene (Morley, 1998).
275
The uplift of north-central Borneo caused a mass of sediment into deltas in
north and east Borneo. From c. 20 Ma, there has probably always been
land exposed in the region of Sulawesi. From 15 to 5 Ma more of Borneo
emerged, and volcanic activity and land mass collisions led to intermittent
emergence of many points of land (Hall, 1998). However, concurrently,
deep basins also formed (e.g. Sulu Sea, Banda Sea) which would have
formed new barriers at the same time as new pathways were also forming.
At the present moment “there are more highland areas, and a greater area
of land [in SE Asia] than at any time during the last 30 million years” (Hall,
1998, p. 122).
12.2.4:
Summary of main points:
Cretaceous
G ondw analand.
0.
Sea opens between S. Africa and Argentina.
130 Ma
early Cretaceous
M adagascar / India separate from Africa.
c. 105 Ma
M adagascar reached present position relative to Africa (Hallam,
1994, p. 139).
95-80 Ma
All land connections between Africa and South America lost.
c. 90 Ma
India separates from Madagascar/Africa (Hallam, 1994, p. 139).
c. 65 Ma
landbridge forms between Africa and South America (Rio Grande
Rise - Walvis Ridge).
Eocene
mId-Eocene
Sea levels rise.
Indian plate collides with Asia.
Tropical flora in western Europe.
end Eocene
Walvis Ridge (South Atlantic Ocean, southern Africa) submerged.
Global cooling.
mid Oligocene
Global sea levels fall by up to 100 m.
W allace’s line - barrier to plant dispersal.
late Oligocene
Rio Grande Rise (South Atlantic Ocean, South America)
submerged.
early Miocene
Africa collides with Eurasia.
Miocene
East Malesian / Sundan / Australian floras mix.
45-26 Ma
Africa / M adagascar land bridge (McCall, 1997, p. 663).
30-20 Ma
major global rise in aridity.
c. 25 Ma
N. Australia in contact with Sulawesi/Halmahera arc;
discontinuous land connection across Philippines into Sulawesi
(Hall, 1998).
mid-late Miocene
aridification, southern Africa; forest fragmented.
early Pliocene
Panam a Isthmus emerges.
276
12.3 Geographic Origins
12.3.1 Introduction: Either Begonia is a very ancient group, and its modern
day distribution is explicable in terms of plate tectonic events (the
explanation preferred by Sharp (1996, 2000), who argues vociferously if not
convincingly for a Gondwanan origin for the genus) or we need to look to
more recent events (e.g. dispersal and land bridges formed during sea
level fluctuations) to explain its biogeography. The age of the genus
Begonia is pertinent to this question; there is, however, no fossil record to
guide us. Guo and Ricklefs (2000) give the Cucurbitales a phylogenetic
grade of six (compared to, for example, zero for the gymnosperms, one for
the magnoliids, four for the Brassicales), suggesting that they consider
them to be a relatively derived group among angiosperme. However,
simplistic arguments (ancient group = vicariance; modern group =
dispersal) will not necessarily reflect modern day distribution patterns;
ancient events can be overlaid by more recent events, and vicariance can
occur contemporaneously with, after, or prior to, dispersal.
Gondwanaland: Nothofagus is the classic example of a genus with a
“typical austral distribution” (Humphries & Parenti, 1999, p. 129). Early
Nothofagus pollen is recorded from the Cretaceous in Australia and
Antarctica, South America and New Zealand; it has not been found in South
Africa and India. Morley (1998) uses this as evidence that the latter were
“well separated from Gondwanaland at the time of its [Nothofagus] initial
radiation” (p. 215). Nothofagus subsequently dispersed from Australasia to
Papua New Guinea and Irian Jaya, apparently correlating with the uplift of
the New Guinea mountains; it appears in the Birds’ Head of Irian Jaya in
the late Miocene but did not disperse further west, presumably because it
could not disperse across water (Morley, 1998). Begonia, on the other
hand, is found in South Africa, India and South America. Its absence from
Australia/New Zealand suggests that it was not dispersed across
Gondwanaland when the continent broke up.
277
Figure 12.1: ITS phylogeny of Begonia, with geography marked on
_ [~ California
S.W. Asia; Himalayas
Hawai
Cameroon, Principe, SaoTome. Pagalu
Tanzania
Tanzania, Kenia, Uganda
DATISCA
DATISCA
HILLEBR.
SEXALARIA
ROSTROB.
ROSTROB.
IGNOTA
iucunda
CRISTASEM.
thomeana
asplenifolia
FILICIBEG.
staudtii
LOASIBEG.
LOASIBEG.
scapigera
LOASIBEG.
duncan-thomasii
letouzeyi
LOASIBEG.
SCUTOBEG.
dewildei
LOASIBEG.
prismatocarpa
LOASIBEG.
scutifolia
LOASIBEG.
potamophlla
LOASIBEG.
quadrialata
MEZIERIA
meyerl-johannls
NERVIPLAC.
m aaecassa
bogneri
ERMINEA
MEZIERIA
salaziensis
anakarensis
QUADRILO.
QUADRILO.
m ananjabensis
QUADRILO.
francoisii
QUADRILO.
TETRAPHIL.
longipetiolata
lor. rnopafocarpa
TETRAPHIL.
SQUAMIB.
poculifera
molleri
TETRAPHIL.
mannii
TETRAPHIL.
kisuluana
TETRAPHIL.
horticola
TETRAPHIL.
subscutata
TETRAPHIL.
capilllpes
TETRAPHIL.
gabonensis
TETRAPHIL.
sutherlandii
AUGUSTIA
geranioides
AUGUSTIA
ROSTROB.
sonderiana
AUGUSTIA
dregei 'partita'
AUGUSTIA
dregei
dregei homonyma AUGUSTIA
?
GAERTIA
edmondoi
GAERTIA
integerrima
SOLANANT.
solananthera
SOLANANT.
heracleifolia
GIREOUDIA
sp., U172
GIREOUDIA
GIREOUDIA
involucrata
WEILBACH.
vioiifolia
WEILBACH.
imperialis
GIREOUDIA
sericoneura
peltata
GIREOUDIA
GIREOUDIA
thelmei
GIREOUDIA
manicata.
maynensis
KNESBECK.
BARYA
boliviensis
EUPETAL.
cinnabarlna
KNESBECK.
incarnata
HYDRIST.
fissistyla
glomerata
cannabina
sandwichensis
annobonensis
engleri
johnstonii
■El— Ç
Congo; D.R. Congo
■Gabon; Sao Tome
' Gabon
• Cameroon; Nigeria
■Cameroon; Nigeria; Gabon; Congo
■Cameroon
■Cameroon; Gabon; Congo
■Gabon
■Cameroon; Eq. Guinea; Ivory Coast
■Cameroon; Eq. Guinea; Gabon; Angola; D.R. Congo
• Cameroon; Gabon; Congo
west & west central Africa
■east Africa
■Madagascar
• Madagascar
' Reunion, Mauritius
' Madagascar
■Madagascar
' Madagascar
' Madagascar
■Nigeria; D.R. Congo
• Cameroon; D.R. Congo; Sao Tome; Principe
• Nigeria to Tanzania; Angola
■SaoTome
west & central Africa
■Nigeria to Uganda; south to Angola
■Congo; D.R. Congo; Ugaijda
• Cameroon to Congo &TD.R. Congo
• Cameroon; Eq. Guinea; Gabon
■Gabon?
■S. Africa; D.R. Congo; Tanzania; Zambia; Mozambique
■ S. Africa
■S. Africa; Zambia; Mozambique
■S. Africa
■S. Africa
■S. Afnca
AF
tu-
AM
r - t
rE H
fuUlS
■Brazil
■Brazil (Rio de Janeiro)
■Brazil (Rio da Janeiro; Minas Gerais; Sao Paulo)
Brazil (Rio de Janeiro)
Mexico; Guatemala; Honduras
Trinidad
Costa Rica; Nicaragua; Panama
Mexico (Chipias?)
Mexico
Mexico (Chipias; Oaxaca)
Mexico; Guatemala
Mexico (Chipias; Veracruz)
Mexico; Guatemala; Honduras; Nicaragua
Ecuador; Pern
Bolivia (Chuquisaca; Santa Cmz; Tarija)
Bolivia (Acero; Cordillera)
Mexico
Bolivia (Yungas)
Bolivia
Guadeloupe
Jamaica
Cuba
Martinique
sp., Bolivia
odorata
minor
cubensis
obliqua
?
Colombia; Ecuador; Peru; Venezuela
Venezuela (Merida; Sucre; Amazon)
Colombia; Ecuador
Colombia
Colombia; Ecuador; Venezuela
□
Mexico (Oaxaca)
Brazil
Brazil
Bolivia (La Paz, Yungas; Santa Cruz)
Venezuela; Guyana; Trindad
B
B
B
B
B
B
B
B.
ISaJfisis
?
Ecuador
Brazil (Rio de Janeiro)
Brazii (Rio de Janeiro)
Paraguay
Brazil (Santa Catarina; Parana)
RUIZOPAV.
RUIZOPAV.
RUIZOPAV.
LEPSIA
LEPSIA
KNESBECK.
QUADRIPER.
TRACHEL.
sp., TrachelocarpusTRACHEL.
KNESBECK.
woolnyi
convolvulacea
sp., macE
acerifoli
valida
à
echinosepala
sp., macGL
?
Brazil (Rio de Janeiro)
Brazil (Sao Paulo)
Brazil (Rio de Janeiro; Minas Gerais)
Brazil (Rio de Janeiro; Minas Gerais)
Brazil (Sao Paulo to Minas Gerais)
278
?
meridensis
holtonis
fuchsioides
jam esoniana
olbia
gracilis
herbacea
ulmifolia
Mexico; West Indies; Guatemala to Peru
Brazil (Ceara; Bahia; Rio de Janeiro)
BEGONIA
BEGONIA
BEGONIA
BEGONIA
oxyphylla
rufoserica
angularis
lobata
luxurians
DONALDIA
?
WAGENER.
WAGENER.
?
KNESBECK.
PRITZELIA
TETRACH.
PRITZELIA
PRITZELIA
PRITZELIA
PRITZELIA
PRITZELIA
PRITZELIA
PRITZELIA
SCHEIDW.
r|n]AS
China (Yunnan)
China (Yunnan)
fallax
IGNOTA
socotrana
PELTAUG.
sam hahensis
PELTAUG.
porter!
COELOC.
COELOC.
morsel
COELOC.
masoniana
masoniana maculata COELOC.
R ID LEY.
kingiana
IGNOTA
amphioxis
P
E TE R M .
malachosticta
P E TE R M .
chlorosticta
P E TE R M .
isoptera
P E TE R M .
incisa
aequata
P E TE R M .
serratipetala
P E TE R M .
sp., of serratipetala P E TE R M .
P E TE R M .
brevirimosa
P E TE R M .
sp., of brevirimosa
S
YM B E G .
sanguinea
S YM B E G .
sp., 136
S
YM B E G .
sp., 121
sp., Philippine
DIPLOCL.
R EIC H E N .
floccifera
?
sp., nam
DIPLOCL.
grandis holostyla
DIPLOCL.
grandis grandis
dipetala
beddomei
sp., Reichenheimia
rajah
R EIC H E N .
gogoensis
B AR YA ND .
oxysperma
sp., 1998 1824
DIPLOCL.
DIPLOCL.
chloroneura
DIPLOCL.
tayabensis
DIPLOCL.
labordei
DIPLOCL.
rubella
IGNOTA
balansana
PLATYC.
versicolor
PLATYC.
sp., Yunnan 26
China (Yunnan)
China (Yunnan)
China (Yunnan)
Nepal
China (Yunnan)
China (Yunnan)
Indonesia (Sulawesi)
Philippines (Mindoro)
India; Nepal; Burma
?
?
India (Himalaya)
India (Himalaya)
China (Yunnan )
Taiwan
Taiwan
Taiwan
Vietnam
India; Nepal; Burma; China
China
China (Yunnan); IndoChina
China (Yunnan)
China (Yunnan); Burma; Thailand
China; Indonesia
China; Indonesia
Indonesia (Sulawesi)
Indonesia (Sulawesi)
sp. nov., Yunnan
longicarpa 1
longicarpa 2
sp., Yunnan 25
hatacoa
sp., Yunnan 33
sp., Sulawesi 254
sp. nov., Philippine
roxburghii
deliciosa
diadema
rex
annulate
sp., Yunnan 21
sp., Taiwan
ravenii
formosana
sp., Platycentrum
pal mata 74
hem sleyana
handelii
menyengensis
acetosefla
longifolia
crassirostris
sp., Sulawesi 252
sp., Sulawesi 253
India; Sri Lanka
Socotran archipelago; Socotra
Socotran archipelago; Sam hah
SO
S.W. China
S.W. China
? Singapore
u
?
Peninsular Malaysia
(Sabah)
Borneo (Sabah)
Borneo (Sarawak)
I
—
Borneo
L
11b
p C
Indonesia (Java)
Philippines (Luzon)
Philippines (Luzon)
New Guinea
New Guinea
New Guinea
New Guinea
New Guinea
New Guinea
New Guinea
Philippines (Luzon)
India
?
Dl
[l2a]---
I— China; Japan
China (Yunnan)
India
India (Assam)
Malaysia
Peninsular Malaysia
Indonesia (Sumatra)
Philippines (Luzon)
Philippines (Palawan)
Philippines (Luzon)
Philippines
China (Szechuan; Yunnan); Burma
EÜl—1_|-^
In^C hina
12c
-c
c
-c
gilSRiS:
PLATYC.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
?
S PH ENA N .
PLATYC.
PLATYC.
PLATYC.
PLATYC.
?
DIPLOCL.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
S PH ENA N .
S PH ENA N .
S PH ENA N .
S PH ENA N .
SPH ENA N .
?
7
(Boxed numbers on clades will be discussed later in this chapter)
Figure 12.1 is the ITS ‘jigsaw’ phylogeny of Begonia (Figure 7.22), with
geographic distributions of species (taken from Doorenbos, Sosef & de
Wilde, 1998) marked on. There are strong geographic correlations in this
phylogeny (e.g. a Madagascan clade; a New Guinea clade). There are two
possible reasons species may show such geographical correlations.
Firstly, if species are poorly dispersed and sister taxa therefore tend to
remain in geographic proximity; secondly, if hybridisation is common and
the pattern relates to reticulation events between geographically (rather
279
then necessarily phylogenetically) proximal taxa. For the purposes of
discussion, the former will be assumed to be responsible for the majority of
the phylogenetic patterns observed. In order to test the latter possibility, a
chloroplast phylogeny could be compared to the patterns reconstructed in
this nuclear ribosomal treatment.
^2.3.2Datisca: The two species in Datisca have a disjunct distribution,
occurring in S.W. Asia and California. Because the Californian species (D.
glomerata) exhibits the unusual breeding system of androdioecy (Liston,
Riesberg & Elias, 1990) while the Asian species (D. cannabina) is
dioecious, the genus has been fairly widely studied (Liston, Riesberg &
Elias, 1989, 1990; Liston, Riesberg & Hanson, 1992; Riesberg, Hanson &
Philbrick, 1992; Swensen, Mullin & Chase, 1994).
Liston, Riesberg and Hanson (1992) dated the divergence of the two
Datisca species at around 10 Ma (late Miocene), based on cp-DNA
mutation rates. This is the last period when there were land connections
between the temperate deciduous forest which spanned the northern
hemisphere. Thus the two species may be the result of the past
fragmentation of a formerly more continuous range. Eurasia and North
America have seen considerable climate fluctuations within even the
Quaternary. Much of the North American temperate flora is thought to be
relictual of a flora formerly far more widely distributed through the northern
hemisphere; many of the disjuncts between eastern Asia and North
America (including the two Datisca species) may be Tertiary relicts formerly
more widespread across higher latitudes during the Palaeogene (Guo &
Ricklefs, 2000). A less reliable prior estimate for divergence times for the
two Datisca species, extrapolated from Nei’s mean genetic identity values
for isozyme data, was 10 - 40 Ma (Liston, Riesberg & Elias, 1989, p. 538);
this is the value quoted by Guo and Ricklefs (2000) in their analysis of
eastern Asian - North American disjuncts.
Divergence times based on ITS are discussed in the next section.
280
^2.3.3Hillebrandia: The Hawaiian Islands are 3,900 km from the closest
continent, with the highest known rate of endemism for any major
archipelago. Emergent land has existed in the location of the islands for
the past c. 70 Ma (Kim et al., 1998). The progenitors of all the c. 1000
species of native angiosperme are thought to have got to the Hawaiian
islands by long-distance dispersal; Malaysia, North America, northern
South America, Australia, New Zealand and South America have all been
proposed to have floristic affinities with Hawaii (Kim et al., 1998). Affinities
of the native plants, which may have been diverging from their mainland
sister groups for up to 70 million years, can be difficult to determine.
Kim et al. (1998) investigated the phylogeny of the endemic Hawaiian
genus Hesperomannia (Asteraceae); they found it to have affinities with
African taxa (c. 15,000 km away); they dated the divergence between the
African and Hawaiian taxa at 17-26 Ma. Seelanan, Schnabel and Wendel
(1997) also found links between African and Hawaiian taxa in the family
Malvaceae, with a sister group relationship between Kokia Lewton (Hawaii)
and Gossypioides Skovsk. ex J.B.Hutch. (East Africa-Madagascar) dated c.
3 Ma (Pliocene), necessitating an hypothesis of long-distance trans
oceanic dispersal. These studies are relevant to Hillebrandia because our
analyses suggest that Hillebrandia is sister to Begonia, and that its nearest
relatives may be found in Africa. This cannot be explained in any way but as
a long distance dispersal event, given that Hawaii is not hypothesised to
have been connected to any mainland. Possibly Hillebrandia belonged to a
more widespread lineage which has undergone extinctions in other
geographic locations. Without finding either fossil evidence or extant
relatives in some other location it is not possible to decide whether this is
the case.
If Begoniaceae ITS DNA sequence divergences occurred following a
regular molecular clock, a date could be put on the Hillebrandia ! Begonia
divergence. Given considerable difficulties in aligning sequences from the
two genera so that many positions have been excluded from our
phylogenetic analyses, comparing ITS rates with those in other plant
groups is not reliable. Calibration by dated fossil remains is not possible,
281
as there are none, and calibration by geological events (e.g. the oldest
known age of emergent land at Hawaii) would be extremely circular.
Further, even within a more recent Asian clade. Begonia ITS does not
appear to show clock-like behaviour (see later discussion) and so there is
no reason to suppose that it may have in the past.
Such (rather compelling) provisos aside, using a molecular clock with
estimates of 0.79% - 1.57% nucleotide substitutions per million years
(Sang et al., 1994; Sang, Crawford & Stuessy, 1995) for ITS (uncorrected
pairwise distances, with the 5.8 region excluded), very approximate values
can be put on clades (see Table 12.2).
Table 12.2:
Rough clade ages assuming an ITS molecular clock
TAXA
SEQUENCE
AGE RANGE
DIVERGENCE
Datisca c. - Datisca g.
Datisca c. - Hillebrandia
9%
6 - 2.5 Ma
42%
27 - 1 3 Ma
Datisca g. - Hillebrandia
44%
2 8 - 1 4 Ma
Datisca - B. johnstonii
34%
2 2 - 1 1 Ma
Datisca - B. valida
45%
29 - 1 4 Ma
Hillebrandia - B. meyerl-johannls
31%
20 - 9 Ma
Hillebrandia - B. solananthera
41%
2 6 - 1 3 Ma
B. nosslbea - B. dewildei
37%
2 4 - 1 1 Ma
However, with pairwise divergence values for ITS 1 and ITS 2 up to c. 45%
(when all the variable regions, which were excluded from analyses, are
included), it is apparent that the alignment pf some regions may be
inaccurate; even were the alignment accurate, there is a high possibility that
multiple hits will lead to underestimates of divergence using uncorrected
pairwise differences.
282
Figure 12.2: Molecular clock - based estimates of lineage age
2 4 - 1 1 Ma (ITS)
26 - 9 Ma ( l \ S ) ' ^
Begonia
%
Hillebrandia
6 - 2.5 Ma (ITS
Datisca
28 - 13 Ma (ITS) Hillebrandia - Datisca
2 9 -1 1 Ma (ITS) Begonia - Datisca
Drawn to scale of upper values of ITS value estimates,
with the lower edges of the ranges marked in bold.
More data is needed to corroborate the basal divergences within
Begoniaceae; estimates using maximum likelihood rather than uncorrected
pairwise distances would also be more informative.
Wagstaff and Dawson (2000) suggest a date of 55 Ma for the Begoniaceae/
Datiscaceae lineage, based on early Eocene Tetramelaceae megafossils
(see Figure 12.3). They also have an Oligocene leaf, stem and raceme
fossil and lower Miocene pollen for Coriaria.
Figure 12.3: rbcL phylogeny of Coriariaceae, Corynocarpaceae,
Tetramelaceae, Datiscaceae and Begoniaceae
- from Figure 2, Wagstaff & Dawson, 2000 (p. 139)
5
5in
y
b
p
^
6j-^Begonia glabra
Begonia ulmifolia
Begonia metallica * sanguinea
3 T ^ Begonia boisiana
Begonia herbacea
Begonia oxyloba
Hillebrandia sandwicensis
Datisca cannabina
Datisca glomerata
Telrameles nudiflora
Octomeles sumatrana
Corynocarpus rupestris
,1? Co/y#M>cai7>itf c/iftftttw u r
*"i2
— T
dissimilis
Corynocarpus laevigatas
Corynocarpus similis
5S m ybp
- Coriaria ruscifolia
Coriaria sarmentosa
Coriaria arborea
Coriaria myrtifolia
283
This suggests that the Begoniaceae / Datiscaceae lineage is at least 55
Ma (the fossil cannot give an upper limit for lineage age, and we cannot tell
how long after the Begoniaceae / Datiscaceae lineage evolved the
Begoniaceae evolved, so this date cannot be used as direct evidence for
the age of Begoniaceae). rbcL branch lengths from the dated node to the
terminals range from 23 (node to Datisca glomerata) to 51 (node to B.
ulmifolia) (Wagstaff & Dawson, 2000). The relative rates test (Doyle & Gaut,
2000) gives a value of r = 0.451 (and so, does not support a time-calibrated
clock).
It is possible, based on fossil evidence and on ITS and 268 molecular
divergence values, that the Begoniaceae (Begonia and Hillebrandia) may
be in the region of 60 to 20 million years old; more fossil evidence (and
sequence from more genes) is needed to narrow this estimate.
284
12.3 A Begonia - relationships from the ciadograms
12.3.4.1 Continental relationships: Africa has been suggested as the area
of origin for Begonia (e.g. van den Berg, 1995, p. 75); although species
depauperate compared to the rest of the tropics (c. 140 species as
compared to c. 1360 species), African taxa occur in morphologically
isolated clades (e.g. Tetraphila-, Loasibegonia-Scutobegonia), separated
by suites of characters (e.g. flower colour, fruit fleshiness, seed and pollen
micromorphology). The relationships suggested by this ITS analysis are
summarised in Figure 12.4.
Figure 12.4: ITS-based geographic relationships of Begonia species
S.AFR1CA
AMERICA INDIA
SOCOTRA
ASIA
The paraphyly of African taxa can be interpreted in two ways: either with the
African lineage older than lineages in Asia and America, or with there being
two African lineages, one sister to the rest of Begonia, and the other, sister
to all the American species of Begonia, derived from a more recent west to
east dispersal event. These two options are shown in Figure 12.5. The
explanation which has the most basal lineages in Begonia as African (i) is
preferable to the other (ii) in terms of parsimony.
285
Figure 12.5: Geographic origins of Begonia lineages
12.5 a:
CLADOGRAMS
Africa basal
ii.
Basal region unknown
AMERICA
AFRICA
1ERICA
SOCOTI
12.5 b.
SOCOTRA
ASIA
AFRICA
ASIA
BLOCK DIAGRAMS
Africa basal
AMERICA
INDIA
A FR IC A
ASIA
AFRICA
i.
AFRICA AMERICA
AFRICA
ii.
ASIA
AMERICA
Basal region unknown
AFRICA
ASIA
One possible scenario (hypothesis one) is as follows:
The ancestral Begonia evolved on Africa. The main African lineage
contained all the taxa which were to become sections Rostrobegonia,
Sexalaria, Tetraphila, Squamibegonia, Cristasemen, Loasibegonia,
Scutobegonia, Filicibegonia, and all the Madagascan species. There was
another lineage, possibly with an easterly distribution, across to the land
mass which was to become India (see Figure 12.6 a). About 90 million
years ago India separated from Africa/Madagascar and moved north,
carrying on it some taxa from this lineage, the Begonia species which were
to populate Asia. One lineage dispersed from India onto Socotra
286
(Peltaugustia)', the rest of the species arrived in Asia in the mid Eocene;
from there, they radiated out across Asia, with one clade (Platycentrum)
diversifying particularly on the geologically active landscape of the
Himalayas, and the other {Petermannia), particularly across the emerging
and submerging islands of Malesia.
Other species from the eastern African lineage migrated towards the south
of Africa and spread across to the west coast. From there, one lineage
(Augustia) spread through southern Africa, while the other, the ancestor to
all the American species, crossed (possibly) via the Walvis Ridge/Rio
Grande Rise (probably before the onset of the Oligocene); the Rio Grande
Rise was submerged by the late Oligocene, so Begonia would have arrived
in America by this date. They then radiated, and crossed through Central
America into Mexico, over the Panama Isthmus during the early Pliocene.
Figure 12.6: Begonia biogeography, hypothesis one
12.6 a:
Fitting lineages across a modern-day world map
latycentru
c. 35 Ma:
Walvis RIdg
etermannial | j n e
^bmergqd
early Pliocene:
Panama Isthmus
floras merged
c. 25 Ma; no
Begonia
crossed this
[Augustia
Oligocene:
Walvis Ridge/ Rio
Grande Rise
c. 25 Ma:
Rio Grande Rise submerged
287
90 Ma
Indian raft
c. 4 5 Ma, mid Eocene:
India - Eurasia collide
12.6 b:
Fitting dates onto the cladogram
AFRICA
S.AFRICA
AMERICA INDIA
SOCOTRA
ASIA
c. 35 Ma
c. 45 Ma
c. 90 Ma
Southern / Eastern
African lineage (in bold)
Although the order of these events fits the cladogram perfectly (see Figure
12.6 b), in order for India to carry Begonia to Asia, the date of origin for the
genus would be over 90 million years ago (when India absolutely
separated from Africa/Madagascar. Nearly all the diversity in Asia (c. 660
species) must have evolved during the last c. 45 million years, since India
collided with Asia; most of the diversity in America (c. 600 species - de
Lange & Bouman, 1999) would have occurred in the last 25 or so million
years (although some diversification could have occurred on the Indian
plate and/or South Atlantic land-brldge/islands). The Australian and south
east Asian floras came into contact about 25 million years ago; as Begonia
has not been found on Australia or New Zealand, it seems likely that the
genus had not reached islands like New Guinea at this point in time (rather
than that it could have crossed to Australia and did not); Australia and New
Zealand contain a large amount of habitat apparently suitable for Begonia,
There are several examples of genera (e.g. Dipterocarpaceae Blume,
Gonystylus Teijsm. & Binnend. (Gonystylaceae Gilg), Ixonanthes Jack
(Linaceae DC ex Perleb.), Eugeissona Griffith. (Arecaceae) and Durio
Adans. (Bombacaceae Kunth.)) which are today considered typically
Malesian, having apparently rafted from Africa, radiated in Asia, and
subsequently suffered range (and species number) reductions in Africa
and India (Morley, 1998). Southern Africa, after all, suffered from
aridification, forest fragmentation and savanna expansion about 10 million
years ago; many Begonia species require a damp climate and forest cover
to survive; it is possible that whole lineages were lost, and that the
paraphyly of African Begonia (if extinct species were included) would be
288
more apparent.
Still, so old a date sits a little uncomfortably on what is not generally
considered a particularly basal angiosperm genus (and with the fossil date
on the Begoniaceae/Datiscaceae clade of c. 55 Ma - Wagstaff & Dawson,
2000; Figure 12.3). Further, India, with massive geological activity and
periods of aridification, would not have made a very hospitable raft for
Begonia. An alternative hypothesis (hypothesis two) could be that the
lineage of Begonia which went on to give rise to section Augustia/ American
taxa/ Asian taxa separated into two clades while in Africa (see Figure 12.7
a); one migrated north; the other, south/south east (diversifying into
Augustia! all the America species, as described). The clade which moved
north would have been able to cross into Eurasia about 23 million years
ago, when Africa and Eurasia collided.
Figure 12.7: Begonia biogeography, hypothesis two
12.7 a:
Fitting lineages across a modern-day map
c. 23 Ma:
Africa - Eurasia
collide \
[Platycentnji
c. 35 Me:
Walvis Ridgi
‘etermannial |jr j0
'^bmerg^ |
early Pliocene:
Panama Isthmus
floras merged
c. 25 Me; no
Begonia
crossed this
\
Augustia
Oligocene:
Walvis Ridge/ Rio
Grande Rise
c. 25 Ma:
Rio Grande Rise submerged
289
12.7 b:
Fitting dates onto the cladogram
AFRICA
S.AFRICA
AMERICA INDIA
SOCOTFtA
ASIA
c. 35 Ma
c. 23 Ma
The chronological inconsistency (in the ciadograms the Asian clade
predates the American clade; see Figure 12.7 b) may be explained by
extinctions in the north of Africa (along the bold line). Further, as the climate
in Eurasia is now largely inhospitable to Begonia, taxa would have been
lost from across Arabia (surviving only in Socotra). The sister relationship
between Socotran and Indian taxa could be explained by lineage splitting in
North Africa or Eurasia, closer geographically to the Socotran islands
(Figure 12.8 b), with possible extinctions of other members of the lineages,
prior to Begonia reaching, and radiating in, Asia, rather than by a dispersal
event from India (Figure 12.8 a).
Figure 12.8: Asian and Socotran Begonia lineages
12.8a
12.8 b
SOCOTRA
INDIA
SOCOTRA
ASIA
N.AFRICA/
EURASIA
AFRICA
AFRICA
The following discussion is more concerned with the relationships within
than between the continents; clade numbers are those marked onto the ITS
phylogeny. Figure 12.1 (and were also used in Chapter 11 to discuss
cytology - see Figure 11.1).
290
12.3.4.2
African clades
The African relationships from Figure 12.1 are redrawn in Figure 12.9 for
convenience.
Figure 12.9: ITS-based relationships of African Begonia taxa
Cameroon, Principe, Sao Tome. Pagalu
Tanzania
Tanzania, Kenia, Uganda
B. annobonensis
B. engleri
B. johnstonii
Congo; D.R. Congo
Gabon; Sao Tome
Gabon
Cameroon; Nigeria
Cameroon; Nigeria; Gabon; Congo
Cameroon
Cameroon; Gabon; Congo
Gabon
Cameroon; Eq. Guinea; Ivory Coast
Cameroon; Eq. Guinea; Gabon; Angola; D.R. Congo
Cameroon, Gabon; Congo
west & west central Africa
east Africa
Madagascar
Madagascar
Reunion, Mauritius
Madagascar
Madagascar
Madagascar
Madagascar
Nigeria; D.R. Congo
Cameroon; D.R. Congo; Sao Tome; Principe
Nigeria to Tanzania; Angola
SaoTome
west & central Africa
Nigeria to Uganda; south to Angola
Congo; D.R. Congo; Uganda
Cameroon to Congo & D.R. Congo
Cameroon; Eq. Guinea; Gabon
Gabon?
S. Africa; D.R. Congo;Tanzania; Zambia; Mozambique
S. Africa
S. Africa; Zambia; Mozambique
S. Africa
S. Africa
S. Africa
B.
B.
B.
B.
g
R.
B-
B.
8.
B.
B.
g
g’
b !
g
g‘
B.
B.
B.
B.
R.
B.
g
g|
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
iucunda
thomeana
asplenifolia
staudtii
scapigera
duncan-thomasii
letouzeyi
dewildei
prismatocarpa
scutifolia
potamophila
quadrialata
meyeri-johannis
m adecassa
bogneri
salaziensis
anakarensis
mananjabensis
nossibea
francoisii
longipetiolata
lor. rnopalocarpa
poculifera
molleri
mannii
kisuluana
horticola
subscutata
capilllpes
gabonensis
sutherlandii
geranioides
sonderiana
dregei ‘partita’
dregei ^
dregei homonyma
S E X A LA R IA
ROSTROB.
ROSTROB.
IGNOTA
C R IS TA S E M .
FILICIBEG.
LOASIBEG.
LOASIBEG.
LOASIBEG.
LOASIBEG.
LOASIBEG.
LOASIBEG.
LOASIBEG.
M E Z IE R IA
N E R V IPLA C .
QUADRILO.
QUADRILO.
QUADRILO.
QUADRILO.
TETRA PH IL.
TE TRA PH IL.
SQUAM IB.
TE TRA PH IL.
TE TRA PH IL.
TE TRA PH IL.
TE TRA PH IL.
TE TRA PH IL.
A UG USTIA
A UG USTIA
ROSTROB.
A U G USTIA
A U G USTIA
A U G U S TIA
AMERICA
ASIA
Clade 1 : This clade appears as sister to all other east, west and central
African species of Begonia (see Figures 12.9, 12.10).
Figure 12.10:
Map of geographic distribution of species in Clade 1
and Clade 1 (Africa)
Cameroon, Principe, Sao Tome. Pagalu B. annobonensis S E X A LA R IA
Tanzania
B. engleri
ROSTROB.
Tanzania, Kenia, Uganda
B. johnstonii
ROSTROB.
B. annobonensis (section Sexalaria) is a monocarpic species which can go
291
through several generations in a year. It is distributed from west Africa to
the islands of Sao Tome and Pagalu. The other two taxa (B. engleri and B.
johnstonii, section Rostrobegonia) are found on the east African mainland.
Sampling more of the species from within section Rostrobegonia may give
this clade a more continuous range. The section Rostrobegonia appears
polyphyletic, so it is not possible to simply extrapolate its distribution from
the distributions of species currently assigned to it.
Clade 2: This next African clade includes species from sections
Cristasemen, Filicibegonia, Loasibegonia and Scutobegonia (see Figure
12.11).
Figure 12.11:
Map of geographic distribution of species in Clade 2
and Clade 2 (Africa)
Congo; D.R. Congo
Gabon; Sao Tome
Gabon
Cameroon; Nigeria
Cameroon; Nigeria; Gabon; Congo
Camemon
Cameroon; Gabon; Congo
Gabon
Cameroon; Eq. Guinea; Ivory Coast
Cameroon; Eq. Guinea; Gabon; Angola; D.R. Congo
Cameroon; Gat>on; Congo
west & west central Afnca
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
iucunda
IGNOTA
thomeana
C R ISTA SE M .
asplenifolia
FILICIBEG.
staudtii
LOASIBEG.
scapigera
LOASIBEG.
duncan-thomasii LOASIBEG.
letouzeyi
LOASIBEG.
dewildei
SCUTOBEG.
prismatocarpa
LOASIBEG.
scutifolia
LOASIBEG.
potamophila
LOASlBEG.
quadrialata
LOASIBEG.
Many species within this group have relatively large, bright yellow, flowers,
monochasial inflorescences, and, with the exception of the lianescent, ivy
like B. thomeana (section Cristasemen), they are all rhizomatous herbs.
Species are distributed through west central Africa, from Guinea, east to the
Democratic Republic of Congo, Rwanda and Burundi, and south to Angola,
and west to the island of Sao Tome, Gulf of Guinea (B. thomeana). The
idea that these species are related is not novel; De Lange and Bouman
(1992) group sections Filicibegonia, Loasibegonia and Scutobegonia
together according to seed characteristics.
Sosef (1994) looked at the biogeographic relationships of species within
the sections Loasibegonia and Scutobegonia in an attempt to identify
Pleistocene rain forest réfugia. Although he managed to trace a few
vicariance events, he suggests that the method he used was only capable
292
of tracing events of comparatively recent origin (the last glacial) and that
vicariance events during previous glacial periods have been obscured “by
renewed dispersal resulting in the display of floristic affinities rather than of
vicariance in the data” (Sosef, 1994, p. 134). It may be, particularly on
continental land masses, that biogeographic inferences should be
restricted to broad (continental-scale) patterns rather than country-bycountry comparisons. Also, if it is the case that there are several overlaid
patterns in Begonia, for nowhere is this more likely to be true than for Africa,
which appears to hold the oldest lineages in the genus.
Clade 3: This clade includes species from sections Mezieria, Tetraphila,
Squamibegonia and all the Madagascan species of Begonia (see Figure
12.12).
Figure 12.12:
Map of geographic distribution of species in Clade 3
and Clade 3 (Africa)
2^ ,
Kssrsu*»
§; fsirassi™'*
I; teSnsi,
Madagascar
B.
Madagascar
B.
Madagascar
B.
Madagascar
B.
Nigeria: D.R. Congo
B.
Cameroon; D.R. Congo; SaoTome; Principe
B.
Nigeria to Tanzania; Angola
B.
SaoTom e
B.
west & central Africa
B.
Nigeria to Uganda; soulti to Angola
B.
Congo; D.R. Congo; Uwnda
°
Cameroon to Congo & D.R. Congo
B.
Cameroon; Eq. Guinea; Gatxsn
B.
Gatxsn?
B.
mim
anakarensis
QUADRILO.
m ananjabensis QUADRILO.
nossibea
QUADRILO.
francoisii
QUADRILO.
longipetiolata
TETRA P H IL
lor. rnopalocarpaTETRAPHIL
poculifera
SQUAM IB.
mollerj.
TE TR A PH IL
mannii
TETRA P H IL
kisuluana
TETRA P H IL
tiorticola
TE TR A PH IL
subscutata
TETRA P H IL
capilllpes
T E T R A P H Il
gabonensis
TETRA PH IL
Despite great morphological variation within the island, all the sampled
species from Madagascar are monophyletic. This has not previously been
suspected, and demonstrates the potential for morphology to confuse. The
Madagascan clade does include one non-Madagascan taxon, B.
salaziensis, section Mezieria, from the Mascarine Islands (Reunion and
Mauritius) to the east of Madagascar. Africa and Madagascar are currently
c. 700 km apart, posing the question of how a lineage of Begonia got onto
Madagascar.
Unlike Begonia, Streptocarpus Lindl. (Gesneriaceae) is thought to have
colonised Madagascar three times from Africa (Moller & Cronk, in prep.,
293
2001). Both genera are found in similar habitats (predominantly moist,
shaded forest locations). Moller and Cronk (in prep., 2001), using a
conservative estimate of 0.79 - 1.57% nucleotide substitutions per million
years for ITS (Sang et al., 1994; Sang, Crawford & Stuessy, 1995), estimate
maximum divergence time between African and Madagascan taxa to be 50
to 25 million years. Using the same substitution rates gives slightly
younger divergence times for Begonia (between c. 21 and 10 million years,
based on B. duncan-thomasii to B. ankaranensis, uncorrected pairwise
distance 33%). Even doubling the maximal dates on these ranges does
not put them into a suitable time-frame for Gondwanaland - based
vicariance, as Madagascar is thought to have separated from Africa in the
early Cretaceous.
Some form of land bridge between Africa and Madagascar has been
suggested, from the mid Eocene to the early Miocene, 26 to 45 Ma (McCall,
1997). This is not far from the dates based on sequence divergence values
(which will be underestimated for Begonia, given that uncorrected pariwise
values were used), and also is more consistent with an age of c. 60 to 30
Ma for Begonia, as discussed before, than a Gondwanan disjunction would
be.
Section Tetraphila is paraphyletic, also including species from section
Squamibegonia. The species in this Tetraphila/Squamibegonia clade are
widely distributed, not only on mainland Africa, but also to the west of Africa,
in the Gulf of Guinea (on the islands of Sao Tome and Principe) and on the
Mascarine Islands to the east of Africa. It is interesting that these widely
distributed species (some species are recorded with disjunct
mainland/island distributions, or from more than one island) include most
of the fleshy-fruited Begonia species; fleshy-fruitedness is thought to
correlate with bird dispersal, to which ocean is not necessarily a barrier.
Clade 4: These southern African species do not appear to be closely
related to species from the rest of Africa, but appear as sister to an
American clade (see Figures 12.9, 12.13).
294
Figure 12.13:
Map of geographic distribution of species in Clade 4
and Clade 4 (Africa)
s. Africa; D.R. Congo; Tanzania; Zambia; Mozambique
S. Africa
s. Africa; Zambia; Mozambique
S. Africa
S. Africa
S. Africa
B.
B.
B.
B.
B.
B.
sutherlandii
A U G U S T IA
geranioides
A U G U S T IA
sonderana
ROSTROB.
dregei ‘partita’
A U G U S T IA
dregei
A U G U S T IA
dregei ‘h o m o n y m a ’A U G U S T I A
The southern African clade consists largely of species from section
Augustia, although one species currently assigned to section
Rostrobegonia (B. sonderana) is also included. Most of the species are
from South Africa; they have underground tubers and either herbaceous or
woody stems. The most widely distributed species is B. sutherlandii, which
is unusual in that not only has it small tubers, but it can also produce
tubercils in the leaf axes. B. sutherlandii can over-winter outside even when
grown in the Scottish climate; its ability to withstand a range of
temperatures and seasonality probably is responsible for its wide
distribution. Many of the other species in this clade show some ability to
withstand water shortages (and perhaps to regenerate after flash fires?),
perenniating though a combination of tubers, a distinct caudex and/or thick
woody trunks.
295
12.3.4.3
Am ericas
The American relationships from Figure 12.1 are redrawn in Figure 12.14
for convenience.
ITS-based relationships of American Begonia taxa
Figure 12.14:
■AFRICA
■SOUTHERN AFRICA
—
n
\—
■ Brazil
■ Brazil (Rio de Janeiro)
■Brazil (Rio de Janeiro; Minas Gerais; Sao Paulo)
■Brazil (Rio de Janeiro)
■ Mexico; Guatemala; Honduras
■ Trinidad
■ Costa Rica; Nicaragua; Panama
■ Mexico (Chipias?)
• Mexico
■ Mexico (Chipias; Oaxaca)
■ Mexico; Guatemala
■ Mexico (Chipias; Veracruz)
■Mexico; Guatemala; Honduras; Nicaragua
Ecuador; Peru
Bolivia (Chuquisaca; Santa Cruz; Tarija)
Bolivia (Acero; Cordillera)
Mexico
Bolivia (Yungas)
Bolivia
Guadeloupe
Jamaica
Cuba
Martinique
?
Colombia; Ecuador Peru; Venezuela
Venezuela (Merida; Sucre; Amazon)
Colombia; Ecuador
Colomtxa
Colombia; Ecuador Venezuela
Brazil
Mexico (Oaxaca)
Brazil
Brazil
Bolivia (La Paz, Yungas; Santa Cruz)
Venezuela; Guyana; Trindad
?
Mexico; West Indies; Guatemala to Peru
Brazil (Ceara; Bahia; Rio de Janeiro)
?
Ecuador
Brazil (Rio de Janeiro)
Brazil (Rio de Janeiro)
Paraguay
■ BraziI(SantaCatarina; Parana)
B. sp., gutt
B. lubbersii
B. edmondoi
I; SSŒIra
B. heracleifolia
B. sp., U172
B. involucrata
G AERTIA
G AERTIA
SOLANANT.
SOLANANT.
G IREO UD IA
G IREO UD IA
G IREO UD IA
W EILB A C H .
vioiifolia
W EILB A C H .
imperialis
sericoneura
G IREO UD IA
peltata
G IREO UD IA
G IREO UDIA
theimei
manicata
G IREO UD IA
maynensis
K N E SB EC K .
boliviensis
BARYA
cinnabarina
E U PETA L.
K N E SB EC K .
incarnata
H YDR IST.
fissistyla
sp., Bolivia
BEGONIA
odorata
BEGONIA
minor
BEGONIA
cubensis
BEGONIA
obliqua
sp., sych _
?
guaduensis
RUIZOPAV.
meridensis
RUIZOPAV.
holtonis
R UIZOPAV.
fuchsioides
L E P S IA
jam esoniana
LE P S IA
olbia
K N E SB EC K .
gracilis
QU A DR IPER .
TRACHEL.
herbacea
. sp., TrachelocarpusTRACHEL.
K N E SB EC K .
woolnyi
ulmifolia
DONALDIA
sp., 224
?
glabra
W A G EN ER .
convolvulacea
W A G EN ER .
sp., macE
K N E SB EC K .
acerifoli
PR ITZELIA
valida
TETRACH.
■?
echinosepala
sp., macGL
■ Brazil (Rio de Janeiro)
• Brazil (Sao Paulo)
■ Brazil (Rio de Janeiro; Minas Gerais)
■Brazil (Rio de Janeiro; Minas Gerais)
' Brazil (Sao Paulo to Minas Gerais)
oxyphylla
rufoserica
angularis
lobata
luxurians
P R ITZELIA
PR ITZELIA
P R ITZELIA
P R ITZELIA
PR ITZELIA
SC H E ID W .
ASIA
Clade 5: The most basal species in America, from section Gaerdtia, are
found in eastern Brazil (see Figure 12.15).
296
Figure 12.15:
Map of geographic distribution of species in Clade 5,
and Clade 5 (America)
Brazil
Brazil (Rio de Janeiro)
irsli GAERDTIA
B. edmondoi GAERDTIA
These species have somewhat woody stems (they belong to an
horticultural class known as ‘cane begonias’) and generally bifid placentae
which are unusual in that ovules are only on the outer surfaces (although B.
edmondoi has undivided placentae, as do the Southern African species in
the clade basal to this, clade 4, section Augustia). Species in section
Gaerdtia are generally reasonably drought-tolerant; B. lubbersii, in
cultivation, can survive leaf-drop.
Clade 6: Species in this clade are widely distributed, from Brazil to Mexico
(see Figure 12.16).
Figure 12.16:
Map of geographic distribution of species in Clade 6
and Clade 6 (America)
r
Brazil (Rio de Janeiro; Minas Gerais; Sao Paulo)
Brazil (Rio de Janeiro)
Mexico; Guatemala; Honduras
_ P - Trinidad
•—
Costa Rica; Nicaragua; Panama
I
—
Mexico
(Chipias?)
I— Mexico
Mexico (Chipias; Oaxaca)
M j
Mexico; Guatemala
M
I
—
Mexico (Chipias; Veracruz)
Mexico; Guatemala; Honduras; Nicaragua
I
M r—
. integerrima
SOLANANT.
. solananthera SOLANANT.
B. heracleifolia GIREO UD IA
B. sp., U 172
GIREO UD IA
B. involucrata
GIREO UD IA
g
B.
B.
B.
B.
B.
B.
vioiifolia
imperialis
sericoneura
peltata
theimei
manicata
W E ILB A C H .
W E ILB A C H .
GIREO UD IA
GIREO UD IA
GIREO UD IA
GIREO UD IA
Because the species in clade 5 are also Brazilian, the biogeography in
297
clade 6 can be interpreted as a migration north, from Brazil to Mexico. Thus
the Brazilian species B. solananthera and B. integerrima (section
Solananthera) may represent an early lineage within clade 6 (at least, they
form the less speciose half of the basal dichotomy). They are lianescent
climbers and, like the species in the previous clade, are unusual in having
ovules only on the outer surfaces of their bifid placentae; the fruits have
three locules. Within the other half of the dichotomy, B. vioiifolia and B.
imperialis (section Weilbachia) are small rhizomatous herbs; they have
bifid placentation with ovules between the branches, but have only two
locules in the fruits. All the other species have thick, relatively woody stems,
bifid placentation with ovules between the branches, and three locular
fruits. Several of the species in this clade possess asymmetric
inflorescences.
Clade 7: Clade 7 is broadly Andean, from Ecuador to Bolivia (see Figure
12.17).
Figure 12.17:
Map of geographic distribution of species in Clade 7
and Clade 7 (America)
Ecuador; Peru
Bolivia (Chuquisaca: Santa Cruz; Tarija)
Bolivia (Acero; Cordillera)
'."'.Z
Z ZB'.E C K .
[ . mayriensjs
^________ K
B.
N ES
B. boliviensis BARYA
f cinnabarina
‘
B.
ËÜ P É TA L.
B. maynensis, from Ecuador and Peru, has far smaller male than female
flowers. This unusual character is also found in some species from the SE
Asian section Petermannia. In this cladogram 8. maynensis resolves as
sister to two tuberous Bolivian species, 8. cinnabarina and 8. boliviensis.
Both these species have orange to red flowers, and appear to show
adaptations to bird pollination. The androecium of 8. boliviensis in
particular is very similar to that of the New Guinean Symbegonia species;
298
the styles also show some convergence. Both comparative flower size and
the fused, swollen, coloured androecium are likely to be pollinator-specific
adaptations. It is remarkable that within one South American clade and
within one SE Asian clade the same two distinct morphological adaptations
appear to have evolved independently.
6. maynensis has a thick woody stem, while the other species, from the
Andean region, have perenniating tubers (they were involved in the crosses
which gave rise to the modern range of tuberous ‘Elatior’ Begonia cultivars
(Arends, 1970)). B. bolivienesis is currently ascribed to section Barya; the
other two species also ascribed to this section are found in Peru. Although
there are no obvious morphological similarities between B. maynensis and
6. boiiviensis and B. cinnabarina, and despite what appear to be very
different pollination syndromes, clade 7 can therefore be circumscribed
geographically.
Section Casparya could not be sampled, as none of the 24 known species
are in cultivation. The section is distributed in Central America and the
Andean region, and characterised by fruits dehiscing through the backs of
the locules, and being horned rather than winged (Doorenbos, Sosef and
de Wilde, 1998). The relationship of this section to other Begonia sections
is not known; however, when discussing possible pollination syndromes in
other America Begonia, it may be relevant to point out that nectar production
(not otherwise recorded in Begonia) has been observed in B. ferruginea L.f.
(Vogel, 1998), and that morphologially, the flowers bear a striking
resemblance to B. boliviensis.
Lower oxygen levels and overall temperatures in the higher Andean regions
mean that insects are comparatively scarce; this may be what has driven
the change from insect to bird pollination in these species. Pollen is no use
to hummingbirds; Begonia flowers are thought (Vogel, 1998) to mimic other
reward-bearing species, particularly Fuchsia. (This deception is also how
B. fuchsioides, in the apparently unrelated section Lepsia (clade 8b), is
thought to be pollinated). However, it is possible that B. ferruginea is not
the only nectar-bearing species in Begonia; Vogel (1998) found no
299
specialised nectaries in its flowers; thus there would be no evidence of
nectar secretion in herbarium material.
Clade 8: This clade has a wide distribution, through Central and South
America (see Figure 12.18).
Figure 12.18:
Map of geographic distribution of species in Clade 8
and Clade 8 (America)
Mexico
Guadeloupe
Jamaica
Cuba
Martinique
Colombia; Ecuador; Peru; Venezuela
Venezuela (Merida; Sucre; Amazon)
Colombia; Ecuador
Colombia
Colombia; Ecuador Venezuela
incarnata
fissistyla
sp., Bolivia
odorata
minor
cubensis
obliqua
sp., sych .
guaduensis
meridensis
KNESBECK.
H YDR IST.
BEGONIA
BEGONIA
BEGONIA
BEGONIA
?
R UIZOPAV.
R UIZOPAV.
R UIZOPAV.
i?clTsioides L E P S IA
B. jam esoniana L E P S IA
The basal species in this clade is from section Knesbeckia (B. incarnata).
This species has a fleshy/woody stem, and is found in Mexico. Section
Knesbeckia appears to be polyphyletic; as currently delimited, it includes
50 to 55 species distributed from Mexico to Bolivia. Two Bolivian species
(probably) from section Hydristyles (the unidentified taxon is known only
from a single herbarium sheet, and lacks female flowers) are sister to the
rest of the taxa in clade 8. Without far more exhaustive sampling, it is not
appropriate to comment on any biogeographic relationships between
Mexico and Bolivia, as other species from section Knesbeckia, with other
distributions, may resolve between these lineages.
Clade 8a (with the included species from section Begonia) occurs in the
West Indies; its sister clade, 8b (sections Ruizopavonia and Lepsia),
includes species distributed through Colombia, Ecuador, Peru and
Venezuela. The included species from sections Begonia, Ruizopavonia,
Hydristyles and Lepsia are herbs with small, entire leaves, and are
relatively intolerant to water shortages. The leaves tend to be held on a
plane to either side of the stem, and in some species each node includes
300
one smaller and one larger leaf (B. foliosa] B. fuchsioides, section Lepsia).
Clade 9: There is a basal polytomy in this clade, with the positions of B.
olbia and B. gracilis (sections Knesbeckia and Quadriperigonia
respectively), the two species from the morphologically highly distinct
section Trachelocarpus, and the final major American clade (B. wollnyi - B.
luxurians) unresolved in relation to each other (see Figure 12.19).
Figure 12.19:
Map of geographic distribution of species in Clade 9
and Clade 9 (America)
Mexico (Oaxaca)
Brazil
Brazil
Bolivia (La Paz, Yungas; Santa Cmz)
B.
B.
B.
B.
Venezuela; Guyana; Trindad
B.
□
Mexico; West Indies; Guatemala to Pern B.
Brazil (Ceara; Bahia; Rio de Janeiro)
B.
?
Ecuador
Brazil (Rio de Janeins)
Brazil (Rio de Janeiro)
B ^ f^ S a n ta Catarina; Parana)
?
Brazil (Rio de Janeiro)
Brazil (Sao Paulo)
Brazil (Rio de Janeiro; Minas Gerais)
Brazil (Rio de Janeiro; Minas Gerais)
Brazil (Sao Paulo to Minas Gerais)
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
olbia
K N E SB EC K .
gracilis
QU A DR IPER .
herbacea
TRACHEL.
sp., TrachelocarpusTRACHEL.
K N E SB EC K .
woolnyi
ulmifolia
DONALDIA
sp., 224
W A G EN ER .
glabra
convolvulacea
W A G EN ER .
sp.. macE
i^N ESBECK.
acerifoli
PRITZELIA
valida
TETRACH.
PRITZELIA
PR ITZELIA
echinosepala
sp., macGL
PR ITZELIA
P R ITZELIA
oxyphylla
PRITZELIA
rufoserica
angularis
PRITZELIA
PRITZELIA
lobata
S C HEIDW .
luxurians
«
Section Quadriperigonia includes 17 to 19 species, mostly from Mexico,
and is characterised by a terminal inflorescence and propagation by
tubercles (Doorenbos, Sosef & de Wilde, 1998). More species from this
section need to be sampled; the current limitation is lack of living material.
B. olbia is a relatively woody, thick-stemmed species. The species in
section Trachelocarpus are rhizomatous epiphytes, known only from
eastern Brazil. They have distinctive beaked fruits, flowers with an unusual
almondy scent, separate male and female inflorescences, distinctive
seeds (de Lange & Bouman, 1999) and occur on very long branches in ITS
analysis (see Figure 7.4). They also have an indumentum of unusual
droplet-shaped glands (described as ‘pearl-glands’ by Doorenbos, Sosef &
de Wilde, 1998). There is nothing in their morphology which gives any hint
as to possible relationships; it is unfortunate that this phylogeny does not
resolve their position. They have a chromosome number of 56 (counted for
four species in the section); however, this is also found in species from
301
sections Gaerdtia, Solananthera, Knesbeckia, Quadriperigonia and
PritzeliaIScheidweileria, so offers no real clues.
Basal to the last resolved American clade is a fleshy-stemmed, woody,
sometimes deciduous species (8. wollnyi)] sister to 8. wollnyi there are two
clades. Clade 9a includes species from sections Knesbeckia, Pritzeila,
Donaldia and Wageneria, and is distributed from Mexico, through the West
Indies and Brazil, to Peru. Species in this clade tend to have a mass of
small white flowers in a symmetrical inflorescence, and are shrubby in
habit. An exception to the habit is the 8. convolvulacea/B. glabra lineage;
these species, from section Wageneria, are lianescent, with slightly woody
stems. Section Wageneria has in the past been incorporated in section
Pritzelia (e.g. Irmscher) but is separated out by Doorenbos, Sosef and de
Wilde (1998) largely on the basis of its scandent habit.
The other clade, 9b, is almost exclusively Brazilian; with two exceptions (8.
egregia (Tetrachia)', 8. luxurians (Scheidweileria)) all species are in section
Pritzelia. The monotypic section Tetrachia has peltate leaves; section
Scheidweileria is characterised by compound leaves. All other taxa in this
clade have simple basifixed leaves. Again, this clade includes many taxa
with huge inflorescences of small white flowers (although 8. listada and 8.
echinosepala have far smaller inflorescences); further, the ovaries of the
female flowers are densely hairy. With the exception of 8. listada, a small,
rhizomatous species, these taxa are shrubby; indeed, 8. oxyphylla and 8.
luxurians can grow to several metres.
The nesting of 8. luxurians (section Scheidweileria) within section Pritzelia
is highly plausible, given that the key feature differentiating members of
section Scheidweileria from section Pritzelia is leaf morphology (simple
versus compound leaves).
302
12.3.4.4
Asia
The Asian relationships from Figure 12.1 are redrawn in Figure 12.20 for
convenience.
Figure 12.20:
ITS-based relationships of Asian Begonia taxa
AFRICA
AMERICA: SOUTHERN AFRICA
—03-
so
It1a^
India; Sri Lanka
Socotran archipelago; Socotra
Socotran archipelago: Samhah
S.W. China
S.W. China
? Singapore
w
,
?
Peninsular Malaysia
------------ T” Borneo (Sabah)
l_
lllb
Borneo (Sabah)
Borneo (Sarawak)
r - [ Indonesia (Java)
rE3”
Philippines (Luzon)
Philippines (Luzon)
New Guinea
New Guinea
New Guinea
New Guinea
New Guinea
New Guinea
New Guinea
Philippines (Luzon)
India
China; Japan
China (Yunnan)
India
India (Assam)
Malaysia
Peninsular Malaysia
Indonesia (Sumatra)
Philippines (Luzon)
Philippines (Palawan)
Philippines (Luzon)
Philippines
China (Szechuan; Yunnan); Burma
Nepal
Indo-China
China (Yunnan)
China (Yunnan)
China (Yunnan)
China (Yunnan)
China (Yunnan)
Nepal
China (Yunnan)
China (Yunnan)
Indonesia (Sulawesi)
Philippines (Mindoro)
India; Nepal; Burma
India (Himalaya)
India (Himalaya)
China (Yunnan )
“
Taiwan
r
Taiwan
Taiwan
r
Vietnam
India; Nepal; Burma; China
““ China
r
China (Yunnan); IndoChina
China (Yunnan)
China (Yunnan); Burnna; Thailand
China; Indonesia
China; Indonesia
Indonesia (Sulawesi)
Indonesia (Sulawesi)
303
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
fallax
IGNOTA
socotrana
PELTAUG.
samhahensis
PELTAUG.
porter!
morsel
8 8 it8 8 :
COELOC.
masoniana
masoniana m aculataCOELOC.
kingiana
amphioxis
malachostlcta
chlorostlcta
isoptera
incisa
aequata
serratipetala
sp., cf serratipetala
brevirimosa
sp., cf brevirimosa
sanguinea
sp., 136
sp., 121
sp., Philippine
floccifera
R ID LEY,
IGNOTA
P E TE R M .
P E TE R M .
P E TER M .
P E TER M .
P E TER M .
P E TE R M .
P E TE R M .
P E TE R M .
P E TE R M .
SYMBEG.
SYM BEG.
SYMBEG.
DIPLOCL.
R E IC HEN .
sp., nam
grandis holostyla
grandis grandis
dipetala
beddomei
sp., Reichenheimia
rajah
gogoensis
oxysperma
sp., 1998 1824
chloroneura
tayabensis
labordei
rubella
balansana
versicolor
sp., Yunnan 26
sp. nov., Yunnan
longicarpa 1
longicarpa 2
sp., Yunnan 25
hatacoa
sp., Yunnan 33
sp., Sulawesi 254
sp. nov., Philippine
roxburghii
deliciosa
diadema
rex
annulate
sp., Yunnan 21
sp., Taiwan
ravenii
formosana
sp., Platycentrum
palmate 74
hemsleyana
handelii
menyangensis
acetosella
longifolia
crassirostris
sp., Sulawesi 252
sp., Sulawesi 253
?
DIPLOCL.
D IP LO C L
HAAGEA
PLATYC.
R E IC HEN .
R E IC HEN .
R EIC HEN .
BARYAND.
DIPLOCL.
DIPLOCL.
DIPLOCL.
DIPLOCL.
DIPLOCL.
IGNOTA
PLATYC.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
?
SPH ENA N .
PLATYC.
PLATYC.
?
DIPLOCL.
PLATYC.
PLATYC.
PLATYC.
PLATYC.
SPH ENA N .
SPH ENA N .
SPH ENA N .
?
?
Clade 10: This clade is sister to all the Asian Begonia species (see Figure
12.20). For its geographic distribution, see Figure 12.21.
Figure 12.21:
Map of geographic distribution of species in Clade 10
and Clade 10 (Asia / Socotra)
India; Sri Lanka
Socotran archipelago: Socotra
Socotran archipelago; Samhah
IGNOTA
B. fallax
PELTAUG.
B. socotrana
8 . sam hahensis PELTAUG.
The sister group relationship of some Indian and Socotran species, which
has already been discussed in relation to Figure 12.7, is unexpected in that
most recent authors have considered the Socotran species to be related to
southern African species from the section Augustia (e.g. van den Berg,
1983, using pollen characters). However, Hooker (1881) suggested that
there may be a link between B. socotrana and some peltate fleshy-leaved
Indian species from section Reichenheimia, like B. floccifera. Although this
relationship was suggested by some analyses (see Chapter 5, Figures 5.5,
5.6, 5.7, 5.8, 5.9, 5.10) it is not resolved in the tree under discussion. B.
fallax, the sister to the Socotran species, is a shruby plant which was
placed in section Diploclinium by de Candolle (1864); Doorenbos, Sosef
and de Wilde (1998) hint instead at an affinity with section Haagea.
Sequence divergence is high between the two Socotran endemics and
other species in Begonia, and the Socotran species both show
morphological adaptations (in the form of perenniating bulbils) to what is a
very unusual environment for a Begonia, dry and seasonal. The period of
reproductive isolation in an unusual environment may mean that the
morphological characters suggesting affinity with section Augustia are
misleading. The Bremer support values for the Socotra/B. fallax clade are
low (four for the 177-taxon matrix, Figure 7.3; two for the morphologicalanalysis ITS matrix. Figure 10.9). In the combined ITS/morphology
analysis. Figure 10.11, the Socotran species resolve as sister to everything
304
American, South African and Asian, while B. fallax resolves close to section
Haagea (Bremer support value three). Thus it seems that it is too early to
make the definitive statement about the position of this lineage, as adding
more data may alter the ways its relationships are reconstructed yet again.
In this ITS phylogeny, the Socotran-lndian clade shares a common
ancestor with all the other Asian species of Begonia (and Symbegonia). It
may be that there are western Asian/Indian species which are basal in
Asia; collections from across India are sorely needed. B. samhahensis
was only discovered in 1995; perhaps more species of Begonia remain to
be discovered in such atypical locations.
Clades 11 and 12: Some of the biogeographic patterns in SE Asia are
“difficult to relate simply to geology" - such as why the distance between
Borneo and Sulawesi (across Wallace’s Line) appears difficult for plant
groups to cross.
From Figure 12.20, it can be seen that all the sampled Begonia species
from Borneo are in section Petermannia, and in the same lineage as taxa
from Peninsular Malaysia (basal), Java, Luzon and New Guinea (clade
11b). However, the three sampled taxa from Sulawesi resolve within the
predominantly Chinese Platycentrum clade (clade 12c). This is despite the
morphological similarity of one of the Sulawesi taxa (no. 254) to section
Petermannia. The analyses here are sectional rather than species level,
so the true patterns can only be hinted at, and it possible that there are
other Sulawesi species which have close relatives in Borneo.
Clade 11: Most of the species in this clade are Malesian (see Figure
12.22). The two halves of clade 11 are highly unbalanced, with c. 12
species in clade 11a, and c. 200 in clade 11 b (assuming that the sections
Coelocentrum and Petermannia are monophyletic, as the initial results
presented here suggest).
305
Figure 12.22:
Map of geographic distribution of species in Clade 11
and Clade 11 (Asia)
Clade 1 1 a
1
—
Clade 1 1 b
S.W. China
S.W. China
? Singapore, Hort.
IÎÎ9
r-[
Peninsular Malaysia
Borneo (Sabah)
Borneo (Sabah)
Borneo (Sarawak)
Indonesia (Java)
Philippines (Luzon)
Philippines (Luzon)
New Guinea
New Guinea
j — New Guinea
"1— New Guinea
New Guinea
I— New Guinea
New Guinea
i:S?oTlSi
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
B.
88ib8S:
m asoniana
COELOC.
masoniana maculataCOELOC.
kingiana
RIDLEY.
amphioxis
IGNOTA
malachostlcta
PETERM.
chlorostlcta
PETERM.
Isoptera
PETERM.
Incisa
PETERM.
aequata
PETERM.
serratipetala
PETERM.
sp., cf serratipetala PETERM.
brevirimosa
PETERM.
sp., cf brevirimosa
PETERM.
i:l?."T3§“
S. sp.. 121
S Y M B EG .
Clade 11a: This clade consists of species from section Coelocentrum] the
section is distributed in south-western China and VietNam. B. masoniana
was ‘discovered’ in a botanic garden in Singapore; there are no records of
where it came from (Mason, 1957; Irmscher, 1959). Because every other
known species in this section is from a relatively small area of northern
VietNam / Yunnan / Guangxi it seems probable that B. masoniana is also
from this region. The section is characterised by having unilocular ovaries
with parietal placentation. This has been considered (e.g. Jin & Wang,
1994) as a primitive condition in Begonia, linking the species with some
from section Mezieria in Africa, and therefore it has been suggested that
species from section Coelocentrum are basal in Asia. There is no
evidence for the primitivity of section Coelocentrum here (as Irmscher,
1939, suspected): unilocular ovaries appear to have evolved separately in
Africa and Asia (where they have evolved at least twice, once in section
Coelocentrum and once in the morphologically peculiar Petermanniarelative, B. amphioxis).
306
Clade 11b: The lineage of section Petermannia may have entered the
Malesian islands via the Malaysian archipelago; its ancestor presumably
migrated south from the continent. The two species on Sabah (including B.
amphioxis as a member of the section) are monophyletic; the next clade
consists of species from Sarawak and Java. Species from Luzon are
paraphyletic, due to a monophyletic clade of seven taxa from New Guinea
(including species of Begonia and of Symbegonia). What evidence there is
suggests that oceans provide barriers to Begonia dispersal in this lineage
at least, with a high degree of island endemism, and apparently no species
crossing the Torres Strait (between New Guinea and Australia) or the Timor
Sea to Australia. Of course, species may have crossed into Australia and
subsequently suffered extinction; equally, there may be as-yet undiscovered
Begonia on the continent. The former is thought unlikely as we are dealing
with (comparatively) recent events; the latter, in part, because there is a
vibrant amateur Begonia group in Queensland, Australia, which would
surely have spotted them!
Clade 12: Lack of resolution at the base of this major Asian clade creates
problems with interpretation. The relationships between clades from the
Philippines, India, China, Malaysia / Sumatra and the major 'Platycentrum'
clade are unresolved (see Figure 12.23).
Figure 12.23:
Map of geographic distribution of species in Clade 12
and Clade 12 (Asia)
307
Philippines (Luzon)
India
China; Japan
China (Yunnan)
India
India (Assam)
Malaysia
Peninsular Malaysia
Indonesia (Sumatra)
Philippines (Luzon)
Philippines (Palawan)
Philippines (Luzon)
Philippines
China (Szechuan; Yunnan); Burma
în ^ C h in a
China (Yunnan)
China (Yunnan)
China (Yunnan)
China (Yunnan)
China (Yunnan)
Nepal
China (Yunnan)
China (Yunnan)
Indonesia (Sulawesi)
Philippines (Mindoro)
India; Nepal; Burma
?
?
India (Himalaya)
India (Himalaya)
China (Yunnan )
Taiwan
Taiwan
Taiwan
Vietnam
India; Nepal; Burma; China
China
China (Yunnan); IndoChina
China (Yunnan)
China (Yunnan); Burma; Thailand
China; Indonesia
China; Indonesia
Indonesia (Sulawesi)
Indonesia (Sulawesi)
B. sp., Philippine
B. floccifera
DIPLOCL.
R E IC HEN .
?
B. sp., nam
DIPLOCL.
B. grandis holos^la
B. grandis grandis
DIPLOCL.
HAAGEA
B. dipetala
PLATYC.
B. beddomei
B. sp., Reichenheimia REIC HEN .
REIC HEN .
B. rajah
R EIC HE N .
B. gogoensis
BAR YA ND .
B. oxysperma
B. sp., 1998 1824
DIPLOCL.
B. chloroneura
DIPLOCL.
DIPLOCL.
B. tayabensis
DIPLOCL.
B. iabordei
DIPLOCL.
B. rubella
IGNOTA
B. balansana
PLATYC.
B. versicolor
PLATYC.
B. sp., Yunnan 26
B. sp. nov., Yunnan
PLATYC.
PLATYC.
B. longicarpa 1
PLATYC.
B. longicarpa 2
B. sp., Yunnan 25
PLATYC.
PLATYC.
B. hatacoa
B. sp., Yunnan 33
PLATYC.
B. sp., Sulawesi 254
?
B. sp. nov., Philippine SPHENAN.
B. roxburghii
B. deliciosa
B. diadem a
B. rex
PLATYC.
B. annulate
B. sp., Yunnan 21
PLATYC.
?
B. sp., Taiwan
B. ravenii
DIPLOCL.
B. formosana
PLATYC.
B. sp., Platycentrum
PLATYC.
B. palmata 74
PLATYC.
PLATYC.
B. hem sleyana
SPHENAN.
B. handelii
SPHENAN.
B. menyangensis
SPHENAN.
B. acetosella
SPHENAN.
B. longifolia
SPHENAN.
B. crassirostris
?
B. sp., Sulawesi 252
?
B. sp., Sulawesi 253
One clade (12a; section Reichenheimia) suggests migration from Malaysia
to Sumatra; another (12b) shows the monophyly of four Philippine taxa.
Within the largest resolved clade (12c), the basal taxa are from China, Indo
China, Burma and Nepal. Many of the species within this clade are
unresolved; this resolution is not the result of conflict between many
different most parsimonious trees in the consensus tree (the topology has
been taken from the compartment analysis of these taxa, which resulted in
only ten most parsimonious trees). Rather, the lack of resolution is due to
low levels of sequence divergence, which may be due to a rapid radiation
(faster than ITS can track).
Harking back to the phylogram presented for the compartment analysis,
section Platycentrum (Figure 7.15; presented again here as Figure 12.24)
and for the same taxa within the complete culled ITS analysis phylogram
(Figure 7.4), there appears to be a rapid radiation (with little internal
resolution) followed by a period of lineage differentiation.
308
Figure 12.24:
Phylogram for Platycentrum clade compartment
analysis (copied from Figure 7.14)
r-C
lOchanges
B. chlorosticta
B. masoniana
B. balansana
“ B. versicolor
B. sp., Yunnan 26
B. sp. nov. Yunnan
________ IB. longicarpa A
B. longicarpa B
B. sp., Yunnan 25
B. hatacoa
i “ B. sp., Sulawesi 254
B. sp., Philippine
B. roxburghii
r~~ B. diadema
B. deliciosa
B. hemsleyana
B. sp., Yunnan 33
B. sp., Yunnan 21
B. annulata
--------------- B. rex
B. sp., Taiwan
I
B. ravenii
B. formosana
B. sp., Platycentrum.
B. palmata 74
B. palmata 75
B. palmata 227
B. handelii
B. menyangensis
B. acetosella
B. longifolia
B. crassirostris
B. sp., Sulawesi 252
B. sp., Sulawesi 253
c
172 parsimony-informative
characters
Tree length = 559
Cl = 0.70
01 ex uninformative = 0.58
Rl = 0.67
Many of the species in this clade are currently found around China - India Himalaya - Burma - VietNam. The uplift of the Himalayas and Tibet
continued long after the initial collision of India and Asia (estimates of a
data for this collision vary, from the late Palaeocene, c. 60 Ma (Powell &
Conaghan, 1973) to the Eocene (c. 40 Ma, Molnar & Tapponnier, 1975)) and
had a significant impact on climate (Hallam, 1994): grassland spread
where once was forest, and xerophytic scrub developed in rain-shadow
areas. The Tibetan plateau reached its present elevation only 8 Ma; it is
309
thought that the “late Cenozoic climatic system was stongly influenced by
the Tibetan plateau” (Windley, 1995), which had far-reaching effects
including increases in the intensity of the Indian monsoon and changes in
the vegetation patterns in Pakistan.
It is possible that the radiation in this group correlates with this Himalayan
uplift and its associated effect on climate, which may have led to the
fragmentation of ancestral ranges and subsequent divergence in isolation.
However, the 'Platycentrum' clade also has a number of morphological
character changes associated with it, which could be interpreted as ‘key
innovations’. The majority of the species in this clade have two-locular
ovaries, while the majority of Begonia species overall have three locules.
This morphological change appears to correlate with the mode of seed
dispersal. Seeds from the three-locular fruits are wind dispersed, while, in
these two-locular species, the fruit recurves and the two smaller wings on
the fruit form a cup which catches raindrops, shaking the seeds loose (de
Lange & Bouman, 1999) (see Figure 12.25).
Figure 12.25:
T.S., two-locular fruit, section Platycentrum
RAIN
DROP
m
Assuming that rain-splash dispersal is advantageous over wind dispersal
in some situations (wind dispersal tends to rely on dry fruit and may be
problematic in a monsoon climate, for example) the ‘innovation’ of these
two-locular fruits could have allowed the lineage which possessed it to
radiate.
Further evidence for evolution of seed dispersal in this clade is a probable
transition from rain-splash to zoochory, in the fleshy fruited Sphenanthera
species.
310
Corning back to the question of Himalayan uplift versus morphological key
innovations as a driving force for Platycentrum radiation, it is worth asking
whether molecular clock estimates for this clade correlate with the timing of
the Himalayan uplift.
The ITS phylogram for the Platycentrum compartment (Figure 7.15) has
branch lengths ranging from 15 (polytomy to B. hemsleyana) to 40
(polytomy to B. palmata] polytomy to B. roxburghii). The relative rate ratio ‘r’
between these species is 0.375; only if r = 1 is there evidence for a timecalibrated molecular clock (Doyle & Gaut, 2000). N.B. the alignment of
sequences from this region was not ambiguous and no positions were
excluded due to uncertainty. Another DNA region may behave in a more
clock-like manner, and thus be more suitable for molecular clock based
hypotheses.
The uncorrected pairwise divergence within this Platycentrum i
Sphenanthera clade range from 1.4% (between closely related species) to
11.5% (across the unresolved part of the tree). Using a conservative
estimate of 0.79 - 1.57% nucleotide substitutions per million years (Sang et
al., 1994; Sang, Crawford & Stuessy, 1995) provides dates in the order of
0.89 - 0.45 Ma between B. longifolia and B. acetosella, i.e. Pleistocene; 8 3.5 Ma between B. roxburghii and B. palmata, i.e. late Miocene. If the
radiation of the Platycentrum clade did occur in the Miocene, the initial
collision of India and Asia would have happened over 20 million years
previously, and Tibet would have more or less reached its present
elevation. However, given that ITS does not appear to evolve in a clock-like
fashion in Begonia, there is little basis for accepting these dates as
evidence.
Within the ‘Platycentrum’ clade, species have radiated across Sulawesi /
Philippines, China, the Himalayan region, Taiwan, Vietnam, Burma,
Thailand and Indonesia. Certainly within the species attributed to section
Sphenanthera (B. handelii - B. crassirostris) a migration appears to have
occurred from China to Indonesia; a separate southern migration into
Malesia is required to explain the ‘Sulawesi no. 254’ / ’Philippine sp. nov.’
clade.
311
Dioecy is widespread in angiosperms, being present in 37 of Engler and
Prantl’s 51 orders (Bawa, 1980) (and remains highly polyphyletic in the
more phylogenetic classifications produced by the A.P.G. e.g. Soltis, Soltis
& Chase, 1999). The section Sphenanthera contains several species
which are dioecious^\ e.g. B. roxburghii, 6 . menyangensis and 8 . handelii,
which are included in this ITS phylogeny. The section does not appear to
be monophyletic, as the dioecious species resolve in two separate clades
(suggesting two separate gains of dioecy). These two clades are also
supported by gross morphology, as B. roxburghii is a ‘cane’ Begonia, with
tall upright stems to c. one metre, while 8. menyangensis and 8. handelii
are more or less a caulescent, producing masses of large, strongly scented
pale flowers near the ground surface. In the light of Bawa’s (1980)
suggestion that dioecy correlates with fleshy-fruitedness, it is interesting
that dioecy is found only among the fleshy-fruited members of the
Platycentrum / Sphenanthera clade. The majority of dioecious species are
reported to be insect pollinated and animal dispersed, particularly in the
tropics (Bawa, 1980). It is not known what disperses the seeds of the
fleshy-fruited species in section Sphenanthera.
It would be interesting to compare population genetic structure of
nucleotide and organelle markers in order to estimate pollen to seed flow
ratios in sympatric Begonia species with different fruit types (e.g.
zoochorous, rain splash dispersed, wind dispersed).
Without including taxa from the full distribution of Begonia in this region
(e.g. species from Fiji, Flaimahera) detailed island biogeographic
conclusions cannot be made. Flowever, Begonia, a genus with a range of
narrow endemics (and very few widely dispersed species), appears
eminently suited to biogeographic considerations; the presence of at least
two unrelated clades of taxa on the south east Asian islands offers the
possibility of using cladistic biogeography to compare and contrast
independent distribution patterns.
It can be difficult to determine dioecy based on herbarium collections, as plants may
produce separate male and female inflorescences, which can be separated temporally.
However, these reports are based on observations over many years, of plants in
cultivation.
312
12.4 Why is Begonia a large genus?
The traditional sections in the genus Begonia conform to the ‘hollow curve’
distribution described in the first chapter of this thesis. Simplistically, this
suggests that a lot of things look very similar (therefore are included in a
few big sections) and a few things look very different (therefore are included
in small to monotypic sections). Returning to the graph shown in Chapter 4
(Figure 4.1) it can be seen that over half the known species of Begonia are
contained in only seven sections; the remainder are contained in 55
sections (Figure 12.26).
Figure 12.26:
The number of species per section for Begonia
(from Figure 4.1)
14
13
12
N 11
°
10
9
193
c. 142
122
c. 110
68
62
c. 55
8
7
6
-
54
3
2
14
0
I
Peterm annia
Diploclinium
Pritzelia
Platycentrum
Gireoudia
Begonia
Knesbeckia
TOTAL 752
li
11
193
No. species
Flowever, given that many of these sections (particularly sections
Knesbeckia and Diploclinium) are not good monophyletic groups, it is
clearly preferable to consider phylogeny over traditional classification.
The first question is whether Begonia is a big genus because it is old
(Willis, 1922, Age and Area hypothesis) or because it is young (Cronk,
1989, Relict hypothesis). The evidence strongly favours Cronk’s
hypothesis: the less basal clades (e.g. in America and Asia) are more
species rich, more widely distributed and less differentiated
morphologically; the older lineages (in Africa) are less speciose and better
313
differentiated morphologically^®. Following Cronk (1989), the younger
lineages in Begonia could be described as being in 'bloom' phase, while
the African species may have been ‘depleted by extinction’, leaving them
phenetically distinctive.
Looking back to the ITS phylogram (Figure 7.4) allows consideration of tree
‘stemminess’ (see Figures 1.2 to 1.5 for description). Figure 12.27 is
reproduced from part of Figure 7.24, and shows branch lengths for the
culled manual alignment ITS analysis. Most of the species included in the
African clades are clustered relatively close to the ends of long branches,
while the American and Asian clades, on the other hand, generally have
shorter internal branch lengths. Although this is a broad generalisation, it
supports the view that the African lineages are more ancient and divergent
than the (younger) lineages in Asia and America. From a simplistic
perspective, a casual glance at the ITS matrix (Appendix, 14.7) shows far
greater difficulty in aligning African taxa with each other than aligning all the
Asian and American species together.
although, as Africa Is also the best studied region taxonomically, it could be argued
that these African sections are better delimited.
314
Figure 12.27:
Tree shape, from a phylogram produced by analysis of
the manually aligned, culled ITS data set
(reproduced from Figure 7.24)
Africa
America
5 changes
Asia
Accepting that African lineages show greater divergence than Asian and
American lineages, it is worth asking whether the extant species in the
different continents show a similar trend. One way of assessing this
(assuming that there is some sort of regularity to sequence nucleotide
divergences, i.e. some form of molecular clock) is comparing pairwise
divergences between species in different lineages. Clearly there are risks
of erroneous inference in such an exercise, due to differential taxon
sampling within clades, and the delimitation of the clades selected for
comparison. The clades which have been used correspond to
monophyletic groups, separated by an obvious morphological disjunction.
Comparing traditional sections was not possible due to the paraphyletic
nature of the larger sections in the ITS phylogeny. Relative sampling
densities are discussed below.
315
For section Loasibegonia ITS sequences were obtained for nine of its 19
species. Unfortunately, there is a possibility that the section is paraphyletic,
with Scutobegonia nested within it. Only one of the 21 recognised species
in section Scutobegonia could be included (i.e. ten species have been
sampled from a clade of perhaps 40 species). The uncorrected pairwise
divergences in this clade range from 13% to 1.3%
Another African clade,
Tetraphila i Squamibegonia, has been sampled for ten out of c. 30 species.
Divergences range from 10.3% to 1.1% within the clade.
These can be compared to values obtained for lineages in Asia and
America. Only a very small proportion of the species in these lineages have
been sampled ( 1 2 - 1 3 species out of over 200, Petermannia / Symbegonia
clade; 28 out of over 130, Platycentrum / Sphenanthera clade; 15 out of
over 160, Pritzelia / Weilbachia / Donaldia / Scheidweileria clade). The
uncorrected pairwise divergence values are 0.6% to 8.1% (Petermannia /
Symbegonia clade); 0.1% to 9.5% (Platycentrum / Sphenanthera clade)
and 0% to 20% (Pritzelia ! Weilbachia / Donaldia / Scheidweileria clade).
Divergence ranges are generally higher in the two African lineages, but
there is considerable overlap - enough to say that there must be
equivalently recent species in all clades. The lower sampling levels in Asia
and America mean that the extremes of ranges are less likely to have been
included; therefore the true overlap could be higher. Although there are
many weaknesses in this informal analysis, a preliminary generalisation is
that Begonia species on Africa are unlikely to be orders of magnitude older
than species in Asia and America (and in fact the species are probably of
roughly comparable ages despite the ages of the lineages). This is being
found increasingly in plant phylogenetics - even ancient lineages are
currently composed of modern species (e.g. Selaginella, Bateman pens,
comm., 2000; Araucaria, Setoguchi et al., 1998 - see section 1.4.4 B).
The other major factor in 'tree-shape', which was mentioned in the
introduction and which tells us something about diversification, is balance.
Because the alignment of all 177 taxa in the global ITS analysis is extremely gappy
and, in places, ambiguous, uncorrected pairwise divergence values from the
Compartment analyses (section 7.3.3) are cited.
316
However, because there are problems with the monophyly of some of the
traditional sections, it can be difficult to know how many species are truly in
each clade on the tree.
Figure 12.28 gives very approximate figures for species number per clade,
taken from Doorenbos, Sosef and de Wilde (1998) and reliant on the
assumption that no members of the sections included in each clade truly
belong in another clade. This is, however, false for the African section
Rostrobegonia (clade 1) which has one member (8. sonderana) which
resolves in the Augustia clade (clade 4). Another highly problematic section
is American, Knesbeckia, which resolves in several clades (clades 7, 8 and
9). Due to the uncertaintly surrounding their placement, its 50 - 55 species
have not been added onto the totals for any clade (which partly explains why
the total number of species in the South African / American clade (c. 612) is
not the total of the numbers of species in individual clades (477); the rest of
these ‘missing’ species belong to sections which have not been included
in the analysis). Unsampled sections also explain the discrepancy
between the total Asian species (c. 645) and the sum of the clades in Asia /
Socotra (463). Although section Diploclinium is also polyphyletic, all its
species fall within clade 12 in analyses so far.
317
Figure 12.28: ITS phylogeny of Begoniaceae, with approximate species no.
85.
MAD
DATISC A
D.
D ATISC A
D.
HILLEBR.
H.
SE X A LA R IA B.
ROSTROB. B.
ROSTROB. B.
IGNOTA
B.
C R IS T A S E M B .
FILICIBEG. B.
LOASIBEG. B.
LOASIBEG. B.
LOASIBEG. B.
LOASIBEG. B.
SCUTOBEG. B.
LOASIBEG. B.
LOASIBEG. B.
LOASIBEG. B.
LOASIBEG. B.
M E ZIE R IA B
n e r v ip l a c b :
ER M IN EA
B.
M E ZIE R IA B.
QUADRILO. B.
QUADRILO. B.
QUADRILO. B.
QUADRILO. B.
TETRAPHIL. B.
TETRAPHIL. B.
SQUAM IB. B.
TETRAPHIL. B.
TETRAPHIL. B.
îiîgJgHltj:
S.AF
95
A M _7à
A U G USTIA
ROSTROB.
AUG USTIA
AUG USTIA
A UG USTIA
?
GAERTIA
GAERTIA
SOLANANT.
SOLANANT.
GIREO UD IA
GIREO UD IA
GIREO UD IA
J
C yVEILBACH:
n I
G IREO UDIA
n j
GIREO UD IA
30
T j-G IR E O U D IA
V a ^ G IR E O U D IA
m i
K N ESB EC K .
■
L t " BARYA
B:
B.
B.
B.
B.
B.
B.
r - H YDRIST.
^ ?
BEGONIA
BEGONIA
BEGONIA
BEGONIA
?
RUIZOPAV.
RUIZOPAV. B.
RUIZOPAV. B.
LE P S IA
LE P S IA
I - KNESB EC K.B.
T -Q U A D R IP E R B .
J -T R A C H E L .
B.
B.
^TR A CH EL.
KNESB EC K.B.
DONALDIA B.
?
B.
W A G EN ER . B.
W A G EN ER . B.
?
B.
K N E S B E C K .B .
PR ITZELIA B.
B.
TETRACH.
PRITZELIA B.
PRITZELIA B.
PRITZELIA B.
l
PRITZELIA
PRITZELIA
PRITZELIA
PRITZELIA
SC HEIDW .
iucunda
thomeana
asplenifolia
staudtii
scapigera
duncan-thomasü
letouzeyi
dewildei
prismatocarpa
scutifolla
potamophila
quadrialata
meyeri-johannls
m aaecassa
bognerl
saTaziensis
anakarensis
mananjabensis
nossibea
francoisii
longipetiolata
lor. rnopalocarpa
poculifera
molleri
mannil
kisuluana
horticola
subscutata
capillipes
gabonensis
sutherlandii
geranloides
sonderiana
dregei ‘partita’
dregei
dregei ‘homonyma’
sp., gutt
lubbersii
edmondol
integerrima
solananthera
heracleifolia
sp.. U172
B.
B.
B.
B.
B.
B.
B.
B.
|.
B.
B.
B.
B. involucrata
120
180
glomerata
cannabina
sandwichensis
annobonensis
englerl
johnstonii
violifolia
imperialis
sericoneura
peltata
theimei
manicata
maynensis
boliviensis
cinnabarina
incarnata
fissistyla
sp., Bolivia
odorata
minor
cubensis
obliqua
s p .,W c h .
guadUensis
meridensis
holtonis
fuchsioides
jam esoniana
olbia
gracilis
herbacea
sp., Trachelocarpus
wooinyi
ulmifolia
gfâbr?'^
convolvulacea
sp., macE
acerifoli
valida
a
echinosepala
sp., mac
oxyphylla
rufoserica
angularis
lobata
luxurians
318
IGNOTA
B. fallax
PELTAUG B. socotrana
PELTAUG B. samhahensis
COELOC. B. porteri
COELOC. B. morsei
COELOC. B. masoniana
COELOC. B. mason, mac.
R ID LE Y . B. kingiana
IGNOTA
B. amphioxis
P E TE R M . B. malachosticta
P E TE R M . B. chlorosticta
P E TE R M . B. isoptera
P E TE R M . B. incisa
P E TE R M . B. aequata
P E TE R M . B. serratipetala
P E TE R M . B. sp. cf serratipet.
P E TE R M . B. brevirimosa
P E TE R M . B. sp. cf brevirim.
S Y M B E G . S. sanguinea
S Y M B E G . S. sp., 136
S YM B E G 5 . sp., 121
DIPLOCL B. sp.. Philippine
REIC HEN B. floccifera
?
B. sp., naum
D PLOCL. B. grandis holost.
D P L O C L B. grandis grandis
HAAGIA
B. dipetala
PLATYC
B. beddomei
R E C H E N B. sp., Reich.
REIC HEN . B. rajah
REIC HEN . B. gogoensis
B ARYAND B. oxysperma
D PLOCL. B. sp., 1998 1824
DIPLOCL B. chloroneura
DIPLOCL. B. tayabensis
DIPLOCL. B. labordei
D PLOCL. B. rubella
GNOTA
B. balansana
PLATYC. B. versicolor
PLATYC.
B. sp., Yunnan 26
B. sp. nov. Yunnan
PLATYC.
PLATYC
B. longicarpa 1
PLATYC. B. longicarpa 2
PLATYC. B. sp., Yunnan 25
6 . hatacoa
PLATYC.
PLATYC.
B. sp. Yunnan 33
B. sp. Sulawesi254
?
SPH ENA N B. sp. nov. Philipp.
B. roxburghii
B. deliciosa
B. diadema
PLATYC.
B. rex
B. annulata
B. sp., Yunnan 21
PLATYC.
B. sp., Taiwan
?
DIPLOCL. B. ravenii
B. formosana
PLATYC.
B. sp., Platycent.
PLATYC.
B. palmata 74
PLATYC.
B. hem sleyana
PLATYC.
SPH ENA N B. handelii
SPH ENA N B. menyengensis
SPH ENA N B. acetosella
SPH ENA N B. longifolia
SPH ENA N B. crassirostris
?
B. sp. Sulawesi252
7
B. sp. Sulawesi253
Figure 12.29 provides a summary of the numbers of species per clade
(with provisos as to accuracy, as mentioned previously).
Following Guyer and Slowinski’s (1993) definition of ‘unbalanced’ (having
90% or more of the total number of taxa along the more diverse branch of
the dichotomy), unbalanced nodes are marked onto Figure 12.29 with open
circles.
Summary diagram of species number per clade,
Figure 12.29:
for the 12 clades described previously
Hillebrandia
Cristasemen; Loasibegonia; Scutobegonia
Madagascar: Mezieria; Tetraphila; Squamibegonia
Rostrobegonia; Sexalaria
120
A M ER IC A
Hydristyles; Begonia; Ruizopavonia; Lepsia
180
Quadriperigonia; Trachelocarpus; Donaldia;
Wageneria; Pritzelia, Tetrachia; Scheidweileria
612
Barya; Eupetalum
Solananthera; Gireoudia; Weilbachia
AFRICA
Gaerdtia
Augustia
Peltaugustia; Ignota
ASIA
130
Coelocentrum; Ridleyela; Petermannia;
Symbegonia
330
Diploclinium; Reichenheimia; Haagia; Baryandra;
Playcentrum; Sphenanthera
(clades are not drawn to scale)
The basal nodes in Begoniaceae, and also in both the American and the
Asian clades, are unbalanced. This means that there are differences in the
relative diversification and / or extinction rates between sister groups.
It is not possible to prove that extinction has occurred purely on the basis of
a phylogeny; however it seems likely in the case of a genus which is almost
319
exclusively confined to moist tropical / subtropical forest, and which has
been in Africa over a period when forests are thought to have contracted
and aridification occurred. If the genus did migrate north from Africa into
Eurasia, extinctions are also likely to have occurred there, as it is another
region which has suffered aridification, and temperature cooling.
Thus
extinction could explain the unbalanced nature of many of the nodes within
this ITS phylogeny (e.g. the African / rest of Begonia dichotomy unbalanced
due to increased extinction in the African lineage; the unbalance in the
Asian lineage due to increased extinction in the North of Africa and
Eurasia).
12.5 Overview: The Evolution of Begonia
There is no hard evidence about the age of the genus Begonia: there are no
fossils within the family Begoniaceae (and only the 55 Ma Tetramelaceae
fossil cited in Wagstaff & Dawson, 2000, from a closely related family).
Rough estimates based on sequence divergence are also difficult: ITS is
very divergent between African lineages (which leads to alignment
problems, which means that pairwise differences are highly unreliable
between unrelated clades). It seems likely, however, that the alignment
difficulties between African clades, and between Africa and (Asia/ America)
confirm that African lineages are older than the other lineages in Begonia.
(It is possible that Broulliet’s 1995 pens, comm., that ITS is slow in Begonia,
was due to not including species from Africa in his pilot study).
The similar numbers of species in America and Asia are interesting. Either
Begonia has equivalent spéciation rates in both continents and has been in
each for similar amounts of time, or spéciation and / or extinction rates
differ on each continent and the balance is purely down to chance. There
are certainly many undescribed species in Asia; I am less familiar with
America. It may be that, if these could be taken into account, Asia would
have more species.
Key innovations are difficult to prove; the presence of them should correlate
with increased species richness (Dodd, Silvertown & Chase, 1999).
320
However, unbalanced clades appear to correlate to geographic rather than
morphological changes; thus it appears that the key factor generating
Begonia species is radiation into new habitats. Whether this is adaptive,
into new niches, is debatable. Begonia do fill several obvious ecological
niches (e.g. geophyte, epiphyte) but the majority of species grow happily
under very similar conditions in cultivation, and the evidence for radical
pollinator or disperser specialisation is slim (e.g. bird pollination in
Symbegonia, Barya and Casparya] ant dispersal in species of Tetraphila
(Bouman & de Lange, 1982); bird dispersal in species of Tetraphila,
Squamibegonia and Mezieria', rain-splash dispersal in Platycentrum).
One fairly simple measure, which does not rely absolutely on a molecluar
clock, is lineage diversification rate (In N / 1, where t = the age of a clade,
and N = the number of species in it) (Wojchiechowski, Sanderson & Hu,
1999) (as discussed in Chapter 1, section 1.5.1). The genus Begonia
contains c. 1400 species; I have been reluctant to put an absolute age on it;
based on the datings of land bridges I have hypothesised Begonia might
have used and Tetramelaceae fossils, a rough (and very broad) estimate
would be 60 to 35 million years ago (probably Eocene). These values give
diversification rates of between 0.12 and 0.21 (rates for the whole of
Begonia will be biased downwards, as I expect extinctions to have occurred
in Africa and Eurasia). Erikkson and Bremer’s (1992) median value for
continental plant families is 0.12 spp/Ma; clearly without a narrower date for
the origin of Begonia it is not possible to say whether the genus shows
above-average diversification.
The estimated dates for the Asian and American clades are purely
speculative, based on biogeographic hypotheses with little corroborative
evidence. Assuming Begonia did leave Africa along the Walvis ridge, the
lineage must have separated by 35 Ma. The estimated diversification rate
for the c. 600 American species is then 0.18 spp/Ma. A date of c. 25 Ma for
the c. 645 Asian species would give a diversification rate of 0.26 spp/Ma.
None of these values approach the estimation (Wojciechowski, Sanderson
& Hu, 1999) of 0.71 spp/Ma for Astragalus. From these calculations it would
appear that lineages in Begonia have far lower diversification rates than the
321
extremely large genus Astragalus. To obtain a value as high as c. 0.71 for
1400 species, the genus would have had to have originated in the mid
Miocene, c. 10.2 Ma).
What are lacking are studies on spéciation within Begonia. Hybridisation
and polyploidy have been discussed in Chapter 11 and may contribute
towards isolation and diversification. In addition, the geographical
constraints to clade distribution indicate that allopatric spéciation may be
important in Begonia. Supporting evidence, of limited dispersal providing
the potential for reproductive isolation by distance, comes from population
level studies by Matolweni, Balkwill and McLellan (2000). They showed
differential allelic fixation and high Fst values (the proportion of variation
partitioned between populations) over even small geographic distances.
Further studies are required in order to assess the scale over which
populations become reproductively isolated, and the potential for localised
adaptation and differentiation, particularly in the face of the homogenising
effect of gene flow from sympatric relatives.
322
12.6 Taxonomic Changes Recommended
The aim of this thesis was to produce a phylogeny for the genus Begonia,
and consequently the taxon sampling was directed at covering the
morphological and geographical range of the genus. Although there are
some sections (e.g. Loasibegonia) which are well represented, the levels
of sampling per section are not adequate to produce a robust species level
revision. Also, further analyses with increased sampling may reveal hidden
homoplasy (Sanderson, 1990) and alter the overall topology. Furthermore,
many of the taxa are represented by only one molecular data set (ITS); it is
possible that alternate data sets (perhaps from different genomes) will
affect the clades resolved. Thus any taxonomic comments are to be taken
as preliminary.
However, in gross and micro- morphology there are some convincing
examples of convergence in Begonia - for example, the similarity of flowers
(particularly anther and style types) in Symbegonia in Asia and section
Barya in South America, associated with bird pollination; also the
homoplasy in endothecial cell types between section Petermannia in Asia
and section Solananthera in South America. These cases, between widely
phylogenetically separate taxa, should act as a warning: morphological
convergences between closely related taxa have far more potential to
mislead and may contribute to lack of monophyly in traditional sections.
12.6.1 Genera:
There is a notable exception to the ‘preliminary’ nature
of most of the comments in this chapter. Symbegonia has not always
received generic status (e.g. Brummitt, 1992), and on the basis of results
here and in other studies, should clearly be regarded, at most, as a section
of Begonia. Although the ITS phylogeny does not resolve Symbegonia as
monophyletic, and includes it within the section Petermannia, the
morphological synapomorphies of the erstwhile genus (its extremely
distinctive androecium and unique anther endothecial cells) suggest that
adding more sequence data may recover its monophyly (i.e. that the
problem is the lack of ITS characters in this part of the phylogeny). The
inclusion of Symbegonia in Begonia does not just rest on ITS and 26S data
alone - trnC-trnD (Badcock, 1998), rbcL and 18S (Swensen, Luthi &
323
Rieseberg, 1998) sequence data and morphological data all place
Symbegonia deeply within Begonia.
Some may argue against the sinking of this genus into Begonia, given that
it is easily recognisable in the field as a separate entity (Sands, pens,
comm., 2000). However, not only are there several other sections in the
genus for which such an argument could be made {Tetraphila (Africa),
Peltaugustia (Socotran archipelago) and Trachelocarpus (America) for
example), but treating Symbegonia as a separate genus implies that it is
comparable to other genera - anyone unfamiliar with the true relationships
may wonder how one genus in the Begoniaceae is so species rich (with
around 1400 species) while another contains only around 14 species.
Obviously, in the light of phylogeny, such comparisons are meaningless.
One important consideration is the role sections should have: are they
practical subdivisions or should they reflect common evolutionary history?
All the available evidence suggests that the taxon Symbegonia has evolved
from within section Petermannia, rendering Petermannia paraphyletic if
Symbegonia is even given sectional status. As yet, Begonia classifications
do not go below the sectional level; with about 200 species in section
Petermannia (and the additional c. 14 from Symbegonia) there is clearly a
need for some subsectional division. Until this is in place, ‘losing’
Symbegonia amongst this huge morass of species would be foolish and
its sectional status should therefore be upheld on this purely practical
criterion.
The Begoniaceae appear to be a good natural group; within the family, the
characters which separate Hiliebrandia and Begonia are clear-cut, relating
to tepal number, to the mode of dehiscence of the fruits, and to the position
of the ovary. No such suite can be cited to distinguish sections of Begonia]
although it may be possible to hive off some of the distinct African sections
as separate genera, the obvious morphological divisions would leave
Begonia para- (or even poly-) phyletic. Further, even given the (perhaps
laudable) aim of restricting Begonia to a more manageable size, excising
Africa would not accomplish it - although most of the morphological and
324
molecular divergence of the genus is African, most of the species are Asian
and American. There are c. 140 species in Africa, and c. 1260 in Asia and
America. The type, 8. obliqua L., is an American species, section Begonia]
therefore the name would remain with the exuberance.
12.6.2 Madagascan species:
The monophyly of the Madagascan
species is certainly strongly suggested by ITS and 268 data. However,
incorporating all Madagascan species within a single section may not be
the best way of dealing with them. Although this would be phylogenetically
informative, this, although desirable, is not the sole purpose of sectional
classifications. There are at least 48 species of Begonia on Madagascar
(de Lange & Bouman, 1992) (judging by a recent RBG Kew expedition to
Ambatoraky reserve on the northeast of the island (Baker, pens, comm.,
2000) there are many more to be found), and one purpose of subgeneric
classification must be to facilitate identification of these in the field. Due to
sampling limitations, it is not possible to say whether the sections which
are currently recognised are monophyletic, as only one individual was
sampled from sections Erminea and Nerviplacentaria. Further, there are
some doubts as to the usefulness of the current sections; the most recent
flora of Madagascar (Keraudren-Aymonin, 1983) abandoned sectional
treatment as untenable. However, there is certainly a place for some form
of subdivision (whether sections or subsections) within the Madagascan
species; a thorough cladistic analysis of the species on the island is
required before this can be attempted.
12.6.3 African species: Section Mezieria resolves as polyphyletic in this
study, despite only two species from the section being included.
Suggestions that there are problems with this section can be found in the
taxonomic revision published by Klazenga, de Wilde and Quene (1994).
They produce a morphological cladogram based on eight characters, which
gives four equally parsimonious trees. Of these trees, they accept the only
one which is fully resolved (which gives a monophyletic Mezieria).
However, the two characters which appear as synapomorphies for the
section show reversals within the section. Furthermore, in two of the other
equally parsimonious trees Mezieria is not monophyletic. Their study
325
includes six species within Mezieria, and two outgroups (section
Baccabegonia and section Squamibegonia). Clearly, in the light of the ITS
phylogeny, this is an inadequate test of monophyly; such a study should
also contain the Madagascan species, as well as species from section
Tetraphila. Such a study is currently being undertaken by Vanessa Plana,
RBGE.
Without including more species from Mezieria in analyses, it is not
possible to draw many conclusions, and perhaps greater sampling will
lead to topological changes. However, on the basis of the ITS analyses
presented here, it appears that B. meyeri-johannis should not be included
in section Mezieria (the type of which is B. salaziensis). The inclusion of B.
meyeri-johannis within section Mezieria has previously been questioned,
because it differs from the other species by “its 5-locular ovaries with 5
styles, unisexual inflorescences and lianoid habit” (Klazenga, de Wilde &
Quene, 1994, p. 310) (although they drew the opposite conclusion, that
there is “neither a need nor a justification to establish a new section to
accommodate B. meyeri-johannis”', loc. cit., p. 310).
There are currently 63 recognised sections and c. 1400 species in Begonia
(mean section size 22.2; a more accurate representation of section size is
in the graph in Chapter 4, Figure 4.1). In the interests of monophyly, this
high number of sections should be reduced (e.g. the loss of sections
Scheidweileria, Squamibegonia, Lepsia, Baryandra). In some cases this
would render large and unwieldy sections even larger and less wieldy; in
these cases, species level revisions are required to search for workable
subdivisions (e.g. subsections). This project is limited to circumscribing
suitable clades as starting points for such revisions (e.g. clades 1 to 12, as
described in this chapter and in chapter 11) and to provide a framework for
future workers to evaluate the phylogenetic placement and taxonomic
affinities of as yet unsampled species.
326
12.7 Summary
While the geographic origins of the family Begoniaceae cannot be
determined on the basis of these analyses, the oldest lineages in the
genus Begonia appear to be found on the African continent. From Africa
Begonia probably dispersed to, and radiated in, Asia and South America. In
South America, it seems likely that Begonia arrived in Brazil, and that
several lineages have migrated north and west from Brazil; independent
clades have members in Mexico and in the Andean region. Within Asia
there are two main clades, one predominantly continental and one
predominantly on the Malesian islands. No taxa are thought to have
reached Australia. Given the hypothesis that Begonia left Africa by a Walvis
Ridge/Rio Grande Rise route to the west (the Walvis ridge would have been
completely submerged by the end of the Eocene, about 35 million years
ago), and into Eurasia to the north east (less than 23 million years ago), the
lineage ‘Begonia’ must have originated, at the latest, during the Eocene
(between 56.5 and 35.4 million years ago).
327
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14
Appendices
14.1
A.
B.
List of large genera - by family
List of large genera - by size
14.2
Famiiies which contain iarge genera
14.3
List of fossil record for large genera
14.4
Comparison between ITS tree, Loasibegonia I
Scutobegonia, and S osef s (1994) tree
14.5
Herbarium specimens included in morphological
analyses
359
14.1A:
Large Vascular Plant Genera, from Mlnelll
1993, arranged according to Species
Number
FAMILY
GENUS
Cyperaceae
Euphorbiaceae
Piperaceae
Fabaceae
Solanaceaea
Begoniaceae
Asteraceae
Fabaceae
Orchidaceae
Melastomataceae
Myrtaceae
Orchidaceae
Piperaceae
Rubiaceae
Lamiaceae
Orchidaceae
Balsaminaceae
Dioscoriaceae
Ericaceae
Orchidaceae
Euphorbiaceae
Moraceae
Ericaceae
Aspleniaceae
Araceae
Caryophylaceae
Fabaceae
Oxalidaceae
Pandanaceae
Selaginellaceae
Alliaceae
Orchidaceae
Convoivulaceae
Cyatheaceae
Acanthaceae
Asteraceae
Euphorbiaceae
Fabaceae
Myrtaceae
Orchidaceae
Ranuncuiaceae
Myrtaceae
Asteraceae
Asteraceae
Asteraceae
Berberidaceae
C arex
2000
Euphorbia
2000
P ip e r
2000
Astragalus
1750
Solarium
1700
Begonia
1400
Senecio
1250
A cacia
1200
Pleurothallis
1120
Miconia
1000
Syzygium
1000
Bulbophyllum
1000
Peperomia
1000
Psychotria
800-1500
Salvia
900
Dendrobium
900
Im patiens
850
Dioscorea
850
Rhododendron
850
Epidendrum
800
Croton
750
Ficus
750
Erica
735
Asplénium
720
Anthurium
700
Silene
700
Indigofera
700
O xalis
700
Pandanus
700
Selaginella
700
Allium
690
Oncidium
680
Ipom oea
650
C yathea
620
Justicia
600
Helichrysum
600
Phyllanthis
600
Crotalaria
600
Eucalyptus
600
Habenaria
600
Ranunculus
600
Eugenia
550
Veronina
500
Cousinia
500
Centaurea
500
Berberis
500
SPP No.
FAMILY
GENUS
SPP No.
Poaceae
Polygonaceae
Rosaceae
Eriocaulaceae
Fabaceae
Ebenaceae
Ericaceae
Fabaceae
Euphorbiaceae
Passifloraceae
Primulaceae
Aquifoliaceae
Dryopteridaceae
Eriocaulaceae
Fabaceae
Fagaceae
Lamiaceae
Lauraceae
Lomariopsidaceae
Melastomataceae
Rubiaceae
Salicaeae
Violaceae
Bromeliaceae
Clusiaceae
Gentianaceae
Asteraceae
Scrophulariacae
Asteraceae
Cyperaceae
Geraniaceae
Lamiaceae
Lycopodiaceae
Rubiaceae
Rubiaceae
Asteraceae
Myrsinaceae
Myrtaceae
Guttiferae
Oleaceae
Urticaceae
Panicum
Polygala
Potentilla
Paepalanthus
Mimosa
Diospyros
Vaccinium
Desmodium
Acalypha
Passiflora
Primula
Ilex
Diplazium
Eriocaulon
Tephrosia
Quercus
Clerodendrum
Litsea
Elaphoglossum
Medinilla
P avetta
Salix
Viola
Tillandsia
Hypericum
G entiana
Artem esia
Peduncularis
Saussurea
Cyperus
Geranium
Hyptis
Huperzia
Galium
Ixora
A s ter
Ardisia
Myricia
Garcinia
Jasminum
Pilea
500
500
500
485
480
475
450
450
430
430
425
400
400
400
400
400
400
400
400
400
400
400
400
380
370
361
350
350
300
300
300
300
300
300
300
250
250
250
200
200
200
A uthorities as given in tab le 1 4.3
360
14.1 B:
Large Vascular Plant Genera, from Mlnelll,
1993, arranged according to Family
FAMILY
GENUS
SPP No.
FAMILY
GENUS
Acanthaceae
Alliaceae
Aquifoliaceae
Araceae
Aspleniaceae
Asteraceae
Asteraceae
Asteraceae
Asteraceae
Asteraceae
Asteraceae
Asteraceae
Asteraceae
Balsaminaceae
Begoniaceae
Berberidaceae
Bromeliaceae
Caryophylaceae
Clusiaceae
Convoivulaceae
Cyatheaceae
Cyperaceae
Cyperaceae
Dioscoriaceae
Dryopteridaceae
Ebenaceae
Ericaceae
Ericaceae
Ericaceae
Eriocaulaceae
Eriocaulaceae
Euphorbiaceae
Euphorbiaceae
Euphorbiaceae
Euphorbiaceae
Fabaceae
Fabaceae
Fabaceae
Fabaceae
Fabaceae
Fabaceae
Fabaceae
Fagaceae
Gentianaceae
Geraniaceae
Guttiferae
Lamiaceae
Justicia
Ailium
Ilex
Anthurium
Asplénium
Senecio
Helichrysum
Centaurea
Cousinia
Veronina
Artem esia
Saussurea
A s ter
Im patiens
Begonia
Berberis
Tillandsia
Silene
Hypericum
Ipomoea
Cyathea
Carex
Cyperus
Dioscorea
Diplazium
Diospyros
Rhododendron
Erica
Vaccinium
Paepalanthus
Eriocaulon
Euphorbia
Croton
Phyllanthis
Acalypha
Astragalus
Acacia
Indigofera
Crotalaria
Mimosa
Desmodium
Tephrosia
Quercus
Gentiana
Geranium
Garcinia
Salvia
600
690
400
700
720
1250
600
500
500
500
350
300
250
850
1400
500
380
700
370
650
620
2000
300
850
400
475
850
735
450
485
400
2000
750
600
430
1750
1200
700
600
480
450
400
400
361
300
200
900
Lamiaceae
Lamiaceae
Lauraceae
Lomariopsidaceae
Lycopodiaceae
Melastomataceae
Melastomataceae
Moraceae
Myrsinaceae
Myrtaceae
Myrtaceae
Myrtaceae
Myrtaceae
Oleaceae
Orchidaceae
Orchidaceae
Orchidaceae
Orchidaceae
Orchidaceae
Orchidaceae
Oxalidaceae
Pandanaceae
Passifloraceae
Piperaceae
Piperaceae
Poaceae
Polygonaceae
Primulaceae
Ranuncuiaceae
Rosaceae
Rubiaceae
Rubiaceae
Rubiaceae
Rubiaceae
Salicaeae
Scrophulariacae
Selaginellaceae
Solanaceaea
Urticaceae
Violaceae
Clerodendrum
400
Hyptis
300
Litsea
400
Elaphoglossum 400
Huperzia
300
Miconia
1000
Medinilla
400
Ficus
750
Ardisia
250
Syzygium
1000
Eucalyptus
600
Eugenia
550
Myricia
250
Jasminum
200
Pleurothallis
1120
Bulbophyllum
1000
Dendrobium
900
Epidendrum
800
Oncidium
680
Habenaria
600
Oxalis
700
Pandanus
700
Passiflora
430
Piper
2000
Peperomia
1000
Panicum
500
Polygala
500
Primula
425
Ranunculus
600
Potentilla
500
Psychotria
800-1500
P av etta
400
Galium
300
Ixora
300
Salix
400
Peduncularis
350
Selaginella
700
Solanum
1700
Pilea
200
Viola
400
Authorities as given in table 14.3
361
SPP No.
14.2;
Families which contain large genera
(as listed in Minelli, 1993), arranged
according to total number of species
(from Mabberley, 1997).
GRADE
FAMILY
DICOT
MONOCOT
DICOT
DICOT
MONOCOT
DICOT
DICOT
DICOT
DICOT
DICOT
MONOCOT
DICOT
DICOT
DICOT
DICOT
DICOT
DICOT
DICOT
MONOCOT
DICOT
FERN
DICOT
DICOT
MONOCOT
DICOT
DICOT
DICOT
DICOT
DICOT
MONOCOT
DICOT
DICOT
MONOCOT
MONOCOT
DICOT
DICOT
DICOT
DICOT
FERN
DICOT
Asteraceae
Orchidaceae
Fabaceae
Rubiaceae
Poaceae
Euphorbiaceae
Lamiaceae
Scrophulariacae
Melastomataceae
Myrtaceae
Cyperaceae
Acanthaceae
Ericaceae
Piperaceae
Solanaceaea
Lauraceae
Rosaceae
Ranuncuiaceae
Bromeliaceae
Caryophylaceae
Dryopteridaceae
Convoivulaceae
Clusiaceae
Araceae
Gentianaceae
Myrsinaceae
Polygonaceae
Moraceae
Urticaceae
Eriocaulaceae
Begoniaceae
Dioscoriaceae
Pandanaceae
Alliaceae
Primulaceae
Balsaminaceae
Violaceae
Oxalidaceae
Aspleniaceae
Geraniaceae
Selaginellaceae
Berberidaceae
Cyatheaceae
Oleaceae
Passifloraceae
Lomariopsidaceae
Ebenaceae
Salicaeae
Aquifoliaceae
Lycopodiaceae
DICOT
TREE FERN
DICOT
DICOT
FERN
DICOT
DICOT
DICOT
CLUBMOSS
No. GENERA
1528
788
642
630
668
313
252
269
188
129
98
229
107
8
94
52
95
62
59
87
47
56
45
47
78
33
46
38
48
9
2
8
3
30
22
2
20
6
1
11
1
15
1
24
17
6
2
2
4
4
No. SPP
No.SPP
No. GENERA
22750
18500
18000
10200
9500
8100
6700
5100
4950
4620
4350
3450
3400
3000
2950
2850
2825
2450
2400
2300
1700
1600
1370
1325
1225
1225
1100
1100
1050
1000
900
880
875
850
825
820
800
775
720
700
700
680
620
615
575
525
485
435
420
380
14.89
23.48
28.04
16.19
14.22
25.88
26.59
18.96
26.33
35.81
44.39
15.07
31.78
375.00
31.38
54.81
29.74
39.52
40.68
26.44
36.17
28.57
30.44
28.19
15.71
37.12
23.91
28.95
21.88
111.11
450.00
110.00
291.67
28.33
37.50
410.00
40.00
129.17
720.00
63.64
700.00
45.33
620.00
25.63
33.82
87.50
242.50
217.50
105.00
95.00
362
14.3;
Large vascular plant genera which appear
in the Plant Fossil Record, arranged by
genus size
FAMILY
GENUS
No. SPP
FOSSIL RECORD
Cyperaceae
Euphorbiaceae
Piperaceae
Fabaceae
Solanaceaea
Begoniaceae
Asteraceae
Fabaceae
Rubiaceae
Orchidaceae
Orchidaceae
Melastomataceae!
Piperaceae
Myrtaceae
Orchidaceae
Lamiaceae
Dioscoriaceae
Balsaminaceae
Ericaceae
Orchidaceae
Euphorbiaceae
Moraceae
Ericaceae
Aspleniaceae
Araceae
Fabaceae
Oxalidaceae
Pandanaceae
Selaginellaceae
Caryophylaceae
Alliaceae
Orchidaceae
Convoivulaceae
Cyatheaceae
Fabaceae
Myrtaceae
Orchidaceae
Asteraceae
Acanthaceae
Euphorbiaceae
Ranuncuiaceae
Myrtaceae
Berberidaceae
Asteraceae
Asteraceae
Poaceae
Polygonaceae
Rosaceae
Asteraceae
Eriocaulaceae
Fabaceae
Ebenaceae
Fabaceae
Poaceae
Ericaceae
Euphorbiaceae
Asteraceae
Passifloraceae
Primulaceae
Lamiaceae
Dryopteridaceae
C arex L.
Euphorbia L.
P ip e r L.
A stragalus L.
Solanum L.
Begonia L.
Senecio L.
Acacia Miller
P sychotria L.
Pleurothallis R.Br.
Bulbophylium Thouars.
Miconia Ruiz & Pavon
Peperom ia Ruiz & Pavon
Syzygium Gaertner
Dendrobium Sw.
Salvia L.
Dioscorea L.
Im patiens L.
Rhododendron L.
Epidendrum L.
Croton L.
Ficus L.
Erica L.
Asplénium L.
Anthurium Schott
Indigofera L.
O xalis L.
P andanus Parkinson
Selaginella Pal.
Silene L.
Allium L.
Oncidium Sw.
Ipom oea L.
C yathea Sm.
Crotalaria L.
Eucalyptus L'Herit.
Habenaria Willd.
Helichrysum Miller
Justicia L.
Phyllanthis L.
Ranunculus L.
Eugenia L.
Berberis L.
Centaurea L.
Cousinia Cass.
Panicum L.
Polygala L.
Potentilla L.
Veronina L.
Paepalanthus Kunth
M im osa L.
Diospyros L.
Desm odium Desv.
F estuca L.
Vaccinium L.
A calypha L.
Mikania Willd.
Passiflora L.
Primula L.
Clerodendrum L.
Diplazium Sw.
2000
2000
2000
1750
1700
1400
1250
1200
1200
1120
1000
1000
1000
1000
900
900
850
850
850
800
750
750
735
720
700
700
700
700
700
700
690
680
650
620
600
600
600
600
600
600
600
550
500
500
500
500
500
500
500
485
480
475
450
450
450
430
430
430
425
400
400
Pliocene
363
Pleistocene
Oligocene
Eocene
Cretaceous
Oligocene
Cretaceous
Miocene
Cretaceous
Pleistocene
Cretaceous
Oligocene
Cretaceous
Pliocene
Oligocene
Pliocene
Cretaceous
Miocene
Oligocene
Lomariopsidaceae
Eriocaulaceae
Aquifoliaceae
Lauraceae
Melastomataceae
Rubiaceae
Fagaceae
Salicaeae
Fabaceae
Violaceae
Bromeliaceae
Araceae
Clusiaceae
Gentianaceae
Asteraceae
Fabaceae
Orchidaceaae
Lauraceae
Scrophulariacae
Cyperaceae
Rubiaceae
Geraniaceae
Lycopodiaceae
Lamiaceae
Rubiaceae
Juncaceae
Campanulaceae
Actinidiaceae
Asteraceae
Ranuncuiaceae
Geraniaceae
Myrsinaceae
Asteraceae
Capparidaceae
Myrtaceae
Apiaceae
Poaceae
Iridaceae
Brassicaceae
Clusiaceae
Oleaceae
Verbeniaceae
Cactaceae
Hyacinthaceae
Urticaceae
Lamiaceae
Dryopteridaceae
Anacardiaceae
Elaphoglossum Schott ex J.Sm.
Eriocaulon L.
Ilex L.
Litsea Lam.
Medinilla Gaudich
P a v e tta L.
Q uercus L.
Salix L.
Tephrosia Pers.
Viola L.
Tillandsia L.
Philodendron Schott
Hypericum L.
G entiana L.
A rtem esia L.
Inga Miller
Liparis Rich.
O cotea Aublet
Peduncularis L.
Cyperus L.
Galium L.
G eranium L.
H uperzia Bernh.
Hyptis Jacq.
Ixora L.
Juncus L.
Lobelia L.
Saurauia Willd.
Saussurea DC
Ciem atis L.
Pelargonium
Ardisia Sw.
A s te r L.
Capparis L.
Myrcia DC ex Guillemin
Eryngium L.
Digitaria Haller
Iris L.
Erysimum L.
Garcinia L.
Jasm inum L.
Lippia L.
Opuntia Miller
Omithogalum L.
Pilea Lindley
Plectranthus L'Herit.
Polystrichum Roth
Rhus L.
400
400
400
400
400
400
400
400
400
400
380
375
370
361
350
350
350
350
350
300
300
300
300
300
300
300
300
300
300
295
270
250
250
250
250
240
220
210
200
200
200
200
200
200
200
200
200
200
Cretaceous
Cretaceous
Palaeocene
Miocene
Neogene
Oligocene
Pleistocene
* denotes genera not in Minelli’s list (1993) but found in a quick look through Mabberley
(1997). List therefore appears to be less reliable for the ‘smaller’ genera; those of less than
400 species are not included in any further discussion.
Fossil record data from the Plant Fossil Record (http://ibs.uel.ac.uk/palaeo/pfr2/pfr.htm) from
searching by extant genus name. Therefore form genera will not have been found.
364
14.4:
Comparison between the ITS tree,
Loasibegonia I Scutobegonia, and
Sosefs (1994) tree
Sosef (1994) produced a cladogram for the sections Loasibegonia and
Scutobegonia. This cladogram was based on an analysis of 132
morphological and anatomical characters, for 44 taxa (four of which were
regarded as outgroups). Of all these ingroup taxa, only nine were
sequenced for ITS. Still, a quick comparison can be made between the
relationships suggested by Sosefs analysis, and those suggested by the
ITS analysis. The branching diagram on the left is the most parsimonious
tree for the ITS data set (from Chapter 7, Figure 7.7, rooted on 8.
aspieniifo!ia)\ the branching diagram on the right is not a most
parsimonious tree for Sosefs data, but represents the relationships
suggested by pruning all the extraneous taxa from his “conclusive
cladogram” (Sosef, 1994, Figure 11.17, p. I l l , rooted on section
Filicibegonia).
Figure 14.1: Comparison between ITS MPT & Sosefs analysis
morphology
(Sosef, 1994, Fig. 11.17)
ITS
(compartment no. 1 )
o---
rO-
B. letouzeyi
“
B. duncan-thomasii “
B. scapigera
LO-
Loasibegonia
o-------
Filicibegonia
—
B. staudtii
“
B. potamophila
""
B. quadrialata
“
B. scutifolia
“
B. prismatccarpa ”
PI
^u to b eg on ia
T T "0
O
represents sections
B. dewildei
“
—
D—
Loasibegonia
—
Di
Oi
if
Scutobegonia
- O
-o
Q represent the groups described in Sosef
365
The only species from section Scutobegonia which was included in the ITS
analysis is B. dewildei. Its position changes radically between the two
trees: in the ITS tree, section Loasibegonia is paraphyletic, and includes
section Scutobegonia] Sosefs tree is consistent with both sections being
monophyletic (as is shown in his unpruned tree). It may be that the
inclusion of more taxa from section Scutobegonia in the ITS analyses will
pull B. dewildei out of section Loasibegonia. Unfortunately the other taxon
from this section which is in cultivation, B. hirsutula, did not amplify for ITS.
It would also be useful to rerun Sosefs analyses using only the taxa
included in the ITS analysis.
Sosef breaks the taxa he has examined into seven monophyletic groups.
ITS shows a sister-group relationships between B. letouzeyi and B.
duncan-thomasii. In Sosefs cladogram there are six taxa in this clade; he
calls it ‘the B. letouzeyi group’. B. scapigera and B. staudtii belong to
Sosefs ‘B. scapigera group’. This is not supported by the ITS data, which
resolve this group as paraphyletic with the B. letouzeyi group’. Sosefs B.
potamophila group’ is represented here by B. potamophila, B.
prismatccarpa, B. scutifolia and B. quadrialata. Although ITS supports the
monophyly of this group, it resolves the relationships within it differently. B.
dewildei is the only included representative from Sosefs B. ferramica
group’.
For an example of the morphological characters which hold together one of
Sosefs groups, see his Figure 11.11 (p. 105), the ‘B. scapigera group’.
This is supported by three synapomorphies:
Ch. 65: Ovary shape (narrowly elliptical - obovate TO narrowly oblong - narrowly elliptic)
Ch. 71: Wing shape (linear - obovate TO linear)
Ch. 114:Placenta shape (lobed, thickened TO not or weakly lobed, strongly thickened).
Each of these characters has overlapping states; further, character 114 has
a reversal in B. staudtii. In the ITS analysis, the clade with B. scapigera, B.
duncan-thomasii and B. letouzeyi has Bremer support value 12, and 100%
bootstrap support. The ITS analysis is not necessarily more reliable, but
caution needs to be taken with morphology, especially when analyses
include quantitative or overlapping characters.
366
14.5
Herbarium specimens inciuded in
morphologicai anaiyses (from E).
B. aequataA. Gray. Wilkie, P., Argent, C.G.C., Mendum, M., Pennington,
R.T., Romero, E.M. & Fuentes, R.E. Philippines RBGE accession
1997 2515: Luzon Island: Camarines Sur.: Naga Province. Barangay
Panicuason: Mt. Isarog, west slope. On tree in lower submontane
forest, 1200 m. 13°39' N,123°21’E. Climber.
B. formosana (Hayata) Masamune. Edinburgh Taiwan Expedition (1993)
no. 24, 31 X 1993. Taiwan: Maioli Hsian, Tahsueh Shan, line 210 at
25 km. Warm temperate coniferous forest, codominant with
Fagaceae. Shady moist woodland slopes in very organic soil.
2145 m. 24° 15' N, 121°5’E.
B. oxysperma A.DC. Wilkie, P., Argent, C.G.C., Mendum, M., Pennington,
R.T., Romero, E.M. & Fuentes, R.E. No. 29142. Philippines: Luzon
Island: Camarines Sur.: Naga Province. Barangay Panicuason: Mt.
Isarog, west slope. On tree in lower submontane forest, mostly on
tree ferns, 1200 m. 13°39' N, 123°2TE. Epiphytic climber.
RBGE accession 1997 2519.
B. rufo-serica Toledo C l 1195, 4 v 1977. RBGE accession no. 1964 3108,
G35. RBGE cultivated plants.
B. serratipetala Irmsch. Reeves no. 588, vii 1983. Waimeram, Paiela
Census Division, Porgera District, Enga Province. Terrestrial - old
garden, also planted near houses by local people. 1800 m.
B. sp. ‘exotica’ (= B. cf. brevirimosa). T.M. Reeves no. 142, xii 1981.
Korombi: Paiela Census Division, Purgera District, Enga Province.
Terrestrial in shaded forest. 1500 m.
B. sp., Sulawesi 252. Argent, G., Mendum, M. & Hendrian no. 00116, 20 ii
2000. Lake Poso, south Sulawesi, c. 2°24’ S, 120°48’ E. Roadside
ditch in shade in disturbed rain forest, c. 1150 m.
B. sp., Sulawesi 253. Argent, G., Mendum, M. & Hendrian no. 00151, 25 ii
2000. Mt Sojol, Central Sulawesi, c. 0° 40’ S, 120° 10’ E. Valley
bottom in shade of rain forest, c. 600 m.
B. sp., Sulawesi 254. Argent, G., Mendum, M. & Hendrian no. 00152, 25 ii
2000. Mt Sojol, Central Sulawesi, c. 0° 40’ S, 120° 10’ E. Valley
bottom in shade of rain forest, c. 600 m.
367
LIEK .
'