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OPEN
The genetic legacy
of fragmentation
and overexploitation
in the threatened medicinal African
pepper‑bark tree, Warburgia
salutaris
Annae M. Senkoro 1,2, Pedro Talhinhas 3, Fernanda Simões 4, Paula Batista‑Santos 3,
Charlie M. Shackleton 1, Robert A. Voeks5, Isabel Marques 6* & Ana I. Ribeiro‑Barros 6*
The pepper‑bark tree (Warburgia salutaris) is one of the most highly valued medicinal plant species
worldwide. Native to southern Africa, this species has been extensively harvested for the bark, which
is widely used in traditional health practices. Illegal harvesting coupled with habitat degradation
has contributed to fragmentation of populations and a severe decline in its distribution. Even
though the species is included in the IUCN Red List as Endangered, genetic data that would help
conservation efforts and future re‑introductions are absent. We therefore developed new molecular
markers to understand patterns of genetic diversity, structure, and gene flow of W. salutaris in
one of its most important areas of occurrence (Mozambique). In this study, we have shown that,
despite fragmentation and overexploitation, this species maintains a relatively high level of genetic
diversity supporting the existence of random mating. Two genetic groups were found corresponding
to the northern and southern locations. Our study suggests that, if local extinctions occurred in
Mozambique, the pepper‑bark tree persisted in sufficient numbers to retain a large proportion of
genetic diversity. Management plans should concentrate on maintaining this high level of genetic
variability through both in and ex-situ conservation actions.
Medicinal plants have been used worldwide since ancient times, being particularly relevant in the developing
world where ca. 80% of the population rely on these resources to fulfil their basic health care needs1–4. Additionally, at the global level the importance of bio-based compounds continues to grow and phytochemical research
towards the identification of new active compounds of medical and nutritional importance is among top research
priorities (e.g.5–14).
Sub-Saharan Africa harbours a vast repository of plant biodiversity, with 45,000 known vascular plant
species15, many of which are used in traditional medicine16–20. However, efforts to safeguard this biodiversity
are often compromised by anthropogenic pressures, with proximal drivers being land transformation, synergistic
impacts of fires, grazing, climate change and harvesting (c.f.17,21–27), and growing commercialisation of medicinal
plant in high demand (c.f.17,28,29). The last is motivated by preferences for certain species due to cultural identity,
traditions, and lower costs in comparison with modern pharmaceuticals, even under circumstances of access to
modern medical facilities21,30. On the other hand, the conservation status of many endemic and native species is
1
Department of Environmental Science, Rhodes University, Grahamstown 6140, South Africa. 2Departmento
de Ciências Biológicas, Universidade Eduardo Mondlane CP 257, Maputo, Moçambique. 3Linking Landscape,
Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, Tapada
da Ajuda, 1349-017 Lisbon, Portugal. 4Instituto Nacional de Investigação Agrária E Veterinária, Av. da República,
Quinta Marquês, Edificio Sede, 2780-157 Oeiras, Portugal. 5Department of Geography and the Environment,
California State University, 800 N State College Blvd, FullertonFullerton, CA 92831, USA. 6Forest Research
Centre (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisbon,
Portugal. *email: isabelmarques@isa.ulisboa.pt; aribeiro@isa.ulisboa.pt
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poorly understood31,32 and many natural populations may be at risk. Current exploitation rates, often in tandem
with other pressures like fire, invasive species, browsing and land transformation, threaten wild populations
unless management methods are established, including community-based approaches17,21,30.
Under the current scenario of climate change and human population growth, the use of genomic tools is valuable to understand species evolution and adaptation in natural ecosystems33,34. The importance of phylogenetic
data, genetic diversity, and population structure analyses to characterize the biodiversity of wild species has
been well-established in numerous studies (e.g.35–39). Microsatellites (Single Sequence Repeats, SSR) are amongst
the most efficient and widely used markers for these studies as they are codominant and highly polymorphic
loci40. Although these markers are species specific, the increasing accessibility to next-generation sequencing41
has enabled the development of SSRs for the so-called orphan, neglected or wild crop relative species (e.g.42–45),
although sequencing large plant genomes still remains a challenge46.
The pepper-bark tree, Warburgia salutaris (Bertol.) Chiov. (Family Canellaceae) is one of the most widely
used and traded medicinal plants in southern Africa47. This slow growing species is part of an early diverging
group of basal angiosperms, thought to be native to eastern and southern Africa48. However, subsequent studies
confined the distribution of W. salutaris to only a sub-region of southern Africa, i.e. South Africa21,49, Eswatini
(previously known as Swaziland)24,50, Zimbabwe29,51–53, Malawi54 and Mozambique55. This species is commonly
used to treat several ailments such as common colds, throat and mouth sores, or coughs47,48.
In the past, sustainable harvesting of medicinal plants was regulated through traditional practises such as
taboos, restrictions and harvesting tools30. However, with commercial demand increasing, W. salutaris groves
were repeatedly raided by harvesters that often debarked the whole tree, especially mature plants56. Severe
harvesting resulted in high tree mortality in many areas and in the extinction of many local populations21,24,57
and consequently, W. salutaris is considered threatened throughout its range50,58,59, and listed as an Endangered
Species in the IUCN Red List57. The most extreme case is that of Zimbabwe, where the species is listed as extinct
in the wild29,60. That resulted in the import of bark supplies in the late 1990s from Mozambique and South
Africa53 being later trafficked from the same countries29. For instance, in South Africa, 43% of W. salutaris
bark in the Johannesburg main market originated from Mozambique, with annual traded amounts estimated
at 500–1000 kg28. As a result, populations of W. salutaris in Mozambique are currently restricted to fragmented
patches in the Lebombo Mountains, Tembe River and Futi Corridor (Fig. 1)48. According to the Red List classification for Mozambique, this species is considered Vulnerable VU A2 cd58. Despite this critical situation, only
a few studies on the populations dynamics of W. salutaris are available; of the 60 research and review papers
available in the Web of Science on W. salutaris on 05 February 2020, only seven addressed this topic21,24,48,61–63
while the vast majority are focused on the medicinal applications of this species. Nevertheless, amplified fragment length polymorphisms (AFLPs) have been used to solve genetic relationships between W. ugandensis, W.
salutaris and W. stuhlmanni showing a high degree of genetic variation among individuals within populations
as well as between populations62.
In this work, we have developed SSRs markers for W. salutaris to investigate the genetic legacy of exploitation
in this slow growing species and to contribute to future re-introduction actions. For that, we have used its best
known area of occurrence, Mozambique (Fig. 1) to addressed the following questions: (1) How is genetic diversity distributed within and among individuals across geographical areas?; (2) Is the genetic structure associated
with the geographical distribution?; and (3) Is there any evidence of inbreeding or lack of gene flow between
populations?
Results
Genetic diversity.
For each locus, the numbers of alleles varied from three (13-N1132836, 16-N1150626
and 18-N1173706 locus) to nine (31-N2284857 and 43-N1009973 locus) with an average of 5.8 ± 2.3 alleles per
locus and a total of 58 alleles considering all loci (Table 1). The average observed and expected heterozygosis
per loci varied from 0.299 ± 0.186 (16-N1150626) to 0.852 ± 0.062 (10-N1110523), and from 0.249 ± 0.109 (16N1150626) to 0.812 ± 0.048 (31-N2284857), respectively.
From the three sampling areas of W. salutaris 156 alleles were found in the 48 individuals sampled, being
the number of alleles higher in LM than in the other two areas (Table 2). The average Shannon’s diversity index
(I) was also higher in LM than in TR and FC. Observed and expected heterozygosis had similar average values
in LM and TR being slightly lower in FC. The polymorphic information content (PIC) had high average values
while inbreeding coefficients (FIS) were low and showing negative values in the three sampling areas.
Population genetic structure and differentiation. The Bayesian clustering program STRUCTURE
found the highest LnP(D) and ΔK values for K = 2 (Fig. 2; Fig. S1). One cluster was predominantly found across
LM and TR areas, while a second one characterized the FC area. Nevertheless, some individuals in this last area
showed signs of genetic admixture between the two genetic groups (* indicated in Fig. 2).
The first two coordinates of the principal coordinate analysis (PCoA) explained 22.9% of the total variation, and populations were spatially separated into the two main groups found by STRUCTURE (Fig. 3). The
neighbour-joining tree revealed several small clusters although mostly with a very low support (< 30% BS) and
overall, with no association between the clusters found and the three geographic areas (Fig. 4) as reported in the
other analyses. However, a clear cluster grouped all the FC geographical area.
The pairwise population FST values varied from 0.049 (TR vs. LM) to 0.114 (FC vs. TR) revealing moderate
levels of genetic differentiation between FC and TR and between FC and LM and lower levels between TR and
LM (Table 3).
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Figure 1. Location of the Lebombo Mountains, Tembe River, and Futi Corridor areas and their respective
villages in southern Mozambique. Maps were generated with Idrisi Selva v.17.02 environment (Clark Labs, Clark
University, www.clarklabs.org).
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Locus
Repeat motif
Accession number
Primer Sequence 5′–3′
Size range
Na
Ho
He
132–174
6
0.487 ± 0.139
0.394 ± 0.101
1-N1002135
(ATG)5
MT515706
F: TATGTTGGGAGAGGG
TGAGG
R: GTTTAACGACTGCAT
CATCCCA
7-N1082598
(AAT)9
MT515707
F: GTTGATCATAGACAC
GCCAAGG
R: GTCGTGCAACCTAGA
GGTCC
161–182
7
0.633 ± 0.085
0.700 ± 0.029
10-N1110523
(TTA)9
MT515708
F: AACCATTGGCACCTC
AAGTC
R: GTTGAAGTTGAGGGA
AGGGATG
244–262
7
0.852 ± 0.060
0.786 ± 0.023
12-N1126672
(TTG)7
MT515709
F: GTTAAATCTGGACCC
ACTTGCC
R: GGGTGAATTAGTGAA
CGTCTTG
161–180
7
0.805 ± 0.125
0.718 ± 0.074
13-N1132836
(AAG)7
MT515710
F: GTTCCTGCTCCGAGA
CCTAGAA
R: TCATGAAGAAATCGC
AACCA
138–144
3
0.304 ± 0.087
0.296 ± 0.086
16-N1150626
(TGG)5
MT515711
F. GTCTTTGGCGAAATC
AGTTGGT
R: GAAGGTTTCCAGGTT
GGTGA
149–159
3
0.299 ± 0.186
0.249 ± 0.109
18-N1173706
(AAG)6
MT515712
F: GAGCTGCCTCGATAT
GGACT
R: GTTATCCAATGGCCA
AGAAACC
164–170
3
0.398 ± 0.105
0.421 ± 0.078
31-N2284857
(TTC)12
MT515713
F: GTCTCTTGCTATCAT
GCGGTCA
R: CAGATTGGAGAATCC
AGACCA
207–263
9
0.771 ± 0.138
0.812 ± 0.078
33-N3477883
(TGA)6
MT515714
F: GTACAAGATTCATGT
GACCGGC
R: GCAAGGCATCATATT
CACGA
184–200
4
0.550 ± 0.171
0.472 ± 0.124
43-N1009973
(AT)10
MT515715
F: GTTGCGCTCATCGAT
CTGTA
R: GTGCGAACTATGATC
GGACGAA
146–185
9
0.439 ± 0.102
0.778 ± 0.027
Table 1. Characteristics and genetic diversity statistics of the 10 polymorphic microsatellite markers
developed for Warburgia salutaris. For each loci, the repeat motif, Genbank accession number, primer
sequence, and size range (bp) is indicated. Na refers to the number of alleles, Ho to observed heterozygosity
(mean ± SE) and He to expected heterozygosity (mean ± SE).
Lebombo Mountains (LM)
Tembe River (TR)
Futi Corridor (FC)
Locus
Na
I
Ho
He
PIC
Na
I
Ho
He
PIC
Na
I
Ho
He
PIC
1-N1002135
3
0.809
0.579
0.499
0.499
3
0.840
0.667
0.491
0.491
2
0.340
0.214
0.191
0.191
7-N1082598
7
1.457
0.526
0.672
0.672
9
1.764
0.800
0.758
0.758
8
1.516
0.571
0.671
0.671
10-N1110523
9
1.942
0.895
0.832
0.832
5
1.480
0.733
0.762
0.762
7
1.649
0.929
0.763
0.763
12-N1126672
7
1.716
0.842
0.795
0.795
7
1.739
1.000
0.789
0.789
4
1.061
0.571
0.569
0.569
13-N1132836
2
0.576
0.421
0.388
0.388
2
0.245
0.133
0.124
0.124
2
0.562
0.357
0.375
0.375
16-N1150626
3
0.455
0.158
0.234
0.234
2
0.637
0.667
0.444
0.444
2
0.154
0.071
0.069
0.069
18-N1173706
3
0.942
0.579
0.564
0.564
3
0.680
0.400
0.407
0.407
2
0.469
0.214
0.293
0.293
31-N2284857
14
2.429
0.947
0.895
0.895
9
1.884
0.867
0.816
0.816
6
1.487
0.500
0.727
0.727
33-N3477883
4
0.954
0.526
0.517
0.517
3
0.468
0.267
0.238
0.238
3
1.090
0.857
0.661
0.661
43-N1009973
11
1.980
0.632
0.801
0.810
9
1.827
0.400
0.798
0.798
5
1.438
0.286
0.724
0.724
Average ± SE
6.300 ± 1.274
1.326 ± 0.213
0.611 ± 0.075
0.620 ± 0.068
0.621 ± 0.216
5.200 ± 0.952
1.156 ± 0.203
0.593 ± 0.089
0.563 ± 0.081
0.563 ± 0.256
4.100 ± 0.722
0.977 ± 0.175
0.457 ± 0.089
0.504 ± 0.080
0.504 ± 0.252
Table 2. Genetic diversity of Warburgia salutaris in the three study areas. Na refers to the number of alleles,
I to Shannonʼs diversity index, Ho to observed heterozygosity (mean ± SE), He to expected heterozygosity
(mean ± SE) and PIC to polymorphic information content.
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Figure 2. Population structure of Warburgia salutaris based on 10 SSRs and using the best assignment result
retrieved by STRUCTURE (K = 2). Each individual sample is represented by a thin vertical line divided into K
coloured segments that represent the individual’s estimated membership fractions in K clusters. Populations and
main geographical areas are indicated below following Table 4. Asterisks indicate individuals with a probably of
membership lower than 90% to the main genetic cluster, as revealed by STRUCTURE.
*HUC18
MAC15
*HUC17
*MSL32
*MSL34
*HUC19
MAC13
*HUC16
MAC14
Axis 2 (11.10%)
HUC20
MAC16
MAC14
MAC22
MAC18
MAC20 MAC17
*PZ44
MSL32
MSL36
KZT21
GS09
KZT16
KZT24
KZT15
KZT32
MAC24
KZT35
PZ41
KZT28
KZT9
GF12
GF2
KZT7
KZT22
GF6
GF5
KZT14
KZT41
KZT6
GF3
GF1
MON47
KZT40
LEBOMBO MOUNTAINS
TEMBE RIVER
FUTI CORRIDOR
Axis 1 (11.83%)
Figure 3. Principal Coordinate analysis (PCoA) of the studied Warburgia salutaris using the scored SSRs
markers. Percentage of explained variance of each axis is given in parentheses. Population labels follow Table 4.
Colour of symbols (circles) indicate the two genetic groups identified by STRUCTURE. Colour of labels follow
the three main geographic areas as depicted in Fig. 1. Asterisks as in Fig. 2.
Discussion
High genetic diversity and admixture in Warburgia salutaris. Assessment of genetic diversity is
critical to understand the ability of a species to cope with changing conditions and environments, especially for
threatened species39,64–68. In this study, we reported for the first time the development of Single Sequence Repeats
(SSR) markers in W. salutaris by employing next generation sequencing (Illumina platform). The 10 SSRs markers were validated and found to be highly polymorphic, with values similar to the ones found in other threatened species such as Acer miaotaiense (PIC = 0.604)69 or Corylus avellana (PIC = 0.778)70. These markers are now
available to extend W. salutaris population studies to a worldwide level. Additionally, the SSRs developed during
this work might potentially be suitable to study genetic diversity in other species within the genus Warburgia,
since only a limited number of studies is available and based on Amplified Fragment Length Polymorphism
(AFLP)62,71, a time-consuming and costly technique. To the best of our knowledge, the present study represents
the first genome size estimation of W. salutaris and only the second within the Canellaceae family having a
genome size 4 × smaller than Canella winterana (2C = 11.7 pg72,73). The relatively small genome size of W. salutaris (see methods) is within the range of the non-expanded genomes of currently known magnoliids (Fig. S2)
and may facilitate future genomic initiatives although further analyses are needed to determine its ploidy level.
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18
* HUC
C1 7
* HU
PZ41
6
*P
Z4
4
* HUC1
* HUC19
HU
6
T1
T2
1
C20
KZ
KZ
T
KZ
24
KZ
T1
3
GF
5
KZ
14
T3
KZT
KZT
5
28
KZT41
45
KZT22
KZT9
KZT7
KZT6
31
MAC11
35
37
3
MSL3
N47
MAC13
MO
MAC1
MAC
5
22
1
GF
MA
C1
4
G
32
S9
T
KZ
MA
C2
0
4
C1
GF6
GF2
*M
6
L3
GF5
MA
6
C1
MA AC17
M
8
MAC1
MS
GF12
24
AC
M
0
SL
T4
32
KZ
34
SL
*M
LEBOMBO MOUNTAINS
0.04
TEMBE RIVER
FUTI CORRIDOR
Figure 4. Unrooted neighbour-joining tree of the studied Warburgia salutaris based on Nei’s Da genetic
distance. Numbers associated with branches indicate bootstrap values (BS) based on 1000 replications. Only BS
above 30 are shown. Colours of branches indicate the two genetic groups identified by STRUCTURE. Colour of
circles near each label indicate the three main geographic areas as depicted in Fig. 1. Asterisks as in Fig. 2.
Population
Lebombo Mountains
Lebombo Mountains
0.000
Tembe River
Tembe River
0.049
0.000
Futi Corridor
0.084
0.114
Futi Corridor
0.000
Table 3. Pairwise population FST values for Warburgia salutaris in the three study areas.
Due to the heavy harvesting pressure to which W. salutaris is subjected in Mozambique28,48, genetic diversity
levels were expected to be low. However, we found high levels of genetic diversity in the three surveyed areas
in comparison to other narrowly distributed species, as for instance, the tropical tree Paypayrola blanchetiana
(Na: 2–5 alleles per locus; Ho: 0.063–0.563 in the two populations; He: 0.063–0.567 in the first population and
0.063–0.627 in the second)39. However, genetic diversity indices of W. salutaris were similar to other species where
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bark has been heavily-exploited, such as Cinchona officinalis (Na: 5.2–7.6 alleles per locus; Ho: 0.580–0.680; He:
0.616–0.717)74 or even lower than Himatanthus drasticus (Na: 6–24; Ho: 0–0.847, He: 0–0.864)34.
High levels of heterozygosis may be due to factors including the reproductive system such as self-incompatibility75 or high gene flow65,76. Results from this work revealed a range of the inbreeding coefficient of -0.492
(TR) to -0.363 (LM), which is much lower than those found in e.g. H. drasticus (0.248–0.303)34, Calotropis
gigantea (0.167), C. procera (0.177)77, or Phoenix theophrasti (0.9)78. The negative inbreeding values found here
suggest the existence of random mating79 among individuals of W. salutaris and might also explain the levels of
heterozygosis found here. Indeed, the related species Warburgia ugandensis has a mixed mating system being
predominantly outcrossing62. Additionally, insect pollinators of W. salutaris such as bees are probably able to
travel over the large agricultural blocks separating the three geographical areas studied here, promoting gene
flow. Genetic admixture between sites might also be facilitated by frugivorous birds that often eat the berries
thereby facilitating the dispersion of seeds. In accordance, we found high levels of genetic admixture between
populations with only two genetic clusters being found, one grouping the northern populations and the other
one, the southern populations.
Our study suggests that, although some local populations might have been severely affected by harvesting,
the pepper-bark tree might have persisted in sufficient numbers in Mozambique to allow outcrossing between
sites, retaining a large proportion of genetic diversity. Although there are no records of the historical distribution of this species, the studied populations could be relicts of once much larger populations that persisted in
specific locations. In addition, recent conservation efforts might have diminished trade in Mozambique, avoiding
severe barking in these populations. Further research should focus on understanding the factors limiting the
regeneration of W. salutaris trees.
Population differentiation between geographic areas. Population differentiation of endangered
species is variable. For example, low differentiation was found between populations of Platanthera leucophaea
(FST < 0.02 over distances < 2 km80) while in H. drasticus the differentiation levels were high (FST from 0.036 to
0.077 over short distances)34. In contrast, the endangered Paeoma rockii revealed a high differentiation between
populations (FST varied from 0.780 to 0.982)81. Despite the narrow distributional area of W. salutaris in Mozambique, this study revealed a high genetic differentiation between the northern populations located in LM and
TR and the southern populations located in FC (Fig. 1). Pairwise FST comparisons showed lower genetic differentiation between LM and TR (0.049), which are separated by only 28 km, than either between LM and FC
areas (0.084, separated by 81 km) or between TR and FC (0.114, separated by 49 km). STRUCTURE analyses
also found a distinct genetic cluster in the FC area, which was also supported by PCoA analyses and the NJ tree.
Contrary to LM and TR areas, where W. salutaris occurs in slopes and forest patches, in the FC area this species
occurs near seasonal pans in thicket vegetation associated with termitaria on clay soils82,83. This might imply
differences in reproductive ecology, particularly regarding flowering phenology and the activity of pollinators,
which would affect gene flow with the other sites, explaining the genetic structure and population differentiation found between the studied sites. Thus, the differentiated FC genetic clusters could be harbouring novel and
important alleles and should be given priority in in situ and ex situ conservation strategies in Mozambique77,84,85.
How to conserve a species widely exploited and needed? Several populations of W. salutaris are
threatened by fire from slash and burn agriculture, as they occur in adjacent patches or in agricultural lands48.
Equally, burning of natural vegetation to improve livestock fodder, poaching, and opening of new areas for
settlements are also potential threats to the species (e.g.86–88). Vegetative propagation of W. salutaris is possible
through tissue culture63 although expensive. This species is being largely cultivated ex situ in South Africa89 and
in small scale in Zimbabwe53 and Mozambique (unpublished data), to encourage the sustainable use of the species. Home gardening would also be important for this species although that requires the involvement of local
communities and understanding their perceptions towards the conservation of this species.
Considering the confined distribution and threatened status, the long-term persistence of W. salutaris should
be secured by conserving the maximum genetic diversity of the species. As it is impossible to designate every
natural wild plant habitat as a protected area, nurseries could be implemented to ensure production stability.
The disclosure of genetic variation and understanding of genetic relatedness within populations is useful for
their sustainable uses90. Knowledge of genetic diversity from other countries as the one reported here would
also help to implement conservation strategies including re-introduction programs, selecting the most suitable
material to be used. Understanding the degree of genetic variation between Mozambique and the neighbouring
countries would facilitate transborder conservation actions. Further studies must also be conducted to detect
and understand how reductions of natural regeneration or fitness are affected by harvesting. Finally, efforts to
educate the local population and landowners on the importance of conserving the natural populations of W.
salutaris should continue.
Methods
Study species. Warburgia salutaris is an evergreen tree, generally 5–10 m tall, but occasionally up to 20 m57.
The flowers are small (< 7 mm in diameter), white to greenish in colour, generally solitary or in tight, few-flowered heads, borne on short, robust stalks in the axils of the leaves from autumn to winter (April–June). Flowers
are bisexual, actinomorphic (having symmetrically arranged perianth parts of similar size or shape that are
divisible into 3 or more equal halves). Flowers are visited by many insect species, most especially bees. The flowers develop rounded, oval berries (30 mm in diameter), usually dark-green and turning purple during ripening
that occurs throughout winter an into early summer (July to December). Dispersion occurs by frugivorous birds
that disperse the seeds, although fruits can also drop near the maternal tree. Leaves are glossy and dark green,
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Accessions
Location
ID
Lat
Long
Accessions
Location
ID
Lat
Long
GF1 (1)
Goba Fronteira
LM
− 26.23266
32.09810
KZT16 (27)
Kazimat
TR
− 26.40994
32.35490
MAC13 (2)
Macanda
LM
− 26.03522
32.12181
KZT21 (28)
Kazimat
TR
− 26.40391
32.36711
MAC14 (3)
Macanda
LM
− 26.03577
32.12150
KZT22 (29)
Kazimat
TR
− 26.40059
32.35109
MAC15 (4)
Macanda
LM
− 26.03778
32.12730
KZT24 (30)
Kazimat
TR
− 26.40206
32.36188
MAC16 (5)
Macanda
LM
− 26.03692
32.12772
KZT28 (31)
Kazimat
TR
− 26.36735
32.37323
MAC17 (6)
Macanda
LM
− 26.05158
32.11803
KZT35 (32)
Kazimat
TR
26.36737
32.37266
MAC18 (7)
Macanda
LM
− 26.05159
32.11565
KZT40 (33)
Kazimat
TR
− 26.36873
32.37078
MAC19 (8)
Macanda
LM
− 26.81118
32.64545
KZT41 (34)
Kazimat
TR
− 26.36929
32.37334
MAC20 (9)
Macanda
LM
− 26.04696
32.11979
KZT46 (35)
Kazimat
TR
− 26.36935
32.37321
MAC22 (10)
Macanda
LM
− 26.04508
32.11982
MON47 (36)
Monucua
TR
− 26.36952
32.32288
MAC24 (11)
Macanda
LM
− 26.03521
32.12181
Huc16 (44)
Huco
FC
− 26.85013
32.60338
GF2 (12)
Goba Fronteira
LM
− 26.26867
32.10719
Huc17 (45)
Huco
FC
− 26.86159
32.60604
GF5 (13)
Goba Fronteira
LM
− 26.23250
32.09818
Huc18 (46)
Huco
FC
− 26.86169
32.60353
GF6 (14)
Goba Fronteira
LM
− 26.23241
32.09815
Huc19 (47)
Huco
FC
− 26.86129
32.60282
GF12 (15)
Goba Fronteira
LM
− 26.23240
32.09822
Huc20 (48)
Huco
FC
− 26.86025
32.60309
GS09 (16)
Goba Sede
LM
− 26.23238
32.09822
MSL32 (49)
Massale
FC
− 26.83979
32.88339
MAC11 (17)
Macanda
LM
− 26.04509
32.11983
MSL33 (50)
Massale
FC
− 26.86458
32.60790
GF3 (18)
Goba Fronteira
LM
− 26.26879
32.10747
MSL34 (51)
Massale
FC
− 26.80948
32.64368
GF4 (19)
Goba Fronteira
LM
− 26.23233
32.09818
MSL36 (52)
Massale
FC
− 26.80590
32.63823
KZT6 (22)
Kazimat
TR
− 26.41303
32.36338
Pz41 (53)
Phuza
FC
− 26.78824
32.67368
KZT7 (23)
Kazimat
TR
− 26.41190
32.36422
Pz42 (54)
Phuza
FC
− 26.78817
32.67434
KZT9 (24)
Kazimat
TR
− 26.40960
32.36578
Pz43 (55)
Phuza
FC
− 26.78814
32.67383
KZT14 (25)
Kazimat
TR
− 26.40414
32.35073
Pz44 (56)
Phuza
FC
− 26.78760
32.67419
KZT15 (26)
Kazimat
TR
− 26.38806
32.35008
Pz45 (57)
Phuza
FC
− 26.81144
32.66415
Table 4. Sampled accessions and locations of Warburgia salutaris sorted by geographical area. LM Lebombo
Mountains, TR Tembe River, FC Futi Corridor.
with a bitter, peppery taste. The stem is covered by a brown bark marked with corky lenticels and is bitter and
peppery and is widely used medicinally. The active compounds (drimanes and sesquiterpenoides) are mostly
found in the inner part of the stem and root bark.
Study area. The present study was carried out in the districts of Matutuine and Namaacha (Mozambique),
in the three areas of known occurrence of W. salutaris48: (1) Lebombo Mountains (LM) also named the western
area, (2) Tembe River (TR) or centre, and (3) Futi Corridor (FC) or eastern area (Fig. 1). The climate is subtropical to tropical, encompassing a wet (October–April) and dry season (May–September). The mean annual temperature ranges from 21 to over 24 °C, and the mean annual rainfall from 600 to 1000 mm88,91. In LM, W. salutaris is accompanied by Acacia nigrescens Oliv., Acacia burkei Benth. and Combretum apiculatum Sond, although
Aloe marlothii A. Berger, Ficus spp. and Euphorbia spp. are found in shallow soils, and Olea africana Miller and
Combretum spp. in steeper stony slopes92,93. In TR, W. salutaris is found in sand forest patches together with
Pteleopsis myrtifolia (M.A.Lawson) Engl. & Diels, Cleistanthus schlechteri Pax (Hutch.), Hymenocardia ulmoides
Oliv. and Monodora junodii Engl. & Diels94. The open savanna woodland links the patches of W. salutaris, being
composed mainly by Strychnos spp., Terminalia sericea Burch. ex DC., Acacia burkei Benth., Combretum molle R.
Br. ex G.Don and Albizia versicolor Oliv.95. In FC, W. salutaris occurs near seasonal pans96 in thicket vegetation
associated to termitaria in clay soils82. Common tree species found in this community include Berchemia zeyheri
(Sond.) Grubov, Pappea capensis Eckl. & Zeyh. and Olea europaea subsp. africana (Miller) P.S. Green97. The
primary economic activities of local residents are subsistence agriculture, livestock rearing, trade of non-timber
forest products and migrant labour to South Africa87,98,99.
Population sampling, DNA extraction, genome size value, and SSR development.
Based on
the areas of occurrence (Senkoro et al., unpublished data), 48 individuals were sampled: 19 individuals from LM,
15 from TR and 14 from LM (Table 4). Fresh, young undamaged leaves were collected for each individual plant
and frozen at − 80 °C until DNA isolation. Total genomic DNA was extracted from 50 mg of ground leaves using
the InnuSPEED Plant DNA Kit (Analytik Jena Innuscreen GmbH, Germany) according to the manufacturer’s
protocol. The average yield and purity were assessed spectrophotometrically by OD230, OD260 and OD280
readings (Nanodrop 2000, Thermo Fisher Scientific, Waltham, MA, USA) and visualized by electrophoresis in
1% agarose gels under UV light. Normalized DNA from five individuals of each population was used to develop
the SSR markers at CD Genomics (cd-genomics.com/hi-ssrseq.html).
For the development of the markers, we first estimated the nuclear DNA content of W. salutaris by flow
cytometry using fresh young leaves that were chopped using a razor blade together with an internal standard in a
Petri dish containing 1 mL of Woody Plant Buffer100 following the protocol described in101. Solanum lycopersicum
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‘Stupické’ (2C = 1.96 pg)102 was used as internal standard. The nuclear suspension was then filtered through a
30 μm nylon filter, and 50 μg/mL of propidium iodide (PI; Sigma-Aldrich, St. Louis, USA) and 50 μg/mL of RNase
(Sigma-Aldrich) were added to stain the DNA only. The fluorescence intensity of nuclei was analysed using a
CyFlow Space flow cytometer (Sysmex, Kobe, Japan). Four independent replicates collected from Kazimat (TR)
were measured. Conversion of mass values into numbers of base pairs was done according to the factor 1 pg = 978
Mbp103. The mean 2C-value of W. salutaris was found to be 2.91 pg (± 0.068), corresponding to an average genome
size of 2845 Mbp (Fig. S2). Samples had an average coefficient of variation of 4.18%.
Genomic libraries were constructed using the KAPAHyper prep kit and sequenced by Illumina Hiseq 2500.
We firstly used SSRHunter1.3 to screen the potential SSRs from the sequenced data that had at least five repeats
(penta-) for 3–5 bp units. Based on the obtained sequences, primers were designed with Primer Premier 5.0
software (Table 1). Fourteen geographically representative samples of W. salutaris (LM, TR and FC; Fig. 1) were
first used to test microsatellite amplification and to troubleshoot amplification conditions. Amplifications were
performed in 15 μl reactions containing: 1.25U TaKaRa Hot startTaq polymerase, 1X Buffer I, 1 mM dNTPs,
5 μM Primer F and R and 100 ng DNA. The PCR amplification conditions were run as follows: 95 °C for 5 min,
94 °C for 30 s, 30 cycles of 56 °C for 30 s, 72 °C for 30 s, 94 °C for 30 s, 10 cycles of 53 °C for 30 s, 72 °C for 30 s
and final extension at 60 °C for 30 min. We then considered 10 markers that presented > 20% polymorphism,
which were used to amplify all samples within this study (Table 1). The amplified fragments were analysed on a
3730 × 1 gene analyzer (Thermo Fischer Scientific) and examined manually for microsatellite peaks. Allele sizes
were determined using GeneMapper 3.2 (Applied Biosystems).
Estimates of genetic diversity.
For each microsatellite locus, genetic polymorphism was assessed in 48
individuals by calculating the number of alleles (Na), observed heterozygosis (Ho), expected heterozygosis (He),
Shannon’s diversity index (I), and inbreeding coefficient (FIS) using GenALEX software version 6.5104. The polymorphic information content (PIC) was calculated as PIC = 1 − ΣPi2, where Pi is the allele frequency for each SSR
marker locus105,106. Values of PIC above 0.5 were considered highly informative, between 0.5 and 0.25 moderately
informative, and below 0.25 less informative107.
Population genetic structure and differentiation. The Bayesian program STRUCTURE v.2.3.4108
was used to infer the population structure and to assign individual plants to subpopulations. Models with a
putative numbers of populations (K) from 1–5, imposing ancestral admixture and correlated allele frequencies
priors, were considered. Ten independent runs with 50 000 burn-in steps, followed by run lengths of 1 000 000
interactions for each K, were computed. The number of clusters in the data was estimated using STRUCTURE
HARVESTER109, which identifies the optimal K based both on the posterior probability of the data for a given
K and the ΔK110. To correctly assess the membership proportions (q values) for clusters identified in STRUCTU
RE, the results of the replicates at the best fit K were post-processed using CLUMPP 1.1.2111. GenALEX software
version 6.5104 was used to calculate the Nei’s genetic distance112 among individuals. A Principle Coordinate
Analysis (PCoA)113 was performed to detect genetic variations between W. salutaris individuals. POPULATION
1.2114 was used to construct an unrooted neighbour-joining tree with 1000 bootstrap replicates. The Wright’s FST
value was computed to estimate population differentiation104. Lower genetic differentiation was considered for
FST below 0.05, moderate from 0.05 to 0.15 and high genetic differentiation above 0.25115.
Received: 27 May 2020; Accepted: 28 September 2020
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Acknowledgements
We are grateful to the Organization for Women in Science for the Developing World (OWSD), Swedish International Development Cooperation Agency (SIDA), Russell E. Train Education for Nature Program, World Wildlife
Fund (Agreement #SS20), Camões, I.P. (Portugal), and the Portuguese Science and Technology Foundation
through the research units UIDB/00239/2020 (CEF) and UID/04129/2020 (LEAF), and the contribution to the
International Rice Research Institute. We would also like to thank our field guides Antonio Tembe, Ernesto Bié,
Filimone Cossa, Luis Cossa, Massale Tembe, Ricardo Mundlovu and Sifiso Masuko for their support during
sample collection. We are also grateful to our colleagues, Domingos Maguengue, Ivete Maquia, and Ana Gomes
during the initial phase of the work and to José Alfredo Amanze for providing the study area map.
Author contributions
A.M.S., C.M.S., R.A.V., and A.I.R.B. conceived the work and the experimental design. A.M.S., C.M.S., and R.A.V.
performed the field data survey and sample collection. A.M.S., P.B.S., F.S., and P.T. performed the laboratorial
analysis. P.T. performe the flow cytometry data analysis. A.M.S., F.S., I.M. and A.I.R.B. performed the microsatellite data analysis. A.M.S., I.M., and A.I.R.B. wrote the first draft and final version of the manuscript, which has
been thoroughly reviewed by all authors.
Competing interests
The authors declare no competing interests.
Additional information
Supplementary information is available for this paper at https://doi.org/10.1038/s41598-020-76654-6.
Correspondence and requests for materials should be addressed to I.M. or A.I.R.-B.
Reprints and permissions information is available at www.nature.com/reprints.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and
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