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ITS2 secondary structure for species circumscription: case study in southern African Strychnos L. (Loganiaceae)

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Abstract

Recently developed computational tools in ITS2 sequence-structure phylogenetics are improving tree robustness by exploitation of the added information content of the secondary structure. Despite this strength, however, their adoption for species-level clarifications in angiosperms has been slow. We investigate the utility of combining ITS2 sequence and secondary structure to separate species of southern African Strychnos, and assess correlation between compensatory base changes (CBCs) and currently recognised species boundaries. Combined phylogenetic analysis of sequence and secondary structure datasets performed better, in terms of robustness and species resolution, than analysis involving primary sequences only, achieving 100 and 88.2 % taxa discriminations respectively. Further, the Strychnos madagascariensis complex is well-resolved by sequence-structure phylogenetic analysis. The 17 Strychnos species corresponded to 14 ITS2 CBC clades. Four of the five taxa in section Densiflorae belong to a single CBC clade, whose members tend to form natural hybrids. Our finding supports the application of ITS2 as a complementary barcoding marker for species identification. It also highlights the potential of comparative studies of ITS2 CBC features among prospective parental pairs in breeding experiments as a rapid proxy for cross compatibility assessment. This could save valuable time in crop improvement. Patterns of CBC evolution and species boundaries in Strychnos suggests a positive correlation. We conclude that the CBC pattern coupled with observed ITS2 sequence paraphyly in section Densiflorae points to a speciation work-in-progress.

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Acknowledgments

This work was supported by the NRF-Thuthuka grant awarded to the first author through YN. The authors thank Masego Kruger-Gaadingwe and David Styles for help with collection of Strychnos specimens, and the curator of the National Herbarium Pretoria for access to materials. We also thank eThekwini Municipality for collection access to conservation areas around Durban.

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Authors and Affiliations

  1. School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Private Bag 3, Wits, Johannesburg, 2050, South Africa

    Adekunle Adebowale

  2. School of Life Sciences, University of KwaZulu-Natal, New Biology Building, South Ring Road, Westville, 3630, South Africa

    Jennifer Lamb, Ashley Nicholas & Yougasphree Naidoo

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  1. Adekunle Adebowale
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Figure S1

Comparison of ITS2 helices II and III across southern African Strychnos. Key: ang = S. angolensis; coc = S. cocculoides; dec = S. decussata; dip = S. diplotricha; ger = S. gerrardii; hen = S. henningsii; inn = S. innocua; luc = S. lucens; mad = S. madagascariensis; mel = S. mellodora; mit = S. mitis; pan = S. panganensis; pot = S. potatorum; pun = S. pungens; spi = S. spinosa; usa = S. usambarensis; xan = S. xantha (EPS 1865 kb)

Figure S2

Comparison of ITS2 helices I and IV across southern African Strychnos. Key: ang = S. angolensis; coc = S. cocculoides; dec = S. decussata; dip = S. diplotricha; ger = S. gerrardii; hen = S. henningsii; inn = S. innocua; luc = S. lucens; mad = S. madagascariensis; mel = S. mellodora; mit = S. mitis; pan = S. panganensis; pot = S. potatorum; pun = S. pungens; spi = S. spinosa; usa = S. usambarensis; xan = S. xantha. The ITS2 sequences identified as (GenBank: JF937984.1) and S. panganensis are incomplete. They lack helix IV. Note the identical sequences of S. angolensis and GenBank: JF937984.1, a possible misidentification as S. henningsii by Frasier (2008), even in the highly variable terminal loop. (EPS 1290 kb)

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Adebowale, A., Lamb, J., Nicholas, A. et al. ITS2 secondary structure for species circumscription: case study in southern African Strychnos L. (Loganiaceae). Genetica 144, 639–650 (2016). https://doi.org/10.1007/s10709-016-9931-0

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