Research Paper

Incomplete lineage sorting and secondary admixture results in the paraphyly of Lecanorchis cerina, L. suginoana, and L. thalassica (Orchidaceae) in Taiwan

Shih-Ying Hwang, Yi-Shao Li, Tsan-Piao Lin

Published on: 02 July 2022

Page: 366 - 376

DOI: 10.6165/tai.2022.67.366

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2022 vol.67 no.3 pp.366-376



?lvarez, I., J.F. Wendel. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylogenet. Evol. 29(3): 417–434.
DOI: 10.1016/S1055-7903(03)00208-2View ArticleGoogle Scholar

Bates, D., M. Maechler, B. Bolker and S. Walker. 2015. Fitting linear mixed effects models using lme4. J. Stat. Soft. 67(1): 1–48.
DOI: 10.18637/jss.v067.i01View ArticleGoogle Scholar

Bodenhofer, U., E. Bonatesta, C. Horej?-Kainrath and S. Hochreiter. 2015. msa: an R package for multiple sequence alignment. Bioinformatics 31(24): 3997–3999.
DOI: 10.1093/bioinformatics/btv494View ArticleGoogle Scholar

Bonin, A., E. Bellemain, E.P. Bronken, F. Pompanon, C. Brochmann and P. Taberlet. 2004. How to track and assess genotyping errors in population genetics studies. Mol. Ecol. 13(11): 3261–3273.
DOI: 10.1111/j.1365-294X.2004.02346.xView ArticleGoogle Scholar

Clement, M.J., Q. Snell, P. Walke, D. Posada and K.A. Crandall. 2002. TCS: estimating gene genealogies. Proc. 16th Int. Parallel Distrib. Process Symp. 2: 184.

Csill?ry, K., M.G.B. Blum, O.E. Gaggiotti and O. Fran?ois. 2010. Approximate Bayesian computation (ABC) in practice. Trends Ecol. Evol. 25(7): 410–418.
DOI: 10.1016/j.tree.2010.04.001View ArticleGoogle Scholar

Doyle, J.J. and J.L. Doyle. 1987. A rapid DNA isolation procedure from small quantities of fresh leaf material. Phytochem. Bull. 19(1): 11–15.

Dray, S. and A.-B. Dufour. 2007. The ade4 package: implementing the duality diagram for ecologists. J. Stat. Soft. 22(4): 1–20.
DOI: 10.18637/jss.v022.i04View ArticleGoogle Scholar

Ebersbach, J., J. Schnitzler, A. Favre and A.N. Muellner-Riehl. 2017. Evolutionary radiations in the species-rich mountain genus Saxifraga L. BMC Evol. Biol. 17(1): 119.
DOI: 10.1186/s12862-017-0967-2View ArticleGoogle Scholar

Evanno, G., S. Regnaut and J. Goudet. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14(8): 2611–2620.
DOI: 10.1111/j.1365-294X.2005.02553.xView ArticleGoogle Scholar

Excoffier, L. and H.E. Lischer. 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 10(3): 564–567.
DOI: 10.1111/j.1755-0998.2010.02847.xView ArticleGoogle Scholar

Farminh?o, J.N.M., S. Verlynde, E. Kaymak, V. Droissart, M. Simo-Droissart, G. Collobert, F. Martos and T. St?vart. 2021. Rapid radiation of angraecoids (Orchidaceae, Angraecinae) in tropical Africa characterized by multiple karyotypic shifts under major environmental instability. Mol. Phylogenet. Evol. 159: 107105.
DOI: 10.1016/j.ympev.2021.107105View ArticleGoogle Scholar

Farris, J.S. 1989. The retention index and the rescaled consistency index. Cladistics 5(4): 417–419.
DOI: 10.1111/j.1096-0031.1989.tb00573.xView ArticleGoogle Scholar

Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39(4): 783–791.
DOI: 10.2307/2408678View ArticleGoogle Scholar

Fox, J. and S. Weisberg. 2011. An R Companion to Applied Regression, 2nd ed. Sage, Thousand Oaks, USA.

Frichot, E. and O. Francois. 2015. LEA: an R package for landscape and ecological association studies. Methods Ecol. Evol. 6(8): 925–929.
DOI: 10.1111/2041-210X.12382View ArticleGoogle Scholar

Funk, D.J. and K.E. Omland. 2003. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Ann. Rev. Ecol. Evol. and Syst. 34(1): 397–423.
DOI: 10.1146/annurev.ecolsys.34.011802.132421View ArticleGoogle Scholar

George, S., J. Sharma and V.L. Yadon. 2009. Genetic diversity of the endangered and narrow endemic Piperia yadonii (Orchidaceae) assessed with ISSR polymorphisms. Amer. J. Bot. 96(11): 2022–2030.
DOI: 10.3732/ajb.0800368View ArticleGoogle Scholar

Goetze, M., C.M. Zanella, C. Palma-Silva, M.V. B?ttow and F. Bered. 2017. Incomplete lineage sorting and hybridization in the evolutionary history of closely related, endemic yellow-flowered Aechmea species of subgenus Ortgiesia (Bromeliaceae). Amer. J. Bot. 104(7): 1073–1087.
DOI: 10.3732/ajb.1700103View ArticleGoogle Scholar

Gow, J.L., C.L. Peichel and E.B. Taylor. 2006. Contrasting hybridization rates between sympatric three spine sticklebacks highlight the fragility of reproductive barriers between evolutionarily young species. Mol. Ecol. 15(3): 739–752.
DOI: 10.1111/j.1365-294X.2006.02825.xView ArticleGoogle Scholar

Hey, J. 2010. Isolation with migration models for more than two populations. Mol. Biol. Evol. 27(4): 905–920.
DOI: 10.1093/molbev/msp296View ArticleGoogle Scholar

Hu, A.-Q., S.W. Gale, Z.-J. Liu, S. Suddee, T.-C. Hsu, G.A. Fischer and R.M.K. Saunders. 2020. Molecular phylogenetics and floral evolution of the Cirrhopetalum alliance (Bulbophyllum, Orchidaceae): Evolutionary transitions and phylogenetic signal variation. Mol. Phylogen. Evol. 143: 106689.
DOI: 10.1016/j.ympev.2019.106689View ArticleGoogle Scholar

Isabel, N., J. Beaulieu, P. Th?riault and J. Bousquet. 1999. Direct evidence for biased gene diversity estimates from dominant random amplified polymorphic DNA (RAPD) fingerprints. Mol. Ecol. 8(3): 477–483.
DOI: 10.1046/j.1365-294X.1999.00597.xView ArticleGoogle Scholar

Jacquemyn, H., R. Brys, D. Adriaens, O. Honnay and I. Rold?n-Ruiz. 2009. Effects of population size and forest management on genetic diversity and structure of the tuberous orchid Orchis mascula. Conserv. Genet. 10(1): 161–168.
DOI: 10.1007/s10592-008-9543-zView ArticleGoogle Scholar

Jombart, T. and I. Ahmed. 2011. Adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics 27(21): 3070–3071.
DOI: 10.1093/bioinformatics/btr521View ArticleGoogle Scholar

Jombart, T., S. Devillard and F. Balloux. 2010. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet. 11(1): 94.
DOI: 10.1186/1471-2156-11-94View ArticleGoogle Scholar

Kamvar, Z.N., J.C. Brooks and N.J. Gr?nwald. 2015. Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality. Front. Genet. 6: 208.
DOI: 10.3389/fgene.2015.00208View ArticleGoogle Scholar

Kimura, M. 1983. The Neutral Theory of Molecular Evolution. Cambridge Univ. Press, Cambridge, UK.
DOI: 10.1017/CBO9780511623486View Article

Kluge, A.G. and J.S. Farris. 1969. Quantitative phyletics and the evolution of Anurans. Syst. Zool. 18(1): 1–32.
DOI: 10.2307/2412407View ArticleGoogle Scholar

Koopman, W.J.M., V. Wissemann, K. de Cock, J. van Huylenbroeck, J. de Riek, G.J.H Sabatino, D. Visser, B. Vosman, C.M. Ritz, B. Maes, G. Werlemark, H. Nybom, T. Debener, M. Linde and J.M. Smulders. 2008. AFLP markers as a tool to reconstruct complex relationships: A case study in Rosa (Rosaceae). Amer. J. Bot. 95(3): 353–366.
DOI: 10.3732/ajb.95.3.353View ArticleGoogle Scholar

Leigh, J.W. and D. Bryant. 2015. PopART: full-feature software for haplotype network construction. Methods Ecol. Evol. 6(9): 1110–1116.
DOI: 10.1111/2041-210X.12410View ArticleGoogle Scholar

Leimu, R., P. Mutikainen, J. Koricheva and M. Fischer. 2006. How general are positive relationships between plant population size, fitness and genetic variation? J. Ecol. 94(5): 942–952.
DOI: 10.1111/j.1365-2745.2006.01150.xView ArticleGoogle Scholar

Lenth, R. 2018. emmeans: Estimated marginal means, aka least-squares means. R package version 1.3.1. Accessed Apr 7. 2018.

Lin, T.P. 2019. The Orchid Flora of Taiwan, a collection of line drawings. NTU Press, Taipei, Taiwan. 1012 pages.
DOI: 10.978.986350/3682View ArticleGoogle Scholar

Linder, C.R. and L.H. Rieseberg. 2004. Reconstructing patterns of reticulate evolution in plants. Amer. J. Bot. 91(10): 1700–1708.
DOI: 10.3732/ajb.91.10.1700View ArticleGoogle Scholar

Mariette, S., V. Le Corre, F. Austerlitz and Kremer, A. 2002. Sampling within the genome for measuring within-population diversity: trade-offs between markers. Mol. Ecol. 11(7): 1145–1156.
DOI: 10.1046/j.1365-294X.2002.01519.xView ArticleGoogle Scholar

Meleshko, O., M.D. Martin, T.S. Korneliussen, C. Schr?ck, P. Lamkowski, J. Schmutz, A. Healey, B.T. Piakowski, A.J. Shaw, D.J. Weston, K.I. Flatberg, P. Sz?v?nyi, K. Hassel and H.K. Sten?ien. 2021. Extensive genome-wide phylogenetic discordance is due to incomplete lineage sorting and not ongoing introgression in a rapidly radiated bryophyte genus. Mol. Biol. Evol. 38(7): 2750–2766.
DOI: 10.1093/molbev/msab063View ArticleGoogle Scholar

Muir, G. and C. Schl?tterer. 2005. Evidence for shared ancestral polymorphism rather than recurrent gene flow at microsatellite loci differentiating two hybridizing oaks (Quercus spp.) Mol. Ecol. 14(2): 549–561.
DOI: 10.1111/j.1365-294X.2004.02418.xView ArticleGoogle Scholar

Nei, M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89(3): 583–590.
DOI: 10.1093/genetics/89.3.583View ArticleGoogle Scholar

Nei, M. 1987. Molecular Evolutionary Genetics. Columbia University Press, New York, USA. 512 pp.
DOI: 10.7312/nei-92038View Article

Nielsen, R. and J. Wakeley. 2001. Distinguishing migration from isolation. A Markov chain Monte Carlo approach. Genetics 158(2): 885–896.
DOI: 10.1093/genetics/158.2.885View ArticleGoogle Scholar

Paradis, E. and K. Schliep. 2019. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35(3): 526–528.
DOI: 10.1093/bioinformatics/bty633View ArticleGoogle Scholar

Pease, J.B., D.C. Haak, M.W. Hahn and L.C. Moyle. 2016. Phylogenomics reveals three sources of adaptive variation during a rapid radiation. PLoS Biol. 14(2): e1002379.
DOI: 10.1371/journal.pbio.1002379View ArticleGoogle Scholar

P?rez-Excobar, O.A., G. Chomicki, F.L. Condamine, A.P. Karremans, D. Bogarin, N.J. Matxke, D. Silvestro and A. Antonelli. 2017. Recent origin and rapid speciation of Neotropical orchids in the world’s richest plant biodiversity hotspot. New Phytol. 215(2): 891–905.
DOI: 10.1111/nph.14629View ArticleGoogle Scholar

Petit, R.J. and L. Excoffier. 2009. Gene flow and species delimitation. Trends Ecol. Evol. 24(7): 386–393.
DOI: 10.1016/j.tree.2009.02.011View ArticleGoogle Scholar

Pritchard, J.K., M. Stephens and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155(2): 945–959.
DOI: 10.1093/genetics/155.2.945View ArticleGoogle Scholar

Qu, Y.H., X. Luo, R.Y. Zhang, G. Song, F.S. Zou and F.M. Lei. 2011. Lineage diversification and historical demography of a montane bird Garrulax elliotii—implications for the Pleistocene evolutionary history of the eastern Himalayas. BMC Evol. Biol. 11(1): 174.
DOI: 10.1186/1471-2148-11-174View ArticleGoogle Scholar

R Development Core Team. 2020. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria.

Rokas, A. and S.B. Carroll. 2006. Bushes in the tree of life. PLoS Biol. 4(11): e352.
DOI: 10.1371/journal.pbio.0040352View ArticleGoogle Scholar

Rozas, J., A. Ferrer-Mata, J.C. S?nchez-DelBarrio, S. Guirao-Rico, P. Librado, S.E. Ramos-Onsins and A. S?nchez-Gracia. 2017. DnaSP 6: DNA sequence polymorphism analysis of large datasets. Mol. Biol. Evol. 34(12): 3299–3302.
DOI: 10.1093/molbev/msx248View ArticleGoogle Scholar

Schliep, K.P. 2011. phangorn: phylogenetic analysis in R. Bioinformatics 27(4): 592–593.
DOI: 10.1093/bioinformatics/btq706View ArticleGoogle Scholar

Sten?ien, H.K., A.J. Shaw, B. Shaw, K. Hassel and U. Gunnarsson. 2011. North American origin and recent European establishments of the amphi-Atlantic peat moss Sphagnum angermanicum. Evolution 65(4):1181–1194.
DOI: 10.1111/j.1558-5646.2010.01191.xView ArticleGoogle Scholar

Suetsugu, K., S. Kaida, H. Fukunaga and S. Sawa. 2020. A new form of the mycoheterotrophic plant Lecanorchis japonica (Orchidaceae) from Japan. Acta Phytotax. Geobot. 71(3): 243–248.

Suetsugu, K., S. Kaida, T.-C. Hsu and S. Sawa. 2019. Lecanorchis moritae (Orchidaceae, Vanilloideae), a new mycoheterotrophic species from Amamai-Oshima Island, Japan based on morphological and molecular data. Phytotaxa 404(4): 137–145.
DOI: 10.11646/phytotaxa.404.4.2View ArticleGoogle Scholar

Suetsugu, K., C. Shimaoka, H. Fukunaga and S. Sawa. 2018. The taxonomic identity of three varieties of Lecanorchis nigricans (Vanilleae, Vanilloideae, Orchidaceae) in Japan. PhytoKeys 92: 17–35.
DOI: 10.3897/phytokeys.92.21657View ArticleGoogle Scholar

Sunn?ker, M., A.G. Busetto, E. Numminen, J. Corander, M. Foll and C. Dessimoz. 2013. Approximate Bayesian computation. PLoS Comput. Biol. 9(1): e1002803.
DOI: 10.1371/journal.pcbi.1002803View ArticleGoogle Scholar

Szczeci?ska, M., G. Sramk?, K. Wolosz and J. Sawwicki. 2016. Genetic diversity and population structure of the rare and endangered plant species Pulsatilla patens (L.) Mill in East Central Europe. PLoS One 11(3): e0151730.
DOI: 10.1371/journal.pone.0151730View ArticleGoogle Scholar

Sz?v?nyi, P., S. Terracciano, M. Ricca, S. Giordano and A.J. Shaw. 2008. Recent divergence, intercontinental dispersal and shared polymorphism are shaping the genetic structure of amphi-Atlantic peatmoss populations. Mol Ecol. 17(24): 5364–5377.
DOI: 10.1111/j.1365-294X.2008.04003.xView ArticleGoogle Scholar

Takashima, M., Y. Yamashita, A. Kinoshita, M. Ohta and T. Yukawa. 2019. Taxonomic status of Lecanorchis suginoana (Tuyama) Seriz. (Orchidaceae). Bull. Natl. Mus. Nat. Sci. Ser. B. 45(3): 119–129.

Thompson, J.D., D.G. Higgins and T.J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22(22): 4673–4680.
DOI: 10.1093/nar/22.22.4673View ArticleGoogle Scholar

Vekemans, X., T. Beauwens, M. Lemaire and I. Rold?n-Ruiz. 2002. Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Mol. Ecol. 11(1): 139–151.
DOI: 10.1046/j.0962-1083.2001.01415.xView ArticleGoogle Scholar

Vos, P., R. Hogers, M. Bleeker, M. Reijans, T. van der Lee, M. Hornes, A. Friters, J. Pot, J. Paleman, M. Kuiper and M. Zabeau. 1995. AFLP: a new technique for DNA fingerprinting. Nucl. Acids Res. 23(21): 4407–4414.
DOI: 10.1093/nar/23.21.4407View ArticleGoogle Scholar

WCVP. 2022, World Checklist of Vascular Plants, version 2.0. Facilitated by the Royal Botanic Gardens, Kew. Published on the Internet; Accessed 11 Mar. 2022.

Zhivotovsky, L.A. 1999. Estimating population structure in diploids with multilocus dominant DNA markers. Mol. Ecol. 8(6): 907–913.
DOI: 10.1046/j.1365-294x.1999.00620.xView ArticleGoogle Scholar

Zhou, Y., L. Duvaux, G. Ren, L. Zhang, O. Savolainen and J. Liu. 2017. Importance of incomplete sorting and introgression in the origin of shared genetic variation between two closely related pines with overlapping distributions. Heredity 118(3): 211–220.
DOI: 10.1038/hdy.2016.72View ArticleGoogle Scholar