Phylogenetic incongruence in Cymbidium orchids

doi:10.1016/j.pld.2021.08.002

Abstract

Abstract: Cymbidium, which includes approximately 80 species, is one of the most ornamental and cultivated orchid genera. However, a lack of markers and sparse sampling have posed great challenges to resolving the phylogenetic relationships within the genus. In the present study, we reconstructed the phylogenetic relationships by utilizing one nuclear DNA (nrITS) and seven plastid genes (rbcL, trnS, trnG, matK, trnL, psbA, and atpI) from 70 species (varieties) in Cymbidium. We also examined the occurrence of phylogenetic conflict between nuclear (nrITS) and plastid loci and investigated how phylogenetic conflict bears on taxonomic classification within the genus. We found that phylogenetic conflict and low support values may be explained by hybridization and a lack of informative characteristics. Our results do not support previous classification of the subgenera and sections within Cymbidium. Discordance between gene trees and network analysis indicate that reticulate evolution occurred in the genus Cymbidium. Overall, our study indicates that Cymbidium has undergone a complex evolution.

Key words: Cymbidium, Phylogenetic conflict, nrITS, cpDNA, Reticulate evolution

Guo-Qiang Zhang, Gui-Zhen Chen, Li-Jun Chen, Jun-Wen Zhai, Jie Huang, Xin-Yi Wu, Ming-He Li, Dong-Hui Peng, Wen-Hui Rao, Zhong-Jian Liu, Si-Ren Lan. Phylogenetic incongruence in Cymbidium orchids[J]. Plant Diversity, 2021, 43(06): 452-461.

References

Bateman, R.M., Smith, R.J., Fay, M.F., 2008. Morphometric and population genetic analyses elucidate the origin, evolutionary significance and conservation implications of Orchis angusticruris (O. purpurea, O. simia), a hybrid orchid new to Britain. Bot. J. Linn. Soc. 157, 687-711.
Berg, V.D., 2002. Molecular phylogenetics of Cymbidium (Orchidaceae: Maxillarieae) sequence data from internal transcribed spacers (ITS) of nuclear ribosomal DNA and plastid matK. Lindleyana 17, 102-111.
Cameron, K.M., Chase, M.W., Whitten, W.M., et al., 1999. A phylogenetic analysis of the Orchidaceae: evidence from rbcL nucleotide sequences. Am. J. Bot. 86, 208-224. https://doi.org/10.2307/2656938.
Chase, M.W., Cameron, K.M., Freudenstein, J.V., et al., 2015. An updated classification of Orchidaceae. Bot. J. Linn. Soc. 177, 151-174. https://doi.org/10.1111/boj.12234.
Chen, S.C., Liu, Z.J., Zhu, G.H., et al., 2009. Orchidaceae, Flora of China, vol. 25. Science Press, Beijing & Missouri Botanical Garden Press, Beijing. Chen, G.Z., Huang, J., Zhang, G.Q., et al., 2017. New subtribe Pachitinae (Orchideae) of Orchidaceae: evidence from morphological and molecular analyses. Phytotaxa 329, 114-126. https://doi.org/10.11646/phytotaxa.329.2.2.
Cortis, P., Vereecken, N.J., Schiestl, F.P., et al., 2009. Pollinator convergence and the nature of species' boundaries in sympatric Sardinian Ophrys (Orchidaceae). Ann. Bot. 104, 497-506.
Cribb, P.J., 1998. The Genus Paphiopedilum, second ed. Natural History Publications, Kota Kinabalu and Kew.
Doyle, J.J., Doyle, J.L., 1987. A rapid isolation procedure from small quantities of fresh leaf tissue. Phytochem. Bull. 19, 11-15.
Dressler, R.L., 1981. The Orchids: Natural History and Classification. Cambridge Harvard University Press, New York.
Dressler, R.L., 1993. Phylogeny and Classification of the Orchid Family. Cambridge University Press.
Du Puy, D.J., Cribb, P.J., 2007. The Genus Cymbidium. Royal Botanic Garden, Kew, Richmond.
Edgar, R.C., 2004. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797. https://doi.org/10.1093/nar/gkh340.
Farris, J.S., Källersjö, M., Kluge, A.G., 1995. Constructing a significance test for incongruence. Syst. Biol. 44, 570-572. https://doi.org/10.1093/sysbio/44.4.570.
Francine, C., De Ré, Robe, L.J., et al., 2017. Inferring the phylogenetic position of the Drosophila flavopilosa group: incongruence within and between mitochondrial and nuclear multilocus datasets. J. Zool. Syst. Evol. Res. 55, 208-221 https://doi.org/221. 10.1111/jzs.12170.
Freudenstein, J.V., Rasmussen, F.N., 1999. What does morphology tell us about orchid relationships? A cladistic analysis. Am. J. Bot. 86, 225-248. https://doi.org/10.2307/2656939.
Geuten, K., Smets, E., Schols, P., et al., 2004. Conflicting phylogenies of Balsaminoid families and the polytomy in Ericales: combining data in a Bayesian framework. Mol. Phylogenet. Evol. 31, 711-729. https://doi.org/10.1016/j.ympev.2003.09.014.
Guo, Y.Y., Luo, Y.B., Liu, Z.J., et al., 2015. Reticulate evolution and sea-level fluctuations together drove species diversification of slipper orchids (Paphiopedilum) in South-East Asia. Mol. Ecol. 24, 2838-2855. https://doi.org/10.1111/mec. 13189.
Hunt, P.F., 1970. Notes on Asiatic orchis 5. Kew Bulletin 24, 93-94.
Huson, D.H., Bryant, D., 2006. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23, 254-267. https://doi.org/10.1093/molbev/msj030.
Kanzi, A.M., Trollip, C., Wingfield, M.J., et al., 2020. Phylogenomic incongruence in Ceratocystis: a clue to speciation. BMC Genom. 21, 362.
Lan, S.R., Chen, L.J., Chen, G.Z., et al., 2018. Cymbidium densiflorum (Orchidaceae:Epidendroideae: Cymbidieae): a new orchid species from China based on morphological and molecular evidence. Phytotaxa 345, 51-58. https://doi.org/10.11646/phytotaxa.345.1.6.
Li, M.H., Zhang, G.Q., Lan, S.R., et al., 2015. A molecular phylogeny of Chinese orchids. J. Systemat. Evol. 54, 349-362. https://doi.org/10.1111/jse.12187.
Lindley, J., 1821. Eulophia. Botan. Reg. 7, 573.
Lindley, J., 1826. Epidendreae. Collect. Bot. 17, 16.
Liu, Z.J., Chen, X.Q., 1998. Five new species of Cymbidium from Asia. J. S. China Agric. Univ. 19, 114-118.
Liu, Z.J., Chen, X.Q., 2002. Cymbidium paucifolium, a new species of Orchidaceae from China. J. Wuhan Bot. Res. 20, 350-352.
Liu, Z.J., Chen, X.Q., 2004. Cymbidium micranthum, a new orchid from Yunnan, China. J. Wuhan Bot. Res. 22, 500-502.
Liu, Z.J., Chen, X.Q., 2005. Cymbidium rhizomatosum, a new species of Orchidaceae from Yunnan, China. J. Wuhan Bot. Res. 27, 378-380.
Liu, Z.J., Chen, S.C., Chen, L.J., et al., 2009. The Genus Paphiopedilum in China. Science Press, Beijing.
Liu, Z.J., Chen, X.Q., Ru, Z.Z., et al., 2006. The Genus Cymbidium in China. Science Press, Beijing.
Long, C.L., Dao, Z.L., Li, H., 2003. A new species of Cymbidium (Orchidaceae) from Tibet (Xizang), China. Novon 13, 203-205. https://doi.org/10.2307/3393520.
Miller, M.A., Pfeiffer, W., Schwartz, T., 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: Proceedings of the Gateway Computing Environments Workshop (GCE). New Orleans, LA, pp. 1-8. https://doi.org/10.1109/GCE.2010.5676129.
Pelser, P.B., Kennedy, A.H., Tepe, E.J., et al., 2010. Patterns and causes of incongruence between plastid and nuclear Senecioneae (Asteraceae) phylogenies. Am. J. Bot. 97, 856-873. https://doi.org/10.3732/ajb.0900287.
Pinheiro, F., de Barros, F., Palma-Silva, C., et al., 2010. Hybridization and introgression across different ploidy levels in the Neotropical orchids Epidendrum fulgens and E. puniceoluteum (Orchidaceae). Mol. Ecol. 19, 3981-3994.
Pridgeon, A.M., Cribb, P.J., Chase, M.W., et al., 2009. Genera Orchidacearum, 5. Oxford University Press, Oxford. Epidendroideae (Part 2).
Puy, D.D., Cribb, P., 1988. The Genus Cymbidium. Timber Press, USA, Christopher Helm.
Richardson, A.O., Palmer, J.D., 2007. Horizontal gene transfer in plants. J. Exp. Bot. 58, 1-9. https://doi.org/10.1007/s10142-013-0345-0.
Russell, A., Samuel, R., Klejna, V., et al., 2010. Reticulate evolution in diploid and tetraploid species of Polystachya (Orchidaceae) as shown by plastid DNA sequences and low-copy nuclear genes. Ann. Bot. 106, 37-56. https://doi.org/10.1093/aob/mcq092.
Schlechter, R., 1924. Die Gattungen Cymbidium Sw. und Cyperorchis Bl. Repert. Sp. Nov. Regni. 20, 96-110. https://doi.org/10.1002/fedr.19240200605.
Seth, C.J., Cribb, P.J., 1984. A reassessment of the sectional limits in the genus Cymbidium Swartz. In: Orchid Biology, Reviews and Prospectives 3. Cornell Univ. Press, Ithaca and London.
Sharma, S.K., Dkhar, J., Kumaria, S., et al., 2012. Assessment of phylogenetic interrelationships in the genus Cymbidium (Orchidaceae) based on internal transcribed spacer region of rDNA. Gene 495, 10-15. https://doi.org/10.1016/j.gene.2011.12.052.
Stamatakis, A., Hoover, P., Rougemont, J., 2008. A rapid bootstrap algorithm for the RAxML webeservers. Syst. Biol. 75, 758-771. https://doi.org/10.1080/10635150802429642.
Tamura, K., Peterson, D., Peterson, et al., 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and Maximum Parsimony methods. Mol. Biol. Evol. 28, 2731. https://doi.org/10.1093/molbev/msr121.
Tang, Y., Yukawa, T., Bateman, R.M., et al., 2015. Phylogeny and classification of the east Asian Amitostigma alliance (Orchidaceae: Orchideae) based on six DNA markers. BMC Evol. Biol. 15, 96.
Tu, T., Dillon, M.O., Sun, H., et al., 2008. Phylogeny of Nolana (Solanaceae) of the Atacama and Peruvian deserts inferred from sequences of four plastid markers and the nuclear LEAFY second intron. Mol. Phylogenet. Evol. 49, 561-573.https://doi.org/10.1016/j.ympev.2008.07.018.
Yang, Z.Y., Ran, J.H., Wang, X.Q., 2012. Three genome-based phylogeny of Cupressaceae s.l.: further evidence for the evolution of gymnosperms and Southern Hemisphere biogeography. Mol. Phylogenet. Evol. 64, 452-470. https://doi.org/10.1186/1471-2148-13-84.
Yang, J.B., Tang, M., Li, H.T., et al., 2013. Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses. BMC Evol. Biol. 13, 84.
Yu, W.B., Huang, P.H., Li, D.Z., et al., 2013. Incongruence between nuclear and chloroplast DNA phylogenies in Pedicularis section Cyathophora (Orobanchaceae). PLoS One 8, e74828.
Yukawa, T., Stern, W.L., 2002. Comparative vegetative anatomy and systematics of Cymbidium (Cymbidieae: Orchidaceae). Bot. J. Linn. Soc. 138, 383-419. https://doi.org/10.1046/j.1095-8339.2002.00038.x.
Zhai, J.W., Zhang, G.Q., Li, L., et al., 2014. A new phylogenetic analysis sheds new light on the relationships in the Calanthe alliance (Orchidaceae) in China. Mol. Phylogenet. Evol. 77, 216-222. https://doi.org/10.1016/j.ympev.2014.04.005.
Zhang, G.Q., Chen, G.Z., Liu, Z.J., et al., 2018. Cymbidium daweishanense (Orchidaceae; Epidendroideae), a new species from China: evidence from morphological and molecular analyses. Phytotaxa 374, 249-256. https://doi.org/10.11646/phytotaxa.374.3.6.
Zhang, G.Q., Liu, K.W., Chen, L.J., et al., 2013. A new molecular phylogeny and a new genus, Pendulorchis, of the AerideseVanda alliance (Orchidaceae: Epidendroideae). PLoS One 8, e60097. https://doi.org/10.1371/journal.pone. 0060097.
Zhang, M.Y., Yun, S.C., Gang, H., et al., 2002. A preliminary analysis of phylogenetic relationships in Cymbidium (Orchidaceae) based on nrITS sequence data. Acta Bot. Sin. 44, 588-592.
Zhang, Y.X., Zeng, C.X., Li, D.Z., 2012. Complex evolution in Arundinarieae (Poaceae:Bambusoideae): incongruence between plastid and nuclear GBSSI gene phylogenies. Mol. Phylogenet. Evol. 63, 777-797.

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