Phylogenetics of Subtribe Orchidinae S.l. (Orchidaceae; Orchidoideae) Based on Seven Markers (plastid MatK, PsaB, RbcL, TrnL-F, TrnH-psba, and Nuclear NrITS, Xdh): Implications for Generic Delimitation

Overview

Journal BMC Plant Biol

Publisher Biomed Central

Specialty Biology

Date 2017 Nov 28

PMID 29178835

Citations 20

Authors

Wei-Tao Jin

Andre Schuiteman

Mark W Chase

Jian-Wu Li

Shih-Wen Chung

Tian-Chuan Hsu

Xiao-Hua Jin

Affiliations

Soon will be listed here.

Abstract

Background: Subtribe Orchidinae (Orchidaceae, Orchidoideae) are a nearly cosmopolitan taxon of terrestrial orchids, comprising about 1800 species in 47 to 60 genera. Although much progress has been made in recent years of phylogenetics of Orchidinae, considerable problems remain to be addressed. Based on molecular phylogenetics, we attempt to illustrate the phylogenetic relationships and discuss generic delimitation within Orchidinae. Seven DNA markers (five plastid and two nuclear), a broad sampling of Orchidinae (400 species in 52 genera) and three methods of phylogenetic analysis (maximum likelihood, maximum parsimony and Bayesian inference) were used.

Results: Orchidinae s.l. are monophyletic. Satyrium is sister to the rest of Orchidinae s.l. Brachycorythis and Schizochilus are successive sister to Asian-European Orchidinae s.s. Sirindhornia and Shizhenia are successive sister to clade formed by Tsaiorchis-Hemipilia-Ponerorchis alliance. Stenoglottis is sister to the Habenaria-Herminium-Peristylus alliance. Habenaria, currently the largest genus in Orchidinae, is polyphyletic and split into two distant clades: one Asian-Australian and the other African-American-Asian. Diplomeris is sister to Herminium s.l. plus Asian-Australian Habenaria.

Conclusions: We propose to recognize five genera in the Ponerorchis alliance: Hemipilia, Ponerorchis s.l., Sirindhornia, Shizhenia and Tsaiorchis. Splitting Habenaria into two genera based on morphological characters and geographical distribution may be the least disruptive approach, and it is reasonable to keep Satyrium in Orchidinae.

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References

Inda L, Pimentel M, Chase M . Phylogenetics of tribe Orchideae (Orchidaceae: Orchidoideae) based on combined DNA matrices: inferences regarding timing of diversification and evolution of pollination syndromes. Ann Bot. 2012; 110(1):71-90. PMC: 3380586. DOI: 10.1093/aob/mcs083. View

Sramko G, Attila M, Hawkins J, Bateman R . Molecular phylogeny and evolutionary history of the Eurasiatic orchid genus Himantoglossum s.l. (Orchidaceae). Ann Bot. 2014; 114(8):1609-26. PMC: 4649687. DOI: 10.1093/aob/mcu179. View

Bateman R, Sramko G, Rudall P . Floral miniaturisation and autogamy in boreal-arctic plants are epitomised by Iceland's most frequent orchid, Platanthera hyperborea. PeerJ. 2015; 3:e894. PMC: 4400879. DOI: 10.7717/peerj.894. View

Stamatakis A . RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014; 30(9):1312-3. PMC: 3998144. DOI: 10.1093/bioinformatics/btu033. View

Bytebier B, Antonelli A, Bellstedt D, Linder H . Estimating the age of fire in the Cape flora of South Africa from an orchid phylogeny. Proc Biol Sci. 2010; 278(1703):188-95. PMC: 3013384. DOI: 10.1098/rspb.2010.1035. View

Douzery E, Pridgeon A, Kores P, Linder H, Kurzweil H, Chase M . Molecular phylogenetics of Diseae (Orchidaceae): a contribution from nuclear ribosomal ITS sequences. Am J Bot. 1999; 86(6):887-99. View

Kores P, Molvray M, Weston P, Hopper S, Brown A, Cameron K . A phylogenetic analysis of Diurideae (Orchidaceae) based on plastid DNA sequence data. Am J Bot. 2011; 88(10):1903-14. View

Devey D, Bateman R, Fay M, Hawkins J . Friends or relatives? Phylogenetics and species delimitation in the controversial European orchid genus Ophrys. Ann Bot. 2008; 101(3):385-402. PMC: 2701817. DOI: 10.1093/aob/mcm299. View

Alvarez I, Wendel J . Ribosomal ITS sequences and plant phylogenetic inference. Mol Phylogenet Evol. 2003; 29(3):417-34. DOI: 10.1016/s1055-7903(03)00208-2. View

10.

Tang Y, Yukawa T, Bateman R, Jiang H, Peng H . Phylogeny and classification of the East Asian Amitostigma alliance (Orchidaceae: Orchideae) based on six DNA markers. BMC Evol Biol. 2015; 15:96. PMC: 4479074. DOI: 10.1186/s12862-015-0376-3. View

11.

Katoh K, Standley D . MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30(4):772-80. PMC: 3603318. DOI: 10.1093/molbev/mst010. View

12.

Efimov P . [Sibling species of rein orchid (Gymnadenia:Orchidaceae, Magnoliophyta) in Russia]. Genetika. 2013; 49(3):343-54. DOI: 10.7868/s0016675813020045. View

13.

Bahadur Raskoti B, Jin W, Xiang X, Schuiteman A, Li D, Li J . A phylogenetic analysis of molecular and morphological characters of Herminium (Orchidaceae, Orchideae): evolutionary relationships, taxonomy, and patterns of character evolution. Cladistics. 2021; 32(2):198-210. DOI: 10.1111/cla.12125. View

14.

Batista J, Borges K, de Faria M, Proite K, Ramalho A, Salazar G . Molecular phylogenetics of the species-rich genus Habenaria (Orchidaceae) in the New World based on nuclear and plastid DNA sequences. Mol Phylogenet Evol. 2013; 67(1):95-109. DOI: 10.1016/j.ympev.2013.01.008. View

15.

Devey D, Bateman R, Fay M, Hawkins J . Genetic structure and systematic relationships within the Ophrys fuciflora aggregate (Orchidaceae: Orchidinae): high diversity in Kent and a wind-induced discontinuity bisecting the Adriatic. Ann Bot. 2009; 104(3):483-95. PMC: 2720644. DOI: 10.1093/aob/mcp039. View

16.

Felsenstein J . Phylogenies from molecular sequences: inference and reliability. Annu Rev Genet. 1988; 22:521-65. DOI: 10.1146/annurev.ge.22.120188.002513. View

17.

Pelser P, Kennedy A, Tepe E, Shidler J, Nordenstam B, Kadereit J . Patterns and causes of incongruence between plastid and nuclear Senecioneae (Asteraceae) phylogenies. Am J Bot. 2011; 97(5):856-73. DOI: 10.3732/ajb.0900287. View

18.

Shipunov A, Fay M, Pillon Y, Bateman R, Chase M . Dactylorhiza (Orchidaceae) in European Russia: combined molecular and morphological analysis. Am J Bot. 2011; 91(9):1419-26. DOI: 10.3732/ajb.91.9.1419. View

19.

Ronquist F, Teslenko M, van der Mark P, Ayres D, Darling A, Hohna S . MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012; 61(3):539-42. PMC: 3329765. DOI: 10.1093/sysbio/sys029. View

20.

Nylander J, Ronquist F, Huelsenbeck J, Nieves-Aldrey J . Bayesian phylogenetic analysis of combined data. Syst Biol. 2004; 53(1):47-67. DOI: 10.1080/10635150490264699. View