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

Abstract

BackgroundSubtribe 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.ResultsOrchidinae 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.ConclusionsWe 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.Electronic supplementary materialThe online version of this article (10.1186/s12870-017-1160-x) contains supplementary material, which is available to authorized users.

A Synopsis of Sardinian Studies: Why Is it Important to Work on Island Orchids?

“…Indeed, it interferes with all other aspects of biodiversity, and thus the scarcity of information about the number of species occurring is one of the most relevant deficiencies in biodiversity [45]. Since orchids are highly specialized organisms where eco-ethological adaptations are not always reflected in genotypes, species circumscription has rarely found agreement among taxonomists [26,46,47]. Thus, this debate is a losing game in the presence of a disproportion of knowledge between morphofunctional data and molecular data, as we recorded for many Sardinian orchids (see Table 1 and Supplementary Files 2 and 3).…”

Molecular phylogeny and morphology reveal a new epiphytic species of Habenaria (Orchidaceae; Orchideae; Orchidinae) from Nepal

“…Additionally, we sequenced two samples of the newly collected taxon for the present analyses. The ingroup taxa included a total of 191 sequences of 185 species, representing all of the major clades in the Habenaria and its alliance [6, 7, 8, 9]. Three representative species of Disa P.J.…”

“…were selected as outgroups following previous phylogenetic studies [6, 7, 8]. We added 41 additional samples of Habenaria species than in the past phylogenetic study [7]. A list of sampled species, GenBank accession numbers for all sequences and voucher information are provided in S1 Appendix.…”

“…The sequencing reactions were performed using the ABI Prism Bigdye Terminator Cycle Sequencing Kit (Applied Biosystems, ABI) following the reference Raskoti et al [22]. We selected nucleotide sequences (ITS), and plastid ( matK and rbcl ), which have exhibited their efficacy for understanding phylogenetic relationships at various taxonomic levels within the Orchidinae and other members in Orchidaceae [6, 7, 9, 22–25].…”

“…et W.T. Jin, Bonatea Willd., Diplomeris D. Don, Gennaria Parl., Peristylus Blume) indicated that Habenaria , in the broad sense, is not monophyletic [6, 7]. Despite of past and recent progress on phylogeny of Habenaria and its alliance [6, 7, 8, 9], problems remain to be addressed to solve relationships mainly between Old World and New World species [6, 7].…”