DOI: 10.5061/dryad.66hc0
title: Data from: Phylogeny and classification of the East Asian Amitostigma alliance (Orchidaceae: Orchideae) based on six DNA markers

description: Background: Tribe Orchideae dominates the orchid flora of the temperate
 Northern Hemisphere but its representatives in East Asia had been subject
 to less intensive phylogenetic study than those in Eurasia and North
 America. Although this situation was improved recently by the molecular
 phylogenetic study of Jin et al., comparatively few species were analyzed
 from the species-rich and taxonomically controversial East Asian
 Amitostigma alliance. Here, we present a framework nrITS tree of 235
 accessions of Orchideae plus an in-depth analysis of 110 representative
 accessions, encompassing most widely recognized species within the
 alliance, to elucidate their relationships. Results We used parsimony,
 likelihood and Bayesian approaches to generate trees from data for two
 nuclear (rITS, low-copy Xdh) and four chloroplast (matK, psbA-trnH,
 trnL-F, trnS-trnG) markers. Nuclear and plastid data were analyzed
 separately due to a few hard incongruences that most likely reflect
 chloroplast capture. Our results suggest key phylogenetic placements for
 Sirindhornia and Brachycorythis, and confirm previous assertions that the
 Amitostigma alliance is monophyletic and sister to the Eurasian plus
 European clades of subtribe Orchidinae. Seven robust clades are evident
 within the alliance, but none corresponds precisely with any of the
 traditional genera; the smaller and more morphologically distinct genera
 Tsaiorchis, Hemipilia, Neottianthe and Hemipiliopsis are monophyletic but
 each is nested within a polyphyletic plexus of species attributed to
 either Ponerorchis or the most plesiomorphic genus, Amitostigma. Two
 early-divergent clades that escaped analysis by Jin et al. undermine their
 attempt to circumscribe an expanded monophyletic genus Ponerorchis.
 Conclusions We provide a new framework on the complex phylogenetic
 relationships between Amitostigma and other genera traditionally included
 in its alliance; based on which, we combine the entire Amitostigma
 alliance into a morphologically and molecularly circumscribed Amitostigma
 sensu latissimo that also contains seven molecularly circumscribed
 sections. Our molecular trees imply unusually high levels of morphological
 homoplasy, but these will need to be quantified via a future group-wide
 review of the alliance based on living plants if morphology is to be fully
 integrated into our classification.
description: Alignment of the
 tribe-wide nrITS datasetAlignment of the
 combined nuclear datasetAlignment of the
 combined plastid datasetBayesian tree of the
 tribe-wide nrITS datasetMaximum Likelihood tree
 of the tribe-wide nrITS datasetMaximum Parsimony strict
 consensus tree of the tribe-wide nrITS datasetMaximum Parsimony
 bootstrapping trees of the tribe-wide nrITS datasetMaximum Parsimony
 most-parsimonious trees of the tribe-wide nrITS datasetBayesian tree of the
 combined nuclear datasetMaximum Likelihood tree
 of the combined nuclear datasetMaximum Parsimony strict
 consensus tree of the combined nuclear datasetMaximum Parsimony
 most-parsimonious trees of the combined nuclear datasetMaximum Parsimony
 bootstrapping trees of the combined nuclear datasetBayesian tree of the
 combined plastid datasetMaximum Likelihood tree
 of the combined plastid datasetMaximum Parsimony strict
 consensus tree of the combined plastid datasetMaximum Parsimony
 bootstrapping trees of the combined plastid datasetMaximum Parsimony
 most-parsimonious trees of the combined plastid datasetBayesian tree of the
 nuclear Xdh datasetMaximum Likelihood tree
 of the nuclear Xdh datasetMaximum Parsimony strict
 consensus tree of the nuclear Xdh datasetMaximum Parsimony
 bootstrapping trees of the nuclear Xdh datasetMaximum Parsimony
 most-parsimonious trees of the nuclear Xdh dataset