10.5061/DRYAD.66HC0
Tang, Ying
Chinese Academy of Sciences
Yukawa, Tomohisa
National Museum of Nature and Science
Bateman, Richard M.
Royal Botanic Gardens
Jiang, Hong
Yunnan Academy of Forestry/Yunnan Laboratory for Conservation of Rare,
Endangered and Endemic Forest Plants, State Forestry Administration,
Kunming, China
Peng, Hua
Chinese Academy of Sciences
Data from: Phylogeny and classification of the East Asian Amitostigma
alliance (Orchidaceae: Orchideae) based on six DNA markers
Dryad
dataset
2015
Neottianthe
Hemipilia
Hemipiliopsis
Holocene
Ponerorchis
Amitostigma
Tsaiorchis
2015-05-27T15:35:40Z
2015-05-27T15:35:40Z
en
https://doi.org/10.1186/s12862-015-0376-3
26674056 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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
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