Phylogeny and classification of the East Asian Amitostigma alliance (Orchidaceae: Orchideae) based on six DNA markers
Identifieur interne : 000081 ( Main/Merge ); précédent : 000080; suivant : 000082Phylogeny and classification of the East Asian Amitostigma alliance (Orchidaceae: Orchideae) based on six DNA markers
Auteurs : Ying Tang [République populaire de Chine] ; Tomohisa Yukawa ; Richard M. Bateman ; Hong Jiang ; Hua PengSource :
- BMC Evolutionary Biology [ 1471-2148 ] ; 2015.
Abstract
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
We used parsimony, likelihood and Bayesian approaches to generate trees from data for two nuclear (nrITS, low-copy
We provide a new framework on the complex phylogenetic relationships between
The online version of this article (doi:10.1186/s12862-015-0376-3) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12862-015-0376-3
PubMed: 26006185
PubMed Central: 4479074
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Phylogeny and classification of the East Asian <italic>Amitostigma</italic> alliance (Orchidaceae: Orchideae) based on six DNA markers</title><author><name sortKey="Tang, Ying" sort="Tang, Ying" uniqKey="Tang Y" first="Ying" last="Tang">Ying Tang</name><affiliation><nlm:aff id="Aff1">Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China</nlm:aff><wicri:noCountry code="subfield">650201 Yunnan China</wicri:noCountry></affiliation><affiliation wicri:level="3"><nlm:aff id="Aff2">University of Chinese Academy of Sciences, Beijing, 100049 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>University of Chinese Academy of Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Yukawa, Tomohisa" sort="Yukawa, Tomohisa" uniqKey="Yukawa T" first="Tomohisa" last="Yukawa">Tomohisa Yukawa</name><affiliation><nlm:aff id="Aff3">Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki 305-0005 Japan</nlm:aff><wicri:noCountry code="subfield">Ibaraki 305-0005 Japan</wicri:noCountry></affiliation></author><author><name sortKey="Bateman, Richard M" sort="Bateman, Richard M" uniqKey="Bateman R" first="Richard M" last="Bateman">Richard M. Bateman</name><affiliation><nlm:aff id="Aff4">Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AB UK</nlm:aff><wicri:noCountry code="subfield">TW9 3AB UK</wicri:noCountry></affiliation></author><author><name sortKey="Jiang, Hong" sort="Jiang, Hong" uniqKey="Jiang H" first="Hong" last="Jiang">Hong Jiang</name><affiliation><nlm:aff id="Aff5">Yunnan Academy of Forestry/Yunnan Laboratory for Conservation of Rare, Endangered and Endemic Forest Plants, State Forestry Administration, Kunming, 650204 Yunnan China</nlm:aff><wicri:noCountry code="subfield">650204 Yunnan China</wicri:noCountry></affiliation></author><author><name sortKey="Peng, Hua" sort="Peng, Hua" uniqKey="Peng H" first="Hua" last="Peng">Hua Peng</name><affiliation><nlm:aff id="Aff1">Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China</nlm:aff><wicri:noCountry code="subfield">650201 Yunnan China</wicri:noCountry></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26006185</idno><idno type="pmc">4479074</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4479074</idno><idno type="RBID">PMC:4479074</idno><idno type="doi">10.1186/s12862-015-0376-3</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000164</idno><idno type="wicri:Area/Pmc/Curation">000164</idno><idno type="wicri:Area/Pmc/Checkpoint">000075</idno><idno type="wicri:Area/Ncbi/Merge">000640</idno><idno type="wicri:Area/Ncbi/Curation">000640</idno><idno type="wicri:Area/Ncbi/Checkpoint">000640</idno><idno type="wicri:Area/Main/Merge">000081</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Phylogeny and classification of the East Asian <italic>Amitostigma</italic> alliance (Orchidaceae: Orchideae) based on six DNA markers</title><author><name sortKey="Tang, Ying" sort="Tang, Ying" uniqKey="Tang Y" first="Ying" last="Tang">Ying Tang</name><affiliation><nlm:aff id="Aff1">Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China</nlm:aff><wicri:noCountry code="subfield">650201 Yunnan China</wicri:noCountry></affiliation><affiliation wicri:level="3"><nlm:aff id="Aff2">University of Chinese Academy of Sciences, Beijing, 100049 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>University of Chinese Academy of Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Yukawa, Tomohisa" sort="Yukawa, Tomohisa" uniqKey="Yukawa T" first="Tomohisa" last="Yukawa">Tomohisa Yukawa</name><affiliation><nlm:aff id="Aff3">Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki 305-0005 Japan</nlm:aff><wicri:noCountry code="subfield">Ibaraki 305-0005 Japan</wicri:noCountry></affiliation></author><author><name sortKey="Bateman, Richard M" sort="Bateman, Richard M" uniqKey="Bateman R" first="Richard M" last="Bateman">Richard M. Bateman</name><affiliation><nlm:aff id="Aff4">Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AB UK</nlm:aff><wicri:noCountry code="subfield">TW9 3AB UK</wicri:noCountry></affiliation></author><author><name sortKey="Jiang, Hong" sort="Jiang, Hong" uniqKey="Jiang H" first="Hong" last="Jiang">Hong Jiang</name><affiliation><nlm:aff id="Aff5">Yunnan Academy of Forestry/Yunnan Laboratory for Conservation of Rare, Endangered and Endemic Forest Plants, State Forestry Administration, Kunming, 650204 Yunnan China</nlm:aff><wicri:noCountry code="subfield">650204 Yunnan China</wicri:noCountry></affiliation></author><author><name sortKey="Peng, Hua" sort="Peng, Hua" uniqKey="Peng H" first="Hua" last="Peng">Hua Peng</name><affiliation><nlm:aff id="Aff1">Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China</nlm:aff><wicri:noCountry code="subfield">650201 Yunnan China</wicri:noCountry></affiliation></author></analytic><series><title level="j">BMC Evolutionary Biology</title><idno type="eISSN">1471-2148</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>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 <italic>Amitostigma</italic> 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.</p></sec><sec><title>Results</title><p>We used parsimony, likelihood and Bayesian approaches to generate trees from data for two nuclear (nrITS, low-copy <italic>Xdh</italic>) and four chloroplast (<italic>matK</italic>, <italic>psbA-trnH</italic>, <italic>trnL-F</italic>, <italic>trnS-trnG</italic>) 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 <italic>Sirindhornia</italic> and <italic>Brachycorythis</italic>, and confirm previous assertions that the <italic>Amitostigma</italic> 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 <italic>Tsaiorchis</italic>, <italic>Hemipilia</italic>, <italic>Neottianthe</italic> and <italic>Hemipiliopsis</italic> are monophyletic but each is nested within a polyphyletic plexus of species attributed to either <italic>Ponerorchis</italic> or the most plesiomorphic genus, <italic>Amitostigma</italic>. Two early-divergent clades that escaped analysis by Jin et al. undermine their attempt to circumscribe an expanded monophyletic genus <italic>Ponerorchis</italic>.</p></sec><sec><title>Conclusions</title><p>We provide a new framework on the complex phylogenetic relationships between <italic>Amitostigma</italic> and other genera traditionally included in its alliance; based on which, we combine the entire <italic>Amitostigma</italic> alliance into a morphologically and molecularly circumscribed <italic>Amitostigma sensu latissimo</italic> 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.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12862-015-0376-3) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Lang, K Y" uniqKey="Lang K">K-Y Lang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lang, K Y" uniqKey="Lang K">K-Y Lang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chen, S C" uniqKey="Chen S">S-C Chen</name></author><author><name sortKey="Lang, K Y" uniqKey="Lang K">K-Y Lang</name></author><author><name sortKey="Gale, Sw" uniqKey="Gale S">SW 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Rudall</name></author></analytic></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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