A Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia
Identifieur interne : 000612 ( Pmc/Curation ); précédent : 000611; suivant : 000613A Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia
Auteurs : Jonathan J. Fong [États-Unis, Corée du Sud] ; Jeremy M. Brown [États-Unis] ; Matthew K. Fujita [États-Unis] ; Bastien Boussau [États-Unis, France]Source :
- PLoS ONE [ 1932-6203 ] ; 2012.
Abstract
In resolving the vertebrate tree of life, two fundamental questions remain: 1) what is the phylogenetic position of turtles within amniotes, and 2) what are the relationships between the three major lissamphibian (extant amphibian) groups? These relationships have historically been difficult to resolve, with five different hypotheses proposed for turtle placement, and four proposed branching patterns within Lissamphibia. We compiled a large cDNA/EST dataset for vertebrates (75 genes for 129 taxa) to address these outstanding questions. Gene-specific phylogenetic analyses revealed a great deal of variation in preferred topology, resulting in topologically ambiguous conclusions from the combined dataset. Due to consistent preferences for the same divergent topologies across genes, we suspected systematic phylogenetic error as a cause of some variation. Accordingly, we developed and tested a novel statistical method that identifies sites that have a high probability of containing biased signal for a specific phylogenetic relationship. After removing putatively biased sites, support emerged for a sister relationship between turtles and either crocodilians or archosaurs, as well as for a caecilian-salamander sister relationship within Lissamphibia, with Lissamphibia potentially paraphyletic.
Url:
DOI: 10.1371/journal.pone.0048990
PubMed: 23145043
PubMed Central: 3492174
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These relationships have historically been difficult to resolve, with five different hypotheses proposed for turtle placement, and four proposed branching patterns within Lissamphibia. We compiled a large cDNA/EST dataset for vertebrates (75 genes for 129 taxa) to address these outstanding questions. Gene-specific phylogenetic analyses revealed a great deal of variation in preferred topology, resulting in topologically ambiguous conclusions from the combined dataset. Due to consistent preferences for the same divergent topologies across genes, we suspected systematic phylogenetic error as a cause of some variation. Accordingly, we developed and tested a novel statistical method that identifies sites that have a high probability of containing biased signal for a specific phylogenetic relationship. After removing putatively biased sites, support emerged for a sister relationship between turtles and either crocodilians or archosaurs, as well as for a caecilian-salamander sister relationship within Lissamphibia, with Lissamphibia potentially paraphyletic.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Benton, Mj" uniqKey="Benton M">MJ Benton</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Meyer, A" uniqKey="Meyer A">A Meyer</name></author><author><name sortKey="Zardoya, R" uniqKey="Zardoya R">R Zardoya</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thomson, Rc" uniqKey="Thomson R">RC Thomson</name></author><author><name sortKey="Shaffer, Hb" uniqKey="Shaffer H">HB Shaffer</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Lyson, Tr" uniqKey="Lyson 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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">23145043</article-id><article-id pub-id-type="pmc">3492174</article-id><article-id pub-id-type="publisher-id">PONE-D-12-10241</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0048990</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Biology</subject><subj-group><subject>Computational Biology</subject><subj-group><subject>Sequence Analysis</subject></subj-group></subj-group><subj-group><subject>Evolutionary Biology</subject><subj-group><subject>Evolutionary Systematics</subject><subj-group><subject>Molecular Systematics</subject><subject>Phylogenetics</subject></subj-group></subj-group></subj-group><subj-group><subject>Genomics</subject><subj-group><subject>Genome Databases</subject><subj-group><subject>Sequence Databases</subject></subj-group></subj-group></subj-group><subj-group><subject>Zoology</subject><subj-group><subject>Herpetology</subject></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Mathematics</subject><subj-group><subject>Statistics</subject><subj-group><subject>Statistical Methods</subject></subj-group></subj-group></subj-group></article-categories><title-group><article-title>A Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia</article-title><alt-title alt-title-type="running-head">Phylogenomics of the Vertebrate Phylogeny</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Fong</surname><given-names>Jonathan J.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="aff" rid="aff3"><sup>3</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Brown</surname><given-names>Jeremy M.</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="aff" rid="aff4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Fujita</surname><given-names>Matthew K.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="aff" rid="aff5"><sup>5</sup></xref><xref ref-type="aff" rid="aff6"><sup>6</sup></xref></contrib><contrib contrib-type="author"><name><surname>Boussau</surname><given-names>Bastien</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="aff" rid="aff7"><sup>7</sup></xref></contrib></contrib-group><aff id="aff1"><label>1</label><addr-line>Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America</addr-line></aff><aff id="aff2"><label>2</label><addr-line>Department of Integrative Biology, University of California, Berkeley, California, United States of America</addr-line></aff><aff id="aff3"><label>3</label><addr-line>College of Natural Sciences, Seoul National University, Seoul, Republic of Korea</addr-line></aff><aff id="aff4"><label>4</label><addr-line>Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America</addr-line></aff><aff id="aff5"><label>5</label><addr-line>Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America</addr-line></aff><aff id="aff6"><label>6</label><addr-line>Department of Biology, University of Texas-Arlington, Arlington, Texas, United States of America</addr-line></aff><aff id="aff7"><label>7</label><addr-line>Laboratorie de Biométrie et Biologie Evolutive, Université de Lyon, Villeurbanne, France</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Hejnol</surname><given-names>Andreas</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>Sars International Centre for Marine Molecular Biology, Norway</addr-line></aff><author-notes><corresp id="cor1">* E-mail: <email>jfong@snu.ac.kr</email></corresp><fn fn-type="conflict"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con"><p>Conceived and designed the experiments: JJF MKF. Performed the experiments: JJF MKF. Analyzed the data: JJF MKF JMB BB. Contributed reagents/materials/analysis tools: JMB BB. Wrote the paper: JJF MKF JMB BB.</p></fn></author-notes><pub-date pub-type="collection"><year>2012</year></pub-date><pub-date pub-type="epub"><day>7</day><month>11</month><year>2012</year></pub-date><volume>7</volume><issue>11</issue><elocation-id>e48990</elocation-id><history><date date-type="received"><day>10</day><month>4</month><year>2012</year></date><date date-type="accepted"><day>3</day><month>10</month><year>2012</year></date></history><permissions><copyright-year>2012</copyright-year><copyright-holder>Fong et al</copyright-holder><license><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p></license></permissions><abstract><p>In resolving the vertebrate tree of life, two fundamental questions remain: 1) what is the phylogenetic position of turtles within amniotes, and 2) what are the relationships between the three major lissamphibian (extant amphibian) groups? These relationships have historically been difficult to resolve, with five different hypotheses proposed for turtle placement, and four proposed branching patterns within Lissamphibia. We compiled a large cDNA/EST dataset for vertebrates (75 genes for 129 taxa) to address these outstanding questions. Gene-specific phylogenetic analyses revealed a great deal of variation in preferred topology, resulting in topologically ambiguous conclusions from the combined dataset. Due to consistent preferences for the same divergent topologies across genes, we suspected systematic phylogenetic error as a cause of some variation. Accordingly, we developed and tested a novel statistical method that identifies sites that have a high probability of containing biased signal for a specific phylogenetic relationship. After removing putatively biased sites, support emerged for a sister relationship between turtles and either crocodilians or archosaurs, as well as for a caecilian-salamander sister relationship within Lissamphibia, with Lissamphibia potentially paraphyletic.</p></abstract><funding-group><funding-statement>Funding for this work came from the National Science Foundation (NSF) Doctoral Dissertation Improvement Grant (DEB-0909811 [JJF]), NSF Postdoctoral Fellowship in Biology (DBI-0905867 [JMB], DBI-0905714 [MKF]), Human Frontiers Science Program Postdoctoral Fellowship (BB), Centre National de la Recherche Scientifique (BB), and Museum of Vertebrate Zoology (JJF). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement></funding-group><counts><page-count count="14"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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