A Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia
Identifieur interne : 000536 ( Main/Exploration ); précédent : 000535; suivant : 000537A 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
Affiliations:
- Corée du Sud, France, États-Unis
- Californie, Louisiane, Massachusetts, Texas
- Cambridge (Massachusetts), Lyon, Séoul, Villeurbanne
- Université Harvard, Université nationale de Séoul
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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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Boussau</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Corée du Sud</li><li>France</li><li>États-Unis</li></country><region><li>Californie</li><li>Louisiane</li><li>Massachusetts</li><li>Texas</li></region><settlement><li>Cambridge (Massachusetts)</li><li>Lyon</li><li>Séoul</li><li>Villeurbanne</li></settlement><orgName><li>Université Harvard</li><li>Université nationale de Séoul</li></orgName></list><tree><country name="États-Unis"><region name="Californie"><name sortKey="Fong, Jonathan J" sort="Fong, Jonathan J" uniqKey="Fong J" first="Jonathan J." last="Fong">Jonathan J. Fong</name></region><name sortKey="Boussau, Bastien" sort="Boussau, Bastien" uniqKey="Boussau B" first="Bastien" last="Boussau">Bastien Boussau</name><name sortKey="Brown, Jeremy M" sort="Brown, Jeremy M" uniqKey="Brown J" first="Jeremy M." last="Brown">Jeremy M. Brown</name><name sortKey="Brown, Jeremy M" sort="Brown, Jeremy M" uniqKey="Brown J" first="Jeremy M." last="Brown">Jeremy M. Brown</name><name sortKey="Fong, Jonathan J" sort="Fong, Jonathan J" uniqKey="Fong J" first="Jonathan J." last="Fong">Jonathan J. Fong</name><name sortKey="Fujita, Matthew K" sort="Fujita, Matthew K" uniqKey="Fujita M" first="Matthew K." last="Fujita">Matthew K. Fujita</name><name sortKey="Fujita, Matthew K" sort="Fujita, Matthew K" uniqKey="Fujita M" first="Matthew K." last="Fujita">Matthew K. Fujita</name><name sortKey="Fujita, Matthew K" sort="Fujita, Matthew K" uniqKey="Fujita M" first="Matthew K." last="Fujita">Matthew K. Fujita</name><name sortKey="Fujita, Matthew K" sort="Fujita, Matthew K" uniqKey="Fujita M" first="Matthew K." last="Fujita">Matthew K. Fujita</name></country><country name="Corée du Sud"><noRegion><name sortKey="Fong, Jonathan J" sort="Fong, Jonathan J" uniqKey="Fong J" first="Jonathan J." last="Fong">Jonathan J. Fong</name></noRegion></country><country name="France"><noRegion><name sortKey="Boussau, Bastien" sort="Boussau, Bastien" uniqKey="Boussau B" first="Bastien" last="Boussau">Bastien Boussau</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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