A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic lissamphibia

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Public Library of Science


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.





Funding Information

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. {DEB-0909811 [JJF], DBI-0905867 [JMB], DBI-0905714 [MKF]}

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Copyright © 2012 Fong et al. 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.

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Recommended Citation

Fong J. J., Brown J. M., Fujita M. K. & Boussau B. (2012). A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic lissamphibia. PLoS ONE, 7(11), e48990. doi: 10.1371/journal.pone.0048990