TY  - DATA
ID  - doi:10.5061/dryad.25j6h
T1  - Data from: A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic Lissamphibia
AU  - Fong JJ
AU  - Brown JM
AU  - Fujita MK
AU  - Boussau B
Y1  - 2012/11/07/
N2  - 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.
KW  - tree of life
KW  - higher-level systematics
KW  - non-phylogenetic signal
KW  - systematic error
KW  - data filtering
KW  - discriminant function analysis
KW  - Testudines
KW  - Lissamphibia
JF  - PLoS ONE
PB  - Dryad Data Repository
UR  - http://dx.doi.org/10.5061/dryad.25j6h
DO  - doi:10.5061/dryad.25j6h
ER  -