Data from: A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic Lissamphibia

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.