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Turtle-Archosaur Affinity

From: Ben Creisler

Non-dino stuff new in PLoS ONE:

Jonathan J. Fong, Jeremy M. Brown, Matthew K. Fujita & Bastien Boussau (2012)
A Phylogenomic Approach to Vertebrate Phylogeny Supports a
Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia.
PLoS ONE 7(11): e48990.

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.