Data from: Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

BACKGROUND: The morphological peculiarities of turtles have, for a long
time, impeded their accurate placement in the phylogeny of amniotes.
Molecular data used to address this major evolutionary question have so
far been limited to a handful of markers and/or taxa. These studies have
supported conflicting topologies, positioning turtles as either the sister
group to all other reptiles, to lepidosaurs (tuatara, lizards and snakes),
to archosaurs (birds and crocodiles), or to crocodilians. Genome-scale
data have been shown to be useful in resolving other debated phylogenies,
but no such adequate dataset is yet available for amniotes. RESULTS: In
this study, we used next-generation sequencing to obtain seven new
transcriptomes from the blood, liver, or jaws from four turtles, a caiman,
a lizard, and a lungfish. We used a phylogenomic dataset based on 248
nuclear genes (187,026 nucleotide sites) for 16 vertebrate taxa to resolve
the origins of turtles. Maximum likelihood and Bayesian concatenation
analyses and species tree approaches performed under the most realistic
models of the nucleotide and amino acid substitution processes
unambiguously support turtles as a sister group to birds and crocodiles.
The use of more simplistic models of nucleotide substitution for both
concatenation and species tree reconstruction methods leads to the
artefactual grouping of turtles and crocodiles, most likely because of
substitution saturation at third codon positions. Relaxed molecular clock
methods estimate the divergence between turtles and archosaurs around 255
million years ago. The most recent common ancestor of living turtles,
corresponding to the split between Pleurodira and Cryptodira, is estimated
to have occurred around 157 million years ago, in the Upper Jurassic
period. This is a more recent estimate than previously reported, and
questions the interpretation of controversial Lower Jurassic fossils as
being part of the extant turtles radiation. CONCLUSIONS: These results
provide a phylogenetic framework and timescale with which to interpret the
evolution of the peculiar morphological, developmental, and molecular
features of turtles within the amniotes.