Data from: More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

We present the first genomic-scale analysis addressing the phylogenetic
position of turtles, using over 1,000 loci from representatives of all
major reptile lineages including tuatara. Previously, studies of
morphological traits positioned turtles either at the base of the reptile
tree or with lizards, snakes, and tuatara (lepidosaurs), whereas molecular
analyses typically allied turtles with crocodiles and birds (archosaurs).
A recent analysis of shared microRNA families found that turtles are more
closely related to lepidosaurs. To test this hypothesis with data from
many single-copy nuclear loci dispersed throughout the genome, we used
sequence capture, high-throughput sequencing and published genomes to
obtain sequences from 1,145 ultraconserved elements (UCEs) and their
variable flanking DNA. The resulting phylogeny provides overwhelming
support for the hypothesis that turtles evolved from a common ancestor of
birds and crocodilians, rejecting the hypothesized relationship between
turtles and lepidosaurs.