A phylogenomic analysis of turtles

[Display omitted] •2381 Ultraconserved element (UCE) loci resolve relationships among living turtles.•The UCE phylogeny is used to test and develop a phylogenetic nomenclature.•The UCE phylogeny is more consistent with biogeography and stratigraphy of fossil turtles than morphological hypotheses.•The UCE phylogeny provides a scaffold for paleontological studies. Molecular analyses of turtle relationships have overturned prevailing morphological hypotheses and prompted the development of a new taxonomy. Here we provide the first genome-scale analysis of turtle phylogeny. We sequenced 2381 ultraconserved element (UCE) loci representing a total of 1,718,154bp of aligned sequence. Our sampling includes 32 turtle taxa representing all 14 recognized turtle families and an additional six outgroups. Maximum likelihood, Bayesian, and species tree methods produce a single resolved phylogeny. This robust phylogeny shows that proposed phylogenetic names correspond to well-supported clades, and this topology is more consistent with the temporal appearance of clades and paleobiogeography. Future studies of turtle phylogeny using fossil turtles should use this topology as a scaffold for their morphological phylogenetic analyses.