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

Abstract

We present the first genomic-scale analysis addressing the phylogenetic position of turtles, using over 1000 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 1145 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.

Figure 1.

(a) Depicts the primary morphological hypotheses: turtles most basally branching reptilian lineage [2]² or turtles related to lepidosaurs [3].¹ (b) Depicts the primary molecular hypothesis of a turtle–archosaur alliance [–14]. (c) Depicts the tree derived from miRNA loci [15].

Figure 2.

(a) Reptilian phylogeny estimated from 1145 ultra-conserved loci using Bayesian analysis of concatenated data and species-tree methods, yielding identical topologies. Node labels indicate posterior probability/bootstrap support. (b) Phylogram of the UCE phylogeny generated with STEAC.