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.