A new paper (Crawford et al. 2012) reports that turtle molecules link them to archosaurs, not lepidosaurs.
Here’s the 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.
Ahh, but which archosaurs?
That’s what molecules will never tell you.
At the end we can only confirm with fossil bones
We’ve already uncovered a most parsimonious nesting and a series of gradually accumulating turtle traits in a lineage within the lepidosauromorpha. So if molecules tell a different tale, then someone’s got some ‘splaining to do. Not sure why the molecules would take us one way while the bones take us another.
Turtles are weird.
As always, I encourage readers to see specimens, make observations and come to your own conclusions. Test. Test. And test again.
Evidence and support in the form of nexus, pdf and jpeg files will be sent to all who request additional data.
Crawford NG, Faircloth BC, McCormack JE, Brumfield RT, Winker K, and Glenn TC 2012. More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs. Biology Letters (advance online publication) doi:10.1098/rsbl.2012.0331 online