Last spring when I was in Austin, Kevin Peterson came and gave a talk on the promise of microRNA's in determining phylogenetic relationships of organisms. In a follow-up question Sterling Nesbitt and I asked him if this could be used to solve the debate regarding the relationships of turtles. Peterson replied that they were already working on the problem and that preliminary data suggested that turtles were close to lepidosaurs. You can read more details from the final study below. Fascinating stuff.
Update: Here is the abstract
Lyson, T. R., Sperling, E. A., Heimberg, A. M., Gauthier, J. A., King, B. L., and K. J. Peterson. 2011. MicroRNAs support a turtle + lizard clade. Biology Letters. doi: 10.1098/rsbl.2011.0477
Abstract - Despite much interest in amniote systematics, the origin of turtles remains elusive. Traditional morphological phylogenetic analyses place turtles outside Diapsida—amniotes whose ancestor had two fenestrae in the temporal region of the skull (among the living forms the tuatara, lizards, birds and crocodilians)—and allied with some unfenestrate-skulled (anapsid) taxa. Nonetheless, some morphological analyses place turtles within Diapsida, allied with Lepidosauria (tuatara and lizards). Most molecular studies agree that turtles are diapsids, but rather than allying them with lepidosaurs, instead place turtles near or within Archosauria (crocodilians and birds). Thus, three basic phylogenetic positions for turtles with respect to extant Diapsida are currently debated: (i) sister to Diapsida, (ii) sister to Lepidosauria, or (iii) sister to, or within, Archosauria. Interestingly, although these three alternatives are consistent with a single unrooted four-taxon tree for extant reptiles, they differ with respect to the position of the root. Here, we apply a novel molecular dataset, the presence versus absence of specific microRNAs, to the problem of the phylogenetic position of turtles and the root of the reptilian tree, and find that this dataset unambiguously supports a turtle + lepidosaur group. We find that turtles and lizards share four unique miRNA gene families that are not found in any other organisms' genome or small RNA library, and no miRNAs are found in all diapsids but not turtles, or in turtles and archosaurs but not in lizards. The concordance between our result and some morphological analyses suggests that there have been numerous morphological convergences and reversals in reptile phylogeny, including the loss of temporal fenestrae.