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Re: Turtle-Archosaur Affinity

Whoa. Have a good long look at figure 2. Those numbers for "Other" are, shall we say, impressive; I'd really like to know what "Other" means.

as well as for a  caecilian-salamander sister relationship within
> Lissamphibia, with Lissamphibia potentially paraphyletic.

Awwww. Too bad Jason Anderson officially stopped supporting the hypothesis of modern-amphibian polyphyly in his talk at the SVP meeting. Robert Carroll might be delighted...

Seriously now: I think this paper confirms my opinion, formed from papers on bilaterian phylogeny, that whole genomes are as prone to long-branch attraction or whatever as single genes are. I'll have to cite the paper, but I won't take any of its competing results as strong evidence for anything.

What could be interesting would be data that can only be derived when whole genomes are known, but that behave more like morphological characters. Gene loss (presence/absence) data are one option that comes to mind (they support Ecdysozoa, while whole genomes didn't last time I looked, which was about 10 years ago). Of course, LINE and SINE insertions are another.