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RE: Huge morphological analysis reconfirms deep branch relationships among Squamates

I agree with your points, but Gauthier et al. actually did do the test you 
propose.  As they say on page 54-

"When all snake-like squamates
(and mosasaurians) are removed from the
analysis, and each well-supported fossorial clade
is then added independently, Sineoamphisbaena
hexatabularis groups with polyglyphanodontians
(Figure 13; at least in the 50% majority rule
consensus), Anniella pulchra and Pseudopus
apodus group with anguids (Figure 14), Feylinia
polylepis and Acontias percivali group with
skinks (e.g., see Figure 1), and dibamids lie
within scincoids on the xantusiid stem (Figure
15; the xantusiid line would thereby join the
ranks of so many other autarchoglossan clades
in having produced a fossorial ecomorph)."

And yet strangely, the authors do not realize this makes their legless clade 
too doubtful to seriously endorse.  Snakes and amphisbaenians still emerge as 
anguimorphs when included independently, but that's expected for snakes (since 
large scale relations are so different from molecular analyses anyway) and 
Cryptolacerta was not included, as you say.

Mickey Mortimer

> Date: Sat, 2 Jun 2012 20:58:24 +0800
> From: nanowana@gmail.com
> To: dinosaur@usc.edu; VRTPALEO@usc.edu
> Subject: Huge morphological analysis reconfirms deep branch relationships 
> among Squamates
> The Gauthier et al. paper is a massive milestone, but it's hard to believe
> anybody thinks a morphology-only analysis is worth presenting when there is
> so much molecular evidence out already.
> In my PhD (finished in 1996) I got scolecophidians nested within anilioids
> on morphology, and thought the following procedure was fairly obvious:
> "The effect of convergence associated with fossorial habits must therefore
> be taken
> into account in subsequent research cycles, preferably by some method less
> ad hoc than
> arbitrarily deleting or weighting characters. Reanalysis with removal of
> taxa (in one case
> the three scolecophidian families, in the other the four anilioid taxa)
> converts apparent
> synapomorphies of both groups into autapomorphies of one or the other, and
> should
> allow the systematic position of each to be determined free of the effects
> of convergence
> between them."
> As this was a pretty late thought (2nd last paragraph in the thesis) I
> didn't check if it had been done before, but the answer is: apparently
> not. The same method was subsequently published by Siddall and Whiting
> (1999) as a way of dealing with long-branch attraction in molecular
> analyses, but I've never actually used it in a published analysis (e.g.
> anilioids and scolecophidians got separated by additional data, so it
> wasn't necessary) and I don't know if anyone else has either.
> Conrad (2008) didn't do it, and it looks like Gauthier et al (2012) don't
> do it either. I haven't re-run their analyses with the relevant deletions
> (e.g. including only one of Dibamidae, Amphisbaenia, Serpentes in Conrad)
> but I expect they would end up in different places across the tree when not
> pulled together by convergence. Anyone want to try it?
> Another interesting thing in Gauthier et al. is the fact they cite Müller
> et al (2011) on the stem-amphisbaenian _Cryptolacerta_ but don't include
> this fossil in their analysis. (Facepalm)