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Re: Huge morphological analysis reconfirms deep branch relationships among Squamates.

 Very cool paper, and I agree about the quality of the character
 illustrations.


So do I. It's also cool to have both Gauthier and Rieppel among the authors.


 Though having 68% more characters than Conrad (2008),
(Though not "just under 1000 characters". The abstract says 610 characters, which result in a total of 976 apomorphies all over the tree.) 


 it also has thirty less taxa.
Are there any fossils that Conrad included and the new study lacks? (I don't have access to the paper today. Maybe I'll go to the museum tomorrow again.) 


 Note both group snakes with two other clades of limbless squamates-
 amphisbaenians and dibamids, a group which Gauthier et al. call
 Krypteia. In Conrad these nest within limbless skinks whereas in
 Gauthier et al. they nest in anguimorphs with the legless Anniella.


<Picard & Riker double facepalm>


 Molecular analyses place dibamids as the basalmost living lizards,


Dibamids and/or geckos, no?


 amphisbaenians sister to lacertids,


Beautifully supported by the fossil record, I must add.


 and snakes as sister to iguanians+anguimorphs.
No. Molecular studies apparently can't resolve the Iguania-Anguimorpha-Serpentes trichotomy; different analyses find different resolutions, and the internodes are always scarily short. Lee's recent combined analysis, however, finds Anguimorpha and Pythonomorpha (of which Serpentes is the crown-group) as sister-groups. 


 Similarly, the new Gauthier et al. analysis has mosasaurs as the most
 basal non-iguanians,
That's hard to believe. Where do all the aigialosaurs, dolichosaurs, pontosaurs and whatnots come out? 

Where are *Marmoretta* and *Huehuecuetzpalli*?


 Conrad tried to test this by deleting all taxa except limbless
 burrowers (snakes are basally burrowing in his analysis, and notably
 the burrowing Sineoamphisbaena is sister to Anniella+Krypteia in
 Gauthier et al.'s), and claimed because Krypteia still emerged,
 limbless burrowing characters weren't responsible.
How about looking for correlated _characters_ instead and -- not removing, but merging them?
(I speak from experience when I say characters correlated to others shouldn't simply be removed. In fact, I'll publish on that. Short version: comparing characters is a great way to find mistakes in the coding of all of them.)