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

David Marjanovic wrote-

> 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.)

Conrad includes 129 fossil squamates, Gauthier et al. include 48.  On the other 
hand, that means Conrad uses 93 living squamates, while Gauthier et al. beat it 
out with 144.  Still I'd say Conrad's fossil sample is more important.

> > Molecular analyses place dibamids as the basalmost living lizards,
> Dibamids and/or geckos, no?

Sure.  I was just looking at Vidal and Hedges (2005).

> > 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?

As basal mosasaurs.  Now that I have the paper, I can provide some useful 

"However, when we include snakes, but exclude other snake-like squamates 
(limb-reduced lizards with more than 50 presacral vertebrae), mosasaurians join 
snakes as sister to total-clade Varanoidea"

"We tested traditional hypotheses for the placement of Mosasauria within 
Anguimorpha with the Wilcoxon sign-ranked test compared to our shortest tree 
(Templeton 1983). Mosasauria as sister to Varanidae can be rejected (p0.0192). 
However, we cannot reject the idea that Mosasauria is either basal to the 
varanoid stem (p0.0964), the snake stem (p0.3365), or the stem of the entire 
“Fossorial Group” including snakes (p0.7270). Nor can we reject the hypothesis 
that mosasaurians represent a basal divergence from the anguimorph stem 

"In this series of experiments, we first delete the derived mosasaurids and, 
indeed, we recover the more basal mosasaurians near the root of the fossorial 
autarchoglossan group that is sister to total-group varanoids as in the 
all-species analysis (Figure 10). That relationship persists whether
using only dolichosaurs or the basal mosasauroid Aigialosaurus dalmaticus as 
the sole mosasaurian exemplars (not shown). In contrast, confining the 
mosasaurian sample to derived mosasaurids has some remarkable consequences. 
First, Krypteia now emerges from inside Anguidae, predictably, with the 
snake-like and fossorial Anniella pulchra as its sister taxon and then the 
snake-like Pseudopus apodus as its first outgroup. Second, derived
mosasaurids move outside of Scleroglossa as in the all-species analysis but, 
most surprising, with Sineoamphisbaena hexatabularis as their sister. Deleting 
S. hexatabularis yields the same result— krypteians emerge from inside 
Anguidae. But if both Anniella pulchra and S. hexatabularis are
excluded, that results in an even more dramatic shift: although most other 
details of our all-species tree are conserved, krypteians switch from deeply 
nested within anguid anguimorphs to deeply nested among scincid scincomorphs 
(Figure 11) as inferred by Conrad (2008; thus, an “Anguiophidia” can replace 
“Scincophidia” depending on the fossorial species included)."

So basically, mosasaurs are attracted to snakes if you eliminate the probably 
convergent limbless fossorial taxa, which I believe is where they ended up when 
I constrained Conrad's analysis to give results congruent with molecules.  
However, in Gauthier et al.'s dataset, mosasaurs can plausibly have many 
positions, so their basal position is very poorly supported.  When only basal 
mosasaurs are used, they fall into a more plausible position, but when only 
derived mosasaurs are used, they stay weirdly basal, which I think is rather 
good proof the basal position is erroneous and due to the transformed 
morphology of highly aquatic taxa.  Furthermore, if only derived mosasaurs are 
used AND the limbless Anniella and fossorial Sineoamphisbaena are excluded, 
krypteians are nested with the fossorial legless skinks Feylinia and Acontias 
instead.  Surely that's good evidence snakes are just going by the legless 
fossorial taxa.

> Where are *Marmoretta* and *Huehuecuetzpalli*?

Unincluded and the basalmost pan-squamate respectively.

> > 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.

Gauthier et al. tried different tests, which I would say shows their matrix is 
indeed biased by limbless fossorial characters-

"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"

So most of the taxa go where "they're supposed to" when other fossorial 
limbless ones aren't there to compete. To their credit, Gauthier et al. do 
discuss the possibility of convergence quite extensively and don't rule it out. 
 But it really leaves them in an odd position.  They spend much time and effort 
making this extensive (and probably well coded) analysis, only to find it 
supports what are probably convergently similar groups.  Similar to Livezey and 
Zusi's big bird analysis, though that was poorly coded and lacked most fossils. 
 Gauthier et al. end up saying "we anticipate that imposing the phenotypic tree 
on the genetic dataset will explain much more of these data than vice versa", 
but I don't agree.

The looming issue for Mesozoic dinosaur workers like us is whether our 
similarly extensive analyses are just feeding out convergence.  Are 
coelurosaurs just small tetanurines?  Are Paul or Kurochkin right about 
polyphyletic birds?  Are spinosaurines just convergent with barchonychines due 
to diet?

Mickey Mortimer