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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.  
Though having 68% more characters than Conrad (2008), it also has thirty less 
taxa.  Both are also better than many theropod analyses in using ordered 
characters when appropriate.  I'm highly suspicious of convergence in each 
dataset though.  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.  Molecular analyses 
place dibamids as the basalmost living lizards, amphisbaenians sister to 
lacertids, and snakes as sister to iguanians+anguimorphs.  Similarly, the new 
Gauthier et al. analysis has mosasaurs as the most basal non-iguanians, which 
is suspicious since their aquatic habits differ from other taxa.  This is all 
far too similar to Asher et al.'s (2005) morphological mammal analysis where 
clades were obviously based on gross morphotype (aardvark + anteater + 
armadillo + pangolin; ungulates; golden moles + moles; insectivores sensu lato 
+ rodents + lagomorphs) and the divergent taxa (whales and bats in that case) 
are shoved basally.  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.  But 'krypteians' may just be better adapted to 
it, so converged on more characters.  As it stands, I still trust molecular 
phylogenies for both Placentalia and Squamates.

Mickey Mortimer

> Date: Fri, 1 Jun 2012 12:25:09 -0700
> From: pristichampsus@yahoo.com
> To: dinosaur@usc.edu; vrtpaleo@usc.edu
> Subject: Huge morphological analysis reconfirms deep branch relationships 
> among Squamates.
> Okay, so it turns out that this was a month off from what I was initially 
> told, but the magnum opus on squamate phylogeny has finally been released by 
> the Peabody Museum. This is the culmination of seven years worth of data 
> collection and analysis on 192 taxa with just under 1000 characters. This is, 
> in many ways, a response to the molecular phylogeny of Townsend et al. 2004 
> that rewrote the squamate family tree and nested iguanians deep within 
> scleroglossa. As the authors point out in their analysis, if the molecular 
> phylogenies proposed by Townsend, Vidal, Hedges, and/or Wiens are correct 
> then it would require between 51 and 147 evolutionary reversals. Reversals 
> that, to date, have not shown any evidence in the fossil record.
> Sadly the paper does nothing to resolve the dichotomy between molecular and 
> morphological systematics, as it's results verify many previous morphological 
> analyses, but it is the first to really point out the inherent evolutionary 
> problems with the current molecular topology; a view that seems to have been 
> either missed, or ignored by much of the current literature.
> One other key aspect of this paper (and one that will likely leave it as a 
> constant reference for years to come) is the illustration of all the 
> different characters the authors used. In many ways this makes this paper a 
> bit of a "definitive" atlas for squamate morphological analysis. I'd say this 
> is a must read for anyone doing squamate systematics.
> Abstract and link to the paper are below.
> Long live Scleroglossa and Iguania!
> Jason
> http://reptilis.net
> "I am impressed by the fact that we know less about many modern [reptile] 
> types than we do of many fossil groups." - Alfred S. Romer
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> Assembling the Squamate Tree of Life: Perspectives from the Phenotype and the 
> Fossil Record
> Jacques A. Gauthier, Maureen Kearney, Jessica Anderson Maisano, Olivier 
> Rieppel and Adam D.B. Behlke
> http://www.bioone.org/doi/abs/10.3374/014.053.0101
> Abstra
> lected species—51 extinct and 141 extant—and 976 apomorphies distributed 
> among 610 phenotypic characters to investigate the phylogeny of Squamata 
> (“lizards,”
> including snakes and amphisbaenians). These data enabled us to infer a tree 
> much like those derived from previous morphological analyses, but with better 
> support for some key clades. There are also several novel elements, some of 
> which pose striking departures from traditional ideas about lizard evolution 
> (e.g., that mosasaurs and polyglyphanodontians are on the scleroglossan stem, 
> rather than parts of the crown, and related to varanoids and teiids, 
> respectively). Long-bodied, limb-reduced, “snake-like” fossorial lizards—most 
> notably dibamids, amphisbaenians and snakes—have been and continue to be the 
> chief source of character conflict in squamate morphological phylogenetics. 
> Carnivorous lizards (especially snakes, mosasaurs and varanoids) have proven 
> a close second. Genetic data, presumably less burdened by the potential for 
> adaptive convergence related to fossoriality, were expected to resolve these 
> conflicts. Although recent gene phylogenies
> seem to do so, they also differ radically from any phylogeny based on the 
> phenotype, especially for the most ancient crown squamate divergences that 
> occured during the latter half of the Mesozoic. Our study relied on 
> traditionally prepared specimens as well as
> high-resolution computed tomography scans that afforded unprecendented access 
> to the cranial anatomy of Squamata. This, along with the inclusion of stem 
> fossils, provided an unparalleled sample of the
> phenotype enabling us to more fully explore the extreme incongruences between 
> molecular and morphological topologies for the squamate tree of life. Despite 
> this extensive new database, we were unable to find morphological support for 
> the major rearrangement of the deep divergences in Squamata proposed by 
> recent molecular studies. Instead, our data strongly support the same 
> fundamental topology suggested by most previous morphological studies—an 
> Iguania-Scleroglossa basal split, a sister-group relationship between Gekkota 
> and Autarchoglossa, and the divergence between Anguimorpha and 
> Scincomorpha—and documents the extreme degree of morphological homoplasy 
> required by those molecular topologies.