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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!



"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


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.