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Phylogeny of lizards and snakes (Squamata)

From: Ben Creisler

A new online paper:

John J. Wiens, Carl R. Hutter, Daniel G. Mulcahy, Brice P. Noonan, Ted
M. Townsend, Jack W. Sites, Jr. and Tod W. Reeder (2012)
Resolving the phylogeny of lizards and snakes (Squamata) with
extensive sampling of genes and species.
Biology Letters (advance online publication)
doi:10.1098/rsbl.2012.0703 1744-957X

Squamate reptiles (lizards and snakes) are one of the most diverse
groups of terrestrial vertebrates. Recent molecular analyses have
suggested a very different squamate phylogeny relative to
morphological hypotheses, but many aspects remain uncertain from
molecular data. Here, we analyse higher-level squamate phylogeny with
a molecular dataset of unprecedented size, including 161 squamate
species for up to 44 nuclear genes each (33 717 base pairs), using
both concatenated and species-tree methods for the first time. Our
results strongly resolve most squamate relationships and reveal some
surprising results. In contrast to most other recent studies, we find
that dibamids and gekkotans are together the sister group to all other
squamates. Remarkably, we find that the distinctive scolecophidians
(blind snakes) are paraphyletic with respect to other snakes,
suggesting that snakes were primitively burrowers and subsequently
re-invaded surface habitats. Finally, we find that some clades remain
poorly supported, despite our extensive data. Our analyses show that
weakly supported clades are associated with relatively short branches
for which individual genes often show conflicting relationships. These
latter results have important implications for all studies that
attempt to resolve phylogenies with large-scale phylogenomic datasets.