Data from: Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species

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 data sets.