Data from: Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species

Two common approaches for estimating phylogenies in species-rich groups
are to: (i) sample many loci for few species (e.g. phylogenomic approach),
or (ii) sample many species for fewer loci (e.g. supermatrix approach). In
theory, these approaches can be combined to simultaneously resolve both
higher-level relationships (with many genes) and species-level
relationships (with many taxa). However, fundamental questions remain
unanswered about this combined approach. First, will higher-level
relationships more closely resemble those estimated from many genes or
those from many taxa? Second, will branch support increase for
higher-level relationships (relative to the estimate from many taxa)?
Here, we address these questions in squamate reptiles. We combined two
recently published datasets, one based on 44 genes for 161 species, and
one based on 12 genes for 4161 species. The likelihood-based tree from the
combined matrix (52 genes, 4162 species) shared more higher-level clades
with the 44-gene tree (90% vs. 77% shared). Branch support for higher
level-relationships was marginally higher than in the 12-gene tree, but
lower than in the 44-gene tree. Relationships were apparently not obscured
by the abundant missing data (92% overall). We provide a time-calibrated
phylogeny based on extensive sampling of genes and taxa as a resource for
comparative studies.