Data from: Squamate Conserved Loci (SqCL): a unified set of conserved loci for phylogenomics and population genetics of squamate reptiles

The identification of conserved loci across genomes, along with advances
in target capture methods and high-throughput sequencing, has helped spur
a phylogenomics revolution by enabling researchers to gather large numbers
of homologous loci across clades of interest with minimal upfront
investment in locus design. Target capture for vertebrate animals is
currently dominated by two approaches – anchored hybrid enrichment (AHE)
and ultraconserved elements (UCE) – and both approaches have proven useful
for addressing questions in phylogenomics, phylogeography, and population
genomics. However, these two sets of loci have minimal overlap with each
other; moreover, they do not include many traditional loci that that have
been used for phylogenetics. Here, we combine across UCE, AHE, and
traditional phylogenetic gene locus sets to generate the Squamate
Conserved Loci (SqCL) set, a single integrated probe set that can generate
high-quality and highly complete data across all three loci types. We use
these probes to generate data for 44 phylogenetically-disparate taxa that
collectively span approximately 33% of terrestrial vertebrate diversity.
Our results generated an average of 4.29 Mb across 4709 loci per
individual, of which an average of 2.99 Mb was sequenced to high enough
coverage (≥10×) to use for population genetic analyses. We validate the
utility of these loci for both phylogenomic and population genomic
questions, provide a comparison among these locus sets of their relative
usefulness, and suggest areas for future improvement.