Data from: Exon capture phylogenomics: efficacy across scales of divergence

The evolutionary histories of species are not measured directly, but
estimated using genealogies inferred for particular loci. Individual loci
can have discordant histories, but in general we expect to infer
evolutionary histories more accurately as more of the genome is sampled.
High Throughput Sequencing (HTS) is now providing opportunities to
incorporate thousands of loci in ‘phylogenomic’ studies. Here, we used
target enrichment to sequence c.3000 protein-coding exons in a group of
Australian skink lizards (crown group age c.80 Ma). This method uses
synthetic probes to ‘capture’ target exons that were identified in the
transcriptomes of selected probe design (PD) samples. The target exons are
then enriched in sample DNA libraries prior to performing HTS. Our main
goal was to study the efficacy of enrichment of targeted loci at different
levels of phylogenetic divergence from the PD species. In taxa sharing a
common ancestor with PD samples up to c.20 Ma, we detected little
reduction in efficacy, measured here as sequencing depth of coverage.
However, at around 80 Myr divergence from the PD species, we observed an
approximately two-fold reduction in efficacy. A secondary goal was to
develop a workflow for analysing exon capture studies of phylogenetically
diverse samples, while minimizing potential bias. Our approach assembles
each exon in each sample separately, by first recruiting short sequencing
reads having homology to the corresponding protein sequence. In sum,
custom exon capture provides a complement to existing, more generic target
capture methods and is a practical and robust option across low-moderate
levels of phylogenetic divergence.