Data from: Anchored hybrid enrichment for massively high-throughput phylogenomics

The field of phylogenetics is on the cusp of a major revolution, enabled
by new methods of data collection that leverage both genomic resources and
recent advances in DNA sequencing. Previous phylogenetic work has required
labor-intensive marker development coupled with single-locus PCR and DNA
sequencing on a clade-by-clade and marker-by-marker basis. Here, we
present a new, cost-efficient, and rapid approach to obtaining data from
hundreds of genes for potentially hundreds of individuals for deep and
shallow phylogenetic studies. Specifically, we designed probes for target
enrichment of >500 loci in highly-conserved anchor regions of
vertebrate genomes (flanked by less conserved regions) from five model
species and tested enrichment efficiency in non-model species up to 254
million years divergent from the nearest model. We found that hybrid
enrichment using conserved probes (anchored enrichment) can recover a
large number of unlinked loci that are useful at a diversity of
phylogenetic timescales. This new approach has the potential to not only
expedite resolution of deep-scale portions of the Tree of Life but also to
greatly accelerate resolution of the large number of shallow clades that
remain unresolved. The combination of low cost (~1% of the cost of
traditional Sanger sequencing and ~3.5% of the cost of high-throughput
amplicon sequencing for projects on the scale of 500 loci x 100
individuals) and rapid data collection (~2 weeks of laboratory time) are
expected to make this approach tractable even for researchers working on
systems with limited or non-existent genomic resources.