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

Citation

Lemmon, Alan R.; Emme, Sandra; Lemmon, Emily Moriarty; Emme, Sandra A. (2012), Data from: Anchored hybrid enrichment for massively high-throughput phylogenomics, Dryad, Dataset, https://doi.org/10.5061/dryad.r606d128

Abstract

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.

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