TreeBASE Search-Matrices for study 12669

@ARTICLE{TreeBASE2Ref20665, author = {Alan Richard Lemmon and Emily M. Lemmon and Sandra Emme}, title = {Anchored hybrid enrichment for massively high-throughput phylogenomics}, year = {2012}, keywords = {anchored enrichment, sequence capture, hybrid enrichment, highly-conserved regions, ultraconserved elements, anchor regions, phylogenetics, phylogeography}, doi = {}, url = {http://}, pmid = {}, journal = {Systematic Biology}, volume = {}, number = {}, pages = {}, 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 in any system. 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 250 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 5% of the cost of high-throughput amplicon sequencing for projects on the scale of 500 loci x 100 individuals) and rapid data collection (less than two weeks of laboratory time) are expected to make this approach tractable even for researchers working on systems with limited or non-existent genomic resources.} }