Data from: Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales

Comparative genetic studies of non-model organisms are transforming rapidly due to major advances in sequencing technology. A limiting factor in these studies has been the identification and screening of orthologous loci across an evolutionarily distant set of taxa. Here, we evaluate the efficacy of genomic markers targeting ultraconserved DNA elements (UCEs) for analyses at shallow evolutionary timescales. Using sequence capture and massively parallel sequencing to generate UCE data for five co-distributed Neotropical rainforest bird species, we recovered 776–1516 UCE loci across the five species. Across species, 53–77% of the loci were polymorphic, containing between 2.0 and 3.2 variable sites per polymorphic locus, on average. We performed species tree construction, coalescent modeling, and species delimitation, and we found that the five co-distributed species exhibited discordant phylogeographic histories. We also found that species trees and divergence times estimated from UCEs were similar to the parameters obtained from mtDNA. The species that inhabit the understory had older divergence times across barriers, contained a higher number of cryptic species, and exhibited larger effective population sizes relative to the species inhabiting the canopy. Because orthologous UCEs can be obtained from a wide array of taxa, are polymorphic at shallow evolutionary timescales, and can be generated rapidly at low cost, they are an effective genetic marker for studies investigating evolutionary patterns and processes at shallow timescales.Supplemental FiguresSupplemental-data- GPhoCS-outputSupplementary TablesSupplementary MethodsSupp Methods.docxfullFasta alignments of sequences from ultraconserved elements containing up to eight individuals from each of five study species. All alignments in a given species that contain at least one individual in each of four areas of endemism are included.orthologsFasta alignments of sequences from ultraconserved elements containing up to eight individuals from each of five study species. Only the 166 loci that are present in all five full datasets are included.interspecies_fullFasta alignments of sequences from ultraconserved elements containing up to thirty-six individuals from five study species. Alignments include samples from all species, and any loci for which data was recovered for at least two individuals.interspecies_reducedFasta alignments of sequences from ultraconserved elements containing up to thirty-six individuals from five study species. Alignments include samples from all species, but only loci for which at least one individual is represented in every area of endemism in all study species.mtDNA_UCE_taxaMitochondrial DNA sequences from the gene cytochrome b from the same samples for which UCE data were obtained