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.