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.