Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event. Plectrophenax buntings

Using a large, consistent set of orthologous loci to study relationships among taxa would revolutionize among-lineage comparisons of divergence and speciation processes. Ultraconserved elements (UCEs) offer such marker sets. UCEs are useful for deep phylogenetics, but fewer studies apply them to recent evolutionary events. We used UCEs to study population genomics in snow and McKay’s buntings (Plectrophenax nivalis and P. hyperboreus). Prior work suggested divergence during the last glacial maximum (~18-74 Kya). With ~30× coverage and four individuals of each species, we genotyped both alleles, obtaining a complete dataset of 2,635 variable loci (~3.6 SNPs/locus) and 796 invariable loci. We found no fixed allelic differences between the lineages, and few loci had large allele frequency differences. Nevertheless, individuals were 100% diagnosable to species, and the two taxa showed significant genetic structure (FST = 0.034). The demographic model best fitting the data was one of divergence with gene flow. Estimates of demographic parameters differed from published mtDNA research, with UCE data suggesting lower effective population sizes (~92,500 - 240,500 individuals), a deeper divergence time (~241,000 yrs), and lower gene flow (2.8-5.2 individuals per generation). Our results provide additional evidence that UCEs are useful for answering questions at shallow evolutionary depths.