Speciation despite gene flow in two owls (Aegolius ssp.): Evidence from 2,517 loci with ultraconserved elements (UCEs)

New study systems and tools are needed to understand how divergence and speciation occur between lineages with gene flow. Migratory birds often exhibit divergence despite seasonal migration, which brings populations into contact with one another. We studied divergence between two subspecies of Northern Saw-whet Owls, in which a sedentary population on the islands of Haida Gwaii, British Columbia (Aegolius acadicus brooksi), exists in the presence of the mainland form (A. a. acadicus) during migration but not during the breeding season. Prior research showed fixed mtDNA divergence but left open the question of nuclear gene flow. We used 2,517 ultraconserved element loci (UCEs) to examine the demographic history of this young taxon pair. Although there were no fixed single nucleotide polymorphism (SNP) differences between populations among our genotyped individuals, 100% of the birds were diagnosable and the demographic model best fitting the data was one of split-bidirectional-migration (i.e., speciation with gene flow) using dadi. We dated the split to ~278 Kya, and gene flow was skewed, with ~0.7 individuals/generation coming from acadicus into brooksi and ~4.4 going the opposite direction. Coupled with an absence of evidence of phenotypic hybrids and the birds' natural history, these data suggest brooksi may be a young biological species arising despite historic gene flow.