Asymmetric gene flow across a desert contact zone in a riparian songbird

Abstract Secondary contact is a key point in the speciation process, and fine-scale geography can shape its outcomes. This is especially true for species restricted to fragmented habitats, such as riparian corridors through arid regions. Here we examine the role of disjunct riparian habitat in shaping secondary contact in Bell’s Vireo ( Vireo bellii ), a North American songbird species that contains distinct eastern and western forms. We recovered a unique, discontinuous contact zone along the Rio Grande in New Mexico, where two populations with greater nuclear and mitochondrial genetic affinity for the eastern lineage are separated by a population with an affinity for the western lineage. This point of primarily western ancestry on the Rio Grande corresponded with a stretch where several intermittently flowing tributaries join from the west and may have acted as gene flow corridors. Using a combination of empirical analyses of divergence and diversity across the genome and population genetic simulations, we uncovered evidence of neutral, genome-wide admixture driving the genomic architecture of divergence, rather than evidence for local adaptation or selective sweeps. In sum, this genomic study showed us how fine-scale dispersal corridors can cause idiosyncratic patterns of admixture when habitat is limiting in zones of secondary contact.