Population genetic structure of three species of declining North American swallows: Implications for conservation and management.

North American aerial insectivorous birds have suffered steep population declines over the last half-century. Limited information on the population genetic structure of many aerial insectivores restricts our ability to understand factors affecting population-specific trends and infer population connectivity. To address this gap, we examined the population genetic structure of barn (Hirundo rustica erythrogaster), bank (Riparia riparia riparia), and tree (Tachycineta bicolor) swallows across their breeding ranges in North America. We used restriction site-associated DNA sequencing (RADseq) and higher-resolution low-coverage whole genome sequencing (lcWGS) to study species-specific population genetic structure. Additionally, we used species distribution models (SDM) to determine the potential for Pleistocene glacial refugia as drivers of genetic variation. Multivariate analyses identified population clusters corresponding to western, central, and eastern North America for barn and bank swallows, and shallower structure for tree swallows. Species-specific SDMs provided evidence that suitable habitat for both barn and bank swallows existed in multiple refugia during the Pleistocene, and likely either a single southern refugium or higher gene flow after recolonization for tree swallows, supporting the genetic patterns in our data. Our results suggest historical events, physical barriers and migratory pathways continue to shape and maintain population genetic structure among swallow populations. Our findings can be used to guide future sampling of populations to further differentiate genetic structure and serve as a ‘genoscape’ for studies assessing migratory connectivity of individuals sampled during the non-breeding season.