Population Genomic Structure and Demographic History of Black Guillemots Breeding Across the North Atlantic

ABSTRACT Identifying genetically differentiated populations is important for successful species conservation and management, and collecting baseline population genomic data can allow us to quantify impacts from environmental changes and anthropogenic stressors. Unlike most auks, which breed in a few large colonies, black guillemots ( Cepphus grylle ) are dispersed breeders, whose range spans diverse environmental conditions, from polar to temperate waters. They are harvested in some northern regions and can be an important indicator of coastal ecosystem health, but knowledge of their population genetic structure is limited. We used double‐digest restriction‐site associated DNA sequencing to determine the extent to which regional samples of black guillemots ( n = 172) in the Arctic and North Atlantic oceans differ at presumptively neutral markers. Population genetic analyses identified three genetic clusters: (1) Northwest Atlantic: Gulf of Maine, Gulf of St. Lawrence, and East Canadian Shelf (Nova Scotia); (2) Arctic: Baffin Bay, Hudson Bay, Davis Strait, Labrador Shelf, East Canadian Shelf (Newfoundland), and Fram Strait (Svalbard); and (3) Northeast Atlantic: Denmark Strait (Iceland) and the Baltic Sea. Regions of secondary contact appear to exist in northern Baffin Bay and the Northwest Atlantic. Possible reasons for this pattern of genetic structure include historical isolation in multiple glacial refugia during the Pleistocene and contemporary barriers to gene flow. Comparison of several potential historical scenarios provided strongest support for isolation of black guillemots in two glacial refugia in the Northwest and Northeast Atlantic, followed by range expansion and secondary contact in the Arctic since recession of the glaciers. Our results suggest that management of black guillemots will require an internationally coordinated approach to conserve the genomic variation within this species.