Data from: Reduced-representation sequencing detects trans-Arctic connectivity and local adaptation in polar cod (Boreogadus saida)

Information on connectivity and genetic structure of marine organisms remains sparse in frontier ecosystems such as the Arctic Ocean. Filling these knowledge gaps becomes increasingly urgent, as the Arctic is undergoing rapid physical, ecological, and socio-economic changes. The abundant and widely distributed polar cod (Boreogadus saida) is highly adapted to Arctic waters, and its larvae and juveniles live in close association with sea ice. Through a reduced-representation sequencing approach, this study explored the spatial genetic structure of polar cod at a circum-Arctic scale. Genomic variation was partitioned into neutral and adaptive components to respectively investigate genetic connectivity and local adaptation. Based on 922 high-quality single nucleotide polymorphism (SNP) markers genotyped in 611 polar cod, broad-scale differentiation was detected among three groups: (i) Beaufort-Chukchi seas, (ii) all regions connected by the Transpolar Drift, ranging from the Laptev Sea to Iceland, including the European Arctic, and (iii) West Greenland. Patterns of neutral genetic structure suggested broadscale oceanographic and sea ice drift features (i.e. Beaufort Gyre and Transpolar Drift) as important drivers of connectivity. Genomic variation at 35 outlier loci indicated adaptive divergence of the West Greenland, and the Beaufort-Chukchi Seas populations, possibly driven by environmental conditions. Sea ice decline and changing ocean currents can alter or disrupt connectivity between polar cod from the three genetic groups, potentially undermining their resilience to climate change, even in putative refugia, such as the Central Arctic Ocean and the Arctic Archipelago.