Genomic evidence of regional environment-associated genetic divergence in an Arctic copepod

Abstract Rapid environmental changes are expected to challenge the ability of many marine species and populations to adapt and persist in the coming decades. In the north Atlantic, Calanoid copepods play a foundational role in community and ecosystem dynamics. However, climate associated declines and displacement reported in several regions raise concern about potential impacts on food webs and ecosystem resilience. Characterizing how genomic variation in copepods is structured across contemporary environmental gradients is therefore essential for understanding the processes maintaining diversity and connectivity in this system. Here, we report a reduced-representation population genomic survey of 21 810 loci in the copepod Calanus hyperboreus, a keystone zooplankton species in Arctic and sub-Arctic food webs, surveyed from 14 locations across the northwest Atlantic, Canadian Arctic, and in waters off Greenland and Iceland. Despite the high potential for gene flow, we identify three distinct genetic clusters corresponding to three ecoregions, the Gulf of St Lawrence, Atlantic-influenced, and Arctic-influenced. Genotype–environment association analyses identified loci significantly associated with gradients in salinity, dissolved oxygen, and temperature, contributing to environmentally structured patterns among samples. The results reveal spatially and environmentally structured variation in this foundational zooplankton species, highlighting the role of hydrographic regimes in shaping connectivity and ecosystem dynamics in the North Atlantic.