The Arctic environment plays a critical role in the global climate system and marine biodiversity. The region’s ice-covered expanses provide essential breeding and feeding grounds for a diverse assemblage of marine species, who have adapted to thrive in these harsh conditions and consequently are under threat from global warming. The bearded seal (Erignathus barbatus) is an ice-obligate Arctic species using sea-ice for all aspects of its life-history, rendering it particularly vulnerable to sea-ice loss. It is one of the least studied and hence enigmatic of the Arctic marine mammals, with little knowledge regarding genetic structure, diversity, adaptations and demographic history, consequently hampering management and conservation efforts. Here, we sequenced 70 whole nuclear genomes from across most of the species’ circumpolar range, finding significant genetic structure between the Pacific and the Atlantic subspecies, which diverged during the Penultimate Glacial Period (~192 KYA). Remarkably, we found fine-scale genetic structure within both subspecies, with at least two distinct populations in the Pacific and three in the Atlantic. We hypothesize sea-ice dynamics and bathymetry had a prominent role of in shaping bearded seal genetic structure and diversity. Resulting genomic data can be used to complement the health, physiological, and behavioral research needed to conserve this species. In addition, we provide recommendations for management units that can be used to more specifically assess climatic and anthropogenic impacts on bearded seal populations.

Wildlife management and conservation requires knowledge about a species’ population structure, diversity, demographic history and adaptive potential. However, often such information is lacking, or based on insufficient and sometimes contrasting data. This is the case for the grey seal (Halichoerus grypus), for which there remain uncertainties regarding subspecies and population delineations, diversity and recent evolutionary history, despite numerous genetic and non-genetic studies. Here, we present the first range- and genome-wide population genomic analysis of grey seals based on 3,812 nuclear SNP markers genotyped in 188 samples from 17 distinct localities. Our analyses support the existence of three main grey seal populations centred in the NW Atlantic, NE Atlantic and Baltic Sea, but also point to the existence of previously unrecognised substructure within the NE Atlantic, in particular separating grey seals sampled in Iceland, Norway and Russia from the core NE Atlantic population inhabiting the wider North Sea region. We detected remarkably low levels of genetic diversity in NW Atlantic grey seals, which may be the result of evolutionary founder effects, as well as more recent historic hunting and culling. We also found some localities that deviate from the general isolation by distance pattern, likely reflecting wide-scale metapopulation dynamics associated with recolonisation and recovery of grey seals in regions where they were historically extirpated. Our genetic results allow us to identify at least six grey seal management units across the species’ Atlantic range, but also highlights knowledge gaps that should be addressed in future research into this species.