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.

Spatiotemporal environmental heterogeneity is a major evolutionary driver, which can cause profound phylogeographic complexity, particularly at the periphery of species ranges. Ringed seals display a highly disjoint distribution, occurring in high abundance throughout the circumpolar Arctic, as well as in the Baltic Sea, Lake Saimaa and Lake Ladoga. These relict Fennoscandian ringed seals were traditionally regarded as originating from a single colonisation event after the Last Glacial Maximum (LGM), however recent studies have challenged this perception. Here, we analyse 246 mitogenomes and 180 skulls to unravel the diversity and spatiotemporal pattern of diversification in Fennoscandian ringed seals. Contrary to previous assumptions, our results reveal a complex evolutionary history characterised by pre-LGM diversification from Arctic ringed seals and possibly several Fennoscandian colonisation events. We hypothesize that Saimaa seals originate from Arctic ringed seals, from which they diverged prior to their arrival in Lake Saimaa. Ladoga seals appear to also originate from the Arctic, with secondary colonisation events from paleo-Skagerrak-Kattegat-Baltic, while the Baltic ringed seal have mixed evolutionary origins. Lake Saimaa and to some extent Lake Ladoga ringed seals have experienced a loss of diversity and evolved divergent skull morphologies, likely as a result of colonisation bottlenecks, isolation and dietary specialisation, while Baltic Sea ringed seals have retained remarkably high levels of genetic and morphological diversity. Our study supports the classification of Saimaa, Ladoga and Baltic ringed seals as distinct taxa, and highlights the need for management and conservation efforts to mitigate cumulative impacts of human activities and climate change on Fennoscandian ringed seals. 

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 many 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.