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.

Knowledge of genetic diversity and structure is essential for developing conservation strategies for endangered species. The advances in museum genomics can assist in better understanding the effects of over-hunting on the genome by comparing historical to present-day samples. Blue whales were hunted to the point of near extinction in the mid-twentieth century. Herein, we use whole genome sequencing to elucidate the poorly understood population structure of North Atlantic (NA) blue whales (Balaenoptera musculus musculus). We generated a de novo genome assembly of 2.49 Mbp for a NA blue whale (N50 of 1.46 Mb) to analyze 19 whole genomic sequences and 28 complete mitochondrial genomes. We included present-day and historical samples (earliest from 1900) from the Atlantic and Antarctica to understand the impact of whaling on the genetic diversity. We found low population structuring, but high genetic diversity, suggesting a single, panmictic population in the NA. We identified gene flow from fin whale to blue whales, accounting for ~3.5% of the genome. Introgression between blue and fin whales was observed in all the present-day samples but were lacking in some whales sampled early in the 20th century, which suggests increasing disruption in mate choice concomitant with decline in blue whale population. We also assembled and analyzed the transcriptome and revealed positive selection of oncogenes, which may be involved in reduced cancer rates in this largest of mammals ever known. Our sequencing and population structuring studies provide a genomic framework to guide ongoing conservation strategies for this iconic species.