Contemporary hybridization and localized genomic differentiation between grey seal subspecies

Grey seals are divided into two subspecies, Halichoerus grypus grypus in the Baltic Sea and H. grypus atlantica in the North Atlantic Ocean. Historically, intense hunting caused local extinctions of grey seals across their range and promoted geographical isolation of the subspecies. However, recent population recovery and recolonization have renewed their overlap in a contact zone in Danish and Swedish waters. Here, using whole-genome sequencing data from 119 individuals, we investigate the demographic history of grey seals, the divergence of the subspecies, and genomic signatures of local adaptation and potential hybridization in the contact zone. We estimate that divergence began approximately 10,000 years ago, with gene flow ceasing 2000 years ago. We detect peaks of high genetic differentiation near genes with putative functions in osmo- and thermoregulation, consistent with salinity and temperature differences between the Baltic Sea and the North Atlantic. As evidence of the geographic isolation breaking up, we report a hybrid individual in the southwest Baltic contact zone, with Baltic maternal and Atlantic paternal ancestry, and identify a migrant of Baltic origin in the North Sea. Our study illustrates how local environmental variation and long-term hunting pressure have contributed to divergence between mammal subspecies over a short evolutionary timescale, with recent population recovery, recolonization and hybridization reshaping gene flow dynamics. Broadly, our work emphasizes the importance of studying evolutionary processes amid anthropogenic influences, including both disturbances and conservation successes, where demographic fluctuations, range shifts, altered gene flow, and adaptation to changing environments interact in complex, potentially consequential ways.