Abstract
Whales are key components of marine ecosystems, and several populations are affected by environmental and anthropogenic pressures. Among them, the fin whale, Balaenoptera physalus, from the Mediterranean Sea remains poorly characterized at the genomic level despite its classification as Endangered and ongoing population decline driven by human-induced habitat degradation. While bioacoustics and telemetry studies suggest the presence of both resident and migratory subgroups, the extent of genetic isolation in this population remains unclear. Here, we present the first whole-genome analysis of Mediterranean fin whales to assess genomic variability, genetic load, population structure, and adaptive potential of an immunity locus. By comparing genomes from the Mediterranean with those of fin whales from the North Atlantic, North Pacific, and new sequences from Sea of Cortez, we evaluated the degree of genetic isolation and placed the Mediterranean population within a broader evolutionary and conservation context. Our results show that although Mediterranean fin whales form a distinct genetic cluster, they are not fully isolated from North Atlantic populations. We also detected genetic heterogeneity within the Mediterranean basin, with some individuals showing no admixture and others displaying a substantial ancestry component from a different cluster, consistent with previous observations of subgroups exhibiting different migratory tendencies. Despite showing moderate genomic diversity and some adaptive potential compared to other populations, the Mediterranean population remains vulnerable to genomic erosion due to demographic decline, limited connectivity, and growing environmental stress. These findings underscore the importance of conservation actions and long-term genomic monitoring.