Balaenoptera physalus Genome sequencing and assembly

Whales play a crucial role in marine ecosystems, yet many populations face growingenvironmental pressures. Among them, the fin whale (Balaenoptera physalus) from MediterraneanSea remains poorly characterized at the genomic level despite its classification as Endangered anddecreasing in population size due to habitat degradation, climate change, and human-induceddisturbances. Previous studies based on bioacoustic and telemetry data suggest the presence ofboth resident and migratory subgroups, but the genetic isolation of this population remainsuncertain. Here, we sequenced and analysed for the first time whole genomes of theMediterranean fin whale to provide a comprehensive genomic characterization of thispopulation, assessing its genomic variability, genetic load, population structure and potential foradaptation to environmental stressors. By comparing genomic data from Mediterranean finwhales with populations from the North Atlantic, North Pacific, and Sea of Cortez, we aim todetermine the degree of genetic isolation and contextualize the Mediterranean population withina broader evolutionary and conservation framework. Our results showed that whileMediterranean fin whales form a distinct genetic cluster, they are not completely isolated fromNorth Atlantic populations, with gene flow persisting at low levels. Additionally, we identified acomplex substructure within the Mediterranean, supporting the existence of a residentsubpopulation. Although this population preserves moderate levels of genomic diversity andadaptive potential, it remains vulnerable to genomic erosion due to continued demographicdecline, limited connectivity, and increasing environmental stress. These findings underscore theurgency of targeted conservation actions and long-term genetic monitoring, especially as climatechange accelerates and introduces increasingly unpredictable selective pressures that mayexacerbate the risk of genomic erosion and threaten population viability.