Genomic insights into marine-freshwater transition: evolutionary adaptations in freshwater Pusa seals.

The Baikal seal (Pusa sibirica) and Saimaa ringed seal (Pusa hispida saimensis) are phocid species inhabiting freshwater regions. Unlike their marine relatives, these freshwater Pusa seals face distinct environmental challenges, particularly osmoregulation, making marine-to-freshwater habitat transitions an excellent model for investigating the molecular basis of adaptive evolution. In this study, we performed comprehensive comparative genomic analyses across 14 pinniped species to elucidate the molecular mechanisms underlying habitat transitions. Phylogenomic analysis placed the grey seal as a sister clade to the common ancestor of Baikal seal and Saimaa ringed seal, and Pusa and Halichoerus as a sister clade of the harbor seal. We identified lineage-specific adaptive changes in genes involved in osmoregulation, wound healing, and circadian rhythm-including ACE2, ALMS1, F12, SERPING1, and PER3-that are critical for freshwater Pusa seals to thrive in environments with reduced salinity and distinct ecological pressures. Additionally, we discovered InDel variants in conserved non-coding elements (CNEs) that may influence the expression of osmoregulatory genes, offering new insights into the regulatory mechanisms underpinning freshwater adaptation. Collectively, this study provides a foundational framework for understanding the molecular basis of freshwater adaptation in pinnipeds, and the candidate genes and regulatory elements identified here may serve as valuable targets for future research into osmoregulation and wound healing across vertebrates, including humans.