Seascape Genomics Uncovers Genomic Patterns Shaped by Temperature and Salinity Outlier Loci in Dolphinfish (Coryphaena hippurus Linnaeus, 1758) Across the Atlantic Ocean and Mediterranean Sea

In this study, we explored the population genetic structure and its relation to environmental adaptations of the dolphinfish (Coryphaena hippurus) in the western Atlantic Ocean and Mediterranean Sea. Although previously two populations within the Mediterranean Sea were identified, recent evidence suggests more complex structuring. We employed 3RAD sequencing on 138 samples from the Atlantic and Mediterranean, obtaining a total of 20,072 SNPs of which 24 SNPs were strongly associated with temperature and salinity variables (putative adaptive outlier loci). Results revealed a clear genetic differentiation between the Atlantic and Mediterranean basins, with practically no connectivity between them, confirming the Mediterranean basin's long-term isolation. Within the Mediterranean basin, subtle genetic differences were detected between eastern and western Mediterranean sub-basins based on neutral loci with an increased signal of differences in the outlier loci associated with temperature and salinity that identified further differences into three genetically distinct groups, despite an overall high genetic connectivity. Environmental–genetic association analyses identified salinity, temperature and nitrate as major drivers of genetic variation. The most informative dataset (outlier SNPs related to temperature and salinity) explained over 80% of the genetic variation through a model incorporating multiple oceanographic variables. Overall, this research underscores how high-resolution genomic tools can detect hidden genetic structure and adaptation, even in highly dispersive marine species. These findings are essential for fisheries management, particularly in the Mediterranean Sea, where distinct local adaptations may be at risk from global environmental change. Recognizing and preserving this genetic diversity is crucial for the long-term sustainability of dolphinfish populations under climate and anthropogenic pressures.