Patterns of Population Genomic Variation and Evolutionary History of European Hake in the Northeastern Atlantic

Climate change is driving species to shift their distribution ranges, potentially altering the level of genomic structuring and connectivity between populations. Additionally, fishing practices might further reduce genomic diversity and limit the potential adaptability of species to environmental changes. We use whole-genome sequencing for the first time to explore current and historical patterns of genomic diversity in European hake (Merluccius merluccius) from the Northeast Atlantic, focusing on the recently expanded distribution range in the North Sea. Genomic data revealed a complex scenario in the North Sea and neighbouring regions, with three distinct populations: North Sea, Celtic Sea and Portugal. Individuals from the Kattegat, Skagerrak and west coast of Denmark were highly differentiated from those in the Celtic Sea and waters around Ireland. The Northern North Sea appears as a transition zone, with individuals from higher latitudes assigned to the Celtic Sea group and those from lower latitudes to the North Sea group. The more distant Portuguese individuals appeared as a third distinct population. Although the differentiation among these populations was shallow when the entire dataset was used, a subset of 99,364 outlier markers revealed a much deeper divergence. Demographic analyses indicated that these populations are relatively young and have large effective population sizes and thus without sufficient time to build a signature of differentiation by genetic drift. At the same time, selection for local adaptation is strong enough to overcome the effects of contemporary gene flow. Our findings have important implications for managing the European hake stocks in the Northeastern Atlantic, highlighting the need for management measures that address shifts in species and population distribution due to climate change, as well as needing to account for different populations contributing to fisheries within a single stock. Preserving the genomic diversity within and among fish stocks is crucial for maintaining the long-term resilience of marine ecosystems and the services they provide.