Contrasting population genomic structuring of northern pike ( <scp> <i>Esox lucius</i> </scp> L.) in fresh‐ and brackish water environments: Implications for management and conservation

Understanding the factors that shape population genetic structure is crucial for advancing evolutionary studies and developing effective management and conservation strategies. The northern pike (Esox lucius L.) is a top teleost predator that inhabits fresh and brackish water environments in the northern hemisphere. Pike populations in the brackish Baltic Sea typically display strong genetic structuring, with coastal sympatric populations that separate during spring for spawning in either shallow, sheltered brackish bays or in freshwater tributaries and wetlands. In contrast to the Baltic Sea, genomic structuring in freshwater environments, particularly in large lacustrine systems, remains poorly understood. To address this gap, we used restriction site-associated DNA-sequencing to assess the genetic structure and diversity of northern pike in two ecologically contrasting habitats: freshwater Vänern Lake, Sweden (8932 single nucleotide polimorphisms [SNPs]), and the brackish Baltic Sea around Saaremaa, Estonia (6899 SNPs). The results show strong genetic structuring and lower genetic diversity in brackish environment compared to the higher genetic diversity and extremely low genetic structuring observed in freshwater habitat. We found no evidence of divergent selection within environments. However, we identified 187 outlier SNPs and 62 outlier genes distinguishing the brackish and freshwater environments, potentially reflecting adaptation to salinity. Notably, several of these genes are associated with key biological processes, including osmotic stress regulation (akap13), early development (tfap2a) and pathogens response (tlr18). From a fisheries management perspective, our results indicate that the freshwater system can be managed as a single stock, while strong population structuring among Baltic coastal pike likely requires either large-scale solutions and/or population-specific fine-scale management efforts to maintain the genetic and life-history diversity among brackish coastal pike populations.