ERP140806 PRJEB55862 460aac3a-af61-4702-acfd-d85c421cc6dc Genomic differentiation among European perch Perca fluviatilis in the western Baltic Sea reflects colonisation history and local adaptation Environmental variation across the distribution of wild species can lead to local adaptations. The Baltic Sea was formed when the Fenno-Scandian ice sheet retreated around 12 thousand years ago, creating a new brackish water habitat colonised by both marine and freshwater fish species. These have the same cellular osmotic pressure, but rely on fundamentally different osmoregulation mechanisms to keep it stable; hypo-osmoregulation in freshwater and hyper-osmoregulation in marine water. The western Baltic Sea has fluctuating salinities requiring both types of osmoregulation, which have evolved uniquely in specialised populations of a few freshwater fish species. One of these species is the European perch, which in the Baltic Sea has developed a brackish water phenotype that at all life stages can tolerate environmental salinity levels that are lethal to the freshwater phenotype. However, very little is known about the history and underlying genomic mechanisms facilitating the colonisation and adaptation of perch to the western Baltic Sea. Here, we use Genotyping-By-Sequencing data from six freshwater and six brackish water localities to disclose the evolutionary relationship between the freshwater and brackish water phenotype. Our results showed that the brackish water perch phenotype occurs in multiple distinct genetic clusters. Perch isolated in fjord systems by high salinity sea water clustered with freshwater phenotypes while perch with full access to the sea formed a separate cluster. We also disclosed that gene flow between brackish water phenotypes with full access to the sea has led to lower levels of differentiation and higher diversity than freshwater phenotypes. Adaptation analyses suggest that selection played a substantial role in the colonisation of the Baltic Sea. We also found a link between the historic salinity of the Baltic Sea and the demographic history of the brackish water phenotypes and go on to discuss the implications of our findings for management of brackish water perch in the western Baltic sea. PerchGenomics Environmental variation across the distribution of wild species can lead to local adaptations. The Baltic Sea was formed when the Fenno-Scandian ice sheet retreated around 12 thousand years ago, creating a new brackish water habitat colonised by both marine and freshwater fish species. These have the same cellular osmotic pressure, but rely on fundamentally different osmoregulation mechanisms to keep it stable; hypo-osmoregulation in freshwater and hyper-osmoregulation in marine water. The western Baltic Sea has fluctuating salinities requiring both types of osmoregulation, which have evolved uniquely in specialised populations of a few freshwater fish species. One of these species is the European perch, which in the Baltic Sea has developed a brackish water phenotype that at all life stages can tolerate environmental salinity levels that are lethal to the freshwater phenotype. However, very little is known about the history and underlying genomic mechanisms facilitating the colonisation and adaptation of perch to the western Baltic Sea. Here, we use Genotyping-By-Sequencing data from six freshwater and six brackish water localities to disclose the evolutionary relationship between the freshwater and brackish water phenotype. Our results showed that the brackish water perch phenotype occurs in multiple distinct genetic clusters. Perch isolated in fjord systems by high salinity sea water clustered with freshwater phenotypes while perch with full access to the sea formed a separate cluster. We also disclosed that gene flow between brackish water phenotypes with full access to the sea has led to lower levels of differentiation and higher diversity than freshwater phenotypes. Adaptation analyses suggest that selection played a substantial role in the colonisation of the Baltic Sea. We also found a link between the historic salinity of the Baltic Sea and the demographic history of the brackish water phenotypes and go on to discuss the implications of our findings for management of brackish water perch in the western Baltic sea. ENA-FIRST-PUBLIC 2023-04-03 ENA-LAST-UPDATE 2023-04-03