Assessing SNP-markers to study population mixing and ecological adaptation in Baltic cod

Atlantic cod( Gadusmorhua) is a species of great ecological and economical importance in the BalticSea. Here, two genetically differentiated stocks, the western and the eastern Balticcod, display substantial mechanical mixing, hampering our understanding of cod ecology and impeding stock assessmentsand management. Based on whole-genome re-sequencing data from reference samples obtained from the study area, we designed two different panels of Single Nucleotide Polymorphisms markers (SNPs), which take into account the exceptional genome architecture of cod. A minimum panel of 20 diagnostic SNPs and an extended panel (20 diagnostic and 18 biologically informative SNPs, 38 in total) were developed and validated to distinguish unambiguously between the western and the eastern Balticcod stocks and to enable studies of local adaptationto the specific environment in the BalticSea, respectively. We tested both panels on cod sampled from the southern BalticSea (n = 603) caught in 2015 and 2016. Genotyping results showed that catches from the mixing zone in the Arkona Sea, were composed of similar proportions of individuals of the western and the eastern stock. Catches from adjacent areas to the east, the Bornholm Basin and Gdansk Deep, were exclusively composed of eastern Balticcod, whereas catches from adjacent western areas (Belt Sea andO¨ resund) were composed of western Balticcod. Interestingly, the two Balticcod stocks showed strong genetic differences at loci associated with life-history trait candidate genes, highlighting the species’ potential for ecological adaptation even at small geographical scales. The minimum and the extended panel of SNP markers presented in this study provide powerful tools for future applications in research and fisheries managementto further illuminate the mixing dynamics of cod in the BalticSea and to better understand Balticcod ecology.