Data from: Mixed origin of juvenile cod (Gadus morhua) along the Swedish west coast

Cryptic population structure in exploited fishes poses a major challenge for fisheries management. In Atlantic cod, sympatric ecotypes are well-known, for instance off the coast of northern Norway. Recently, two sympatric cod ecotypes have also been documented in the Skagerrak and Kattegat, where adult cod has declined dramatically. One ecotype has an apparent offshore origin and displays a more migratory lifestyle than the other, which is generally resident at the coast throughout its life. To investigate their relative abundances along the Swedish west coast, juvenile cod were collected at a high spatial resolution along the coast, and genetically assigned to ecotype. The results reveal large proportions of the coastal ecotype in the southern Kattegat, Öresund, and in inshore Swedish Skagerrak, whereas the offshore ecotype dominates in offshore areas. Regression model comparison suggests that differences in bottom depth, rather than distance from the open sea, explains the heterogenous spatial distribution of the two ecotypes. In addition, the two ecotypes display genetic differences suggesting adaptation to different environments. The results underline that successful fisheries management requires identification and consideration of locally adapted sympatric ecotypes.