Cryptic population structure in exploited fish species poses a major challenge for fisheries management. This is especially true if fish stocks consist of sympatric ecotypes that are adapted to specific environmental conditions. Recently, two sympatric ecotypes of cod have been documented in the Skagerrak and Kattegat; one ecotype is of an apparent offshore origin and undertakes offshore spawning migrations, and the other appears to be resident at the coast throughout its life. Their relative contributions of juveniles to the Swedish west coast, however, remain poorly understood. In addition, it is unclear whether coastal ecotype juveniles originate from local spawning populations in Swedish fjords or from elsewhere. Here, we have collected juvenile cod of both ecotypes at 26 unique stations in 2019 and 2020 along the Norwegian Skagerrak coast and Swedish west coast:
Norwegian Skagerrak, beach seine (GMS): Rodstranda ytre, Varoysund, and Gronholmen;
Swedish Skagerrak, mini trawl (GT), beach seine (LV), and coastal trawl (KT): Abyfjorden, Brofjorden, Finnsbo, Skar, Skar Inre, Torgestad, Farlevfjorden, Saltkallefjorden, Ellosefjorden, Havstensfjorden, Byfjorden, Byfjorden N, Byfjorden S, Hakefjorden, and Stigfjorden;
Kattegat, coastal trawl (KT) and fyke net (RY): Kungsbackafjorden, Kullen 1, and Kullen 2;
Oresund, mini trawl (OR): Barseback, Hven NW, Kopenhamn, Vedback, and Lundakra;
along with adult cod from:
the North Sea (GM_NOT);
Skagerrak fjords: Gullmarsfjorden (CodS) and Byfjorden (BF);
Kattegat (KA): 7 NW Kullen and W Fladen; and
Oresund (OL): Barseback, Hven N, and Landskrona.
With the 2b-RAD-derived SNP loci, we performed outlier tests between the ecotypes, and explored potential genetic substructure within the coastal ecotype. The results revealed genetic differences between the ecotypes at genes associated with migratory behaviour, social behaviour, and environmental adaptation. This gives mechanistic insights to how the genetic divergence of these cod ecotypes may have evolved. Despite a lack of obvious population substructure within the coastal ecotype, differences in geographical distribution and genetic adaptations still suggest that local selection pressure may shape the geographical distribution of the two ecotypes. Hence, the results underline that successful fisheries management requires identification and consideration of sympatric ecotypes at small spatial scales. Less...