Wennhage, H. | bioRxiv Science

bioRxiv2026

Establishing a baseline for standardised genetic monitoring of Atlantic cod (Gadus morhua) in Sweden

Protecting populations and genetic diversity within them is critical to conserving the resilience and adaptive potential of species. Fisheries management has long had the ambition of managing species at the population level, but mainly define "fish stocks" based on geographical limits, which can lead to overfishing of sensitive populations in areas where many different populations coexist. Modern genetic methods are now sufficiently cost-effective, fast, and accurate to be integrated into fisheries management, enabling genetic identification and monitoring of fish populations. Here, we establish a genetic baseline for the commercially important fish Atlantic cod (Gadus morhua) in the waters surrounding Sweden, by using standardised sampling procedures and developing a genetic panel of 4000 single nucleotide polymorphisms (SNPs) for cost-effective assignment of population-of-origin and inversion genotypes. Using the SNP panel, we resolve the geographical distribution of three genetically distinct cod populations in the region: offshore, coastal/Western Baltic, and Eastern Baltic cod. While there is considerable spatial overlap between the three populations, they are genetically differentiated across the entire genome, as well as in genomic regions associated with chromosomal inversions. In addition, heterozygosity and effective population size estimates suggest differences in genetic diversity and rates of genetic erosion, underscoring the need to monitor the genetic diversity within each population separately. Repeating this methodology across years provides a first suggestion for establishing spatiotemporally resolved genetic monitoring of Atlantic cod in Sweden - simultaneously accounting for both population structure within the species and the genetic diversity within populations.

genomics↗

bioRxiv2022

Mixed origin of juvenile Atlantic cod (Gadus morhua) along the Swedish west coast

Cryptic population structure in exploited fish species poses a major challenge for fisheries management. Atlantic cod (Gadus morhua) is a species in which the presence of sympatric ecotypes has been known for a long time, for instance off the coast of Northern Norway. More recently, two sympatric ecotypes of cod have also been documented in the Skagerrak and Kattegat; one ecotype is of an apparent offshore origin and undertakes spawning migrations to the North Sea, and the other is resident at the coast throughout its life. However, their relative contributions of juveniles to the Swedish west coast remain poorly understood. The lack of adult cod along the Skagerrak and Kattegat coasts in recent years has led to the hypothesis that the offshore ecotype is the main source of juveniles to the area, but recent studies have shown large proportions of coastal cod inside Norwegian Skagerrak fjords. In this study, juvenile cod were collected at a high spatial resolution along the Swedish west coast, and genetically assigned to each of the two ecotypes. The results reveal that there is a considerable proportion of juvenile coastal cod in the southern Kattegat, Oresund, and in inshore Swedish Skagerrak, but that the offshore ecotype dominates in offshore areas. Model selection suggests that differences in bottom depth, rather than distance from the open sea, may explain the heterogenous spatial distribution of the two ecotypes. In addition, the two ecotypes displayed differences at loci known to be associated with environmental adaptation, suggesting that their spatial distribution is maintained by natural selection in response to specific environmental conditions.

genomics↗