Of Fish and SNPs: The Potential of Genetics for Traceability in European Fisheries Management

The importance of marine organisms for both economical and ecological reasons is enormous; and knowledge of population structure and connectivity is crucial for the sustainable utilisation and conservation of exploited fish stocks. However in most cases our understanding of these spatial patterns of natural variation, both neutral and adaptive, is limited. For marine fish, the maintenance of local stocks containing adaptive diversity is associated with the sustainability and resilience of marine fisheries in the face of climatic and anthropogenic threats. However, many previous studies with genetic markers such as microsatellites have observed weak genetic structure in marine fish and combined with a pelagic larval stage, this has supported the hypothesis that gene flow is extensive and that there is little opportunity for differentiation on local scales. A consequence of the limited opportunity for divergence is the associated assumption that local adaptation would be similarly restricted, except perhaps at macrogeographic levels. However, the application of Single Nucleotide Polymorphisms (SNPs) has the potential to demonstrate previously undetected spatial and temporal population structuring and signatures of adaptive variation. Additionally, SNPs are uniquely applicable for the identification and monitoring of wild fish populations and the traceability of products throughout the food supply chain, allowing effective enforcement of fisheries regulations. Here we demonstrate the utility of SNP panels developed in a European Commission-funded consortium, FishPopTrace, to scenarios that are relevant for the identification of potential illegal fishing and/or mislabeling for two commercially important Atlantic species; cod (Gadus morhua) and herring (Clupea harengus). Markers under selection are typically inappropriate for assessing demographic processes such as gene flow. However, the broad distribution of SNP loci throughout the genome, together with the potential to score large numbers using high throughout approaches, allows for the additional flexibility in traceability studies to establish marker panels with loci that vary in their evolutionary dynamics. Strategies for optimizing population assignment in relation to SNP characteristics and target species biology across various spatial scales will be discussed.