Atlantic salmon in Europe inhabit a diverse range of habitats: from cold northern to warm southern rivers, from high mountain streams to lowland farmland, and from rich eutrophic to nutrient poor oligotrophic waters. Such diversity in environments brings with it diversity in selection pressures and, over time, results in diversity in life history characteristics and associated local adaptations. Different selective pressures and adaptive responses are seen when fish are reared in non-natural environments such as hatcheries. Whilst for fish used for stocking, a hatchery may aim to retain as much wild natural genetic variation as possible, selection for traits associated with a domesticated environment is still a significant, if unintentional, force. In contrast, for those fish used in aquaculture, directional selection for commercially advantageous traits is the main aim of breeding programmes. In both of these situations the results of selection may reduce the fitness of fish in a wild situation, and, if subsequent interactions occur, hybridisation and introgression of the non-native genomes into the wild can decrease the fitness of hybrid individuals and populations as a whole.
Genetic and genomic techniques can be used to help managers understand such interactions and so proved a unique approach to potentially reduce the impact of genetic introgression on wild populations. The first and perhaps most important question for managers is what is the proportion of non-native fish present in a system? Genetic approaches can screen wild and non-native stocks and, using techniques such as Genetic Stock Identification, identify the origin of individuals found within a fishery. More sophisticated analysis can allow the proportion of hybrids to be estimated and proportions of admixture determined for individual fish and populations as a whole. Such information can be used for identifying problematic situations thus helping manager’s make informed decisions on both hatchery use and aquaculture facility siting and practices.
Whilst such genetic approaches can provide invaluable insights into the interactions between and introgression of non-native genomes into wild populations, they are challenging to undertake in some situations. For example, such techniques may be more problematic where historic reference samples are unavailable, if there are multiple potential sources of non-native fish, and/or if the traditional genetic differences between the non-native stocks and the wild fish are fairly small. Recent advances in genomics may provide new tools to investigate such situations, including the discovery of new markers and studies of epigenetic changes.