Quantifying ecological effects of genetic introgression of farmed on wild salmon

QuantEscape2 is a continuation of the knowledge platform QuantEscape and combines expertise from four Norwegian research institutions that study interactions between escaped farmed and wild Atlantic salmon, Salmo salar. In QuantEscape2 we shift emphasis from quantifying introgression to studying the ecological consequences of introgression. A novel method for estimating the proportion of farmed ancestry in individual fish provides us with unique opportunities to study the full variation of phenotypes in the wild, as a function of introgression. Analysis of scales from 7000 adult salmon from 105 wild populations show that increased farmed ancestry in a wild salmon affects its entire life history in the wild. Increased genetic introgression reduces the age at smoltification (outmigration) and reduces the sea age at sexual maturity, and thereby the total age at maturity. This faster pace-of-life is associated with increased individual growth rate at all life stages, and also with smaller eggs. In experiments, we find that farmed and hybrid offspring have higher mortality relative to wild fish. Genomic studies of the major breeding lines of farmed salmon have identified genes and candidate mutations that have been subject to selection in aquaculture. These selective sweeps predominantly target domestication genes related to brain and neural development, including dopamine homeostasis. We are able to characterise the nature of polygenic adaptation in aquaculture, as well as adaptation to certain environmental conditions in the wild, and we can now study the direct effects of aquaculture-selected genetic changes in wild settings. Cohort analysis of age-classified juvenile salmon shows selection against farmed and hybrid genotypes in a northern Norwegian river, in line with experimental evidence. In a large set of controlled experiments using pedigreed material of farmed, hybrid, backcrossed and naturalised farmed salmon, we have studied growth, survival, smoltification and maturation of individuals with known introgression level. We have experimentally identified predation by larger brown trout as one mechanism by which farm and hybrid offspring have increased mortality in the wild. Another experiment analysed why farmed salmon, whose growth rate in aquaculture is 2-3 times that of wild salmon, only grows c. 10% faster in nature. The answer was that this is both a phenotypically plastic response to energy-poor food in the wild and a higher mortality of the more extremely fast-growing domesticated individuals. We have also shown how smolt releases intended to compensate for habitat loss after hydropower regulation, can lead to an increase in introgression of escaped farmed to wild Atlantic salmon, and thereby counteract the intended effect. In an individual-based model it seems that the loss in fitness from the combined effect of escaped farmed salmon and environmental change, is larger than the sum of each loss factor alone. This makes it necessary to understand the most important, natural or anthropogenic, factors that affect the fitness of contemporary populations. QuantEscape2 is and will continue to be a contributor to the knowledge base which is important for the sustainable development of aquaculture and other industries that rely on viable wild salmon populations.

QuantEscape2 has increased our understanding of how escaped farmed salmon affect wild populations. Genetic introgression from farmed to wild salmon is widespread and affects the entire life cycle of wild salmon. Increased farmed ancestry in a salmon leads to younger age at outmigration from the river and lower sea age at return. Growth rate is increased at all life stages, and survival is reduced. Project outcomes include improved management of wild and farmed salmon in Norway. The methods developed to estimate proportions of farmed and wild ancestry, are general and may impact future management of 600 species that are now being bred in aquaculture worldwide.

QuantEscape2 is a continuation of the knowledge platform QuantEscape and combines expertise from four central research institutions that study interactions between escaped farmed and wild Atlantic salmon, Salmo salar. In QuantEscape2 we shift emphasis from quantifying introgression to studying the ecological consequences of introgression. A novel method for estimating the expected proportion of farmed genome in individual fish provides us with unique opportunities to study the full variation of phenotypes in the wild, as a function of introgression. Cohort analyses of age-classified fish provide opportunities for estimating selection against farmed and hybrid genotypes. In a large set of controlled experiments using pedigreed material of farmed, hybrid, backcrossed and naturalised farmed salmon, we provide detailed study of the performance (growth, survival, smoltification and maturation) of individuals with known introgression level. Detailed genomic studies of the breeding lines in QuantEscape unraveled several loci that had been amplified in farmed strains, and we can now study the direct effects of these genetic changes in wild settings. Population-dynamic models will be used to predict future changes where experimentation falls short, and to analyse the interactions between introgression of farmed genes and other anthropogenic disturbances. QuantEscape2 will contribute to the sustainable management of farmed and wild Atlantic salmon, and benefit the aquaculture industry and wild salmon fisheries by providing guidelines for sustainable aquaculture.