Atlantic salmon (Salmo salar) is one of the best researched fishes, and its aquaculture plays a global role in the blue revolution. However, since the 1970s, tens of millions of farmed salmon have escaped into the wild. We review current knowledge of genetic interactions and identify the unanswered questions. Native salmon populations are typically genetically distinct from each other and potentially locally adapted. Outside Norway, introgression remains unquantified, and in all regions, biological changes and the mechanisms driving population-specific impacts remain poorly documented. Nevertheless, existing knowledge shows that the long-term consequences of introgression is expected to lead to changes in life-history traits, reduced population productivity and decreased resilience to future challenges. Only a major reduction in the number of escapees and/or sterility of farmed salmon can eliminate further impacts. K E Y W O R D Saquaculture, evolution, fish farming, fitness, genetic, hybrid

Norwegian aquaculture has grown from its pioneering days in the 1970s to be a major industry. It is primarily based on culturing Atlantic salmon and rainbow trout and has the potential to influence the surrounding environment and wild populations. To evaluate these potential hazards, the Institute of Marine Research initiated a risk assessment of Norwegian salmon farming in 2011. This assessment has been repeated annually since. Here, we describe the background, methods and limitations of the risk assessment for the following hazards: genetic introgression of farmed salmon in wild populations, regulatory effects of salmon lice and viral diseases on wild salmonid populations, local and regional impact of nutrients and organic load. The main findings are as follows: (i) 21 of the 34 wild salmon populations investigated indicated moderate-to-high risk for genetic introgression from farmed escaped salmon. (ii) of 109 stations investigated along the Norwegian coast for salmon lice infection, 27 indicated moderate-to-high likelihood of mortality for salmon smolts while 67 stations indicated moderate-to-high mortality of wild sea trout. (iii) Viral disease outbreaks (pancreas disease, infectious pancreatic necrosis, heart and skeletal muscle inflammation, and cardiomyopathy syndrome) in Norwegian salmon farming suggest extensive release of viruses in many areas. However, screening of wild salmonids revealed low to very low prevalence of the causal viruses. (iv) From ∼500 yearly investigations of local organic loading under fish farms, only 2% of them displayed unacceptable conditions in 2013. The risk of eutrophication and organic load beyond the production area of the farm is considered low. Despite several limitations, especially limited monitoring data, this work represents one of the world’s first risk assessment of aquaculture. This has provided the Norwegian government with the basis upon which to take decisions for further development of the Norwegian aquaculture industry.

Survival, growth, and diet were compared for farmed, hybrid, and wild Atlantic salmon (Salmo salar) families from the eyed egg to the smolt stage in River Guddalselva, Hardangerfjord, Norway. All individuals that survived until the smolt stage were captured in a Wolf trap and identified to one of the 69 experimental families using microsatellite markers. Survival of farmed salmon progeny was significantly lower than that of hybrids and wild progeny. However, survival varied considerably, from 0.17% to 6.4%, among farmed families. Egg size had an important influence on survival. Half-sib hybrid families with a farmed mother had higher survival when fathered by wild salmon than by farmed salmon. The overall relative survival of farmed families compared with that of their hybrid half-sib families fell from 0.86 in the second cohort to 0.62 in the last cohort with increasing fish density. Smolts of farmed parents showed significantly higher growth rates than wild and hybrid smolts. The overlap in diet among types of crosses demonstrates competition, and farm and hybrid progeny therefore will reduce the river’s capacity for production of wild salmon.

Knowledge of aquaculture–environment interactions is essential for the development of a sustainable aquaculture industry and efficient marine spatial planning. The effects of fish and shellfish farming on sessile wild populations, particularly infauna, have been studied intensively. Mobile fauna, including crustaceans, fish, birds and marine mammals, also interact with aquaculture operations, but the interactions are more complex and these animals may be attracted to (attraction) or show an aversion to (repulsion) farm operations with various degrees of effects. This review outlines the main mechanisms and effects of attraction and repulsion of wild animals to/from marine finfish cage and bivalve aquaculture, with a focus on effects on fisheries‐related species. Effects considered in this review include those related to the provision of physical structure (farm infrastructure acting as fish aggregating devices (FADs) or artificial reefs (ARs), the provision of food (e.g. farmed animals, waste feed and faeces, fouling organisms associated with farm structures) and some farm activities (e.g. boating, cleaning). The reviews show that the distribution of mobile organisms associated with farming structures varies over various spatial (vertical and horizontal) and temporal scales (season, feeding time, day/night period). Attraction/repulsion mechanisms have a variety of direct and indirect effects on wild organisms at the level of individuals and populations and may have implication for the management of fisheries species and the ecosystem in the context of marine spatial planning. This review revealed considerable uncertainties regarding the long‐term and ecosystem‐wide consequences of these interactions. The use of modelling may help better understand consequences, but long‐term studies are necessary to better elucidate effects.

This review summarises the state of knowledge of both viral and bacterial diseases of Atlantic cod Gadus morhua, and their diagnosis, prophylaxis and treatment. The most important losses have been at the larval and juvenile stages, and vibriosis has long been the most important bacterial disease in cod, with Listonella (Vibrio) anguillarum dominant among pathogenic isolates. Vaccination of cod against pathogens such as L. anguillarum and Aeromonas salmonicida clearly demonstrates that the cod immune system possesses an effective memory and appropriate mechanisms sufficient for protection, at least against some diseases. Well-known viruses such as the nodavirus that causes viral encephalopathy and retinopathy (VER), infectious pancreatic necrosis virus (IPNV) and viral haemorrhagic septicaemia virus (VHSV) have been isolated from Atlantic cod and can be a potential problem under intensive rearing conditions. No commercial vaccines against nodavirus are currently available, whereas vaccines against IPNV infections based upon inactivated virus as well as IPNV recombinant antigens are available. A number of investigations of the pharmacokinetic properties of antibacterial agents in cod and their efficacy in treating bacterial infections have been reviewed.

Ecology and genetics can influence the fate of individuals and populations in multiple ways. However, to date, few studies consider them when modelling the evolutionary trajectory of populations faced with admixture with non-local populations. For the Atlantic salmon, a model incorporating these elements is urgently needed because many populations are challenged with gene-flow from non-local and domesticated conspecifics. We developed an Individual-Based Salmon Eco-genetic Model (IBSEM) to simulate the demographic and population genetic change of an Atlantic salmon population through its entire life-cycle. Processes such as growth, mortality, and maturation are simulated through stochastic procedures, which take into account environmental variables as well as the genotype of the individuals. IBSEM is based upon detailed empirical data from salmon biology, and parameterized to reproduce the environmental conditions and the characteristics of a wild population inhabiting a Norwegian river. Simulations demonstrated that the model consistently and reliably reproduces the characteristics of the population. Moreover, in absence of farmed escapees, the modelled populations reach an evolutionary equilibrium that is similar to our definition of a ‘wild’ genotype. We assessed the sensitivity of the model in the face of assumptions made on the fitness differences between farm and wild salmon, and evaluated the role of straying as a buffering mechanism against the intrusion of farm genes into wild populations. These results demonstrate that IBSEM is able to capture the evolutionary forces shaping the life history of wild salmon and is therefore able to model the response of populations under environmental and genetic stressors.

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To improve assessments of the environmental risks of aquaculture, a series of simulated escapes of farmed Atlantic salmon (Salmo salar L.) from seawater netpens were performed. Individually tagged post-smolts and adult Atlantic salmon were released from various locations at different times of the year. Post-smolts that escaped during their first summer were capable of rapid migration towards the open sea. A small fraction returned to spawn and were recaptured after 1–3 years at sea (0.4%, range 0.0–1.1%). A total of 13% of the post-smolts that escaped during autumn were reported in nearby fisheries during subsequent months, partly because they had grown large enough to be caught in the gillnets used, but more importantly because migratory behaviour diminished towards the end of the year. The mean recapture rate of adult salmon was high after releases in fjords (7–33%), lower after coastal releases (4–7%), and zero on the outer coast. Most of these recaptures were immature fish recaptured in sea relatively close to the release site during their first months post-release. Recaptures of adult escapees after 1–2 years in the wild were very rare (0.09%), probably because of their low survival. A Monte-Carlo method was developed to estimate the annual numbers of escapees from Norwegian fish farms based on reported catches of escaped farmed salmon in the sea and in rivers and the recapture probabilities reported here. The model provides a tool to estimate numbers of escapees independently from the reported numbers. Importantly, our analysis suggests that the total numbers of post-smolt and adult escapees have been two- to fourfold as high as the numbers reported to the authorities by fish farmers, depending on whether the incomplete sea fishery statistics are compensated for.