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When escapee farmed Atlantic salmon Salmo salar interbreed with wild fish, the introgression of maladaptive genes can lower wild population productivity and alter key life history traits. To date, only a few European studies have compared wild, farm, and hybrid salmon under common conditions in the wild, isolating the influence of genetics on survival and fitness-related traits. Here, we examined the performance of experimentally derived Atlantic salmon fry from 4 cross types (wild, farm, and reciprocal F1 hybrids) during the first summer of growth at 3 locations in southern Newfoundland. Overall survival was high, with the cross type rank order consistent across sites (mean percent recaptured: wild-mother hybrids 26.2% ≈ wild 26.0% > farm 19.2% > farm-mother hybrids 12.8%). Wild fish were smaller than wild-mother hybrids and farm fish, though differed less in size from farm-mother hybrids. At 2 out of 3 sites, wild-mother hybrids were larger than wild and farm-mother hybrid fish but had only a small size advantage over farm fish. Shape differences were small and mainly related to body depth, with the largest differences between wild and farm fish. Wild-mother hybrids had fewer parr marks than other cross types at a single site, and though differences in the size of marks were minimal, farm fish tended to have the narrowest marks. Overall, these results show that genetic differences exist for fitness-related traits among wild, farm, and hybrid juveniles, even over short temporal scales and under favourable environmental conditions, and may contribute to patterns of reduced farm-mother hybrid and feral farm survival in the wild.

It has long been clear that interbreeding between domesticated and wild Atlantic salmon can lead to negative fitness consequences for native populations. Few studies, however, have examined these consequences at critical early life stages, particularly in the context of distinct geographical and ancestral relationships among populations as well domestication selection. In Newfoundland (NF), Canada, while the majority of aquaculture sites use the North American (NA) Saint John River strain, site-specific permission has been granted to farm a strain of European origin (EO). We designed a common-garden experiment to compare fitness-related traits (e.g. development time, survival, size and growth) at different early-life stages (eye development, hatch and yolk absorption) among EO and NA farmed, 2 NF wild and F1 hybrid groups. Significant differences (p < 0.001) were observed in development time, survival, growth and energy conversion among farmed, F1 hybrid and wild populations. While pure populations (farmed and wild) differed amongst one another, we found few differences in fitness-related traits between F1 hybrids and their maternal wild/farmed strains. This suggests that the early-life fitness consequences of F1 hybridization will be largely manifested through the action of maternal effects. Additionally, significant associations between the maternal effects of egg size and alevin development time, size, survival, growth, condition and energy conversion efficiency were found. These findings suggest that early-life fitness-related trait differences among farmed, wild and their related F1 hybrids are generated by the geographic and ancestral relationship and maternal effects of egg size and less so by domestication selection.

Cultured Atlantic salmon Salmo salar are of international socioeconomic value, and the process of domestication has resulted in significant behavioural, morphological, and allelic differences from wild populations. Substantial evidence indicates that direct genetic interactions or interbreeding between wild and escaped farmed Atlantic salmon occurs, genetically altering wild salmon and reducing population viability. However, genetic interactions may also occur through ecological mechanisms (e.g. disease, parasites, predation, competition), both in conjunction with and in the absence of interbreeding. Here we examine existing evidence for ecological and non-reproductive genetic interactions between domestic Atlantic salmon and wild populations and the potential use of genetic and genomic tools to resolve these impacts. Our review identified examples of genetic changes resulting from ecological processes, predominately through pathogen or parasite transmission. In addition, many examples were identified where aquaculture activities have either altered the selective landscape experienced by wild populations or resulted in reductions in population abundance, both of which are consistent with the widespread occurrence of indirect genetic changes. We further identify opportunities for genetic or genomic methods to quantify these impacts, though careful experimental design and pre-impact comparisons are often needed to accurately attribute genetic change to aquaculture activities. Our review indicates that ecological and non-reproductive genetic interactions are important, and further study is urgently needed to support an integrated understanding of aquaculture-ecosystem interactions, their implications for ecosystem stability, and the development of potential mitigation and management strategies.

Genetic interactions (i.e. hybridization) between wild and escaped Atlantic salmon Salmo salar from aquaculture operations have been widely documented, yet the ability to incorporate predictions of risk into aquaculture siting advice has been limited. Here we demonstrate a model-based approach to assessing these potential genetic interactions using a salmon aquaculture expansion scenario in southern Newfoundland as an example. We use an eco-genetic individual-based Atlantic salmon model (IBSEM) parameterized for southern Newfoundland populations, with regional environmental data and field-based estimates of survival, to explore how the proportion of escapees relative to the size of wild populations could potentially influence genetic and demographic changes in wild populations. Our simulations suggest that both demographic decline and genetic change are predicted when the percentage of escapees in a river relative to wild population size is equal to or exceeds 10% annually. The occurrence of escapees in southern Newfoundland rivers under a proposed expansion scenario was predicted using river and site locations and models of dispersal for early and late escapees. Model predictions of escapee dispersal suggest that under the proposed expansion scenario, the number of escapees is expected to increase by 49% and the highest escapee concentrations will shift westward, consistent with the location of proposed expansion (20 rivers total >10% escapees, max 24%). Our results identify susceptible rivers and potential impacts predicted under the proposed aquaculture expansion scenario and illustrate how model-based predictions of both escapee dispersal and genetic impacts can be used to inform both aquaculture management decisions and wild salmon conservation.

Hybridization of escaped farmed Atlantic salmon Salmo salar with wild populations occurs throughout their native range and can threaten wild population stability and persistence. The extent of hybridization is often population-specific and can drive changes in phenotype and genotype. Current understanding of the forces that contribute to the spatial distribution of hybridization is insufficient despite its potential to inform conservation and management efforts. Using a panel of 95 single nucleotide polymorphisms previously validated for identifying parr of farmed, wild, or hybrid descent, we present a novel exploration of inter- and intra-river distribution of hybrids from 33 locations across 9 rivers in southern Newfoundland, Canada. The proportion of hybrids varied significantly across (p < 0.001) and within rivers (p < 0.05 in 4 rivers). Binomial mixed models and logistic regression showed increased proportions of hybrid and feral offspring within smaller rivers (p < 0.0001). Within-river distribution of hybrid parr was strongly associated with the migration effort required to reach spawning sites; the hybrid proportion decreased significantly (p < 0.05) with increased elevation, geographic distance and the presence of obstructions. These observations support previous hypotheses that the distribution of escaped farmed Atlantic salmon can be restricted by migratory challenges, which result in the reduction of hybrid individuals in upstream spawning sites relative to downstream locations. Our research demonstrates that levels of hybridization vary spatially and are associated with landscape features. We suggest that consideration of spatial variation in levels of hybridization will be essential for the evaluation of impacts that escaped farmed salmon impose on wild Atlantic salmon populations.