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.

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.

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We analyzed historical data on the age structure and abundance of males in 22 populations of sockeye salmon (Oncorhynchus nerka) in the Fraser River, British Columbia, to determine geographical and temporal patterns of precocial maturation, its relationship with growth and maturation at other ages, and the value of precocial males as indicators of year-class strength. Most Fraser sockeye males spend two winters at sea before maturing at 3-5 years of age. Precocial males return to spawn at 2, 3, or 4 years of age (ages 0.1, 1.1, and 2.1) and comprised <1 to >33% of male brood year returns among populations. Precocity was lowest among populations that spawned far upstream and highest among populations spawning to the west of the main Fraser River and was not correlated with migration distance. Precocial maturation was related to growth during the second summer in the ocean to brood line and to brood line abundance. The combination of brood line, abundance, and size of precocial males accounted for more than 75% of the variation in total returns in four populations, suggesting that these variables might be used to predict abundance 1 year in advance.

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