Direct and indirect effects of salmon aquaculture on wild salmon populations:

collaborative project led by Ian Bradbury, Fisheries and Oceans Canada

The introduction of non-native populations and species has the potential to negatively influence native populations. Genetic impacts have been shown to lower mean population fitness, alter characters, decrease abundance and reduce viability. However, uncertainty remains regarding the relative magnitude of direct (i.e. introgression and hybridization) and indirect (i.e. competition, parasite introduction, and habitat disruption) genetic interactions.


Genetic interactions between domesticated and wild Atlantic salmon (Salmo salar) have been identified as a significant threat to the persistence of wild populations. In recent decades, Atlantic Salmon have become a model system for understanding direct genetic interactions between domesticated and wild fish stocks.  Aquaculture escapes in southern Newfoundland’s Fortune Bay and Bay D’Espoir provide an opportunity to measure the impact of direct genetic interaction. A recent proposal to expand Atlantic Salmon aquaculture, using largely all-female European sterile triploids into Placentia Bay, Newfoundland provides an ideal study system for examining indirect genetic impacts.

Direct genetic effects of aquaculture are introgression of domestic salmon into the local wild populations. With hybridization, local adaptation can be lost, causing outbreeding depression. Local adaptation can include disease resistance, predator response, reproductive success, and swimming capabilities. Differences between wild and domesticated salmon in these traits can be caused by (deliberate) artificial selection in aquaculture, or unintentional selection due to the aquaculture environment.


A large aquaculture escape event in 2013 in southern Newfoundland provided an opportunity to measure morphological changes associated with different degrees of hybridization. A SNP panel is used to identify salmon caught in local rivers as farmed, hybrid, or wild salmon. We will measure differences in body shape among these groups using geometric morphometric analyses. The results from wild or feral salmon will be compared to those obtained from similar analyses of the morphology of wild-type, farmed and hybrid salmon captively reared in a common garden experiment to assess the effect of rearing environment on morphological differences among groups of salmon with different genetic ancestry.


Indirect genetic effects, unlike direct genetic impacts, may influence native populations regardless of whether fish are contained or escape. Environmental disturbance caused by farmed fish, or pathogens or parasites associated with them, may differentially alter mortality or reproductive success in wild fish, thereby changing patterns of natural selection, or depress abundance reducing adaptive genetic diversity via genetic drift. These effects are more likely to be pronounced in small populations or those with low abundance and/or exhibiting population decline such as the wild population along the south coast on Newfoundland.


We plan to generate a multi-year genomic baseline, which will allow the estimation of effective population size and an exploration of adaptive diversity prior to the proposed expansion. The baseline information collected will enable accurate quantification of indirect genetic effects of open net-pen salmon aquaculture on wild populations and directly inform conservation of wild salmon in Atlantic Canada.     

This is a collaborative project led by Ian Bradbury of Fisheries and Oceans Canada. The morphological work will be the MSc research of Ben Perriman, and the indirect genetic effects will be studied by Beth Watson for her MSc degree.