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Standardizing industry and regulatory genetic screening tests for detecting non-local strains in aquaculture and wild populations of Atlantic salmon in the Bay of Fundy area



Analyses of neutral genetic markers generally reveal a positive relationship between genetic and geographic distance; geographically proximate populations are typically more genetically similar than are geographically distant populations. These finding are consistent with results from tagging studies which often demonstrate high spawning site fidelity (low straying rates) for Atlantic salmon. This reduced gene flow affords the potential for adaptive differences to accrue between geographically separated populations. Introduction of foreign genes can decrease the fitness of a wild population in a given river by producing individuals that are adapted to non-local wild conditions.

Introgression of foreign strains can also decrease wild fitness, and increase the risk of extirpation, by breaking up co-adaptive gene complexes in the F2 and subsequent generations. Almost all molecular genetic studies, involving allozyme, mtDNA, and microsatellite markers carried out to date report large nearly diagnostic differences between European and North American salmon. In fact, mitochondrial DNA studies suggest that European and North American salmon diverged approximately 1 million years before present. Given this amount of genetic divergence, outbreeding depression between North American and European salmon is expected to be high, although no studies that the authors are aware of have evaluated hatching success or early mortality in the F2 of North American/European crosses.

Genetic analyses of aquaculture escapees (identified as such on the basis of scale ring growth patterns and fin erosion) in the Bay of Fundy area have identified alleles at microsatellite loci that are absent or very rare in wild local populations, but very common in European salmon; some salmon have two "European" alleles at multiple loci, some a single "European" allele at multiple loci. Because these rare non-local alleles have been observed at multiple microsatellite loci in the same individuals, these Atlantic salmon are almost certainly to be descended from one or two recently introduced European aquaculture parents. In other words, the pattern of alleles observed at multiple loci is not consistent with either (1) strictly North American ancestry, and chance inheritance of rare non-introduced alleles, or (2) chance inheritance of "European" alleles naturally introduced by historic trans-ocean migrants. The hypothesis of European ancestry of these aquaculture escapees has been further corroborated by analyses of mitochondrial DNA- putative European and North American/European aquaculture hybrids exhibit mitochondrial DNA haplotypes reported in the literature only from continental Europe, Iceland, Northern Newfoundland and Labrador. In recent years, several presumably wild salmon, from two inner Bay of Fundy Rivers, have been identified that exhibit a single European and a single North American allele, at multiple nuclear loci, and are thus likely North American/European aquaculture F1 hybrids (partial European ancestry is further supported by analyses of mitochondrial DNA).

Currently, most of the aquaculture industry screens its broodstock for fish of European ancestry; these analyses are required by the US government before eggs, fry and smolt produced in Canada may be exported to Maine for eventual rearing in sea pens. This genetic screening is based on seven microsatellite loci used by US Fish & Wildlife Services. Analyses used by the Department of Fisheries and Oceans are based on more recent technology (tetranucleotide microsatellites and Single Nucleotide Polymorphisms, or SNPs). Although these different techniques likely yield similar results, the aquaculture industry and the Department of Fisheries and Oceans understand that confirmation that both identify the same individuals as European, North American, F1 or F2 hybrids of European/North American salmon, is necessary to protect both the economic interests of the aquaculture industry and wild endangered populations of the Bay of Fundy.

The project objectives are:

  • Standardization of US Fish & Wildlife Services (USFWS) and DFO genetic assays for the detection of European ancestry in aquaculture and wild Bay of Fundy populations of salmon.
  • Extension of genetic surveys of wild and aquaculture populations in the Bay of Fundy area using an approach that will minimize industry regulatory concerns, while protecting wild endangered populations.
  • To transfer the different genetic screening methods to reciprocal laboratories.
  • To screen aquaculture populations for the presence of non-local Gaspé strain salmon
  • To gather necessary information, and to lay the foundations, for a DFO-aquaculture industry risk assessment of European salmon in wild endangered salmon populations of the inner Bay of Fundy.

Program Name

Aquaculture Collaborative Research and Development Program (ACRDP)


2004 - 2007


Atlantic: Gulf of Maine, Scotian Shelf

Principal Investigator(s)

Patrick O'Reilly

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