Temporal change in genetic integrity suggests loss of local adaptation in a wild Atlantic salmon (Salmo salar) population following introgression by farmed escapees

Abstract

In some wild Atlantic salmon populations, rapid declines in numbers of wild returning adults has been associated with an increase in the prevalence of farmed salmon. Studies of phenotypic variation have shown that interbreeding between farmed and wild salmon may lead to loss of local adaptation. Yet, few studies have attempted to assess the impact of interbreeding at the genome level, especially among North American populations. Here, we document temporal changes in the genetic makeup of the severely threatened Magaguadavic River salmon population (Bay of Fundy, Canada), a population that might have been impacted by interbreeding with farmed salmon for nearly 20 years. Wild and farmed individuals caught entering the river from 1980 to 2005 were genotyped at 112 single-nucleotide polymorphisms (SNPs), and/or eight microsatellite loci, to scan for potential shifts in adaptive genetic variation. No significant temporal change in microsatellite-based estimates of allele richness or gene diversity was detected in the wild population, despite its precipitous decline in numbers over the last two decades. This might reflect the effect of introgression from farmed salmon, which was corroborated by temporal change in linkage-disequilibrium. Moreover, SNP genome scans identified a temporal decrease in candidate loci potentially under directional selection. Of particular interest was a SNP previously shown to be strongly associated with an important quantitative trait locus for parr mark number, which retained its genetic distinctiveness between farmed and wild fish longer than other outliers. Overall, these results indicate that farmed escapees have introgressed with wild Magaguadavic salmon resulting in significant alteration of the genetic integrity of the native population, including possible loss of adaptation to wild conditions.

Prevalence and survival of escaped European seabass Dicentrarchus labrax in Cyprus identified using genetic markers

“…The reduced genetic variability of these new stocks was apparent in all the farms and implies they have been obtained from aquaculture sources rather than the wild (Loukovitis et al 2015). Such a trend could have implications for protecting the wild gene pool if significant numbers of seabass escape from aquaculture sites in the future (Bourret et al 2011). The high level of genetic differentiation between these fish and native populations (Table 3) is likely to increase the level of genetic change resulting from introgression (Glover et al 2013).…”

“…The escape of fish from sea-based aquaculture installations is recognised as a problem due to the potential impact of cultured fish on wild populations in terms of disease (Johansen et al 2011), competition for food (Abrantes et al 2011) and interbreeding (Bourret et al 2011). Cultured fish may be genetically different from wild counterparts as they may originate from other geographic areas and, as a population, may have experienced founder effects, genetic drift, domestication and directional selection as part of the farming process (Ferguson et al 2007).…”

“…The interaction of wild and cultured fish has been studied predominantly in salmonids (reviewed by Jonsson & Jonsson 2006) as they form the primary aquaculture species in terms of seacage production; however, any species reared in sea-based cages or pens can potentially escape and interact with wild conspecifics. Interbreeding between wild and farmed salmon (termed 'introgression') has been shown to occur frequently (Fleming et al 2000), resulting in pronounced changes to the genetic characteristics of the wild population (McGinnity et al 2003, Bourret et al 2011). …”

Native and exotic fishes in a Patagonian reservoir with rainbow trout cage culture: spatial and trophic resource use

“…displacement by competition) expected in systems inhabited by species that may share resources with the escapees (Naylor et al, 2005;Johnston et al, 2010;Johnston and Wilson, 2014). Also, when wild populations of conspecifics exist, genetic introgression of farm-adapted genes could reduce fitness through loss of local adaptations (McGinnity et al, 2003;Skaala et al, 2006;Hindar and Fleming, 2007;Bourret et al, 2011).…”

“…Salmonid escapees are expected to have long-term environmental effects on the receiving communities, given their high dispersion capacity and longevity, in addition to the high frequency and massive nature of escape events (Podemski and Blanchfield, 2006;Arismendi et al, 2009;Bourret et al, 2011;Patterson and Blanchfield, 2013). Ecological impacts include predation, competition and species replacement (Habit et al, 2010;Johnston and Wilson, 2014).…”