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

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.     

Generic genetic differences between farmed and wild Atlantic salmon identified from a 7K SNP-chip

Genetic interactions between farmed and wild conspecifics are of special concern in fisheries where large numbers of domesticated individuals are released into the wild. In the Atlantic salmon (Salmo salar), selective breeding since the 1970's has resulted in rapid genetic changes in commercially important traits, such as a doubling of the growth rate. Each year, farmed salmon escape from net pens, enter rivers, and interbreed with wild salmon. Field experiments demonstrate that genetic introgression may weaken the viability of recipient populations. However, due to the lack of diagnostic genetic markers, little is known about actual rates of gene flow from farmed to wild populations. Here we present a panel of 60 single nucleotide polymorphisms (SNPs) that collectively are diagnostic in identifying individual salmon as being farmed or wild, regardless of their populations of origin. These were sourced from a pool of 7000 SNPs comparing historical wild and farmed salmon populations, and were distributed on all but two of the 29 chromosomes. We suggest that the generic differences between farmed and wild salmon at these SNPs have arisen due to domestication. The identified panel of SNPs will permit quantification of gene flow from farmed to wild salmon populations, elucidating one of the most controversial potential impacts of aquaculture. With increasing global interest in aquaculture and increasing pressure on wild populations, results from our study have implications for a wide range of species.     

Differences in pathogen resistance within and among cultured,conservation-dependent,and endangered populations of Atlantic salmon, <Emphasis Type="Italic">Salmo salar</Emphasis> L.

We report genetic differences for resistance to the pathogen Listonella anguillarum within and among one cultured and two wild Canadian populations of Atlantic salmon, Salmo salar, using a common-garden experimental protocol. Following exposure to the causative agent for vibriosis, parr originating from the endangered Stewiacke River population experienced significantly higher mortality than cultured parr, four generations removed from the Saint John River population, and wild parr from Tusket River. Pathogen resistance differed between sexes; males consistently experienced higher survival than females. There was no evidence that maturity influenced pathogen resistance in male parr. The population and sex differences in pathogen resistance documented here have implications for risk assessments of the demographic consequences of interbreeding between wild and farmed Atlantic salmon.     

Reduced anti-predator responses in multi-generational hybrids of farmed and wild Atlantic salmon (<Emphasis Type="Italic">Salmo salar</Emphasis> L.)

Cultured organisms undergo genetically-based behavioural changes that may reduce their ability to survive in the wild. This has raised concerns that interbreeding between escaped cultured and wild organisms will generate hybrids exhibiting maladaptive behaviours which may ultimately reduce the fitness of the wild counterpart. We compared anti-predator responses in Atlantic salmon (Salmo salar) from two wild North American populations, the major farmed strain used in regional aquaculture, and their wild-farmed hybrids (F₁, F₂, and wild backcross). Anti-predator responses of fry (age 0+ parr) were measured under common environmental conditions, using a model of a natural predator (belted kingfisher, Ceryle alcyon). Farmed fry exhibited significantly reduced anti-predator responses relative to fry from both wild populations. The anti-predator responses of wild-farmed hybrid fry were intermediate to those of the parental populations (pure farmed or wild). The magnitude by which wild-farmed hybrids differed in anti-predator responses from pure wild fish also depended on the wild population. These results suggest that: (1) the observed behavioural differences have a genetic basis; (2) wild-farmed hybrids have, on average, reduced anti-predator responses relative to wild fish; and that (3) the effects of wild-farmed interbreeding on anti-predator responses will differ between wild populations. Our study is consistent with the general hypothesis that continual farmed-wild interbreeding may have detrimental effects on the fitness of wild organisms.     

Hatching Time and Alevin Growth Prior to the Onset of Exogenous Feeding in Farmed,Wild and Hybrid Norwegian Atlantic Salmon

The onset of exogenous feeding, when juveniles emerge from the gravel, is a critical event for salmonids where early emergence and large size provide a competitive advantage in the wild. Studying 131 farmed, hybrid and wild Norwegian Atlantic salmon families, originating from four wild populations and two commercial strains, we investigated whether approximately 10 generations of selection for faster growth has also resulted in increased somatic growth prior to the onset of exogenous feeding. In addition, we tested whether relaxed selection in farms has allowed for alterations in hatching time between farmed and wild salmon. Across three cohorts, wild salmon families hatched earlier than farmed salmon families, while hybrid families displayed intermediate hatching times. While the observed differences were small, i.e., 1–15 degree-days (0–3 days, as water temperatures were c. 5–6°C), these data suggest additive genetic variation for hatching time. Alevin length prior to exogenous feeding was positively related to egg size. After removal of egg size effects, no systematic differences in alevin length were observed between the wild and farmed salmon families. While these results indicate additive genetic variation for egg development timing, and wild salmon families consistently hatched earlier than farmed salmon families, these differences were so small they are unlikely to significantly influence early life history competition of farmed and wild salmon in the natural environment. This is especially the case given that the timing of spawning among females can vary by several weeks in some rivers. The general lack of difference in size between farmed and wild alevins, strongly suggest that the documented differences in somatic growth rate between wild and farmed Norwegian Atlantic salmon under hatchery conditions are first detectable after the onset of exogenous feeding.     

Genetic interactions between marine finfish species in European aquaculture and wild conspecifics

The principal species of marine aquaculture in Europe are Atlantic salmon (Salmo salar), sea bass (Dicentrarchus labrax) and sea bream (Sparus auratus). For Atlantic salmon and sea bass, a substantial part of total genetic variation is partitioned at the geographical population level. In the case of sea bream, gene flow across the Azores/Mediterranean scale appears to be extensive and population structuring is not detected. For Atlantic salmon and sea bass, natural population structure is at risk from genetic interaction with escaped aquaculture conspecifics. The locally adaptive features of populations are at risk from interbreeding with non‐local aquaculture fish. Wild populations, generally, are at risk from interactions with aquaculture fish that have been subject to artificial selection or domestication. Atlantic salmon is the main European aquaculture species and its population genetics and ecology have been well‐studied. A general case regarding genetic interactions can be based on the information available for salmon and extended to cover other species, in the appropriate context. A generalized flow chart for interactions is presented. Salmon escape from aquaculture at all life stages, and some survive to breed among wild salmon. Reproductive fitness in the escaped fish is lower than in native, wild fish because of behavioural deficiencies at spawning. However, as the number of salmon in aquaculture greatly exceeds the number of wild fish, even small fractional rates of escape may result in the local presence of large numbers, and high frequencies, of escaped fish. At present, policy and legislation in relation to minimizing genetic interactions between wild and aquaculture fish is best developed for Atlantic salmon, through the recommendations of the Oslo Agreement developed by the North Atlantic Salmon Conservation Organization and subsequent agreements on their implementation. In future, the potential use of genetically modified fish in aquaculture will make additional policy development necessary. Improved containment is recommended as the key to minimizing the numbers and therefore the effects of escaped fish. Emergency recovery procedures are recommended as a back‐up measure in the case of containment failure. Reproductive sterility is recommended as a future key to eliminating the genetic potential of escaped fish. The maintenance of robust populations of wild fish is recommended as a key to minimizing the effects of escaped fish on wild populations.     

Genetic divergence and interactions in the wild among native, farmed and hybrid Atlantic salmon

There is concern that the progeny resulting from the spawnings of escaped farmed Atlantic salmon may compete with and disrupt native salmon populations. This study compared, both in the hatchery and in the wild, fitness-related traits and examined interactions among farmed, native and hybrid 0+ parr derived from controlled crosses and reared under common conditions. The farmed salmon were seventh-generation fish from the principal commercial strain in Norway and native salmon were from the rivers Imsa and Lone, Norway. In the hatchery, farmed salmon were more aggressive than both native populations and tended to dominate them in pairwise contests. Farmed salmon were also more prone to risk, leaving cover sooner after a simulated predator attack, and had higher growth rates than native fish. Interbreeding between farmed and native fish generally resulted in intermediate expression of the above traits. There was, however, evidence of hybrid vigour in Lone/farmed crosses which were able to dominate both pure Lone and farmed parr in pairwise contests. In the wild, observations of habitat use and diet suggested that the populations compete for territory and food, and both farmed fish and hybrids expressed higher growth rates than native fish. Our results suggest that these innate differences in behaviour and growth, that probably are linked closely to fitness, will threaten native populations through competition and disruption of local adaptations.     

IBSEM: An Individual-Based Atlantic Salmon Population Model

Ecology and genetics can influence the fate of individuals and populations in multiple ways. However, to date, few studies consider them when modelling the evolutionary trajectory of populations faced with admixture with non-local populations. For the Atlantic salmon, a model incorporating these elements is urgently needed because many populations are challenged with gene-flow from non-local and domesticated conspecifics. We developed an Individual-Based Salmon Eco-genetic Model (IBSEM) to simulate the demographic and population genetic change of an Atlantic salmon population through its entire life-cycle. Processes such as growth, mortality, and maturation are simulated through stochastic procedures, which take into account environmental variables as well as the genotype of the individuals. IBSEM is based upon detailed empirical data from salmon biology, and parameterized to reproduce the environmental conditions and the characteristics of a wild population inhabiting a Norwegian river. Simulations demonstrated that the model consistently and reliably reproduces the characteristics of the population. Moreover, in absence of farmed escapees, the modelled populations reach an evolutionary equilibrium that is similar to our definition of a ‘wild’ genotype. We assessed the sensitivity of the model in the face of assumptions made on the fitness differences between farm and wild salmon, and evaluated the role of straying as a buffering mechanism against the intrusion of farm genes into wild populations. These results demonstrate that IBSEM is able to capture the evolutionary forces shaping the life history of wild salmon and is therefore able to model the response of populations under environmental and genetic stressors.     

SSU rRNA gene sequence reveals two genotypes of Spironucleus barkhanus (Diplomonadida) from farmed and wild Arctic charr Salvelinus alpinus

Spironucleus barkhanus isolated from the blood of Arctic charr Salvelinus alpinus from a marine fish farm were genetically compared with S. barkhanus isolated from the gall bladder of wild Arctic charr. The wild Arctic charr were caught in the lake used as the water source for the hatchery from which the farmed fish originated. Sequencing of the small subunit ribosomal RNA gene (SSU rDNA) from these 2 populations showed that the isolates obtained from farmed and wild Arctic charr were only 92.7 % similar. Based on the sequence differences between these isolates, it is concluded that the parasites isolated from the farmed fish have not been transmitted from wild Arctic charr in the hatchery's fresh water source. It is therefore most likely that the farmed fish were infected by S. barkhanus after they were transferred to seawater. S. barkhanus isolated from diseased farmed Arctic charr were 99.7% similar to the isolates obtained from diseased farmed Chinook (Canada) and Atlantic salmon (Norway). The high degree of sequence similarity between S. barkhanus from farmed Arctic charr, Chinook and Atlantic salmon indicates that systemic spironucleosis may be caused by specific strains/variants of this parasite. The genetic differences between the isolates of farmed and wild fish are of such magnitude that their conspecificity should be questioned.     

Migratory behaviour of wild and farmed Atlantic salmon (Salmo salar) during spawning

Migratory behaviour at spawning of wild and newly-escaped farmed Atlantic salmon was analysed by radio telemetry in the River Alta, North Norway. Spawning areas were located by aerial surveys. Farmed females moved significantly more than wild females ( P <0.01). There was no such difference between the two groups of males. About 83% of the wild fish stayed within identified spawning areas for 1 day or longer. The corresponding figure for farmed salmon was only 43% ( P <0.05). Wild salmon stayed 8.1 days inside spawning areas and farmed salmon 5.2 days. The present results suggest that escaped farmed salmon had reduced spawning success compared with wild fish.     

Identification of quantitative genetic components of fitness variation in farmed,hybrid and native salmon in the wild

Feral animals represent an important problem in many ecosystems due to interbreeding with wild conspecifics. Hybrid offspring from wild and domestic parents are often less adapted to local environment and ultimately, can reduce the fitness of the native population. This problem is an important concern in Norway, where each year, hundreds of thousands of farm Atlantic salmon escape from fish farms. Feral fish outnumber wild populations, leading to a possible loss of local adaptive genetic variation and erosion of genetic structure in wild populations. Studying the genetic factors underlying relative performance between wild and domesticated conspecific can help to better understand how domestication modifies the genetic background of populations, and how it may alter their ability to adapt to the natural environment. Here, based upon a large-scale release of wild, farm and wild x farm salmon crosses into a natural river system, a genome-wide quantitative trait locus (QTL) scan was performed on the offspring of 50 full-sib families, for traits related to fitness (length, weight, condition factor and survival). Six QTLs were detected as significant contributors to the phenotypic variation of the first three traits, explaining collectively between 9.8 and 14.8% of the phenotypic variation. The seventh QTL had a significant contribution to the variation in survival, and is regarded as a key factor to understand the fitness variability observed among salmon in the river. Interestingly, strong allelic correlation within one of the QTL regions in farmed salmon might reflect a recent selective sweep due to artificial selection.     

Emergence and maintenance of infectious salmon anaemia virus (ISAV) in Europe: a new hypothesis

The present study describes the use of molecular methods in studying infectious salmon anaemia virus (ISAV), an important pathogen of farmed salmon in Norway, Scotland, the Faeroe Islands, Canada, USA and Chile. The nucleotide sequences of the haemagglutinin gene (HA) from 70 ISAV isolates have been analysed for phylogenetic relationship and the average mutation rate of nucleotide substitutions calculated. The isolates constitute 2 major groups, 1 European and 1 North American group. The isolate from Chile is closely related to the North American isolates. The European isolates can be further divided into 3 separate groups reflecting geographical distribution, time of collection, and transmission connected with farming activity. Based on existing information about infectious salmon anaemia (ISA) and new information emerging from the present study, it is hypothesised that: (1) ISAV is maintained in wild populations of trout and salmon in Europe; (2) it is transmitted between wild hosts mainly during their freshwater spawning phase in rivers; (3) wild salmonids, mainly trout, possibly carry benign wild-type ISAV isolates; (4) a change (mutation) in virulence probably results from deletions of amino acid segments from the highly polymorphic region (HPR) of benign wild-type isolates; (5) ISA emerges in farmed Atlantic salmon when mutated isolates are transmitted from wild salmonids or, following mutation of benign isolates, in farmed salmon after transmission from wild salmonids; (6) farming activity is an important factor in transmission of ISAV between farming sites in addition to transmission of ISAV from wild salmonids to farmed salmon; (7) transmission of ISAV from farmed to wild salmonids probably occurs less frequently than transmission from wild to farmed fish due to lower frequency of susceptible wild individuals; (8) the frequency of new outbreaks of ISA in farmed salmon probably reflects natural variation in the prevalence of ISAV in wild populations of salmonids.     

Phylogenetic Evidence of Long Distance Dispersal and Transmission of Piscine Reovirus (PRV) between Farmed and Wild Atlantic Salmon

The extent and effect of disease interaction and pathogen exchange between wild and farmed fish populations is an ongoing debate and an area of research that is difficult to explore. The objective of this study was to investigate pathogen transmission between farmed and wild Atlantic salmon (Salmo salar L.) populations in Norway by means of molecular epidemiology. Piscine reovirus (PRV) was selected as the model organism as it is widely distributed in both farmed and wild Atlantic salmon in Norway, and because infection not necessarily will lead to mortality through development of disease. A matrix comprised of PRV protein coding sequences S1, S2 and S4 from wild, hatchery-reared and farmed Atlantic salmon in addition to one sea-trout (Salmo trutta L.) was examined. Phylogenetic analyses based on maximum likelihood and Bayesian inference indicate long distance transport of PRV and exchange of virus between populations. The results are discussed in the context of Atlantic salmon ecology and the structure of the Norwegian salmon industry. We conclude that the lack of a geographical pattern in the phylogenetic trees is caused by extensive exchange of PRV. In addition, the detailed topography of the trees indicates long distance transportation of PRV. Through its size, structure and infection status, the Atlantic salmon farming industry has the capacity to play a central role in both long distance transportation and transmission of pathogens. Despite extensive migration, wild salmon probably play a minor role as they are fewer in numbers, appear at lower densities and are less likely to be infected. An open question is the relationship between the PRV sequences found in marine fish and those originating from salmon.     

Translocation of wild populations: conservation implications for the genetic diversity of the black-lipped pearl oyster Pinctada margaritifera

Translocation has been widely studied as a tool for conservation management to restore or enhance degraded populations. On the contrary, few studies have been conducted on translocation for commercial purposes. In this study, we evaluate the genetic consequences of translocation of wild individuals of Pinctada margaritifera on farmed and adjacent wild populations. We tested the hypotheses that translocations would induce high genetic heterogeneity in farmed populations and this heterogeneity would then leak into the adjacent wild populations. In fact, farmed samples exhibit high levels of heterogeneity and low pairwise relatedness compared to wild populations, highlighting the pooling of genetically divergent populations into farms. We also demonstrate that this heterogeneity is transmitted to adjacent wild populations as a result of interbreeding. Adjacent wild populations tend to have higher genetic diversity values and greater pairwise relatedness coefficient with farmed populations than wild populations. Overall, pearl culture in French Polynesia promotes the mixing of unrelated individuals in farmed locations and reduces genetic divergence among geographically distant populations as well as among farmed and wild populations of a same lagoon. We also studied for the first time a farmed population originating from spat collected in a lagoon where release of hatchery-produced larvae occurred 10 years ago and we were able to identify four distinct genetic groups. These groups contribute highly to reproduction and caused considerable genetic drift in the lagoon, suggesting that hatchery-produced larvae are neither sustainable method for pearl culture nor for conserving the diversity of P. margaritifera in French Polynesia.     

Efficiency of allele frequency‐based bayesian programmes for detecting hybridization between farmed and wild salmon

Large escapes of cultured salmon from net‐pens have become inevitable disasters linked to the growth of aquaculture in coastal areas. Hybridization between farmed and wild salmon has been witnessed; but the extent of eventual genetic introgression is controversial as selection against hybrids can maintain distinct gene pools. Individual assignment tests based on genetic data have been widely used in fisheries, due to the importance of accurate population assignment for a variety of purposes including distinction between individuals of native and stocked origin. However the ability of these Bayesian programs to detect hybrids and subsequent generations between closely related populations has been little investigated. Here we present results regarding the efficiency of two new computer programs, structure and New Hybrids in detecting hybridization between farmed and wild salmon from the river Teno (Northern Europe) based on genetic data obtained from 17 microsatellite loci.     

Interactions between natural and farmed fish populations: information from genetic markers

Studies on genetic changes in farmed fish populations are reviewed, and the potential interactions between wild and farm escapee, and between wild and stocked, fish populations are discussed. Examples of the application of genetic markers in studies concerning survival and reproduction of stocked fish, and genetic and ecological interactions between stocks, are given for brook trout, Salvelinus fontinalis , brown trout, Salmo trutta , rainbow trout, Salmo gairdneri , cod, Gadus morhua , Guadalupe bass, Micropterus treculi , walleye, Stizostedion vitreum vitreum and chum salmon, Oncorhynchus keta . The various studies produced different results. Evidence for successful reproduction and genetic interactions between released and wild stocks have been found in a few cases. Stocked genetic material sometimes had a lower reproductive success than wild material. In one case the transplanted genetic material failed to acclimatize, and was apparently lost from the genepool in two generations. Investigations on the genetic and ecological interactions between wild and farmed populations are of great importance to the preservation of wild populations and their genetic resources.     

Long-term studies on genetic interaction between wild and ranched cod Gadus morhua by use of a genetic marked strain

Releases of farmed fish, whether accidental from commercial aquaculture facilities or intentional as part of stock enhancement/ranching activities, are considered to pose a risk to native gene pools. Stock enhancement studies of Atlantic cod, Gadus morhua , based on artificially produced juveniles, were initiated in 1984 in western Norway, and genetic aspects were incorporated. In order to investigate potential interbreeding between released and wild cod, a genetically marked cod strain was developed, being homozygotic for a rare allele ( GPI‐1*30 ) expressed in white muscle tissue. In the period from 1990 to 1994, juveniles from the genetic marked strain were released in large quantities in three locations (Masfjord, Øygarden, Heimarkspollen), giving a significant increase of the marker allele in the local wild cod populations. Recently, studies have been conducted in the same areas to estimate the extent of interbreeding between the wild and released cod. The results, however, revealed no permanent increase of the frequency of the marker allele and/or GPI‐1*30 heterozygotes as would be expected from interbreeding. The recent data are compared with comprehensive genetic data of the cod populations in the areas before the actual releases, covering the full period from 1994 to 2003. The present results are also discussed in relation to fishing pressure on coastal cod, migration information and reproductive success of released, genetically marked cod.