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.     

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.     

Genomewide single nucleotide polymorphism discovery in Atlantic salmon (Salmo salar): validation in wild and farmed American and European populations

A considerable number of single nucleotide polymorphisms (SNPs) are required to elucidate genotype–phenotype associations and determine the molecular basis of important traits. In this work, we carried out de novo SNP discovery accounting for both genome duplication and genetic variation from American and European salmon populations. A total of 9 736 473 nonredundant SNPs were identified across a set of 20 fish by whole‐genome sequencing. After applying six bioinformatic filtering steps, 200 K SNPs were selected to develop an Affymetrix Axiom^® myDesign Custom Array. This array was used to genotype 480 fish representing wild and farmed salmon from Europe, North America and Chile. A total of 159 099 (79.6%) SNPs were validated as high quality based on clustering properties. A total of 151 509 validated SNPs showed a unique position in the genome. When comparing these SNPs against 238 572 markers currently available in two other Atlantic salmon arrays, only 4.6% of the SNP overlapped with the panel developed in this study. This novel high‐density SNP panel will be very useful for the dissection of economically and ecologically relevant traits, enhancing breeding programmes through genomic selection as well as supporting genetic studies in both wild and farmed populations of Atlantic salmon using high‐resolution genomewide information.     

Genomewide introgressive hybridization patterns in wild Atlantic salmon influenced by inadvertent gene flow from hatchery releases

Many salmonid fish populations are threatened by genetic homogenization, primarily due to introgressive hybridization with hatchery‐reared conspecifics. By applying genomewide analysis using two molecular marker types (1986 SNPs and 17 microsatellites), we assessed the genetic impacts of inadvertent gene flow via straying from hatchery releases on wild populations of Atlantic salmon in the Gulf of Finland, Baltic Sea, over 16 years (1996–2012). Both microsatellites and SNPs revealed congruent population genetic structuring, indicating that introgression changed the genetic make‐up of wild populations by increasing genetic diversity and reducing genetic divergence. However, the degree of genetic introgression varied among studied populations, being higher in the eastern part and lower in the western part of Estonia, which most likely reflects the history of past stocking activities. Using kernel smoothing and permutation testing, we detected considerable heterogeneity in introgression patterns across the genome, with a large number of regions exhibiting nonrandom introgression widely dispersed across the genome. We also observed substantial variation in nonrandom introgression patterns within populations, as the majority of genomic regions showing elevated or reduced introgression were not consistently detected among temporal samples. This suggests that recombination, selection and stochastic processes may contribute to complex nonrandom introgression patterns. Our results suggest that (i) some genomic regions in Atlantic salmon are more vulnerable to introgressive hybridization, while others show greater resistance to unidirectional gene flow; and (ii) the hybridization of previously separated populations leads to complex and dynamic nonrandom introgression patterns that most likely have functional consequences for indigenous populations.     

Disease interaction between farmed and wild fish populations

This paper reviews the literature on disease interaction between wild and farmed fish and recommends strategies to reduce the disease risks to both populations. Most, if not all, diseases of farmed fish originate in wild populations. The close contact between farmed and wild fish readily leads to pathogens exchange. Aquaculture creates conditions ( e.g. high stocking levels) conducive to pathogen transmission and disease; hence pathogens can overspill back, resulting in high levels of challenge to wild populations. This is exemplified by sea lice infections in farmed Atlantic salmon. Stocking with hatchery reared fish or aquaculture escapees can affect disease dynamics in wild populations. Whirling disease has been spread to many wild rainbow trout populations in the US with the release of hatchery reared stock. The greatest impact of aquaculture on disease in wild populations has resulted from the movement of fish for cultivation. Examples of exotic disease introduction following movement of live fish for aquaculture with serious consequences for wild populations are reviewed. The salmon parasite, Gyrodactylus salaris, has destroyed wild salmon populations in 44 Norwegian rivers. Crayfish plague has wiped out European crayfish over much of Europe. Eels numbers have declined in Europe and infection with the swimbladder nematode Anguillicola crassus has in part been blamed. The impact of disease in farmed fish on wild populations can mitigated. Risk analysis methods need to be refined and applied to live fish movement and new aquacultural developments. Appropriate biosecurity strategies, based on risk assessments, should be developed to reduce pathogen exchange and mitigate the consequences.     

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.     

Application of genome editing in aquatic farm animals: Atlantic salmon

Gene editing offers opportunities to solve fish farming sustainability issues that presently hampers expansion of the aquaculture industry. In for example Atlantic salmon farming, there are now two major bottlenecks limiting the expansion of the industry. One is the genetic impact of escaped farmed salmon on wild populations, which is considered the most long-term negative effect on the environment. Secondly and the utmost acute problem is the fish parasite salmon lice, which is currently causing high lethality in wild salmonids due to high concentrations of the parasite in the sea owing to sea cage salmon farming. There are also sustainability issues associated with increased use of vegetable-based ingredients as replacements for marine products in fish feed. This transition comes at the expense of the omega-3 content both in fish feed and the fish filet of the farmed fish. Reduced fish welfare represents another obstacle, and robust farmed fish is needed to avoid negative stress associated phenotypes such as cataract, bone and fin deformities, precocious maturity and higher disease susceptibility. Gene editing could solve some of these problems as genetic traits can be altered positively to reach phenotype of interest such as for example disease resistance and increased omega-3 production.

     

Modeling Parasite Dynamics on Farmed Salmon for Precautionary Conservation Management of Wild Salmon

Conservation management of wild fish may include fish health management in sympatric populations of domesticated fish in aquaculture. We developed a mathematical model for the population dynamics of parasitic sea lice (Lepeophtheirus salmonis) on domesticated populations of Atlantic salmon (Salmo salar) in the Broughton Archipelago region of British Columbia. The model was fit to a seven-year dataset of monthly sea louse counts on farms in the area to estimate population growth rates in relation to abiotic factors (temperature and salinity), local host density (measured as cohort surface area), and the use of a parasiticide, emamectin benzoate, on farms. We then used the model to evaluate management scenarios in relation to policy guidelines that seek to keep motile louse abundance below an average three per farmed salmon during the March–June juvenile wild Pacific salmon (Oncorhynchus spp.) migration. Abiotic factors mediated the duration of effectiveness of parasiticide treatments, and results suggest treatment of farmed salmon conducted in January or early February minimized average louse abundance per farmed salmon during the juvenile wild salmon migration. Adapting the management of parasites on farmed salmon according to migrations of wild salmon may therefore provide a precautionary approach to conserving wild salmon populations in salmon farming regions.     

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.     

A global assessment of salmon aquaculture impacts on wild salmonids

Since the late 1980s, wild salmon catch and abundance have declined dramatically in the North Atlantic and in much of the northeastern Pacific south of Alaska. In these areas, there has been a concomitant increase in the production of farmed salmon. Previous studies have shown negative impacts on wild salmonids, but these results have been difficult to translate into predictions of change in wild population survival and abundance. We compared marine survival of salmonids in areas with salmon farming to adjacent areas without farms in Scotland, Ireland, Atlantic Canada, and Pacific Canada to estimate changes in marine survival concurrent with the growth of salmon aquaculture. Through a meta-analysis of existing data, we show a reduction in survival or abundance of Atlantic salmon; sea trout; and pink, chum, and coho salmon in association with increased production of farmed salmon. In many cases, these reductions in survival or abundance are greater than 50%. Meta-analytic estimates of the mean effect are significant and negative, suggesting that salmon farming has reduced survival of wild salmon and trout in many populations and countries.     

Genetic screening of farmed Atlantic salmon escapees demonstrates that triploid fish display reduced migration to freshwater

Each year, hundreds of thousands of farmed Atlantic salmon escape from fish farms into the wild. Some of these escapees enter freshwater, and manage to interbreed with native populations. To hinder further genetic introgression in native populations, the use of sterile triploid salmon within commercial aquaculture is being examined. However, if triploid escapees migrate into freshwater, they may still have ecological impacts on local populations. In the present study, we used microsatellite DNA genotyping to determine the ploidy of 3794 farmed escapees captured in 17 Norwegian rivers in the period 2007–2014. Although a previous study has reported an average of 2 % triploids in Norwegian fish farms during this exact period, here, we only observed 7 (0.18 %) triploids among the escapees captured in freshwater. In addition, we identified three trisomic escapees. For the triploids where the within-river capture location was determined, they were only observed in the lower reaches and not on the spawning grounds. It is concluded that propensity for triploid Atlantic salmon to migrate into freshwater following escape from a fish farm is significantly lower than for normal diploid salmon escapees. Therefore, commercial production of triploids should not only be seen as an effective way of stopping genetic introgression, it will also significantly reduce the numbers of escapees entering rivers, which in turn limits ecological interactions and potential disease transmission.     

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.     

Ecological model of interactions between escaped and wild Atlantic salmon Salmo salar

Atlantic salmon in Maine were once abundant but have become depleted, and are listed as endangered under the federal Endangered Species Act. Historically, salmon numbers in Maine may have been as high as 100 000 adults, but habitat loss, pollution and overfishing have contributed to the decline of the species. In 2000, only 110 adults returned to spawn in Maine rivers. Maine produces c. 15 000 metric tons/year of aquacultured Atlantic salmon from a total of nearly 600 coastal net pens. Escapees from these pens may interact with the wild salmon. The dynamics of salmon populations under such conditions are poorly understood. In order to illuminate the role aquaculture may play in such a system, we have developed a model for simulating population trajectories for both wild salmon and competing populations derived from aquaculture escapes. The model simulates a small population of wild salmon based in a stream/estuary system, into which an aquaculture facility is losing fish to escapes. Biological parameters in the model were estimated as much as possible from data in the USFWS report on Maine salmon. We used the model to investigate the consequences of a variety of ecological interactions between the wild and cultured fish including competitive, genetic and disease effects. Initial results indicate that many of these effects allow the aquaculture‐derived population to supplant the wild fish, but that wild populations may still persist under some conditions.     

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.     

Microsatellite DNA variation in wild populations and farmed strains of turbot from Ireland and Norway: a preliminary study

Turbot Scophthalmus maximus is the focus of a rapidly expanding aquaculture industry, while at the same time wild catches appear to be in decline. As a preliminary investigation into the effects of hatchery rearing, genetic variation at three polymorphic microsatellite loci was assessed in two wild populations and two farmed strains of turbot, from Ireland and Norway. Although a considerable loss of rare alleles was observed in the Irish farmed strain, no statistically significant reductions were found in mean heterozygosity or allelic diversity in farmed strains compared to wild populations. Significant genetic heterogeneity was found between wild and farmed samples from each country but not between the two wild populations. Genetic differentiation between the farmed strains was presumed to be caused by drift in the hatcheries. The utility of these particular microsatellite loci in comparing these samples and the importance of molecular genetic testing of farmed strains is stressed.     

A standardized method for quantifying unidirectional genetic introgression

Genetic introgression of domesticated to wild conspecifics is of great concern to the genetic integrity and viability of the wild populations. Therefore, we need tools that can be used for monitoring unidirectional gene flow from domesticated to wild populations. A challenge to quantitation of unidirectional gene flow is that both the donor and the recipient population may be genetically substructured and that the subpopulations are subjected to genetic drift and may exchange migrants between one another. We develop a standardized method for quantifying and monitoring domesticated to wild gene flow and demonstrate its usefulness to farm and wild Atlantic salmon as a model species. The challenge of having several wild and farm populations was circumvented by in silico generating one analytical center point for farm and wild salmon, respectively. Distributions for the probability that an individual is wild were generated from individual‐based analyses of observed wild and farm genotypes using STRUCTURE. We show that estimates of proportions of the genome being of domesticated origin in a particular wild population can be obtained without having a historical reference sample for the same population. The main advantages of the method presented are the standardized way in which genetic processes within and between populations are taken into account, and the individual‐based analyses giving estimates for each individual independent of other individuals. The method makes use of established software, and as long as genetic markers showing generic genetic differences between domesticated and wild populations are available, it can be applied to all species with unidirectional gene flow. Results from our method are easy to interpret and understand, and will serve as a powerful tool for management, especially because there is no need for a specific historical wild reference sample.     

Genetic population structure in flatfishes and potential impact of aquaculture and stock enhancement on wild populations in Europe

Marine fish wild stocks are known to be heavily depleted by overfishing and flatfish species are no exception. Wild catches being soon insufficient for responding to consumer demand, the cultivation of marine species appeared as a logical response to the need of seafood. Nevertheless, fish aquaculture also entails major impacts on wild populations from which genetic ones are now better known. The hybridization between domestic and native strains potentially have a genetic impact on recipient populations as long as 1) domestic populations are distinct from native wild ones (through domestication process, genetic improvement of captive stocks) and/or 2) the native wild populations are structured (metapopulation structure, local adaptation). Some of the flatfish species exhibit population differentiation and even local adaptation and the release of domestic genetically modified fishes (selected, transgenic) could threaten their survival in case of introgression. The impact of aquaculture on flatfishes is probably still low as land-based farms and low production levels guaranty low rates of escapes and therefore limited contacts between wild and farmed strains. However, flatfish aquaculture is regarded by experts as a rapidly growing domain that will greatly develop soon. In our opinion, this perspective, added to the quite good performances of farmed flatfishes when released into the wild, fully justifies a stronger interest from the scientific community to the conservation of their wild stocks.     

An extended panel of single nucleotide polymorphisms in Atlantic salmon (<Emphasis Type="Italic">Salmo salar</Emphasis> L.) mitochondrial DNA

A total of 6,324 base pairs, distributed on eight different regions of the mitochondrial DNA (mtDNA) were re-sequenced for 32 specimens of Norwegian farmed and wild Atlantic salmon. A total of 16 new and three previously reported single nucleotide polymorphisms (SNPs) were detected. These SNPs were validated using 240 farm and 119 wild Norwegian salmon. Alignments of sequences obtained in this study and previously published sequences revealed another 15 previously unreported SNPs. The panel of mitochondrial SNPs detected in the present study will, in combination with previously identified SNPs, prove useful in designing efficient assays for analyzes of mtDNA variation.