Comparative genetic variability of pink salmon from different parts of their range: native Pacific, artificially introduced White Sea and naturally invasive Atlantic Scottish rivers.

Trans-oceanic movement, stocking and subsequent establishment of Pacific pink salmon (Oncorhynchus gorbuscha) into the Atlantic White Sea area have resulted in their spreading further across the northern Atlantic, with spawning being reported in a number of regions within this area. Such expansions of non-native species bring potential risks to the ecosystems in question. It has not yet been established if the spawning events of pink salmon observed are the result of self-sustaining populations in these areas, or are because of repeated invasions of strayers from the White Sea stocks. In 2017 pink salmon were observed in a number of Scottish rivers in historically large numbers. This study set out to examine genetic variation in these fish and compare this to fish in Pacific founder regions and the White Sea translocated populations. A total of 286 samples from Scotland, the Atlantic White Sea, the Pacific Okhotsk region and Northern Pacific Bering Sea were screened using a 1018 bp sequenced region of the Cytochrome b mtDNA gene and 205 of these samples for 13 microsatellites. Significant bottleneck and founder effects were observed in the White Sea stocks in both mitochondrial and nuclear DNA, including loss of diversity and changes in haplotype and allele proportions. Scottish fish were indistinguishable from White Sea populations and as such it was not possible to determine if the fish were strayers from this region or returning fish from previous spawning events in Scotland. Therefore, although the fish caught in Scotland have their origins in the White Sea population, it may not be easy to determine whether self-sustaining populations have, or are becoming, established in the UK using genetic analysis and other techniques may need to be used.

A century of genetic homogenization in Baltic salmon-evidence from archival DNA.

Intra-species genetic homogenization arising from anthropogenic impacts is a major threat to biodiversity. However, few taxa have sufficient historical material to systematically quantify long-term genetic changes. Using archival DNA collected over approximately 100 years, we assessed spatio-temporal genetic change in Atlantic salmon populations across the Baltic Sea, an area heavily impacted by hydropower exploitation and associated with large-scale mitigation stocking. Analysis was carried out by screening 82 SNPs in 1680 individuals from 13 Swedish rivers. We found an overall decrease in genetic divergence and diminished isolation by distance among populations, strongly indicating genetic homogenization over the past century. We further observed an increase in genetic diversity within populations consistent with increased gene flow. The temporal genetic change was lower in larger wild populations than in smaller wild and hatchery-reared ones, indicating that larger populations have been able to support a high number of native spawners in relation to immigrants. Our results demonstrate that stocking practices of salmon in the Baltic Sea have led to the homogenization of populations over the last century, potentially compromising their ability to adapt to environmental change. Stocking of reared fish is common worldwide, and our study is a cautionary example of the potentially long-term negative effects of such activities.

Close relatives in population samples: Evaluation of the consequences for genetic stock identification.

Determining the origin of individuals in mixed population samples is key in many ecological, conservation and management contexts. Genetic data can be analyzed using genetic stock identification (GSI), where the origin of single individuals is determined using Individual Assignment (IA) and population proportions are estimated with Mixed Stock Analysis (MSA). In such analyses, allele frequencies in a reference baseline are required. Unknown individuals or mixture proportions are assigned to source populations based on the likelihood that their multilocus genotypes occur in a particular baseline sample. Representative sampling of populations included in a baseline is important when designing and performing GSI. Here, we investigate the effects of family sampling on GSI, using both simulated and empirical genotypes for Atlantic salmon (Salmo salar). We show that nonrepresentative sampling leading to inclusion of close relatives in a reference baseline may introduce bias in estimated proportions of contributing populations in a mixed sample, and increases the amount of incorrectly assigned individual fish. Simulated data further show that the induced bias increases with increasing family structure, but that it can be partly mitigated by increased baseline population sample sizes. Results from standard accuracy tests of GSI (using only a reference baseline and/or self-assignment) gave a false and elevated indication of the baseline power and accuracy to identify stock proportions and individuals. These findings suggest that family structure in baseline population samples should be quantified and its consequences evaluated, before carrying out GSI.

Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins.

Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such signatures is fundamental for detecting genomic regions of biological relevance to domestication and improving management practices. In aquaculture, domestication was carried out independently in different locations worldwide, which provides opportunities to study the parallel effects of domestication on the genome of individuals that have been selected for similar traits. In this study, we aimed to detect potential genomic signatures of domestication in two independent pairs of wild/domesticated Atlantic salmon populations of Canadian and Scottish origins, respectively. Putative genomic regions under divergent selection were investigated using a 200K SNP array by combining three different statistical methods based either on allele frequencies (LFMM, Bayescan) or haplotype differentiation (Rsb). We identified 337 and 270 SNPs potentially under divergent selection in wild and hatchery populations of Canadian and Scottish origins, respectively. We observed little overlap between results obtained from different statistical methods, highlighting the need to test complementary approaches for detecting a broad range of genomic footprints of selection. The vast majority of the outliers detected were population-specific but we found four candidate genes that were shared between the populations. We propose that these candidate genes may play a role in the parallel process of domestication. Overall, our results suggest that genetic drift may have override the effect of artificial selection and/or point toward a different genetic basis underlying the expression of similar traits in different domesticated strains. Finally, it is likely that domestication may predominantly target polygenic traits (e.g., growth) such that its genomic impact might be more difficult to detect with methods assuming selective sweeps.

Modeling fitness changes in wild Atlantic salmon populations faced by spawning intrusion of domesticated escapees.

Genetic interaction between domesticated escapees and wild conspecifics represents a persistent challenge to an environmentally sustainable Atlantic salmon aquaculture industry. We used a recently developed eco-genetic model (IBSEM) to investigate potential changes in a wild salmon population subject to spawning intrusion from domesticated escapees. At low intrusion levels (5%-10% escapees), phenotypic and demographic characteristics of the recipient wild population only displayed weak changes over 50 years and only at high intrusion levels (30%-50% escapees) were clear changes visible in this period. Our modeling also revealed that genetic changes in phenotypic and demographic characteristics were greater in situations where strayers originating from a neighboring wild population were domestication-admixed and changed in parallel with the focal wild population, as opposed to nonadmixed. While recovery in the phenotypic and demographic characteristics was observed in many instances after domesticated salmon intrusion was halted, in the most extreme intrusion scenario, the population went extinct. Based upon results from these simulations, together with existing knowledge, we suggest that a combination of reduced spawning success of domesticated escapees, natural selection purging maladapted phenotypes/genotypes from the wild population, and phenotypic plasticity, buffer the rate and magnitude of change in phenotypic and demographic characteristics of wild populations subject to spawning intrusion of domesticated escapees. The results of our simulations also suggest that under specific conditions, natural straying among wild populations may buffer genetic changes in phenotypic and demographic characteristics resulting from introgression of domesticated escapees and that variation in straying in time and space may contribute to observed differences in domestication-driven introgression among native populations.

Range-wide parallel climate-associated genomic clines in Atlantic salmon.

Clinal variation across replicated environmental gradients can reveal evidence of local adaptation, providing insight into the demographic and evolutionary processes that shape intraspecific diversity. Using 1773 genome-wide single nucleotide polymorphisms we evaluated latitudinal variation in allele frequency for 134 populations of North American and European Atlantic salmon (Salmo salar). We detected 84 (4.74%) and 195 (11%) loci showing clinal patterns in North America and Europe, respectively, with 12 clinal loci in common between continents. Clinal single nucleotide polymorphisms were evenly distributed across the salmon genome and logistic regression revealed significant associations with latitude and seasonal temperatures, particularly average spring temperature in both continents. Loci displaying parallel clines were associated with several metabolic and immune functions, suggesting a potential basis for climate-associated adaptive differentiation. These climate-based clines collectively suggest evidence of large-scale environmental associated differences on either side of the North Atlantic. Our results support patterns of parallel evolution on both sides of the North Atlantic, with evidence of both similar and divergent underlying genetic architecture. The identification of climate-associated genomic clines illuminates the role of selection and demographic processes on intraspecific diversity in this species and provides a context in which to evaluate the impacts of climate change.

Accuracy of Assignment of Atlantic Salmon (Salmo salar L.) to Rivers and Regions in Scotland and Northeast England Based on Single Nucleotide Polymorphism (SNP) Markers.

Understanding the habitat use patterns of migratory fish, such as Atlantic salmon (Salmo salar L.), and the natural and anthropogenic impacts on them, is aided by the ability to identify individuals to their stock of origin. Presented here are the results of an analysis of informative single nucleotide polymorphic (SNP) markers for detecting genetic structuring in Atlantic salmon in Scotland and NE England and their ability to allow accurate genetic stock identification. 3,787 fish from 147 sites covering 27 rivers were screened at 5,568 SNP markers. In order to identify a cost-effective subset of SNPs, they were ranked according to their ability to differentiate between fish from different rivers. A panel of 288 SNPs was used to examine both individual assignments and mixed stock fisheries and eighteen assignment units were defined. The results improved greatly on previously available methods and, for the first time, fish caught in the marine environment can be confidently assigned to geographically coherent units within Scotland and NE England, including individual rivers. As such, this SNP panel has the potential to aid understanding of the various influences acting upon Atlantic salmon on their marine migrations, be they natural environmental variations and/or anthropogenic impacts, such as mixed stock fisheries and interactions with marine power generation installations.

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.

Finding markers that make a difference: DNA pooling and SNP-arrays identify population informative markers for genetic stock identification.

Genetic stock identification (GSI) using molecular markers is an important tool for management of migratory species. Here, we tested a cost-effective alternative to individual genotyping, known as allelotyping, for identification of highly informative SNPs for accurate genetic stock identification. We estimated allele frequencies of 2880 SNPs from DNA pools of 23 Atlantic salmon populations using Illumina SNP-chip. We evaluated the performance of four common strategies (global F ST, pairwise F ST, Delta and outlier approach) for selection of the most informative set of SNPs and tested their effectiveness for GSI compared to random sets of SNP and microsatellite markers. For the majority of cases, SNPs selected using the outlier approach performed best followed by pairwise F ST and Delta methods. Overall, the selection procedure reduced the number of SNPs required for accurate GSI by up to 53% compared with randomly chosen SNPs. However, GSI accuracy was more affected by populations in the ascertainment group rather than the ranking method itself. We demonstrated for the first time the compatibility of different large-scale SNP datasets by compiling the largest population genetic dataset for Atlantic salmon to date. Finally, we showed an excellent performance of our top SNPs on an independent set of populations covering the main European distribution range of Atlantic salmon. Taken together, we demonstrate how combination of DNA pooling and SNP arrays can be applied for conservation and management of salmonids as well as other species.

Genotypic and phenotypic correlates with proliferative kidney disease-induced mortality in Atlantic salmon.

Heritable variation in resistance to pathogens has been reported in many fish species, but little is known about its genetic architecture. To extend understanding, an investigation was made of the association of resistance to proliferative kidney disease (PKD) in 4 second filial generation (F2) families of Atlantic salmon with molecular markers from different genetic linkage groups in the species' genome, following a natural disease outbreak. PKD causes serious mortality in cultured salmonids. In addition to mortality, associations with growth-related traits were also examined, as immune responses are energetically costly and have been observed to reduce growth. Associations were investigated for 34 microsatellite markers and 5 restriction fragment length polymorphism (RFLP) loci from 3 regions of the growth hormone 1 gene (GH1). The phenotypic and genotypic character of survivors was compared with unexposed fish derived from the same families. Mortality was not size-selective, but growth in the survivors was reduced, and fish had a lower condition factor than unexposed fish, suggesting an energetic cost to resistance. Five markers showed significant allele frequency differences between survivors and unexposed fish, albeit in single families. Prior to correction for multiple tests, 2 of these markers were also linked to variation in growth-related traits among survivors, along with a further 7 markers. Though sample sizes constrained the power of the analysis, the study points to regions of the salmon genome that may contain quantitative trait loci related to PKD resistance, on which further work on the genetic architecture of PKD resistance in this species could focus.

Identification of genetic markers associated with Gyrodactylus salaris resistance in Atlantic salmon Salmo salar.

Gyrodactylus salaris Malmberg, 1957 is a freshwater monogenean ectoparasite of salmonids, first recorded in Norway in 1975 and responsible for extensive epizootics in wild Atlantic salmon Salmo salar L. The susceptibility of different populations of Atlantic salmon to G. salaris infection differs markedly, with fish from the Baltic being characterised as relatively resistant whereas those from Norway or Scotland are known to be (extremely) susceptible. Resistance to Gyrodactylus infection in salmonids has been found to be heritable and a polygenic mechanism of control has been hypothesised. The current study utilises a 'Quantitative trait loci' (QTL) screening approach in order to identify molecular markers linked to QTL influencing G. salaris resistance in B1 backcrosses of Baltic and Scottish salmon. Infection patterns in these fish exhibited 3 distinct types; susceptible (exponential parasite growth), responding (parasite load builds before dropping) and resistant (parasite load never increases). B1 backcross fish were screened at 39 microsatellite markers and single marker-trait associations were examined using general linear modelling. We identified 10 genomic regions associated with heterogeneity in both innate and acquired resistance, explaining up to 27.3% of the total variation in parasite loads. We found that both innate and acquired parasite resistance in Atlantic salmon are under polygenic control, and that salmon would be well suited to a selection programme designed to quickly increase resistance to G. salaris in wild or farmed stocks.

Gene expression profiles of some immune relevant genes from skin of susceptible and responding Atlantic salmon (Salmo salar L.) infected with Gyrodactylus salaris (Monogenea) revealed by suppressive subtractive hybridisation.

Suppressive subtractive hybridisation was used to examine the genetic basis of susceptibility and resistance of the Atlantic salmon (Salmo salar) to Gyrodactylus salaris infection. Selected immune relevant genes are listed and two genes, for myeloid leukemia differentiation protein (Mcl-1) and opioid growth factor receptor (OGFr), obtained from the susceptible salmon library were characterised. Both sequences showed high amino acid identity and similarity with human and mouse isoforms, and their possible involvement in the response of salmon to G. salaris is discussed. Quantitative reverse transcriptase-PCR was performed for both genes. Upregulation of Mcl-1 in B1 backcross salmon of the susceptible phenotypic category compared with resistant salmon was demonstrated. The possible relationship of the salmon Mcl-1 and cytokines (interleukin 1beta) in the G. salaris-induced host response is discussed. Potential involvement of OGFr in the depletion of mucous cells during prolonged and heavy G. salaris infection, via suppression of DNA synthesis and profound decrease in basal cell proliferation, is proposed. However, only two of six susceptible fish showed high upregulation of OGFr, which might indicate that its expression is localised to sites of wounds resulting from a heavy burden of G. salaris.