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Evolution of iteroparity is shaped by the trade-off between current and future reproduction.We studied variation in iteroparity among 205 050 individual Atlantic salmon caught in 179 rivers spanning 14◦ of latitude. The proportion of repeat spawners (iteroparous individuals) averaged 3.8% and ranged from 0% to 26% across rivers. Females were more often repeat spawners than males and had lower cost of reproduction in terms of lost body mass between spawning events. Proportion of repeat spawners for a given sea age at maturity, and the ratio of alternate to consecutive repeat spawners, increased with increasing population mean sea age at maturity. By combining smolt age, sea age at maturity, and age at additional spawning events, we identified 141 unique life-history types, and repeat spawners contributed 75% of that variation. Our results show that repeat spawners are important for life-history variation and suggest that the association between mean sea age and the frequency of repeat spawning is adaptive rather than a pleiotropic side effect arising from selection on sea age. age at maturity, life-history evolution, local adaptation, repeat spawning, trade-off

Many post-smolt tissues were collected and screened as part of the EU funded SALSEA-Merge (Project No. 212529) part of the Seventh Framework Programme and co-sponsored by the Atlantic Salmon Trust and the Total Foundation., Gilbey, J., Utne, K.R., Wennevik, V., Beck, A.C., Kausrud, K., Hindar, K., Garcia de Leaniz, C., Cherbonnel, C., Coughlan, J., Cross, T.F., Dillane, E., Ensing, D., García-Vázquez, E., Hole, L.R., Holm, M., Holst, J.C., Jacobsen, J.A., Jensen, A.J., Karlsson, S., Ó Maoiléidigh, N., Mork, K.A., Nielsen, E.E., Nøttestad, L., Primmer, C.R., Prodöhl, P., Prusov, S., Stevens, J.R., Thomas, K., Whelan, K., McGinnity, P., Verspoor, E.

There is a general paucity of knowledge regards spatial variation in marine resource use for many taxa, even those of high socio-economic importance such as Atlantic salmon. While it is known that the oceans around the Faroe Islands support a salmon feeding ground, the relative use of this feeding ground by different age classes across different stocks remains largely unexplored. Using a combination of genetic stock assignment and run-reconstruction models, we observed a consistent pattern whereby the proportion of multi-sea winter (MSW) salmon for a given reporting group was substantially greater around the Faroes than the MSW proportion for that reporting groups among the prefisheries abundance. Surprisingly, MSW fish from Ireland and UK were as likely to occur around the Faroes as were MSW fish from more north-eastern regions such as the Teno river and the Barents and White Seas. MSW fish from Southern Norway were the most likely to be caught at the Faroes. While 1SW salmon from Ireland and UK as well as from Southern Norway occurred at similar rates around the Faroes, 1SW fish from more north-eastern reporting groups were nearly entirely absent from the same feeding ground. In combination with previous studies that examine the marine distribution of Atlantic salmon, our results strongly indicate that the oceans around the Faroes play host to a predominantly MSW salmon feeding ground and that use of this resource varies both within the age classes of a given stock as well as between different stocks. Furthermore, these results suggest that MSW fish from certain stocks might preferentially undertake migrations to the Faroes. Variation in spatial resource use may help to buffer salmon stocks against localised negative changes in marine conditions.

The viability of wild Atlantic salmon populations is threatened by genetic introgression from escaped farmed salmon. Farmed Atlantic salmon are genetically improved for important commercial traits and a life in captivity but are poorly adapted to the natural environment. The rate of gene flow from escaped farmed to wild salmon depends on their spawning success and on offspring survival at various life stages. We here investigate relative survival of introgressed juvenile Atlantic salmon (parr) in a river in northern Norway. The studied population has experienced genetic introgression from farmed salmon for about four generations (20 years). We followed two cohorts of parr from the year of hatching (0+) to the age of 2 years (2+). Farmed genetic introgression was quantified at the individual level and on a continuous scale using diagnostic SNPs. Population-level genetic introgression decreased from 0+ to 2+ by 64% (2011 cohort) and 37% (2013 cohort). This change was driven by a 70% (2011 cohort) and 49% (2013 cohort) lower survival from age 0+ to 2+ in introgressed parr compared to parr of wild origin. Our observations show that there is natural selection against genetic introgression with a potential cost of lower productivity. aquaculture, Atlantic salmon, farmed salmon, genetic introgression, Salmo salar, survival

Description, Early and late life history and growth are affected by farmed salmon introgression across 105 wild populations of Atlantic salmon., After a half a century of salmon farming, we have yet to understand how the influx of genes from farmed escapees affects the full life history of Atlantic salmon (Salmo salar L.) in the wild. Using scale samples of over 6900 wild adult salmon from 105 rivers, we document that increased farmed genetic ancestry is associated with increased growth throughout life and a younger age at both seaward migration and sexual maturity. There was large among-population variation in the effects of introgression. Most saliently, the increased growth at sea following introgression declined with the population’s average growth potential. Variation at two major-effect loci associated with age at maturity was little affected by farmed genetic ancestry and could not explain the observed phenotypic effects of introgression. Our study provides knowledge crucial for predicting the ecological and evolutionary consequences of increased aquaculture production worldwide.

Norway is the world’s largest producer of farmed Atlantic salmon and is home to ∼400 rivers containing wild salmon populations. Farmed escapees, a reoccurring challenge of all cage-based marine aquaculture, pose a threat to the genetic integrity, productivity, and evolutionary trajectories of wild populations. Escapees have been monitored in Norwegian rivers since 1989, and, a second-generation programme was established in 2014. The new programme includes data from summer angling, autumn angling, broodstock sampling, and snorkelling surveys in >200 rivers, and >25 000 scale samples are analysed annually. In 2014–2017, escapees were observed in two-thirds of rivers surveyed each year, and between 15 and 30 of the rivers had >10% recorded escapees annually. In the period 1989–2017, a reduction in the proportion of escapees in rivers was observed, despite a >6-fold increase in aquaculture production. This reflected improved escape prevention, and possibly changes in production methods that influence post-escape behaviour. On average, populations estimated to experience the greatest genetic introgression from farmed salmon up to 2014 also had the largest proportions of escapees in 2014–2017. Thus, populations already most affected are those at greatest risk of further impacts. These data feed into the annual risk-assessment of Norwegian aquaculture and form the basis for directing mitigation efforts.

Use of fast-growing domesticated and/or genetically-modified strains of fish is becoming increasingly common in aquaculture, increasing the likelihood of deliberate or accidental introductions into the wild. To date, their ecological impacts on ecosystems remain to be quantified. Here, using a controlled phenotype manipulation by implanting growth hormone in juvenile Atlantic salmon (Salmo salar), we found that growth-enhanced fish display changes in several phenotypic traits known to be important for ecosystem functioning such as habitat use, morphology and excretion rate. Further, these phenotypic changes were associated with significant impacts on the invertebrate community and key stream ecosystem functions such as primary production and leaf-litter decomposition. These findings provide novel evidence that introductions of growth-enhanced fish into the wild can affect the functioning of natural ecosystems and represent a form of intraspecific invasion. Consequently, environmental impact assessments of growth-enhanced organisms need to explicitly consider ecosystem-level effects. This article is protected by copyright. All rights reserved.

This is the peer reviewed version of the following article: Aykanat, T., Rasmussen, M., Ozerov, M., Niemelä, E., Paulin, L., Vähä, J.-P., ...Primmer, C. R. (2020). Life‐history genomic regions explain differences in Atlantic salmon marine diet specialization. Journal of Animal Ecology, ?(?), 1-15., which has been published in final form at https://doi.org/10.1111/1365-2656.13324. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. 1. Animals employ various foraging strategies along their ontogeny to acquire energy, and with varying degree of efficiencies, to support growth, maturation and subsequent reproduction events. Individuals that can efficiently acquire energy early are more likely to mature at an earlier age, as a result of faster energy gain which can fuel maturation and reproduction. 2. We aimed to test the hypothesis that heritable resource acquisition variation that covaries with efficiency along the ontogeny would influence maturation timing of individuals. 3. To test this hypothesis, we utilized Atlantic salmon as a model which exhibits a simple, hence trackable, genetic control of maturation age. We then monitored the variation in diet acquisition (quantified as stomach fullness and composition) of individuals with different ages, and linked it with genomic regions (haploblocks) that were previously identified to be associated with age‐at‐maturity. 4. Consistent with the hypothesis, we demonstrated that one of the life‐history genomic regions tested (six6) was indeed associated with age‐dependent differences in stomach fullness. Prey composition was marginally linked to six6, and suggestively (but non‐significantly) to vgll3 genomic regions. We further showed Atlantic salmon switched to the so‐called ‘feast and famine’ strategy along the ontogeny, where older age groups exhibited heavier stomach content, but that came at the expense of running on empty more often. 5. These results suggest genetic variation underlying resource utilization may explain the genetic basis of age structure in Atlantic salmon. Given that ontogenetic diet has a genetic component and the strong spatial diversity associated with these genomic regions, we predict populations with diverse maturation age will have diverse evolutionary responses to future changes in marine food web structures.

Structural variants (SVs) are a major source of genetic and phenotypic variation, but remain challenging to accurately type and are hence poorly characterized in most species. We present an approach for reliable SV discovery in non-model species using whole genome sequencing and report 15,483 high-confidence SVs in 492 Atlantic salmon (Salmo salar L.) sampled from a broad phylogeographic distribution. These SVs recover population genetic structure with high resolution, include an active DNA transposon, widely affect functional features, and overlap more duplicated genes retained from an ancestral salmonid autotetraploidization event than expected. Changes in SV allele frequency between wild and farmed fish indicate polygenic selection on behavioural traits during domestication, targeting brain-expressed synaptic networks linked to neurological disorders in humans. This study offers novel insights into the role of SVs in genome evolution and the genetic architecture of domestication traits, along with resources supporting reliable SV discovery in non-model species., This study presents and validates a novel approach to reliably identify structural variations (SVs) in non-model genomes using whole genome sequencing, which was used to detect 15,483 SVs in 492 Atlantic salmon, shedding light on their roles in genome evolution and the genetic architecture of domestication.

Domestication involves adapting animals to the human-controlled environment. Genetic changes occurring during the domestication process may manifest themselves in phenotypes that render domesticated animals maladaptive for life in the wild. Domesticated Atlantic salmon frequently interbreed with wild conspecifics, and their offspring display reduced survival in the wild. However, the mechanism(s) contributing to their lower survival in the wild remains a subject of conjecture. Here, we document higher susceptibility to predation by brown trout in fast-growing domesticated salmon, as compared to their slow-growing wild conspecifics, demonstrating that directional selection for increased growth comes at a cost of decreased survival when under the risk of predation, as predicted by the growth/predation risk trade-off. Despite earlier documentation of altered risk-taking behavior, this study demonstrates for the first time that domestication of Atlantic salmon has lead to increased predation susceptibility, and that this consitutes a mechanism underpinning the observed survial differences in the wild.

New knowledge challenges long‐established practices of fish stocking and transfer because of increasing scientific consensus that the release of cultivated fish can pose risks to biodiversity; however, stocking can also improve fisheries, creating difficult decision trade‐offs regarding its use. Accordingly, controversy persists about fish stocking and transfer. No studies, however, have embraced a multinational perspective to understand the important governance dimensions of the success and failure of salmonid stocking and transfer policies. The present study has analysed the historical development and contemporary governance of the stocking and transfer of native and non‐native salmonids of the genera Salmo, Salvelinus, and Oncorhynchus in five legislative units around the North Atlantic Ocean: the Atlantic Provinces of Canada, France, Germany, Norway, and Sweden. The study is based on the analyses of published and unpublished literature, and a survey of experts. Current salmonid stocking policies and practices varied significantly among jurisdictions; the degree of policy change varied, from radical and rapid changes de jure and de facto in Atlantic Canada and Norway to incremental mostly de jure changes in France and Germany. Rapid policy change in Atlantic Canada, Norway, and partly in Sweden can be explained by the socio‐political importance of salmonid fisheries, stocking regulations based on policy objectives to conserve wild Atlantic salmon (Salmo salar), well‐documented examples of the harmful consequences of transfers of non‐native species, and well‐developed vertical governance linkages. The policy changes resemble that of the ‘punctuated equilibrium policy framework’. By contrast, France and Germany place less socio‐political emphasis on salmonids, have stocking regulations less directed at wild salmonids, more local‐level decision making, more species‐rich fish communities, and little evidence of adverse ecological impacts of the transfer and stocking of salmonids. This has led to small, incremental changes in stocking policy de facto that are reflective of the ‘advocacy coalition policy framework’.

Atlantic salmon (Salmo salar L.) populations from different river origins mix in the North Atlantic during the marine life stage. To facilitate marine stock identification, we developed a genetic baseline covering the European component of the species’ range excluding the Baltic Sea, from the Russian River Megra in the north-east, the Icelandic Ellidaar in the west, and the Spanish Ulla in the south, spanning 3737 km North to South and 2717 km East to West. The baseline encompasses data for 14 microsatellites for 26 822 individual fish from 13 countries, 282 rivers, and 467 sampling sites. A hierarchy of regional genetic assignment units was defined using a combination of distance-based and Bayesian clustering. At the top level, three assignment units were identified comprising northern, southern, and Icelandic regions. A second assignment level was also defined, comprising eighteen and twenty-nine regional units for accurate individual assignment and mixed stock estimates respectively. The baseline provides the most comprehensive geographical coverage for an Atlantic salmon genetic data-set, and a unique resource for the conservation and management of the species in Europe. It is freely available to researchers to facilitate identification of the natal origin of European salmon.

Parasites often depend on their hosts for long distance transport, and genetic population structure can be strongly affected by host specificity and dispersal. Freshwater pearl mussel (Margaritifera margaritifera) populations have previously been found to naturally infest either primarily Atlantic salmon (‘salmon-mussel’) or exclusively brown trout (‘trout-mussel’) across a wide geographic range. Here, we experimentally test whether this intraspecific variation in natural infestation can be explained by host specificity in freshwater pearl mussel. Our experiments show that when both host species were exposed to larvae from salmon- and trout-mussel respectively, salmon-mussel larvae almost never infested brown trout and vice versa. This suggests that host specificity can explain variation in natural infestation among the studied freshwater pearl mussel populations. Host specificity provides a link to the species’ variable population genetic structure, as mussel populations limited to Atlantic salmon, the host with stronger dispersal, show higher genetic diversity and weaker differentiation than populations limited to brown trout as host.

We report on the data from an extensive monitoring programme for the occurrence of escaped farmed Atlantic salmon (Salmo salar) in Norwegian rivers for 25 years. This monitoring started as a 3-year research programme in 1989 and was followed by management authorities to cover the proportional occurrence of escaped farmed Atlantic salmon in rivers during summer and autumn before spawning. Farmed salmon were distinguished from wild salmon by growth patterns in the scales. More than 362 000 salmon were registered by this programme. Here we present the historical data on escaped farmed salmon in catches 1989–2013 and a methodology for calculating averages across summer and autumn capture in rivers, across years and in regions, using weighted and unweighted observations. Catches of escaped farmed salmon show large spatial and temporal variation, with the early 1990s and early 2000s being periods of large influxes of farmed fish. Western Norway and parts of middle and northern Norway have shown particularly high incidences of escaped farmed fish. Because escaped farmed Atlantic salmon are competing and interbreeding with wild Atlantic salmon, as well as increasing the spread of disease-causing agents, they have become a major force driving the abundance and evolution of Atlantic salmon. aquaculture, Atlantic salmon, escaped farmed salmon, fisheries management, Salmo salar.

Background Invasive species represent a major challenge for the conservation of biodiversity. The invasive ectoparasitic fluke Gyrodactylus salaris is considered one of the major threats to the Atlantic salmon (Salmo salar), and the parasite has so far been detected in 50 rivers in Norway. Aims We investigate environmental DNA (eDNA) as a tool for detecting and assessing relative abundance of G. salaris and Atlantic salmon, upstream and downstream of a recently constructed artificial migration barrier in the River Driva in Norway. In addition, we also use eDNA to assess abundance of the less pathogenic G. derjavinoides and its main host, the brown trout (S. trutta). Material & Methods We filtered 1 L and 10 L of water through a 0.45 μm cellulose filter and a 2.0 μm glass fiber filter, respectively, at nine different localities along the river. Concentrations of eDNA were assessed using droplet digital PCR (ddPCR) and compared to parasite abundance based on conventional methodology using electrofishing and the counting of individual parasites on juvenile salmon. Results All four species could successfully be detected from water samples using two different protocols varying in sample volumes, filter types, and DNA‐isolation methods. However, eDNA‐occupancy modeling revealed that the probability of detecting the two gyrodactylid species was higher when filtering 10 L water through a 2.0 μm glass fiber filter (p > .99) than when filtering 1 L water through a 0.45 μm cellulose filter (p = .48–.78). The eDNA concentrations of the two fish species were markedly higher below the migration barrier, reflecting the expected higher biomass of fish. For the two gyrodactylid parasites, eDNA concentrations showed a peak upstream of the migration barrier and decreased below the migration barrier. The observed pattern was consistent with parasite abundance based on conventional methodology. Discussion Assessing abundance in rivers using eDNA is challenging and potentially influenced by downstream accumulation and dilution from tributaries, but our results suggest that G. salaris eDNA concentrations were indicative of parasite abundance. Conclusion We conclude that eDNA is an efficient way of monitoring gyrodactylid parasites and their salmonid hosts, and we suggest that eDNA should be incorporated into future monitoring of G. salaris.

The Ryman-Laikre (R-L) effect is an increase in inbreeding and a reduction in total effective population size (NeT ) in a combined captive-wild system, which arises when a few captive parents produce large numbers of offspring. To facilitate evaluation of the R-L effect for scenarios that are relevant to marine stock enhancement and aquaculture, we extended the original R-L formula to explicitly account for several key factors that determine NeT , including the numbers of captive and wild adults, the ratio of captive to wild Ne/N (β), productivity of captive and wild breeders, and removal of individuals from the wild for captive breeding. We show how to provide quantitative answers to questions such as: What scenarios lead to no loss of effective size? What is the maximum effective size that can be achieved? and What scenarios insure that NeT will be no smaller than a specified value? Important results include the following: (1) For large marine populations, the value of β becomes increasingly important as the captive contribution increases. Captive propagation will sharply reduce NeT unless the captive contribution is very small or β is very large (∼103 or higher). (2) Very large values of β are only possible if wild Ne/N is tiny. Therefore, large wild populations undergoing captive enhancement at even modest levels will suffer major reductions in effective size unless wild Ne is a tiny fraction of the census size (about 10-4 or lower).

Stocking of hatchery produced fish is common practise to mitigate declines in natural populations and may have unwanted genetic consequences. Here we describe a novel phenomenon arising where broodstock used for stocking may be introgressed with farmed individuals. We test how stocking affects introgression in a wild population of Atlantic salmon (Salmo salar) by quantifying how the number of adult offspring recaptured in a stocked river depend on parental introgression. We found that hatchery conditions favour farmed genotypes such that introgressed broodstock produce up to four times the number of adult offspring compared to non-introgressed broodstock, leading to increased introgression in the recipient spawning population. Our results provide the first empirical evidence that stocking can unintentionally favour introgressed individuals and through selection for domesticated genotypes compromise the fitness of stocked wild populations., Stocking of hatchery produced fish is widely used to supplement wild fish populations. Here, the authors show that supplementary stocking can unintentionally favour introgressed individuals with domestic genotypes and compromise the fitness of a wild population of Atlantic salmon.

Escaped farmed Atlantic salmon interbreed with wild Atlantic salmon, leaving off- spring that often have lower success in nature than pure wild salmon. On top of this, presence of farmed salmon descendants can impair production of wild‐type recruits. We hypothesize that both these effects connect with farmed salmon having acquired higher standard metabolic rates (SMR, the energetic cost of self‐maintenance) during domestication. Fitness‐related advantages of phenotypic traits associated with both high SMR and farmed salmon (e.g., social dominance) depend on environmental con- ditions, such as food availability. We hypothesize that farmed offspring have an ad- vantage at high food availability due to, for example, dominance behavior but suffer increased risks of starvation when food is scarce because this behavior is energy‐de- manding. To test these hypotheses, we first compare embryo SMR of pure farmed, farmed‐wild hybrids and pure wild offspring. Next, we test early‐life performance (in terms of survival and growth) of hybrids relative to that of their wild half‐siblings, as well as their competitive abilities, in semi‐natural conditions of high and low food availability. Finally, we test how SMR affects early‐life performance at high and low food availability. We find inconclusive support for the hypothesis that domestication has induced increased SMR. Further, wild and hybrid juveniles had similar survival and growth in the semi‐natural streams. Yet, the presence of hybrids led to decreased survival of their wild half‐siblings. Contrary to our hypothesis about context‐depend- ency, these effects were not modified by food availability. However, wild juveniles with high SMR had decreased survival when food was scarce, but there was no such effect at high food availability. This study provides further proof that farmed salmon introgression may compromise the viability of wild salmon populations. We cannot, however, conclude that this is connected to alterations in the metabolic phenotype of farmed salmon. domestication, natural selection, RMR, Salmo salar, semi‐natural, SMR This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2018 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

Atlantic salmon (Salmo salar) is one of the best researched fishes, and its aquaculture plays a global role in the blue revolution. However, since the 1970s, tens of millions of farmed salmon have escaped into the wild. We review current knowledge of genetic interactions and identify the unanswered questions. Native salmon populations are typically genetically distinct from each other and potentially locally adapted. Farmed salmon represent a limited number of wild source populations that have been exposed to ≥12 generations of domestication. Consequently, farmed and wild salmon differ in many traits including molecular-genetic polymorphisms, growth, morphology, life history, behaviour, physiology and gene transcription. Field experiments have demonstrated that the offspring of farmed salmon display lower lifetime fitness in the wild than wild salmon and that following introgression, there is a reduced production of genetically wild salmon and, potentially, of total salmon production. It is a formidable task to estimate introgression of farmed salmon in wild populations where they are not exotic. New methods have revealed introgression in half of ~150 Norwegian populations, with point estimates as high as 47%, and an unweighted average of 6.4% across 109 populations. Outside Norway, introgression remains unquantified, and in all regions, biological changes and the mechanisms driving population-specific impacts remain poorly documented. Nevertheless, existing knowledge shows that the long-term consequences of introgression is expected to lead to changes in life-history traits, reduced population productivity and decreased resilience to future challenges. Only a major reduction in the number of escapees and/or sterility of farmed salmon can eliminate further impacts. aquaculture, evolution, fish farming, fitness, genetic, hybrid publishedVersion

Man-made barriers such as dams affect the movement of aquatic species, reducing gene flow and genetic variability. Such encroachments may also lead to selective changes in life history and behaviour. Hydropower construction worldwide has fragmented many previously continuous fish habitats, leading to loss of populations and production. It is therefore important to assess potential impacts on habitats before such developments begin. Here, the potential ecological and evolutionary consequences of planned hydropower development on two migratory salmonid fishes – brown trout (Salmo trutta) and European grayling (Thymallus thymallus) – were assessed, combining telemetry with population genetics. Almost 200 fish were radio-tagged and tracked weekly between March and November. Using microsatellite markers, the genetic population structure was assessed and the number of migrants among different river sections identified for both species. Overall, both species displayed extensive within- and between-river movement, with larger home ranges in grayling than in trout. Regular movements between distinct spawning, feeding and wintering areas were common. These vital habitats were often located within areas of planned hydropower development. Both species exhibited significant population genetic structuring within the study area, with waterfalls acting as impassable barriers to upstream gene flow for grayling. The structuring was more developed for trout than for grayling. However, downstream gene flow was common, resulting in a highly admixed trout population below a waterfall. The large-scale movement patterns and extensive connectivity of the system indicate that habitat fragmentation and changes in water flow will adversely affect both species, but most strongly the trout. The reduction in water flow over large and productive stretches of the river might select for less migratory genotypes in both species. The loss of particular genotypes may reduce the biocomplexity of the system and overall population resilience. Copyright © 2013 John Wiley & Sons, Ltd.

The endangered freshwater pearl mussel (Margaritifera margaritifera) requires brown trout or Atlantic salmon as a host to complete its life cycle. In Norway, populations have been identified using almost exclusively either salmon or trout as hosts, even when both hosts are present. In this study we tested the hypothesis that the genetic variation in freshwater pearl mussel is host-dependent. A total of 587 specimens from 25 different localities were assayed for genetic variation at eight microsatellite loci. Within populations, the trout-mussel populations had significantly lower allelic richness and expected heterozygosity than the salmon-mussel populations. The genetic differentiation among trout-mussel populations was very large (FST = 0.332), and significantly larger than among salmon-mussel populations (FST = 0.023). Host affiliation explained more of the genetic differentiation among freshwater pearl mussel populations (FCT = 0.150) than geographical location (FCT = 0.013). Collectively these results suggest that there is strong reproductive isolation between freshwater pearl mussel populations. More importantly, our results indicate that trout- and salmon-mussel populations are differently genetically structured. Because of the mandatory parasitic larval stage on trout and salmon, the host-dependent genetic variation has implications for restoration and management plans for this species.

This paper describes the first observations of escaped farmed Atlantic salmon Salmo salar in the Arctic Ocean. Among 138 individuals of Atlantic salmon captured at the west coast of the Spitsbergen Island at Svalbard in the period 2008−2010, 11 individuals (8%) were classified as escaped farmed salmon based on genetic analysis and scale characters. The escaped individuals entered the ocean as a result of several different escape events. They had all escaped either at the smolt stage or early in the post-smolt stage, and had stayed one winter at sea. The growth of the escaped fish while at sea and their sizes were similar to those of wild fish captured at the same time in the same area. This suggests that farmed Atlantic salmon that have escaped early during the post-smolt period may grow, migrate, and disperse throughout the ocean like their wild counterparts, and survive to adulthood. Salmo salar · Salmon farming · Svalbard · Genetic assignment · Distribution Escaped farmed Atlantic salmon grow, migrate and disperse throughout the Arctic Ocean like wild salmon

Estimates of fish abundance from electrofishing surveys depend on accurate estimation of capture probability. We examine in this paper how estimates of capture probability and abundance of Atlantic salmon from multi-pass removal sampling can be improved by comparing the results of an experimental programme of closed electrofishing sites within selected rivers in west-central Norway, and those obtained from open electrofishing sites established for monitoring long-term juvenile Atlantic salmon population abundance within the Burrishoole catchment, western Ireland. We first establish that the Carle & Strub method provides a more robust estimate of population abundance than the Zippin and Seber methods. We then show how prior information on capture probability may be used to improve the accuracy of the abundance estimate in open sites. We also show that the use of prior information with single-pass electrofishing may improve the accuracy of the abundance estimate so that it is comparable with that of multi-pass electrofishing in terms of stock prediction while requiring less sampling effort.

Interbreeding between domesticated and wild animals occurs in several species. This gene flow has long been anticipated to induce genetic changes in life-history traits of wild populations, thereby influencing population dynamics and viability. Here, we show that individuals with high levels of introgression (domesticated ancestry) have altered age and size at maturation in 62 wild Atlantic salmon Salmo salar populations, including seven ancestral populations to breeding lines of the domesticated salmon. This study documents widespread changes to life-history traits in wild animal populations following gene flow from selectively bred, domesticated conspecifics. The continued high abundance of escaped, domesticated Atlantic salmon thus threatens wild Atlantic salmon populations by inducing genetic changes in fitness-related traits. Our results represent key evidence and a timely warning concerning the potential ecological impacts of the globally increasing use of domesticated animals. © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

Farmed Atlantic salmon (Salmo salar) escape from net pens and enter rivers to spawn, potentially resulting in genetic introgression and reduced fitness of wild salmon. Here, we quantify genetic introgression of farmed to wild salmon, using molecular genetic markers, in populations from 147 salmon rivers, representing three-quarters of the total wild salmon spawning population in Norway. For 109 rivers with adult modern samples and sample sizes of 20 or more, the average level of farmed genetic introgression was 6.4% (median = 2.3%), with a range between 0.0% and 42.2%. Fifty-one of these rivers showed significant farmed genetic introgression when compared with historical reference samples. We observed a highly significant correlation between estimated farmed introgression and average proportion of escaped farmed salmon. We quantify levels of introgression as unweighted averages or weighted by population sizes, to compare geographical regions and to compare levels of introgression in rivers and fjords designated as locations deserving a high level of protection. We found a generally lower level of introgression in National Salmon Rivers and National Salmon Fjords subjected to formal protection by parliament. We conclude that farmed to wild genetic introgression is high in a large proportion of Norwegian salmon rivers, with the highest levels found in the most intensive areas of salmon farming. The extensive genetic introgression documented here poses a serious challenge to the management of farmed and wild Atlantic salmon in Norway and, in all likelihood, in other regions where farmed-salmon escape events occur with regularity

Atlantic salmon (Salmo salar) is one of the most extensively studied fish species in the world due to its significance in aquaculture, fisheries and ongoing conservation efforts to protect declining populations. Yet, limited genomic resources have hampered our understanding of genetic architecture in the species and the genetic basis of adaptation to the wide range of natural and artificial environments it occupies. In this study, we describe the development of a medium-density Atlantic salmon single nucleotide polymorphism (SNP) array based on expressed sequence tags (ESTs) and genomic sequencing. The array was used in the most extensive assessment of population genetic structure performed to date in this species. A total of 6176 informative SNPs were successfully genotyped in 38 anadromous and freshwater wild populations distributed across the species natural range. Principal component analysis clearly differentiated European and North American populations, and within Europe, three major regional genetic groups were identified for the first time in a single analysis. We assessed the potential for the array to disentangle neutral and putative adaptive divergence of SNP allele frequencies across populations and among regional groups. In Europe, secondary contact zones were identified between major clusters where endogenous and exogenous barriers could be associated, rendering the interpretation of environmental influence on potentially adaptive divergence equivocal. A small number of markers highly divergent in allele frequencies (outliers) were observed between (multiple) freshwater and anadromous populations, between northern and southern latitudes, and when comparing Baltic populations to all others. We also discuss the potential future applications of the SNP array for conservation, management and aquaculture.

Summary 1. Although life-history theory predicts that juvenile growth rates should be high, there is substantial evidence that most juveniles grow below their physiological maximum. The endocrine system plays an important role in the determination of fundamental life-history traits, and hormones often serve as a link between an organism’s environment and the expression of a trait. Particularly, growth is a life-history trait, which is strongly associated with growth hormone (GH) in fish, as well as most vertebrates. 2. To elucidate trade-offs related to elevated GH in fish in a natural environment, we experimentally administrated GH exogenously to juvenile Atlantic salmon using sustained-release GH implants, at an earlier ontogenetic stage than previously achieved (1AE5 months). We assessed the effects on growth, dispersal and survival in contrasting environments. 3. Exogenous GH treatment increased the growth rate when fish were fed ad libitum in captivity. However, in a natural stream, GH treatment had a significant negative effect on growth and no apparent effect on survival or dispersal. This contrasts with previous studies conducted at later developmental stages, which show either a positive growth effect or no effect of elevated GH levels. 4. This study shows that environmental conditions strongly affect the response to GH and that under some natural conditions, it may also reduce growth. We suggest that the endogenous plasma GH levels may be maximizing growth during early, but not later, juvenile stages in nature.

This study explores the ecological and economic impacts of interactions between escaped farmed and wild Atlantic salmon (Salmo salar, Salmonidae) over generations. An age- and stage-structured bioeconomic model is developed. The biological part of the model includes age-specific life-history traits such as survival rates, fecundity and spawning successes for wild and escaped farmed salmon, as well as their hybrids, while the economic part takes account of use and non-use values of fish stock. The model is simulated under three scenarios using data from the Atlantic salmon fishery and salmon farming in Norway. The social welfare is derived from harvest and wild salmon while the economic benefits of fishing comprise both sea and river fisheries. The results reveal that the wild salmon stock is gradually replaced by salmon with farmed origin, while the total social welfare and economic benefit decline, although not at the same rate as the wild salmon stock.

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.

Triploidy could prevent escaped farm salmon breeding in the wild, while also improving nutrient quality within farmed fillets. Despite these potential advantages, triploid Atlantic salmon have not been widely used in aquaculture, and their reproductive function has yet to be fully evaluated. Here, we compare reproductive function and fillet composition between triploid and diploid farm salmon under standard aquaculture rearing conditions. We show that female triploids are sterile and do not develop gonads. By contrast, males produce large numbers of motile spermatozoa capable of fertilizing wild salmon eggs. However, compared with diploids, reproductive development and survival rates of eggs fertilized by triploid males were significantly reduced, with less than 1% of eggs sired by triploid males reaching late-eyed stages of development. Analyses of fillets showed that total lipid and fatty acid quantities were significantly lower in triploid than in diploid Atlantic salmon fillets. However, when fatty acids were normalized to total lipid content, triploid fillets had significantly higher relative levels of important omega-3 longchain polyunsaturated fatty acids. Our results show that: (i) escaped triploid farm salmon are very unlikely to reproduce in the wild and (ii) if able to match diploid fillet lipid content, triploid farm salmon could achieve better fillet quality in terms of essential fatty acids. aquaculture, nutrition, polyploidy, sustainability, sterility, sperm

Levels of genetic variability at 12 microsatellite loci and 19 single nucleotide polymorphisms in mitochondrial DNA were studied in four farm strains and four wild populations of Atlantic salmon. Within populations, the farm strains showed significantly lower allelic richness and expected heterozygosity than wild populations at the 12 microsatellite loci, but a significantly higher genetic variability with respect to observed number of haplotypes and haplotype diversity in mtDNA. Significant differences in allele- and haplotype-frequencies were observed between farm strains and wild populations, as well as between different farm strains and between different wild populations. The large genetic differentiation at mitochondrial DNA between wild populations (FST = 0.24), suggests that the farm strains attained a high mitochondrial genetic variability when created from different wild populations seven generations ago. A large proportion of this variability remains despite an expected lower effective population size for mitochondrial than nuclear DNA. This is best explained by the particular mating schemes in the breeding programmes, with 2–4 females per male. Our observations suggest that for some genetic polymorphisms farm populations might currently hold equal or higher genetic variability than wild populations, but lower overall genetic variability. In the short-term, genetic interactions between escaped farm salmon and wild salmon might increase genetic variability in wild populations, for some, but not most, genetic polymorphisms. In the long term, further losses of genetic variability in farm populations are expected for all genetic polymorphisms, and genetic variability in wild populations will be reduced if escapes of farm salmon continue.

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.

Polyandry and post-copulatory sexual selection provide opportunities for the evolution of female differential sperm selection. Here, we examined the influence of variation in major histocompatibility (MH) class I allelic composition upon sperm competition dynamics in Atlantic salmon. We ran in vitro fertilization competitions that mimicked the gametic microenvironment, and replicated a paired-male experimental design that allowed us to compare differences in sperm competition success among males when their sperm compete for eggs from females that were genetically either similar or dissimilar at the MH class I locus. Concurrently, we measured variation in spermatozoal traits that are known to influence relative fertilization success under these conditions. Contrary to the findings demonstrating mechanisms that promote MH complex heterozygosity, our results showed that males won significantly greater relative fertilization success when competing for eggs from genetically similar females at the MH class I. This result also showed covariation with the known influences of sperm velocity on relative fertilization success. We discuss these unexpected findings in relation to sperm–egg recognition and hybridization avoidance mechanisms based upon immunogenetic variation.

To what degree are population differences in resource use caused by competition and the occupation of adjacent positions along environmental gradients evidence of competition? Habitat use may be the result of a competitive lottery, or restricted by competition. We tested to what extent population differences in habitat use of two salmonids, cutthroat trout (Oncorhynchus clarki) and Dolly Varden charr (Salvelinus malma) were influenced by interspecific competition. We hypothesized that the depth distribution of Dolly Varden charr would be affected by competition from the more littoral and surface-oriented cutthroat trout, and that the depth distribution of cutthroat trout would be little affected by competition from Dolly Varden charr. Sympatric populations of cutthroat trout and Dolly Varden charr were created by reciprocal transfers of previously allopatric populations in two experimental lakes. We found evidence of asymmetric competition, as Dolly Varden charr were displaced from littoral habitats when sympatric with cutthroat trout, whereas cutthroat trout remained unaffected by the presence of Dolly Varden charr. Evolved differences between the species, and differences between experimental lakes, also contributed to population differences in habitat use, but asymmetric competition remained as the main driver of different depth distributions in sympatry.

A study was undertaken to examine the responses of three Atlantic salmon Salmo salar strains to growth hormone (GH) treatment. A positive growth response to sustained-release GH implants was found in two wild strains (Namsen and Imsa) as well as one domesticated strain (AquaGen). The data revealed that the growth-selected AquaGen strain has further growth potential, however, a stronger growth response was observed in the wild strains which outgrew the domesticated strain after GH treatment. These observations suggest that some growth potential may have been lost during the selection for rapid growth in the AquaGen strain. In September, the parr were GH implanted and in December sampled for plasma GH and insulin-like growth factor I (IGF-I) levels, liver, muscle and gill GH receptor, IGF-I mRNA levels, gill Na+,K+-ATPase activity, muscle and liver lipid content and body silvering. Low temperature and seasonal growth cessation probably explains the relatively limited GH effects found. Body silvering in all strains was positively correlated to size. GH increased IGF-I plasma levels in the Namsen strain inspite of liver IGF-I mRNA levels being lower in GH-treated fish.

The present study aimed to investigate the morphological and genetic differentiation of lowland and montane populations of the Pieris napi species complex in Norway and to make inferences about the subspecific status of Pieris napi adalwinda and Pieris napi napi. We measured 22 morphological characters on 228 individuals from eight populations in Central Norway (20–1100 m a.s.l.). In addition, lowland and mountain animals were reared at a high altitude locality. Half the animals from either locality were reared on mountain plant, and the other half on a lowland plant. Finally, a fragment of the mitochondrial cytochrome b gene was sequenced for individuals from Central and South-eastern Norway and Germany. Principal component analysis of morphological characters showed a zone of abrupt change from lowland to mountain morphological character states between populations at 506 m and 730 m a.s.l., respectively. The transplant experiment showed that the morphological differences have a genetic basis and that food plants have no impact on morphology. Limited, but significant, molecular genetic differentiation was found between lowland and mountain animals, but the phylogenetic analysis, however, showed that the lowland form (P. n. napi) is paraphyletic and the montane form (P. n. adalwinda) is monophyletic. Further study is required before taxonomic recognition can be applied. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 92, 727–745.

Males and females share many traits that have a common genetic basis, however selection on these traits often differs between the sexes leading to sexual conflict. Under such sexual antagonism, theory predicts the evolution of genetic architectures that resolve this sexual conflict. Yet, despite intense theoretical and empirical interest, the specific genetic loci behind sexually antagonistic phenotypes have rarely been identified, limiting our understanding of how sexual conflict impacts genome evolution and the maintenance of genetic diversity. Here, we identify a large effect locus controlling age at maturity in 57 salmon populations, an important fitness trait in which selection favours earlier maturation in males than females, and show it is a clear example of sex dependent dominance reducing intralocus sexual conflict and maintaining adaptive variation in wild populations. Using high density SNP data and whole genome re-sequencing, we found that vestigial-like family member 3 (VGLL3) exhibits sex-dependent dominance in salmon, promoting earlier and later maturation in males and females, respectively. VGLL3, an adiposity regulator associated with size and age at maturity in humans, explained 39.4% of phenotypic variation, an unexpectedly high effect size for what is usually considered a highly polygenic trait. Such large effects are predicted under balancing selection from either sexually antagonistic or spatially varying selection. Our results provide the first empirical example of dominance reversal permitting greater optimisation of phenotypes within each sex, contributing to the resolution of sexual conflict in a major and widespread evolutionary trade-off between age and size at maturity. They also provide key empirical evidence for how variation in reproductive strategies can be maintained over large geographical scales. We further anticipate these findings will have a substantial impact on population management in a range of harvested species where trends towards earlier maturation have been observed

The extensive phenotypic polymorphism in the European whitefish has triggered evolutionary research in order to disentangle mechanisms underlying diversification. To illuminate the ecological distinctiveness in polymorphic whitefish, and evaluate taxonomic designations, we studied nine Norwegian lakes in three watercourses, which each harboured pairs of divergent whitefish morphs. We compared the morphology and life history of these morphs, documented the extent of genetic differentiation between them, and contrasted the niche use of sympatric morphs along both the habitat and resource axes. In all cases, sympatric morphs differed in the number of gill rakers, a highly heritable trait related to trophic utilization. Individual growth rate, age and size at maturity, diet and habitat use also differed between morphs within lakes, but were remarkably similar across lakes within the same morph. Microsatellite analyses confirmed for all but one pair that sympatric morphs were significantly genetically different, and that similar morphs from different lakes likely have a polyphyletic origin. These results are most compatible with the process of parallel evolution through recurrent postglacial divergence into pelagic and benthic niches in each of these lakes. We propose that sparsely and densely rakered whitefish sympatric pairs may be a likely case of ecological speciation, mediated in oligotrophic lakes with few trophic competitors.

Hindar, K., Fleming, I. A., McGinnity, P., and Diserud, O. 2006. Genetic and ecological effects of salmon farming on wild salmon: modelling from experimental results. � ICES Journal of Marine Science, 63: 1234e1247. Cultured salmonids are released or escape into the wild in large numbers and may make up significant proportions of wild salmonid populations in fresh- and saltwater, causing considerable concern for the fitness and productivity of these populations. This paper focuses on the effects of escaped farmed Atlantic salmon (Salmo salar) on wild salmon. Farmed salmon have been under artificial selection for growth and other economically important traits for 30 years and are genetically different in their origin at the molecular and quantitative genetic levels. Escaped farmed salmon spawn in the wild with limited success. Their offspring outgrow those of wild origin but suffer higher mortality. Whole-river experiments in Ireland and Norway have shown that the lifetime success of farmed salmon is reduced relative to wild salmon. Based on data from these experiments, we model the future of wild salmon populations experiencing invasions of escaped farmed salmon. Simulations with a fixed intrusion rate of 20% escaped farmed salmon at spawning suggest that substantial changes take place in wild salmon populations within ten salmon generations (w40 years). Low-invasion scenarios suggest that farmed offspring are unlikely to become established in the population, whereas high-invasion scenarios suggest that populations are eventually mixtures of hybrid and farmed descendants. Recovery of the wild population is not likely under all circumstances, even after many decades without further intrusion. Managers of wild salmon will have difficulty in obtaining broodstock of the original wild population after a few generations of high intrusion. We conclude that further measures to reduce escapes of farmed salmon and their spawning in wild populations are urgently needed.