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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

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.

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.

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.

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.

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.

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.

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.

Electrophoretic studies of proteins remain a primary source of insight into genetic diversity in many species including the Atlantic salmon Salmo salar, one of the most culturally and economically important fish species of the North Atlantic region. Since 1966, >350 scientific papers on protein variation have been published encompassing 25 000+ salmon from over 400 locations in >200 river systems across the species' distribution. Variation has been detected at 30% of the 110 protein loci screened, though most studies examine

Combining morphological and genetic analysis, we compared patterns of diversification within and between morphs among sympatric European whitefish (Coregonus lavaretus L.) populations in Lake Femund, Norway. Seven external populations, from potential colonization routes into Lake Femund were included. We found that deep-, shallow-, river- and bay spawning populations are distinct morphs in Lake Femund. Within morphs, populations range from being similar genetically (Fst=0-0.005) among deep-spawning populations to being highly differentiated (Fst=0.153) between bay-spawning populations. Between morphs, genetic differences ranged from a low (Fst=0.008-0.022) between deep- and shallow-spawning populations to high difference (Fst=0.125-0.143) between shallow- and bay-spawning populations. A higher proportion of molecular variance was seen among (3.9%) than within morphs (2.8%). The adaptive gene combinations behind the four morphs seem to have originated within the lake, although the lake could have been colonized from more than one source population.

Mjelnerad, I. B., Refseth, U. H., Karlsen, E., Balstad, T., Jakobsen, K. S. and Hindar, K. 1997. Genetic differences between two wild and one farmed population of Atlantic salmon (Salmo salar) revealed by three classes of genetic markers. Hereditas 127: 239-248. Lund, Sweden. ISSN 0018-0661. Received April 7, 1997. Accepted August 21, 1997 Genetic diversity within and between two wild and one farmed population of Atlantic salmon was estimated by 12 variable enzyme loci, three single locus- and one multilocus DNA minisatellite probe. The farmed salmon were fifth-generation fish from one of the principal commercial strains in Norway and the wild salmon were from the rivers Numedalslagen and Tana, Norway. All three classes of markers detected significant differentiation between the populations, with the farmed population being genetically most divergent. The farmed fish showed less genetic variability than the wild populations, as all techniques revealed a lower (14 %-45 %) number of variable bands/alleles in this group. However, only multilocus DNA fingerprinting detected a significantly lower level of heterozygosity within the farmed population. Estimates of average heterozygosity within populations were almost identical for single locus and multilocus minisatellites (0.558 and 0.548, respectively), which were more than three times higher than for polymorphic allozymes (0.162). Estimates of interpopulation genetic differentiation, however, gave highly concordant results between the allozymes and minisatellites (Fst range: 0.106-0.135). Our results show that fifth generation farmed Atlantic salmon differ significantly from wild salmon in loci others than those chosen for selection in the breeding program. The study also suggests that the choice of genetic markers for studies of Atlantic salmon depends on the aim of the study (within- versus between-population variability).

Management of a group of Atlantic salmon (Salmo salar) populations that are harvested together in the ocean, but separately in freshwater, is looked at from a genetic perspective. A model that estimates total effective population size from local effective population sizes and migration patterns is applied to a system of ten salmon populations in the Sognefjorden district, western Norway. This population system is dominated numerically by the River Lærdalselva population, which may act as a source of migrants into nine smaller populations in a “source–sink” metapopulation. The total effective population size of this system is to a large extent dependent on the effective population size of the Lærdalselva population, but the contribution per spawner to the total effective population size is greater for a fish from the smaller populations than for a fish from Lærdalselva. The results are discussed in light of conservation genetic theory, and empirical results on the fitness consequences of loss of genetic variation in salmonids. The genetic consequences of harvesting need to be assessed both at the levels of local populations and the metapopulation.

A numerical method for computing the eigenvalue variance effective size of a subdivided population connected by any fixed pattern of migration is described. Using specific examples it is shown that total effective size of a subdivided population can become less than the sum of the subpopulation sizes as a result of directionalities in the pattern of migration. For an extension of the model with threshold harvesting and local deterministic logistic population dynamic we consider the problem of maximizing the total harvesting yield with constraints on the total effective size. For some simple source-sink systems and more complicated population structures where subpopulations differ in their degree of isolation, it is shown to be optimal, for a given total effective size, to raise the harvesting thresholds relatively more in small and in isolated populations. Finally, we show how the method applies to populations which are supplemented, either intentionally or unintentionally. It is shown that the total effective size can be reduced by several orders of magnitude if the captive component of a population is much smaller than the wild component, even with symmetric backward migration.

A model of the migration pattern in a metapopulation of sea beet (Beta vulgaris L. ssp. maritima), based on the continuous distributions of seed and pollen movements, is fitted to gene frequency data at 12 isozyme and RFLP loci by maximum likelihood by using an approximation of the simultaneous equilibrium distribution of the gene frequencies generated by the underlying multivariate stochastic process of genetic drift in the population. Several alternative restrictions of the general model are fitted to the data, including the island model, a model of complete isolation, and a model in which the seed and pollen dispersal variances are equal. Several likelihood ratio tests between these alternatives are performed, and median bias in the estimated parameters is corrected by using parametric bootstrapping. To assess the fit of the selected model, the predicted covariances are compared with covariances computed from the data directly. The dependency of estimated parameters on the ratio between effective and absolute subpopulation sizes, which is treated as a known parameter in the analysis, is also examined. Finally, we note that the data also appear to contain some information about this ratio.

Eggs and alevins were collected from 36 redds in the River Vosso in late March 1996. The redds had been made by 20 individual female Atlantic salmon and 12 female brown trout. Species-specific allozyme variation was used to distinguish trout from salmon and egg size and pigment analyses were used to distinguish farmed from wild salmon females. Nine (45%) of the 20 female salmon spawners in the sample were of confirmed farmed origin, because their offspring contained synthetic astaxanthin which is an additive to commercial fish feed. Most of the remaining female salmon were also likely to have been farmed escapees because only about half of the actual farmed spawners can be identified by their astaxanthin content due to intake of carotenoids from natural food sources. The estimated peak spawning for both confirmed and putative farmed females was 32 d earlier than peak spawning of wild females. Egg survival was high and similar to previous estimates for wild and farmed salmon in the River Vosso. Based on the astaxanthin content in sampled eggs and the time of peak spawning it is concluded that most Atlantic salmon fry that hatched in the River Vosso in 1996 were produced by escaped farmed females. The frequency of redds made by farmed females was in accordance with their estimated representation (81%) in the population of spawners during autumn 1995.

This work forms part of the SALSEA-Merge research project (Project No. 212529) and was funded by the European Union under theme six of the 7th Framework programme, Ellis, J.S., Gilbey, J., Armstrong, A., Balstad, T., Cauwelier, E., Cherbonnel, C., Consuegra, S., Coughlan, J., Cross, T.F., Crozier, W., Dillane, E., Ensing, D., de Leániz, C.G., García-Vázquez, E., Griffiths, A.M., Hindar, K., Hjorleifsdottir, S., Knox, D., Machado-Schiaffino, G., McGinnity, P., Meldrup, D., Nielsen, E.E., Olafsson, K., Primmer, C.R., Prodohl, P., Stradmeyer, L., Vähä, J.-P., Verspoor, E., Wennevik, V., Stevens, J.R.

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 loci underlying 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 Atlantic salmon (Salmo salar), 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 that reduces intralocus sexual conflict and maintains adaptive variation in wild populations. Using high-density single nucleotide polymorphism data across 57 wild populations and whole genome re-sequencing, we find that the vestigial-like family member 3 gene (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% of phenotypic variation, an unexpectedly large proportion 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 allowing greater optimization 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 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.

Farm Atlantic salmon escape and invade rivers throughout the North Atlantic annually, which has generated growing concern about their impacts on native salmon populations. A large–scale experiment was therefore undertaken in order to quantify the lifetime success and interactions of farm salmon invading a Norwegian river. Sexually mature farm and native salmon were genetically screened, radio tagged and released into the River Imsa where no other salmon had been allowed to ascend. The farm fishes were competitively and reproductively inferior, achieving less than one–third the breeding success of the native fishes. Moreover, this inferiority was sex biased, being more pronounced in farm males than females, resulting in the principal route of gene flow involving native males mating with farm females. There were also indications of selection against farm genotypes during early survival but not thereafter. However, evidence of resource competition and competitive displacement existed as the productivity of the native population was depressed by more than 30%. Ultimately, the lifetime reproductive success (adult to adult) of the farm fishes was 16% that of the native salmon. Our results indicate that such annual invasions have the potential for impacting on population productivity, disrupting local adaptations and reducing the genetic diversity of wild salmon populations.

Ecologically and morphologically polymorphic species pose several difficulties for conservation genetics. First, the genetic relationships among the different phenotypes must be established. Second, the ecological factors maintaining the polymorphism must be understood. Third, intervention to protect threatened populations must integrate population genetic and ecological considerations. Here, I have discussed these issues based on information about the biology and management of salmonid fishes in particular. A number of salmonid species contain coexisting phenotypes which differ in life history, habitat use, and morphology. Population genetic studies of these species typically show that there is less genetic differentiation between coexisting life-history types than between the same life-history type sampled from geographically separate localities. The life-history polymorphisms appear to be one way by which salmonid populations adapt to heterogeneous environments. How can this genetic and ecological knowledge be integrated in the conservation of polymorphic populations? First, anthropogenic activities that lead to the loss of genetic variation within and between populations should be discouraged. Second, anthropogenic activities should be evaluated with respect to their effect on the life history polymorphism itself, even though this aspect is less well understood. Knowledge about the evolutionary response of natural populations to novel selection regimes may lead to a more detailed view about how populations should be managed from the perspective of conservation genetics.

The systematica of coexisting morphotypes of Arctic charr, Salvelinus alpinus, has been a matter of dispute ever since the days of Linnaeus. Widespread allelic variation at an esterase locus has led some investigators to propose that the morphotypes reflect a complex of at least three sibling species. We tested this hypothesis by examining 42 electrophoretically detectable loci in natural and transplanted charr populations from 15 localities in S Norway. The absolute values of Nei's genetic distance between morphotypes and populations are small (typically in the order of 0.001), and morphotype changes may occur without accompanying changes in frequencies of esterase alleles. Differentiation among localities explains far more of the total gene diversity than differences between morphotypes in the four cases of naturally occurring sympatric morphotypes examined. The data are consistent with an intraspecific population structuring based on locality, and the multiple species hypothesis is rejected.

In this paper, we investigate the reproductive strategy maintaining dwarf and normal phenotypes of an Arctic charr (Salvelinus alpinus) population. Both morphs occurred together in the spawning area, but the peak abundance of dwarf spawners was significantly deeper, and later in the spawning period, than normal spawners. Both phenotypes attained sexual maturity at the same age and did not differ in length-specific fecundity or egg diameter. Our data support the hypothesis that the females matured sexually at the age that maximizes their fitness within the constraints imposed by growth and survival. The two female morphs appeared not to have equal fitness; these differences may be due to random events. The males were more heterogeneous by size than the females when maturing sexually. This may be due to intrasexual competition between males making large males the principal spawners. The dwarf males may circumvent the effects of intrasexual competition by mimicking immature fish, sneak at the redds of normal females, and participate in the spawning acts of normal charr pairs. Also, they may fertilize the eggs of dwarf females spawning in deeper areas.The two charr morphs developed from a uniform young phenotype (parr). The dwarf spawners were precocious individuals maturing sexually in their parr stage, whereas normal spawners had a color shift, analogous to smoltification in anadromous charr, before they attained sexual maturity. The different spawning coloration of the two morphs may be due to sexual selection.Key words: spawning, growth, fecundity, mortality, sexual selection, maturing strategy

The aim of the present study was to test possible habitat and food segregation between two charr morphs in Vangsvatnet Lake. The charr population of Vangsvatnet consists of one pale phenotype with parr marks along the flanks and poorly developed spawning coloration (dwarf charr), and another phenotype with silvery flanks in nonbreeding condition and bright red spawning colors (normal charr). The habitus of the two morphs indicated that they were adapted to different niches during the growth season. The analyses of distribution and food showed that there was marked habitat and food segregation between the two morphs during summer, when dwarf charr dwelled deep-benthic and normal charr roamed in the limnetic zone. The segregation broke down in periods of food abundance, indicating that the habitat segregation was due to intraspecific competition for food. A comparison of charr morphs of Vangsvatnet with the nearby Lønavatnet Lake suggested that the number of charr morphs is adapted to local environmental conditions, among which lake morphology, food availability, and other fish species are important. We hypothesize that the number of charr morphs within a locality depends on the number of available niches during the growth season.Key words: polymorphism, camouflage, distribution, ontogeny, intra- and inter-specific competition