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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.

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.

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.

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.

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.

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.

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.

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.

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.

We compared mitochondrial DNA and gill-raker number variation in populations of the European whitefish Coregonus lavaretus (L.) species complex to illuminate their evolutionary history, and discuss mechanisms behind diversification. Using single-strand conformation polymorphism (SSCP) and sequencing 528 bp of combined parts of the cytochrome oxidase b (cyt b ) and NADH dehydrogenase subunit 3 (ND3) mithochondrial DNA (mtDNA) regions, we documented phylogeographic relationships among populations and phylogeny of mtDNA haplotypes. Demographic events behind geographical distribution of haplotypes were inferred using nested clade analysis (NCA) and mismatch distribution. Concordance between operational taxonomical groups, based on gill-raker numbers, and mtDNA patterns was tested. Three major mtDNA clades were resolved in Europe: a North European clade from northwest Russia to Denmark, a Siberian clade from the Arctic Sea to southwest Norway, and a South European clade from Denmark to the European Alps, reflecting occupation in different glacial refugia. Demographic events inferred from NCA were isolation by distance, range expansion, and fragmentation. Mismatch analysis suggested that clades which colonized Fennoscandia and the Alps expanded in population size 24 500–5800 years before present, with minute female effective population sizes, implying small founder populations during colonization. Gill-raker counts did not commensurate with hierarchical mtDNA clades, and poorly with haplotypes, suggesting recent origin of gill-raker variation. Whitefish designations based on gill-raker numbers were not associated with ancient clades. Lack of congruence in morphology and evolutionary lineages implies that the taxonomy of this species complex should be reconsidered.

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.

Fluctuating asymmetry, the random departure from perfect bilateral symmetry, is a common measure of developmental instability that has been hypothesized to be inversely correlated with heterozygosity. Although this claim has been widely repeated, several studies have reported no such association. Therefore, we test the generality of this association, using meta-analysis, by converting test statistics for the relationship between heterozygosity (H) and fluctuating asymmetry (FA) into a common effect size, the Pearson's product-moment correlation coefficient. We have analysed a database containing 41 studies with a total of 118 individual samples. Overall we found an unweighted mean negative effect size; r=-0.09 (i. e. a negative correlation between H and FA). Significant heterogeneity in effect size was mainly caused by a difference between ectothermic and endothermic animals, and to a lesser extent by the use of different study designs (i.e. within-population vs. among-populations). Mean effect size for endothermic animals was positive and significantly different from the mean effect size for ectothermic animals. Only for within-population studies of ectothermic animals did we find a significantly negative effect size (r=-0.23 +/- 0.09). The distribution of effect sizes in relation to sample size provided little evidence for patterns typical of those produced by publication bias. Our analysis suggests, at best, only a weak association between H and FA, and heterozygosity seems to explain only a very small amount of the variation in developmental instability among individuals and populations (r2=0.01 for the total material).

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.

Arctic charr, Salvelinus alpinus (L.), commonly exhibits two coexisting morphotypes, dwarf and normal charr, which are characterized by differences in adult body size and colouration. We tested whether or not the morphotypic differences were genetically determined in rearing experiments with offspring of the two morphs and of their crosses. The experiments suggest that this ecological polymorphism in Arctic charr is largely environmentally determined. When reared under similar conditions, offspring of each of the two morphs differed little in size at the same age, and they had the same early developmental rate and maturation pattern. Moreover, the presence of parr marks along the flanks of the fish, one characteristic of dwarf charr, depended on body size and not on parental morph. Genetic differences between the morphs were suggested for growth rate during the second year of life, and for jaw morphology. Comparisons between charr life histories in captivity and in the wild suggest that ecological polymorphism in Arctic charr is chiefly a result of variation in growth conditions between different habitats.

The genetic diversity of metapopulations is influenced not only by the effective sizes (N e ) of individual subpopulations, but also by the total effective size of the metapopulation (meta-N e ). We estimated meta-N e of four neighbouring Atlantic salmon populations connected by gene flow using genetic estimates of subpopulation N e s and migration rates derived from capture–recapture data. The $$ meta{\hbox{-}}\hat{N}_{e} $$ was lower than the sum of $$ \hat{N}_{e} $$ s of the subpopulations, suggesting that genetic diversity harboured by the four river salmon metapopulation is lower than what would have been expected by viewing individual subpopulations separately. In addition, $$ meta{\hbox{-}}\hat{N}_{e} $$ was found to be sensitive to changes in $$ \hat{N}_{e} $$ of the subpopulation from which net emigration rate was largest, so as that the genetic diversity of the metapopulation would be best preserved by avoiding any reductions in N e of this subpopulation. Yet, this subpopulation is the one that has historically—and still is—experiencing the highest exploitation rate in the metapopulation system.

The role of competition in a lacustrine community of two salmonid species, cutthroat trout Oncorhynchus clarki and Dolly Varden char Salvelinus malma, was studied in three coastal British Columbia lakes Habitat use by the species alone (allopatric) and in coexistence with each other (sympatric) was investigated by gill netting at 0-40 m depth contours (surface to bottom) so that several habitats (littoral, epipelagic. pelagic, epibenthic) were sampled From June to October, trout used mainly littoral and epipelagic habitats in sympatry and allopatry Char used all habitats in allopatry. and deep habitats (pelagic, epibenthic) not frequented by trout in sympatry The two species were thus spatially segregated with depth in sympatry Diel (day, night) and seasonal changes (spring, summer, autumn) in habitat use were not pronounced The shift in habitat use by experimentally allopatric char but not trout suggests that the effects of competition between sympatric trout and char for habitat resources are greater on the char

This paper addresses the genetic consequences of aquaculture on natural fish populations. The study is motivated by rapidly increasing numbers of intentionally and accidentally released fish and is based on empirical observations reported in the literature. A wide variety of outcomes, ranging from no detectable effect to complete introgression or displacement, has been observed following releases of cultured fish into natural settings. Where genetic effects on performance traits have been documented, they always appear to be negative in comparison with the unaffected native populations. These findings are consistent with theoretical considerations of the implications of elevated levels of gene flow between cultured and locally adapted natural populations; they raise concerns over the genetic future of many natural populations in the light of increasing numbers of released fish. Strategies for the genetic protection of native populations from the effects of aquaculture are outlined including more secure containment, the use of sterilized fish, and modifying the points of rearing and release. We recommend strong restrictions on gene flow from cultured to wild populations and effective monitoring of such gene flow.

We present an application of Bayesian hierarchical modelling of stock–recruitment (SR) relationships aiming at estimating Biological Reference Points (BRP) for European Atlantic salmon (Salmo salar) stocks. The structure of the hierarchical SR model developed distinguishes two nested levels of randomness, within-river and between rivers. It is an extension of the classical Ricker model, where the parameters of the Ricker function are assumed to be different between rivers, but drawn from a common probability distribution conditionally on two covariates: river size and latitude. The output of ultimate interest is the posterior predictive distribution of the SR parameters and their associated BRP for a new river with no SR data. The flexible framework of the Bayesian hierarchical SR analysis is a step towards making the most comprehensive use of detailed stock monitoring programs for improving management advice. Posterior predictive inferences may be imprecise due to the relative paucity of information introduced in the analysis compared to the variability of the stochastic process modeled. Even in such cases, direct extrapolation of results from local data-rich stocks should be dismissed as it can lead to a major underestimation of our uncertainty about management parameters in sparse-data situations. The aggregation of several stocks under a regional complex improves the precision of the posterior predictive inferences. When several stocks are managed jointly, even imprecise knowledge about each component of the aggregate can be valuable. The introduction of covariates to explain between stock variations provides a significant gain in the precision of the posterior predictive inferences. Because we must be able to measure the covariates for all the stocks of interest, i.e. mostly sparse-data cases, the number of covariates which can be used in practice is limited. The definition of the assemblage of stocks which we model as exchangeable units, conditionally on the covariates, remains the most influential choice to be made when attempting to transfer information from data-rich to sparse-data situations.

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.

The aim of this paper is to contribute to the development of strategies for assessing ecological impacts of transgenic tree species. Norway spruce (Picea abies (L.) Karst.) plays a key role in boreal ecosystems from Norway to Siberia and is also an economically very important species. A hypothetical release of transgenic spruce is selected for this case-study exercise, modified from [1].

The farming of salmon and other marine finfish in open net pens continues to increase along the world's coastlines as the aquaculture industry expands to meet human demand. Farm fish are known to escape from pens in all salmon aquaculture areas. Their escape into the wild can result in interbreeding and competition with wild salmon and can facilitate the spread of pathogens, thereby placing more pressure on already dwindling wild populations. Here we assess the ecological, genetic, and socioeconomic impacts of farm salmon escapes, using a risk-assessment framework. We show that risks of damage to wild salmon populations, ecosystems, and society are large when salmon are farmed in their native range, when large numbers of salmon are farmed relative to the size of wild populations, and when exotic pathogens are introduced. We then evaluate the policy and management options for reducing risks and discuss the implications for farming other types of marine finfish.

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

Resource utilization by cutthroat trout (CT) and Dolly Varden charr (DV) was studied 8 years after experimental transfers from sympatry had established reproducing allopatric populations in two nearby fishless lakes. Allopatric DV significantly increased their utilization of shallow-dwelling zoobenthos, and increased their vertical distribution in comparison to that in sympatry. In contrast, allopatric CT showed little change in the proportions of major prey types utilized, and, if anything, restricted their vertical distribution in comparison to that in sympatry. The results can be explained by the hypothesis that the resource use of DV is strongly influenced by interspecific competition from CT, whereas CT largely remains unaffected by this interaction. An alternative hypothesis, that lake differences can explain the differences in resource use between sympatry and allopatry, was evaluated by comparing food resource availability and other biotic and abiotic characteristics of the three study lakes. None of these could account for the shift in resource use by DV between sympatry and allopatry, but lake differences may explain why allopatric CT showed a restricted habitat use in comparison with their sympatric donor stock. The results of this whole-lake transfer experiment are consistent with earlier reported field and laboratory studies, and suggest that the aggressive dominance of CT is the most important mechanism by which DV are displaced from littoral and near-surface habitats in sympathy with CT.

Reproductive potentials of transplanted curthroat trout (Salmo clarki) and Dolly Varden charr (Salvelinus malma) and of their donor stocks were estimated from life history data. We found good agreement between observed and predicted age at maturity in all populations, and cannot reject the hypothesis that the fish matured at the age maximizing the overall lifetime reproductive potential (\(\Delta \mu _{\iota } = 0 = In \left( {{{a_i^p } \mathord{\left/ {\vphantom {{a_i^p } {a_i^L }}} \right. \kern-\nulldelimiterspace} {a_i^L }}} \right) + A_i + {{B_i } \mathord{\left/ {\vphantom {{B_i } T}} \right. \kern-\nulldelimiterspace} T}\)). Our estimates were insensitive to probable variations in female fecundity, adult mortalityrate and maximum body length. Small changes in either juvenile mortality-rate or individual growth-rate had marked effects on the estimations, as did changes in the Malthusian parameter (r). Three alternative mechanistic explanations of how age at maturity is determined could be rejected. We suggest that fish are able to adjust the maturity age non-genetically to changes in growth-rate, and that temporal variations in juvenile survival-rate allow coexistence of genotypes coding for different ages at maturity at the same growth-rate.