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In this study, radio telemetry was used to examine the upstream spawning migration behaviour of anadromous brown trout (sea trout), Salmo trutta L., in a boreal river system, the River Isojoki, western Finland. The aim was to study the movement activity and migration characteristics of trout during the upstream spawning migration, as well as to locate the important spawning habitats and study the spawning characteristics. Furthermore, the authors analysed how flow conditions and a hydropower dam, with adjacent fishways, affected the upstream spawning migration. Tagged trout spawned in both the main stem and four tributaries, with spawning taking place from early October to November. The movement activity of radio-tagged trout was influenced by a hydropower dam (Perus dam), with spring migrators spending prolonged periods at the dam area, postponing the migration upstream. Flow conditions affected the total time spent at the dam area, as well as the movement activity in the free-flowing sections above the dam, with increasing flow stimulating activity. In addition, time of river ascent and location of spawning area had a significant effect on the movement activity of tagged trout. These results are further evidence that synergistic effects of flow and migratory obstacles can negatively influence migrations of anadromous fish, regardless of constructed fishways. The management of flow regimes and the efficiency of fishways are vital, as climate change will likely influence the flow and increase the water temperature of boreal river systems, further aggravating issues caused by obstacles.

The spawning and egg development of invasive pink salmon Oncorhynchus gorbuscha were investigated in the large River Teno in the Barents Sea area where they spawned for the first time on a large scale in 2021. The spawning period started in early August and egg development was rapid. All eggs were eyed by mid-September and the first juveniles hatched in late September. In early October most eggs had hatched. Degree-days in water temperature suggested that egg deposition had mostly taken place in early August. Early egg development is discussed in relation to possible consequences for survival.

Understanding the drivers of evolution is a fundamental aim in biology. However, identifying the evolutionary impacts of human activities is challenging because of a lack of temporal data and limited knowledge of the genetic basis of most traits. Here, we identify the drivers of evolution toward maturity at an earlier age in Atlantic salmon through two types of fisheries-induced evolution acting in opposing directions: an indirect effect linked with harvest of a salmon prey species (capelin) at sea (selection against late maturation) and a direct effect due to net fishing in rivers (selection against early maturation). Because capelin are harvested as an aquaculture feed protein source, we hereby determine an indirect path by which salmon aquaculture may influence wild salmon populations.

This is the peer reviewed version of the following article: "Circumpolar patterns of Arctic freshwater fish biodiversity: A baseline for monitoring", which has been published in final form at https://doi.org/10.1111/fwb.13405. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions Climate change, biological invasions, and anthropogenic disturbance pose a threat to the biodiversity and function of Arctic freshwater ecosystems. Understanding potential changes in fish species distribution and richness is necessary, given the great importance of fish to the function of freshwater ecosystems and as a resource to humans. However, information gaps limit large‐scale studies and our ability to determine patterns and trends in space and time. This study takes the first step in determining circumpolar patterns of fish species richness and composition, which provides a baseline to improve both monitoring and conservation of Arctic freshwater biodiversity. Information on species presence/absence was gathered from the Circumpolar Biodiversity Monitoring Program's Freshwater Database and used to examine patterns of freshwater fish γ‐, α‐, and β‐diversity across 234° of longitude in the Arctic. The metrics of diversity provided information on species richness and composition across hydrobasins, ecoregions, and Arctic zones. Circumpolar patterns of fish species biodiversity varied with latitude, isolation, and coarse ecoregion characteristics; patterns were consistent with historic and contemporary barriers to colonisation and environmental characteristics. Gamma‐diversity was lower in the high Arctic compared to lower latitude zones, but α‐diversity did not decrease with increasing latitude below 71°N, reflecting glacial history. Alpha‐diversity was reduced to a single species, Arctic charr Salvelinus alpinus, in ecoregions above 71°N, where γ‐diversity was the lowest. Beta‐diversity indicated little variation in the composition and richness of species across the High Arctic; at lower latitudes, ecoregions contained more species, although species composition turned over across large spatial extents. In an analysis of five ecoregions in the circumpolar Arctic, physical isolation, and ecoregion area and topography were identified as strong drivers of γ‐, α‐, and β‐diversity. Physical isolation reduced the γ‐ and α‐diversity, and changes in β‐diversity between adjacent locations were due mainly to losses in species richness, rather than due to differences in species composition. Heterogeneity of habitats, environmental gradients, and geographic distance probably contributed to patterns of fish dissimilarity within and across ecoregions. This study presents the first analysis of large‐scale patterns of freshwater fish biodiversity in the circumpolar Arctic. However, information gaps in space, time, and among taxonomic groups remain. Future inclusion of extensive archive and new data will allow future studies to test for changes and drivers of the observed patterns of biodiversity. This is important given the potential impacts of ongoing and accelerating climate change, land use, and biotic exchange on Arctic fish biodiversity.

In hydropeaking rivers, flow regulation typically follows demands in electricity consumption. One hundred and twenty one adult salmon were tagged with radio transmitters to study their spawning run migration patterns in hydropeaking conditions. The fish were released in small groups into the rivers Kemijoki and Iijoki, in Finland. Typically, salmon made subsequent up‐ and downstream movements ascending upstream to the tailrace of the power station and then descending again downstream to lower water velocities. The rate of these migration attempts was higher in mid‐summer and at relatively high flows. On an hourly basis, the pattern of migration attempts followed a trend of increasing attempts at dawn and higher discharges and a decreasing trend towards dusk and low flows. It was concluded that day length and discharge were the most important environmental factors, while temperature had less effect on the pattern of migration attempts.

In species with complex life cycles, life history theory predicts that fitness is affected by conditions encountered in previous life history stages. Here, we use a four-year pedigree to investigate if time spent in two distinct life history stages has sex-specific reproductive fitness consequences in anadromous Atlantic salmon (Salmo salar). We determined the amount of years spent in fresh water as juveniles (freshwater age, FW, measured in years), and years spent in the marine environment as adults (sea age, SW, measured in sea winters) on 264 sexually mature adults collected on a river spawning ground. We then estimated reproductive fitness as the number of offspring (reproductive success) and the number of mates (mating success) using genetic parentage analysis (>5000 offspring). Sea age is significantly and positively correlated with reproductive and mating success of both sexes whereby older and larger individuals gained the highest reproductive fitness benefits (females: 62.2% increase in offspring/SW and 34.8% increase in mate number/SW; males: 201.9% offspring/SW and 60.3% mates/SW). Younger freshwater age was significantly related to older sea age and thus increased reproductive fitness, but only among females (females: -33.9% offspring/FW and -32.4% mates/FW). This result implies that females can obtain higher reproductive fitness by transitioning to the marine environment earlier. In contrast, male mating and reproductive success was unaffected by freshwater age and more males returned at a younger age than females despite the reproductive fitness advantage of later sea age maturation. Our results show that the timing of transitions between juvenile and adult phases has a sex-specific consequence on female reproductive fitness, demonstrating a life-history trade-off between maturation and reproduction in wild Atlantic salmon.

The River Teno is the most visited river for recreational wild salmon fishing in Finland and is one of the most productive wild salmon rivers in Northern Europe. Despite the popularity of recreational fishing in the area, no estimates are available for its economic value. This study uses a travel cost recreation demand model to estimate the recreational value of salmon fishing in the Teno river area. Following a two-step estimation procedure outlined by McConnell, we show that on-site time per trip is endogenous. The estimated consumer surplus per trip ranges from 235 to 338 euros. The estimated total recreational value of salmon fishing in the area is 2.6–3.7 million euros. Also, according to the empirical results, the number of fishing trips per angler is strongly affected by the angler’s previous salmon catch in the Teno river area, which underlines the importance of the proper and sustainable management of recreational salmon fisheries.

Connectivity problems in fish migration in regulated rivers have been widely studied, but few studies have rigorously compared parallel migration success between regulated and free-flowing rivers. Here, survival and migration speed of downstream migrating radio-tagged Atlantic salmon (Salmo salar) smolts were studied in two large neighboring rivers in the northern Baltic Sea area: one without and one with dams. Both rivers have a free-flowing upper section, where the survival and migration speed of salmon smolts were similar. Survival along the lower section of the free-flowing river was about six times higher than in the lower part of the regulated river with five hydropower plants. Migration speed of smolts was also significantly faster in the river without dams. These severe problems in downstream connectivity in the regulated river pose challenging tasks for restoration of salmon populations.

Atlantic salmon (Salmo salar L.) display significant variation in life history traits, including migration patterns and age at maturity. Hatchery rearing has been shown to affect the life history, and rearing-induced changes may include unfavourable consequences, e.g. shortened sea migration period and smaller size at maturity. We report on a new phenomenon of life history of reared Atlantic salmon in the Baltic Sea area: small-sized salmon returning to freshwater only a few months after release as smolts. These “one-sea-summer (1SS)” salmon were ca. 35 cm in length and weighed ca. 400 g, being clearly larger than smolts, but substantially smaller than one-sea-winter (1SW) salmon from the same cohorts. Almost all 1SS salmon were mature males and, at release, had been longer than the overall mean. Stable isotope analysis suggested that the 1SS salmon had been feeding in different sea areas than 1SW and multi-sea-winter salmon, likely in nearby Bothnian Bay, which is typically not a salmon feeding area. If an increasing proportion of the released salmon are not undertaking a normal marine migration (≥1SW) and are returning to estuaries and rivers as 1SS fish, the success and profitability of the reared salmon releases will decline even more than the reduced post-smolt survival is suggesting. We suggest that alternative rearing practices (e.g. enriched rearing environments and advanced diets) should be considered in hatchery production for shaping the reared smolts towards a closer resemblance to wild smolts.

Co-inheritance in life-history traits may result in unpredictable evolutionary trajectories if not accounted for in life-history models. Iteroparity (the reproductive strategy of reproducing more than once) in Atlantic salmon (Salmo salar) is a fitness trait with substantial variation within and among populations. In the Teno River in northern Europe, iteroparous individuals constitute an important component of many populations and have experienced a sharp increase in abundance in the last 20 years, partly overlapping with a general decrease in age structure. The physiological basis of iteroparity bears similarities to that of age at first maturity, another life-history trait with substantial fitness effects in salmon. Sea age at maturity in Atlantic salmon is controlled by a major locus around the vgll3 gene, and we used this opportunity demonstrate that these two traits are co-inherited around this genome region. The odds ratio of survival until second reproduction was up to 2.4 (1.8-3.5 90% CI) times higher for fish with the early-maturing vgll3 genotype (EE) compared to fish with the late-maturing genotype (LL). The L allele was dominant in individuals remaining only one year at sea before maturation, but the dominance was reversed, with the E allele being dominant in individuals maturing after two or more years at sea. Post hoc analysis indicated that iteroparous fish with the EE genotype had accelerated growth prior to first reproduction compared to first-time spawners, across all age groups, whereas this effect was not detected in fish with the LL genotype. These results broaden the functional link around the vgll3 genome region and help us understand constraints in the evolution of life-history variation in salmon. Our results further highlight the need to account for genetic correlations between fitness traits when predicting demographic changes in changing environments.

Salmon spawning in their local habitat have a clear reproductive advantage over dispersers from nearby populations., A long-held, but poorly tested, assumption in natural populations is that individuals that disperse into new areas for reproduction are at a disadvantage compared to individuals that reproduce in their natal habitat, underpinning the eco-evolutionary processes of local adaptation and ecological speciation. Here, we capitalize on fine-scale population structure and natural dispersal events to compare the reproductive success of local and dispersing individuals captured on the same spawning ground in four consecutive parent-offspring cohorts of wild Atlantic salmon (Salmo salar). Parentage analysis conducted on adults and juvenile fish showed that local females and males had 9.6 and 2.9 times higher reproductive success than dispersers, respectively. Our results reveal how higher reproductive success in local spawners compared to dispersers may act in natural populations to drive population divergence and promote local adaptation over microgeographic spatial scales without clear morphological differences between populations.

Many wild Atlantic salmon (Salmo salar) populations are threatened by introgressive hybridization from domesticated fish that have escaped from aquaculture facilities. A detailed understanding of the hybridization dynamics between wild salmon and aquaculture escapees requires discrimination of different hybrid classes; however, markers currently available to discriminate the two types of parental genome have limited power to do this. Using a high‐density Atlantic salmon single nucleotide polymorphism (SNP) array, in combination with pooled‐sample allelotyping and an Fst outlier approach, we identified 200 SNPs that differentiated an important Atlantic salmon stock from the escapees potentially hybridizing with it. By simulating multiple generations of wild–escapee hybridization, involving wild populations in two major phylogeographic lineages and a genetically diverse set of escapees, we showed that both the complete set of SNPs and smaller subsets could reliably assign individuals to different hybrid classes up to the third hybrid (F3) generation. This set of markers will be a useful tool for investigating the genetic interactions between native wild fish and aquaculture escapees in many Atlantic salmon populations.

The effects of four different tagging methods (PIT, anchor T-tag, Carlin tag and dummy radio transmitter) on survival, behaviour and growth of Atlantic salmon smolts during their downstream migration were examined in semi-natural circular channels during a natural migration period in spring. Survival of smolts was high and tagging wounds healed well in all tagging groups. Tag loss rates were generally low, being the highest (2.5%) in the dummy radio transmitter group. Total length and body mass of the tagged and untagged smolts did not differ at the end of the experiment. Migration activity of smolts generally showed similar patterns among the treatments. However, Carlin-tagged smolts started their migration slightly later than the PIT-tagged fish, and smolts tagged with Carlin tag or dummy radio transmitter showed less overall migration activity than fish with PIT tag.

Genetic correlations in life history traits may result in unpredictable evolutionary trajectories if not accounted for in life-history models. Iteroparity (the reproductive strategy of reproducing more than once) in Atlantic salmon (Salmo salar) is a fitness trait with substantial variation within and among populations. In the Teno River in northern Europe, iteroparous individuals constitute an important component of many populations and have experienced a sharp increase in abundance in the last 20 years, partly overlapping with a general decrease in age structure. The physiological basis of iteroparity bears similarities to that of age at first maturity, another life history trait with substantial fitness effects in salmon. Sea age at maturity in Atlantic salmon is controlled by a major locus around thevgll3gene, and we used this opportunity demonstrate that the two traits are genetically correlated around this genome region. The odds ratio of survival until second reproduction was up to 2.4 (1.8-3.5 90% CI) times higher for fish with the early-maturingvgll3genotype (EE) compared to fish with the late-maturing genotype(LL). The association had a dominance architecture, although the dominant allele was reversed in the late-maturing group compared to younger groups that stayed only one year at sea before maturation.Post hocanalysis indicated that iteroparous fish with theEEgenotype had accelerated growth prior to first reproduction compared to first-time spawners, across all age groups, while this effect was not detected in fish with theLLgenotype. These results broaden the functional link around thevgll3genome region and help us understand constraints in the evolution of life history variation in salmon. Our results further highlight the need to account for genetic correlations between fitness traits when predicting demographic changes in changing environments.

Annual run size and timing of Atlantic salmon smolt migration was estimated using Bayesian model framework and data from six years of a video monitoring survey. The model has a modular structure. It separates sub-processes of departing, traveling and observing, of which the first two together define the arrival distribution. The sub-processes utilize biological background and expert knowledge about the migratory behavior of smolts and about the probability to observe them from the video footage under varying environmental conditions. Daily mean temperature and discharge were used as environmental covariates. The model framework does not require assuming a simple distributional shape for the arrival dynamics and thus also allows for multimodal arrival distributions. Results indicate that 20% - 43% of smolts passed the Utsjoki monitoring site unobserved during the years of study. Predictive studies were made to estimate daily run size in cases with missing counts either at the beginning or in the middle of the run, indicating good predictive performance.

Elucidating the genetic basis of adaptation to the local environment can improve our understanding of how the diversity of life has evolved. In this study, we used a dense SNP array to identify candidate loci potentially underlying fine-scale local adaptation within a large Atlantic salmon (Salmo salar) population. By combining outlier, gene-environment association and haplotype homozygosity analyses, we identified multiple regions of the genome with strong evidence for diversifying selection. Several of these candidate regions had previously been identified in other studies, demonstrating that the same loci could be adaptively important in Atlantic salmon at subdrainage, regional and continental scales. Notably, we identified signals consistent with local selection around genes associated with variation in sexual maturation, energy homeostasis and immune defence. These included the large-effect age-at-maturity gene vgll3, the known obesity gene mc4r, and major histocompatibility complex II. Most strikingly, we confirmed a genomic region on Ssa09 that was extremely differentiated among subpopulations and that is also a candidate for local selection over the global range of Atlantic salmon. This region colocalized with a haplotype strongly associated with spawning ecotype in sockeye salmon (Oncorhynchus nerka), with circumstantial evidence that the same gene (six6) may be the selective target in both cases. The phenotypic effect of this region in Atlantic salmon remains cryptic, although allelic variation is related to upstream catchment area and covaries with timing of the return spawning migration. Our results further inform management of Atlantic salmon and open multiple avenues for future research.

A long-held, but poorly tested, assumption in natural populations is that individuals that disperse into new areas for reproduction are at a disadvantage compared to individuals that reproduce in their natal habitat, underpinning the eco-evolutionary processes of local adaptation and ecological speciation. Here, we capitalize on fine-scale population structure and natural dispersal events to compare the reproductive success of local and dispersing individuals captured on the same spawning ground in four consecutive parent-offspring cohorts of wild Atlantic salmon (Salmo salar). Parentage analysis conducted on adults and juvenile fish showed that local females and males had 9.6 and 2.9 times higher reproductive success than dispersers, respectively. Our results reveal how dispersal disadvantage in reproductive success may act in natural populations to drive population divergence and local adaptation over microgeographic spatial scales without clear morphological differences or physical barriers to gene flow.

Elucidating the genetic basis of adaptation to the local environment can improve our understanding of how the diversity of life has evolved. In this study we used a dense SNP array to identify candidate loci underlying fine-scale local adaptation within a large Atlantic salmon (Salmo salar) population. By combining outlier, gene-environment association, and haplotype homozygosity analyses, we identified multiple regions of the genome with strong evidence for diversifying selection. Several of these candidate regions had previously been identified in other studies, demonstrating that the same loci be adaptively important in Atlantic salmon at sub-drainage, regional and continental scales. Notably, we identified signals consistent with local selection around genes associated with variation in sexual maturation, energy homeostasis, behaviour, and immune defence. These included the large-effect age-at-matunty gene vgll3, the known obesity gene mc4r, and major histocompatibility complex II. Most strikingly, we confirmed a genomic region on Ssa09 that was extremely differentiated among subpopulations, and that is also a candidate for local selection over the global range of Atlantic salmon. This region co-localized with a genomic region strongly associated with spawning ecotype in sockeye salmon (Oncorhynchus nerka), with circumstantial evidence that the same gene (six6) may be the selective target in both cases. The phenotypic effect of this region in Atlantic salmon remains cryptic, although allelic variation is related to river flow volume and co-vanes with timing of the return spawning migration. Our results further inform management of Atlantic salmon and open multiple avenues for future research.

Despite decades of research assessing the genetic structure of natural populations, the biological meaning of low yet significant genetic divergence often remains unclear due to a lack of associated phenotypic and ecological information. At the same time, structured populations with low genetic divergence and overlapping boundaries can potentially provide excellent models to study adaptation and reproductive isolation in cases where high-resolution genetic markers and relevant phenotypic and life history information are available. Here, we combined single nucleotide polymorphism (SNP)-based population inference with extensive phenotypic and life history data to identify potential biological mechanisms driving fine-scale subpopulation differentiation in Atlantic salmon (Salmo salar) from the Teno River, a major salmon river in Europe. Two sympatrically occurring subpopulations had low but significant genetic differentiation (FST = 0.018) and displayed marked differences in the distribution of life history strategies, including variation in juvenile growth rate, age at maturity and size within age classes. Large, late-maturing individuals were virtually absent from one of the two subpopulations, and there were significant differences in juvenile growth rates and size at age after oceanic migration between individuals in the respective subpopulations. Our findings suggest that different evolutionary processes affect each subpopulation and that hybridization and subsequent selection may maintain low genetic differentiation without hindering adaptive divergence.

Delaying sexual maturation can lead to larger body size and higher reproductive success, but carries an increased risk of death before reproducing. Classical life history theory predicts that trade-offs between reproductive success and survival should lead to the evolution of an optimal strategy in a given population. However, variation in mating strategies generally persists, and in general, there remains a poor understanding of genetic and physiological mechanisms underlying this variation. One extreme case of this is in the Atlantic salmon (Salmo salar), which can show variation in the age at which they return from their marine migration to spawn (i.e. their 'sea age'). This results in large size differences between strategies, with direct implications for individual fitness. Here, we used an Illumina Infinium SNP array to identify regions of the genome associated with variation in sea age in a large population of Atlantic salmon in Northern Europe, implementing individual-based genome-wide association studies (GWAS) and population-based FST outlier analyses. We identified several regions of the genome which vary in association with phenotype and/or selection between sea ages, with nearby genes having functions related to muscle development, metabolism, immune response and mate choice. In addition, we found that individuals of different sea ages belong to different, yet sympatric populations in this system, indicating that reproductive isolation may be driven by divergence between stable strategies. Overall, this study demonstrates how genome-wide methodologies can be integrated with samples collected from wild, structured populations to understand their ecology and evolution in a natural context.

The accuracy of underwater snorkel counts of adult Atlantic salmon, Salmo salar L., was analysed in a small tributary of the River Teno before and during the spawning period using two independent verification methods (video counts and radio-tagged fish) with known numbers of fish. The observation efficiency of snorkelling crews was generally high, but that of an inexperienced crew (65–72%) was significantly lower than an experienced crew (81–82%). Habitat type affected the accuracy of snorkelers, especially those of the inexperienced crew. The efficiency of snorkelers was high in pool-type habitats (75–100%) but decreased considerably in faster flowing turbulent habitats (43–82%), where the inexperienced crew provided the lowest estimates. Thus, snorkel counting is a valid method for estimating Atlantic salmon spawning population densities in small rivers with adequate underwater visibility and with a sufficiently experienced snorkelling crew.

Weekly exploitation rates of Atlantic salmon, Salmo salar L., in the River Utsjoki, Finland, were estimated from catch reports during the 2003, 2004, 2006 and 2007 seasons, and recordings of all Atlantic salmon ascending the river using a submerged video camera array. In all years, mean weekly fishing mortality rates were significantly higher in June than July to August, with a falling trend throughout the fishing season. Owing to overlap in size between one-sea-winter (1SW) and multi-sea-winter (MSW) salmon, the estimated fishing mortality rates were based on all sea-age categories combined. By the second week in June, 18.3-34.7% of large salmon (only MSW) had ascended, compared with 2.2-6.4% of small salmon (1SW and some MSW). Indirectly, the earlier start of ascent of large salmon to River Utsjoki indicated that in-river fishing mortality of MSW salmon is higher than for 1SW salmon. A later opening of the fishing season may be used to reduce the in-river fishing mortality, especially for the MSW component.

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

Spatial and temporal migratory behaviour of wild Atlantic salmon smolt (Salmo salar L.) was investigated at the River Utsjoki, a tributary of the sub-Arctic River Tana, using submerged video cameras that covered the entire water column across the river. The matrix of cameras provided information on the exact time, position in water column, and swimming direction of individual smolts. The smolt migration started in the beginning of June and ended in the middle of July, i.e. during the period of midnight sun. In contrast to most other studies, smolts migrated all day, with a peak from 07:00 to 10:00 h. Hours of sunshine and change in water level explained 55% of day-to-day variation in numbers of migrating smolts. Most smolts migrated actively (head first) in lower part of the water column with only 4% observed in the upper 30 cm surface water layer.

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.

Background: DNA extracted from historical samples is an important resource for understanding genetic consequences of anthropogenic influences and long-term environmental change. However, such samples generally yield DNA of a lower amount and quality, and the extent to which DNA degradation affects SNP genotyping success and allele frequency estimation is not well understood. We conducted high density SNP genotyping and allele frequency estimation in both individual DNA samples and pooled DNA samples extracted from dried Atlantic salmon (Salmo salar) scales stored at room temperature for up to 35 years, and assessed genotyping success, repeatability and accuracy of allele frequency estimation using a high density SNP genotyping array.Results: In individual DNA samples, genotyping success and repeatability was very high (> 0.973 and > 0.998, respectively) in samples stored for up to 35 years; both increased with the proportion of DNA of fragment size > 1000 bp. In pooled DNA samples, allele frequency estimation was highly repeatable (Repeatability = 0.986) and highly correlated with empirical allele frequency measures (Mean Adjusted R-2 = 0.991); allele frequency could be accurately estimated in > 95% of pooled DNA samples with a reference group of at least 30 individuals. SNPs located in polyploid regions of the genome were more sensitive to DNA degradation: older samples had lower genotyping success at these loci, and a larger reference panel of individuals was required to accurately estimate allele frequencies.Conclusions: SNP genotyping was highly successful in degraded DNA samples, paving the way for the use of degraded samples in SNP genotyping projects. DNA pooling provides the potential for large scale population genetic studies with fewer assays, provided enough reference individuals are also genotyped and DNA quality is properly assessed beforehand. We provide recommendations for future studies intending to conduct high-throughput SNP genotyping and allele frequency estimation in historical samples.

Understanding the mechanisms by which populations adapt to their environments is a fundamental aim in biology. However, it remains challenging to identify the genetic basis of traits, provide evidence of genetic changes and quantify phenotypic responses. Age at maturity in Atlantic salmon represents an ideal trait to study contemporary adaptive evolution as it has been associated with a single locus in the vgll3 region and has also strongly changed in recent decades. Here, we provide an empirical example of contemporary adaptive evolution of a large-effect locus driving contrasting sex-specific evolutionary responses at the phenotypic level. We identified an 18% decrease in the vgll3 allele associated with late maturity in a large and diverse salmon population over 36 years, induced by sex-specific selection during sea migration. Those genetic changes resulted in a significant evolutionary response only in males, due to sex-specific dominance patterns and vgll3 allelic effects. The vgll3 allelic and dominance effects differed greatly in a second population and were likely to generate different selection and evolutionary patterns. Our study highlights the importance of knowledge of genetic architecture to better understand fitness trait evolution and phenotypic diversity. It also emphasizes the potential role of adaptive evolution in the trend towards earlier maturation observed in numerous Atlantic salmon populations worldwide. Age at maturity in Atlantic salmon has been associated with a single locus with sex-specific effects. Here, the authors show rapid evolution towards early maturity in males of a large salmon population induced by sex-specific selection during sea migration.