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publicJan 2023View details →

Postrelease exploration and stress tolerance of landlocked and anadromous Atlantic salmon and their hybrids

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publicMay 2022View details →

Atlantic salmon survival at sea: temporal changes that lack regional synchrony

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publicMar 2025View details →

Data from: Smallmouth bass (Micropterus dolomieu) and chain pickerel (Esox niger) identified as Atlantic salmon (Salmo salar) smolt predators in a reservoir system

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publicNov 2023View details →

Pre-fertilisation gamete thermal environment influences reproductive success, unmasking opposing sex-specific responses in Atlantic Salmon

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opencc-zeroMay 2020View details →

Data from: Divergent and linked selection shape patterns of genomic differentiation between European and North American Atlantic salmon (Salmo salar)

As populations diverge many processes can shape genomic patterns of differentiation. Regions of high differentiation can arise due to divergent selection acting on selected loci, genetic hitchhiking of nearby loci, or through repeated selection against deleterious alleles (linked background selection); this divergence may then be further elevated in regions of reduced recombination. Atlantic salmon (Salmo salar) from Europe and North America diverged >600,000 years ago and despite some evidence of secondary contact, the majority of genetic data indicate substantial divergence between lineages. This deep divergence with potential gene flow provides an opportunity to investigate the role of different mechanisms that shape the genomic landscape during early speciation. Here, using 184,295 SNPs and 80 populations, we investigate the genomic landscape of differentiation across the Atlantic Ocean with a focus on highly differentiated regions and processes shaping them. We found evidence of high (mean FST=0.26) and heterogeneous genomic differentiation between continents. Genomic regions associated with high trans-Atlantic differentiation ranged in size from single loci (SNPs) within important genes to large regions (1-3Mbp) on four chromosomes (Ssa06, Ssa13, Ssa16, and Ssa19). These regions showed signatures consistent with selection, including high linkage disequilibrium despite no local reduction in recombination. Genes and functional enrichment of processes associated with differentiated regions may highlight continental differences in ocean navigation and parasite resistance. Our results provide insight into potential mechanisms underlying differences between continents, and evidence of near fixed and potentially adaptive trans-Atlantic differences concurrent with a background of high genome-wide differentiation supports subspecies designation in Atlantic salmon.

opencc-zeroJul 2020View details →

Data from: Genetic growth potential, rather than phenotypic size, predicts migration phenotype in Atlantic salmon

Knowledge of the relative importance of genetic versus environmental determinants of major developmental transitions is pertinent to understanding phenotypic evolution. In salmonid fishes, a major developmental transition enables a risky seaward migration that provides access to feed resources. In Atlantic salmon, initiation of the migrant phenotype, and thus age of migrants, is presumably controlled via thresholds of a quantitative liability, approximated by body size expressed long before the migration. However, how well size approximates liability, both genetically and environmentally, remains uncertain. We studied 32 Atlantic salmon families in two temperatures and feeding regimes (fully fed, temporarily restricted) to completion of migration status at age 1 year. We detected a lower migrant probability in the cold (0.42) than the warm environment (0.76), but no effects of male maturation status or feed restriction. By contrast, body length in late summer predicted migrant probability and its control reduced migrant probability heritability by 50–70%. Furthermore, migrant probability and length showed high heritabilities and between-environment genetic correlations, and were phenotypically highly correlated with stronger genetic than environmental contributions. Altogether, quantitative estimates for the genetic and environmental effects predicting the migrant phenotype indicate, for a given temperature, a larger importance of genetic than environmental size effects.

opencc-zeroAug 2020View details →

Data from: Cis-regulatory differences in isoform expression associate with life history strategy variation in Atlantic salmon

A major goal in biology is to understand how evolution shapes variation in individual life histories. Genome-wide association studies have been successful in uncovering genome regions linked with traits underlying life history variation in a range of species. However, lack of functional studies of the discovered genotype-phenotype associations severely restrains our understanding how alternative life history traits evolved and are mediated at the molecular level. Here, we report a cis-regulatory mechanism whereby expression of alternative isoforms of the transcription co-factor vestigial-like 3 (vgll3) associate with variation in a key life history trait, age at maturity, in Atlantic salmon (Salmo salar). Using a common-garden experiment, we first show that vgll3 genotype associates with puberty timing in one-year-old salmon males. By way of temporal sampling of vgll3 expression in ten tissues across the first year of salmon development, we identify a pubertal transition in vgll3 expression where maturation coincided with a 66% reduction in testicular vgll3 expression. The late maturation allele was not only associated with a tendency to delay puberty, but also with expression of a rare transcript isoform of vgll3 pre-puberty. By comparing absolute vgll3 mRNA copies in heterozygotes we show that the expression difference between the earlyand late maturity alleles is largely cis-regulatory. We propose a model whereby expression of a rare isoform from the late allele shifts the liability of its carriers towards delaying puberty. These results exemplify the potential importance of regulatory differences as a mechanism for the evolution of life history traits.

opencc-zeroNov 2020View details →

Population genomics reveals repeated signals of adaptive divergence in the Atlantic salmon of northeastern Europe

Our ability to examine genetic variation across entire genomes have enabled many studies searching for the genetic basis of local adaptation. These studies have identified numerous loci as candidates for differential local selection, however relatively few have examined the overlap among candidate loci identified from independent studies of the same species in different geographic areas or evolutionary lineages. We used an allelotyping approach with a 220K SNP array to characterize the population genetic structure of Atlantic salmon in northeastern Europe and ask whether the same genomic segments emerged as outliers among populations in different geographic regions. Genome-wide data recapitulated the phylogeographic structure previously inferred from mtDNA and microsatellite markers. Independent analyses of three genetically and geographically distinct groups of populations repeatedly inferred the same 17 haploblocks to contain loci under differential local selection. The most strongly supported of these replicated haploblocks had known strong associations with life history variation or immune response in Atlantic salmon. Our results are consistent with these genomic segments harbouring large-effect loci which have a major role in Atlantic salmon diversification and are ideal targets for validation studies.

opencc-zeroJan 2021View details →

Space invaders: searching for invasive Smallmouth Bass (Micropterus dolomieu) in a renowned Atlantic Salmon (Salmo salar) river

Humans have the ability to permanently alter aquatic ecosystems and the introduction of species is often the most serious alteration. Non-native Smallmouth Bass (Micropterus dolomieu) were identified in Miramichi Lake c. 2008, which is a headwater tributary to the Southwest Miramichi River, a renowned Atlantic Salmon (Salmo salar) river whose salmon population is dwindling. A containment programme managed by the Department of Fisheries and Oceans, Canada (DFO) was implemented in 2009 to confine Smallmouth Bass (SMB) to the lake. We utilized environmental DNA (eDNA) as a detection tool to establish the potential escape of SMB into the Southwest Miramichi River. We sampled at 26 unique sites within Miramichi Lake, the outlet of Miramichi Lake (Lake Brook), which flows into the main stem Southwest Miramichi River, and the main stem Southwest Miramichi River between August and October 2017. We observed n=6 positive detections located in the lake, Lake Brook, and the main stem Southwest Miramichi downstream of the lake. No detections were observed upstream of the confluence of Lake Brook and the main stem Southwest Miramichi. The spatial pattern of positive eDNA detections downstream of the lake suggests the presence of individual fish versus lake-sourced DNA in the outlet stream discharging to the main river. Smallmouth Bass were later confirmed by visual observation during a snorkeling campaign, and angling. Our results, both eDNA and visual confirmation, definitively show Smallmouth Bass now occupy the main stem of the Southwest Miramichi.

opencc-by-4.0Dec 2023View details →

Sex-specific associations of the maturation locus vgll3 with exploratory behaviour and boldness in Atlantic salmon juveniles

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opencc-zeroMar 2024View details →

Data from: Introgression of non-native mitochondrial haplotypes from farmed to wild Atlantic salmon

Farmed salmon escape and interbreed with wild Atlantic salmon on a large scale. We studied introgression of mitochondrial haplotypes from farmed Atlantic salmon originating from the Eastern Atlantic phylogenetic group to wild salmon of the Barents-White Sea phylogenetic group. We find that farmed genetic introgression introduced novel, non-native haplotypes into the Barents-White Sea phylogenetic group. The mitochondrial genome has important functional effects and is inherited as a haploid from the mother. Hence, the observed introgression across natural genetic barriers is expected to cause long-lasting functional maladaptation of the hybrids in the maternal line. As the use of farmed Atlantic salmon from non-native phylogenetic groups is widespread in aquaculture, the impact on wild Atlantic salmon may be more severe than previously recognized. Our results highlight the ecological risks of releasing non-native wild and domesticated animals.

opencc-by-4.0Nov 2023View details →

F I G U R E 4 in Movement and habitat shift responses of juvenile Atlantic Salmon (Salmo salar) to annually permanent stream flooding

F I G U R E 4 Summary of Fulton's condition factor related to location, 2016–2017.

opencc-by-4.0Nov 2023View details →

F I G U R E 3 Mass specific growth rates among locations, 2016–2017 in Movement and habitat shift responses of juvenile Atlantic Salmon (Salmo salar) to annually permanent stream flooding

F I G U R E 3 Mass specific growth rates among locations, 2016–2017.

opencc-zeroOct 2021View details →

Selection against individuals from genetic introgression of escaped farmed salmon in a natural population of Atlantic salmon

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

opencc-by-4.0Nov 2021View details →

The quest for successful Atlantic salmon restoration: perspectives, priorities, and maxims

Data supporting publication https://academic.oup.com/icesjms/advance-article/doi/10.1093/icesjms/fsab201/6425092?casa_token=nTwNIhkC314AAAAA:FBK2iqeXsVgELsFGUxQAMjyWoOU6p2uJMe9UZ5ynGrdWIH6JxDSqN16EanyKWvZdtf1F3KdN4RW9Vg

opencc-zeroApr 2022View details →

Network analysis reveals that acute stress exacerbates gene regulatory responses of the gill to seawater in Atlantic salmon

The transition from freshwater to seawater represents a physiological challenge for Atlantic salmon smolts preparing for downstream migration. Stressors occurring during downstream migration to the ocean impair the ability of smolts to maintain osmotic/ionic homeostasis in seawater. The molecular mechanisms underlying this interaction are not fully understood, especially at the organ level. We combined RNA-Seq with measures of whole-animal homeostasis to examine gene expression dynamics in the gills of smolts associated with impaired seawater tolerance after an aquaculture-related stressor. Smolts were given a 24 h seawater tolerance test before and after exposure to an acute handling/confinement stress. RNA-Seq followed by differential expression and weighted gene correlation network analysis (WGCNA) was used to quantify the transcriptional response of the gill to handling/confinement stress, seawater and their interaction. Exposure to acute stress was associated with a general stress response and impaired osmotic/ionic homeostasis in seawater. We identified gene networks in the gill exhibiting response to acute stress alone, seawater alone, and others exhibiting combined effects of both stress and seawater. Our findings indicate that acute handling/ confinement stress increases the intensity of seawater-related gene expression and suggest that increased investment in mechanisms related to ion transport may be part of a compensatory response to impaired seawater tolerance in smolts.

opencc-zeroMay 2024View details →

Code from: Early survival in Atlantic salmon is associated with parental genotypes at loci linked to timing of maturation

Large effects loci often contain genes with critical developmental functions with potentially broad effects across life-stages. However, the life-stage-specific fitness consequences are rarely explored. In Atlantic salmon, variation in two large-effect loci, six6 and vgll3, is linked to age at maturity, and several physiological and behavioural traits in early life. By genotyping the progeny of wild Atlantic salmon that were planted into natural streams with nutrient manipulations, we tested if genetic variation in these loci is associated with survival in early life. We found that higher early life survival was linked to the genotype associated with late maturation in the vgll3, but with early maturation in the six6 locus. These effects were significant in high-nutrient, but not in in low-nutrient streams. The differences in early survival were not explained by additive genetic effects in the offspring generation, but by maternal genotypes in the six6 locus, and by both parents' genotypes in the vgll3 locus. Our results suggest that indirect genetic effects by large-effect loci can be significant determinants of offspring fitness. This study demonstrates an intriguing case of how large-effect loci can exhibit complex fitness associations across life stages in the wild and indicates that predicting evolutionary dynamics is difficult.

opencc-zeroJun 2024View details →

The negative association of sea lice from fish farms on recreational fishing catches of Atlantic salmon

The question of whether and to what extent sea-louse (L. salmonis) infestations from salmon farms influence wild Atlantic salmon survival has been subject to sustained scientific debate and political controversy. Documenting the population-level effects of sea lice on wild salmon remains inherently challenging. We employ comprehensive sea-lice data and recreational catch data from Norway to assess the impact of farm sea-louse infestations on wild salmon catches in different production areas (PAs). Our analysis finds a significant correlation between declines in wild Atlantic salmon catches and increasing amounts of adult female sea lice per km2. The effect is most pronounced in PA 4 on the west coast of Norway, an area within the government's "traffic light" management system where out-migrating salmon smolts are deemed to face high exposure to louse-induced mortality risk. Our model predicts below-average catches when the total sea louse load exceeds the government's limit of 0.1 average adult female sea louse per farmed fish within some production areas. Furthermore, our results indicate that the risk of below-average catches increases by approximately 47% when salmon farms exceed this limit (estimated risk ratio of 1.47, 95 % CI [1.10, 1.96]). Synthesis and Applications: Our study expands the existing body of evidence demonstrating a negative association between fish farming and the ecosystem services provided by wild salmon stocks. It has important implications for aquaculture management. First, it shows that farm sea lice directly affect peoples, rights holders, and interest groups, such as landowners and anglers, who rely on viable populations of wild salmon. Second, it suggests that a >0.1 sea lice limit may be insufficient to prevent subpar catches in some areas. Furthermore, in the context of allowing further growth in farmed salmon biomass, setting absolute sea-louse limits for entire production areas may be a more effective regulatory instrument than setting average lice limits per farmed fish. Our findings contribute to advancing a scientific basis for setting appropriate louse limits on farm and area scales.

opencc-zeroJul 2024View details →

Ontogenetic variation in the marine foraging of Atlantic salmon functionally links genomic diversity with a major life history polymorphism

The ecological role of heritable phenotypic variation in free-living populations remains largely unknown. Knowledge of the genetic basis of functional ecological processes can link genomic and phenotypic diversity, providing insight into polymorphism evolution and how populations respond to environmental change. By quantifying the marine diet, of sub-adult Atlantic salmon, we assessed how foraging behavior changes along the ontogeny, and in relation to genetic variation in two loci with major effect on age-at-maturity (six6 and vgll3). We used a two-component, zero-inflated negative binomial model to simultaneously quantify foraging frequency (zero-inflation components) and foraging outcome (count component), separately for fish and crustaceans in the diet. We found that older salmon forage for both prey types more actively (as evidenced by increased foraging frequency), but with a decreased efficiency (as evidenced by fewer prey items in the diet), suggesting an age-dependent shift in foraging dynamics. The vgll3 locus was linked to age-dependent changes in foraging behavior: younger salmon with vgll3LL (the genotype associated with late maturation) tend to forage crustaceans more often than those with vgll3EE (the genotype associated with early maturation), while the pattern was reversed in older salmon. Vgll3 LL genotype was also linked to marginal increase in fish acquisition especially in younger salmon, while six6 was not a factor explaining the diet variation. Our results suggest a functional role for variation in marine feeding behavior linking genomic diversity at vgll3 with age-at-maturity among salmon, with potential age-dependent trade-offs maintaining the genetic variation. A shared genetic basis between dietary ecology and age-at-maturity likely subjects Atlantic salmon populations to evolution induced by bottom-up changes in marine productivity.