Atlantic Salmon Populations Research Articles

Examining fish scale biomineral from Atlantic salmon populations.

Fish scale microchemistry can be used to make life-history inferences, although ecological studies examining scale composition are relatively rare. Salmon scales have an external layer of calcium phosphate hydroxyl apatite (HAP). The structure, hardness, and calcium content of this layer have been shown to vary within and between species. This variation may lead to misinterpretation of trace element profiles. This study uses backscatter scanning electron microscopy with electron dispersive spectrometry to compare scales from salmon populations and to present a more detailed analysis of scale HAP than was previously available. Our findings extend the range of salmon populations for which HAP Ca is available and confirm previous findings that the HAP Ca is relatively invariable within this species.

Occurrence of the invasive pink salmon (Oncorhynchus gorbuscha, Walbaum 1792) in Greenland 2020 and 2021 as revealed using citizen science, snorkeling, and environmental DNA metabarcoding of fishes in the Kapisillit River

The occurrence of the invasive pink salmon ( Oncorhynchus gorbuscha, Walbaum 1792) in Greenland was initially described in 2019 using social media to collect data on their presence. In this study we continue data collection through social media and initiate a monitoring program of the Kapisillit River in Southwest Greenland using snorkeling and environmental DNA (eDNA) metabarcoding in 2020 and 2021. The Kapisillit River is the only freshwater system in Greenland, where the red-listed Atlantic salmon ( Salmo salar, Linnaeus 1758) is known to spawn. This genetically unique population of Atlantic salmon has been found to decline, wherefore there is general conservation concern that the occurrence of pink salmon at some point can become an additional stressor to the “Kapisillit salmon”. In 2021, pink salmon were present near all larger populated areas in Greenland and likely more abundant than in 2019. From visual observations and using eDNA, the presence of pink salmon was documented in the Kapisillit River in 2021. From the number of individuals observed combined with the spatial distribution of eDNA detections in the river, we suggest that the pink salmon invasion in the Kapisillit River is at an early stage.

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 changes. By quantifying the marine diet of Atlantic salmon, we assessed how foraging behaviour changes along the ontogeny, and in relation to genetic variation in two loci with major effects on age at maturity (six6 and vgll3). We used a two-component, zero-inflated negative binomial model to simultaneously quantify foraging frequency and foraging outcome, separately for fish and crustaceans diets. 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 in the diet), suggesting an age-dependent shift in foraging dynamics. The vgll3 locus was linked to age-dependent changes in foraging behaviour: Younger salmon with vgll3LL (the genotype associated with late maturation) tended to forage crustaceans more often than those with vgll3EE (the genotype associated with early maturation), whereas the pattern was reversed in older salmon. Vgll3 LL genotype was also linked to a 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 marine feeding behaviour 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.

Sex-specific overdominance at the maturation vgll3 gene for reproductive fitness in wild Atlantic salmon.

Linking reproductive fitness with adaptive traits at the genomic level can shed light on the mechanisms that produce and maintain sex-specific selection. Here, we construct a multigenerational pedigree to investigate sex-specific selection on a maturation gene, vgll3, in a wild Atlantic salmon population. The vgll3 locus is responsible for ~40% of the variation in maturation (sea age at first reproduction). Genetic parentage analysis was conducted on 18,265 juveniles (parr) and 685 adults collected at the same spawning ground over eight consecutive years. A high proportion of females (26%) were iteroparous and reproduced two to four times in their lifetime. A smaller proportion of males (9%) spawned at least twice in their lifetime. Sex-specific patterns of reproductive fitness were related to vgll3 genotype. Females showed a pattern of overdominance where vgll3*EL genotypes had three-fold more total offspring than homozygous females. In contrast, males demonstrated that late-maturing vgll3*LL individuals had two-fold more offspring than either vgll3*EE or vgll3*EL males. Taken together, these data suggest that balancing selection in females contributes to the maintenance of variation at this locus via increased fitness of iteroparous vgll3*EL females. This study demonstrates the utility of multigenerational pedigrees for uncovering complex patterns of reproduction, sex-specific selection and the maintenance of genetic variation.

Body length changes for Atlantic salmon (Salmo salar) over five decades exhibit weak spatial synchrony over a broad latitudinal gradient.

Understanding the factors that drive spatial synchrony among populations or species is important for management and recovery of populations. The range-wide declines in Atlantic salmon (Salmo salar) populations may be the result of broad-scale changes in the marine environment. Salmon undergo rapid growth in the ocean; therefore changing marine conditions may affect body size and fecundity estimates used to evaluate whether stock reference points are met. Using a dataset that spanned five decades, 172,268 individuals, and 19 rivers throughout Eastern Canada, we investigated the occurrence of spatial synchrony in changes in the body size of returning wild adult Atlantic salmon. Body size was then related to conditions in the marine environment (i.e., climate indices, thermal habitat availability, food availability, density-dependence, and fisheries exploitation rates) that may act on all populations during the ocean feeding phase of their life cycle. Body size increased during the 1980s and 1990s for salmon that returned to rivers after one (1SW) or two winters at sea (2SW); however, significant changes were only observed for 1SW and/or 2SW in some mid-latitude and northern rivers (10/13 rivers with 10 of more years of data during these decades) and not in southern rivers (0/2), suggesting weak spatial synchrony across Eastern Canada. For 1SW salmon in nine rivers, body size was longer when fisheries exploitation rates were lower. For 2SW salmon, body size was longer when suitable thermal habitat was more abundant (significant for 3/8 rivers) and the Atlantic Multidecadal Oscillation was higher (i.e., warmer sea surface temperatures; significant for 4/8 rivers). Overall, the weak spatial synchrony and variable effects of covariates on body size across rivers suggest that changes in Atlantic salmon body size may not be solely driven by shared conditions in the marine environment. Regardless, body size changes may have consequences for population management and recovery through the relationship between size and fecundity.

Methodological influence on detecting temperature effects on growth variability in juvenile Atlantic salmon

In the context of warming freshwater habitats, protection of Atlantic salmon populations requires an understanding of the effects of temperature on somatic growth during the juvenile life stage. However, quantifying the effect of temperature on growth is challenging given differences among methodologies, metrics of growth, and their underlying assumptions. Using short term studies (2000–2002) in two Canadian populations of wild Atlantic salmon (Margaree and Miramichi rivers), we investigate whether different hierarchical modeling approaches influence the derivation of temperature-growth relationships, by contrasting seasonal growth trajectories (von Bertalanffy; VBGF) to size-at-age data models built with instantaneous growth rates. Size-at-age data analysed seasonally with the VBGF framework failed to detect an effect of temperature, whereas instantaneous growth rates from the same dataset were strongly related to temperature metrics. However, instantaneous growth rates cannot be used to extrapolate predictions into meaningful metrics for fisheries management (e.g., size at the end of the growing season). Nevertheless, we show that size at the end of the growing season can be predicted with VBGF models accounting for site-level variation, which in turn are related to temperature metrics, as observed for instantaneous growth rates. Taken together, these results show that combining these two approaches (size-at-age, growth rates) can circumvent their intrinsic drawbacks and reveal essential ecological patterns that may otherwise remain undetected. In cases where instantaneous growth rates are not available, relating predicted size-at-age from hierarchical VBGF to temperature provides an interesting alternative for detecting subtle environmental effects, even if the VBGF parameters or its residuals are unrelated to temperature metrics.

Accuracy of genomic prediction using multiple Atlantic salmon populations

BackgroundThe accuracy of genomic prediction is partly determined by the size of the reference population. In Atlantic salmon breeding programs, four parallel populations often exist, thus offering the opportunity to increase the size of the reference set by combining these populations. By allowing a reduction in the number of records per population, multi-population prediction can potentially reduce cost and welfare issues related to the recording of traits, particularly for diseases. In this study, we evaluated the accuracy of multi- and across-population prediction of breeding values for resistance to amoebic gill disease (AGD) using all single nucleotide polymorphisms (SNPs) on a 55K chip or a selected subset of SNPs based on the signs of allele substitution effect estimates across populations, using both linear and nonlinear genomic prediction (GP) models in Atlantic salmon populations. In addition, we investigated genetic distance, genetic correlation estimated based on genomic relationships, and persistency of linkage disequilibrium (LD) phase across these populations.ResultsThe genetic distance between populations ranged from 0.03 to 0.07, while the genetic correlation ranged from 0.19 to 0.99. Nonetheless, compared to within-population prediction, there was limited or no impact of combining populations for multi-population prediction across the various models used or when using the selected subset of SNPs. The estimates of across-population prediction accuracy were low and to some extent proportional to the genetic correlation estimates. The persistency of LD phase between adjacent markers across populations using all SNP data ranged from 0.51 to 0.65, indicating that LD is poorly conserved across the studied populations.ConclusionsOur results show that a high genetic correlation and a high genetic relationship between populations do not guarantee a higher prediction accuracy from multi-population genomic prediction in Atlantic salmon.

Post‐glacial recolonization and multiple scales of secondary contact contribute to contemporary Atlantic salmon (Salmo salar) genomic variation in North America

AbstractAimIn northern environments, periods of isolation during Pleistocene glaciations and subsequent recolonization and secondary contact have had a significant influence on contemporary diversity of many species. The recent advent of high‐resolution genomic analyses allows unprecedented power to resolve genomic signatures of such events in northern species. Here, we provide the highest resolution genomic characterization of Atlantic salmon in North America to date to infer glacial refugia and the geographic scales of post‐glacial secondary contact.LocationNorth America.TaxonAtlantic salmon, Salmo salar.MethodsSamples were collected for 5455 individuals from 148 populations, encompassing the majority of the Atlantic salmon's native range in North America, from Labrador to Maine. Individuals were genotyped using a 220K single nucleotide polymorphism array aligned to the Atlantic salmon (Salmo salar) genome. Spatial genetic structure (principal component analysis, k‐means clustering, admixture) was evaluated in conjunction with genomic comparisons of these identified lineages to infer the refugia during the last glacial maximum and regions of secondary contact following recolonization.ResultsSpatial genomic analyses identified three phylogeographic groups, consistent with the northward recolonization from two southern glacial refugia in North America (a western Maritime lineage and an eastern Newfoundland and Labrador lineage), with subsequent differentiation of the eastern lineage into two separate groups. Secondary contact among these North American groups was observed within the northern Gulf of St. Lawrence, and evidence of trans‐Atlantic secondary contact was detected within the eastern Newfoundland and Labrador lineage. Comparison of groups from insular Newfoundland with those from mainland Labrador suggests genomic regions displaying high differentiation were characterized by elevated European admixture, suggesting a possible role of European secondary contact in population divergence.Main ConclusionsThese findings present the first evidence suggesting that genomic diversity in extant North American Atlantic salmon populations has resulted from allopatric isolation in two glacial refugia followed by both regional and trans‐Atlantic recolonization and secondary contact and demonstrate the power of genomic tools to resolve historical drivers of diversity in wild populations.

Temporal allele frequency changes in large-effect loci reveal potential fishing impacts on salmon life-history diversity.

Fishing has the potential to influence the life-history traits of exploited populations. However, our understanding of how fisheries can induce evolutionary genetic changes remains incomplete. The discovery of large-effect loci linked with ecologically important life-history traits, such as age at maturity in Atlantic salmon (Salmo salar), provides an opportunity to study the impacts of temporally varying fishing pressures on these traits. A 93-year archive of fish scales from wild Atlantic salmon catches from the northern Baltic Sea region allowed us to monitor variation in adaptive genetic diversity linked with age at maturity of wild Atlantic salmon populations. The dataset consisted of samples from both commercial and recreational fisheries that target salmon on their spawning migration. Using a genotyping-by-sequencing approach (GT-seq), we discovered strong within-season allele frequency changes at the vgll3 locus linked with Atlantic salmon age at maturity: fishing in the early season preferentially targeted the vgll3 variant linked with older maturation. We also found within-season temporal variation in catch proportions of different wild Atlantic salmon subpopulations. Therefore, selective pressures of harvesting may vary depending on the seasonal timing of fishing, which has the potential to cause evolutionary changes in key life-history traits and their diversity. This knowledge can be used to guide fisheries management to reduce the effects of fishing practices on salmon life-history diversity. Thus, this study provides a tangible example of using genomic approaches to infer, monitor and help mitigate human impacts on adaptively important genetic variation in nature.

Selection among critically endangered landlocked salmon (Salmo salar m. sebago) families in survival and growth traits across early life stages and in different environments.

Endangered wild fish populations are commonly supported by hatchery propagation. However, hatchery-reared fish experience very different selective pressures compared to their wild counterparts, potentially causing genotype-by-environment interactions (G × E) in essential fitness traits. We experimentally studied early selection in a critically endangered landlocked Atlantic salmon population, first from fertilization to the swim-up stage in a common hatchery setting, and thereafter until the age of 5 months in two contrasting rearing environments. Swim-up progeny were moved either to standard indoor hatchery tanks involving conventional husbandry or to seminatural outdoor channels providing only natural food. After the first summer, sampled survivors were assigned to their families by genotyping. Early survival until the swim-up stage was mostly determined by maternal effects, but also involved significant variation due to sires and full-sib families (potential genetic effects). High on-growing survival in hatchery tanks (88.7%) maintained a more even distribution among families (relative share 1.5%-4.2%) than the seminatural environment (0.0%-5.4%). This heterogeneity was mostly maternal, whereas no independent paternal effect occurred. Heritability estimates were high for body size traits in both environments (0.62-0.69). Genetic correlations between the environments were significantly positive for body size traits (0.67-0.69), and high body condition in hatchery was also genetically linked to rapid growth in the seminatural environment (0.54). Additive and phenotypic growth variation increased in the seminatural environment, but scaling effects probably played a less significant role for G × E, compared to re-ranking of genotypes. Our results suggest that not only maternal effects, but also genetic effects, direct selection according to the environmental conditions experienced. Consistently high genetic variation in growth implies that, despite its low overall genetic diversity and long history in captive rearing (>50 years), this landlocked Atlantic salmon population still possesses adaptive potential for response to change from hatchery rearing back to more natural conditions.

Variable parallelism in the genomic basis of age at maturity across spatial scales in Atlantic Salmon.

Complex traits often exhibit complex underlying genetic architectures resulting from a combination of evolution from standing variation, hard and soft sweeps, and alleles of varying effect size. Increasingly, studies implicate both large-effect loci and polygenic patterns underpinning adaptation, but the extent that common genetic architectures are utilized during repeated adaptation is not well understood. Sea age or age at maturation represents a significant life history trait in Atlantic Salmon (Salmo salar), the genetic basis of which has been studied extensively in European Atlantic populations, with repeated identification of large-effect loci. However, the genetic basis of sea age within North American Atlantic Salmon populations remains unclear, as does the potential for a parallel trans-Atlantic genomic basis to sea age. Here, we used a large single-nucleotide polymorphism (SNP) array and low-coverage whole-genome resequencing to explore the genomic basis of sea age variation in North American Atlantic Salmon. We found significant associations at the gene and SNP level with a large-effect locus (vgll3) previously identified in European populations, indicating genetic parallelism, but found that this pattern varied based on both sex and geographic region. We also identified nonrepeated sets of highly predictive loci associated with sea age among populations and sexes within North America, indicating polygenicity and low rates of genomic parallelism. Despite low genome-wide parallelism, we uncovered a set of conserved molecular pathways associated with sea age that were consistently enriched among comparisons, including calcium signaling, MapK signaling, focal adhesion, and phosphatidylinositol signaling. Together, our results indicate parallelism of the molecular basis of sea age in North American Atlantic Salmon across large-effect genes and molecular pathways despite population-specific patterns of polygenicity. These findings reveal roles for both contingency and repeated adaptation at the molecular level in the evolution of life history variation.

Sustaining high-value salmonid populations in regulated rivers: Insights from individual-based modelling of brown trout and Atlantic salmon

To combat climate change, societal pressure to develop fossil-free hydroelectricity is growing. There is a great need, however, for environmental assessment tools that can predict the effects of streamflow regulation on biodiversity in hydropower-regulated rivers. Ecological modelling lets practitioners: 1) set broad bounds on population-level responses of key species and 2) identify knowledge gaps and prioritize research needs. Individual-based models (IBMs) are powerful tools for assessing relative benefits of alternative management actions, and therefore help to develop more sustainable hydropower solutions. We applied the inSALMO 7.3-SD IBM for populations of brown trout (Salmo trutta) and Atlantic salmon (S. salar) in the lower Gullspång River, Sweden. We simulated the effects of various minimum hydropeaking flow releases (from 9 to 21 m3/s) on outmigration production. We found that the number of age-1 outmigrants of both species decreased with increasing minimum flow release of the hydropeaking scenarios. The number of age-2 trout outmigrants did not change considerably with increasing the minimum release, but decreased sharply at the highest flow. The most age-2 salmon outmigrants were produced by flow scenarios with minimum releases of 15 and 18 m3/s. The model predicts, therefore, varying species- and life stage-specific effects of flow regulation. Moreover, increased flow caused juveniles to stay in the river longer and outmigrate at larger size, which exposes them to simulated predation longer but could increase post-outmigration survival. By providing insights into mechanisms driving population dynamics, IBMs can help promote the sustainability of high-conservation-value fish species.

Six decades of ecohydrological research connecting landscapes and riverscapes in the Girnock Burn, Scotland: Atlantic salmon population and habitat dynamics in a changing world

AbstractLong‐term data are crucial for understanding ecological responses to climate and land use change; they are also vital evidence for informing management. As a migratory fish, Atlantic salmon are sentinels of both global and local environmental change. This paper reviews the main insights from six decades of research in an upland Scottish stream (Girnock Burn) inhabited by a spring Atlantic salmon population dominated by multi‐sea‐winter fish. Research began in the 1960s providing a census of returning adults, juvenile emigrants and in‐stream production of Atlantic salmon. Early research pioneered new monitoring techniques providing new insights into salmon ecology and population dynamics. These studies underlined the need for interdisciplinary approaches for understanding salmon interactions with physical, chemical and biological components of in‐stream habitats at different life‐stages. This highlighted variations in catchment‐scale hydroclimate, hydrology, geomorphology and hydrochemistry as essential to understanding freshwater habitats in the wider landscape context. Evolution of research has resulted in a remarkable catalogue of novel findings underlining the value of long‐term data that increases with time as modelling tools advance to leverage more insights from “big data”. Data are available on fish numbers, sizes and ages across multiple life stages, extending over many decades and covering a wide range of stock levels. Combined with an unusually detailed characterization of the environment, these data have enabled a unique process‐based understanding of the controls and bottlenecks on salmon population dynamics across the entire lifecycle and the consequences of declining marine survival and ova deposition. Such powerful datasets, methodological enhancements and the resulting process understanding have informed and supported the development of fish population assessment tools which have been applied to aid management of threatened salmon stocks at large‐catchment, regional and national scales. Many pioneering monitoring and modelling approaches developed have been applied internationally. This history shows the importance of integrating discovery science with monitoring for informing policy development and assessing efficacy of management options. It also demonstrates the need to continue to resource long‐term sites, which act as a focus for inter‐disciplinary research and innovation, and where the overall value of the research greatly exceeds the costs of individual component parts.

Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations.

Genomic structural variants (SVs) are now recognized as an integral component of intraspecific polymorphism and are known to contribute to evolutionary processes in various organisms. However, they are inherently difficult to detect and genotype from readily available short-read sequencing data, and therefore remain poorly documented in wild populations. Salmonid species displaying strong interpopulation variability in both life history traits and habitat characteristics, such as Atlantic salmon (Salmo salar), offer a prime context for studying adaptive polymorphism, but the contribution of SVs to fine-scale local adaptation has yet to be explored. Here, we performed a comparative analysis of SVs, single nucleotide polymorphisms (SNPs) and small indels (<50 bp) segregating in the Romaine and Puyjalon salmon, two putatively locally adapted populations inhabiting neighboring rivers (Québec, Canada) and showing pronounced variation in life history traits, namely growth, fecundity, and age at maturity and smoltification. We first catalogued polymorphism using a hybrid SV characterization approach pairing both short- (16X) and long-read sequencing (20X) for variant discovery with graph-based genotyping of SVs across 60 salmon genomes, along with characterization of SNPs and small indels from short reads. We thus identified 115,907 SVs, 8,777,832 SNPs and 1,089,321 short indels, with SVs covering 4.8 times more base pairs than SNPs. All three variant types revealed a highly congruent population structure and similar patterns of F ST and density variation along the genome. Finally, we performed outlier detection and redundancy analysis (RDA) to identify variants of interest in the putative local adaptation of Romaine and Puyjalon salmon. Genes located near these variants were enriched for biological processes related to nervous system function, suggesting that observed variation in traits such as age at smoltification could arise from differences in neural development. This study therefore demonstrates the feasibility of large-scale SV characterization and highlights its relevance for salmonid population genomics.

Ecological interactions between farmed Atlantic salmon and wild Atlantic cod populations in Norway: A review of risk sources and knowledge gaps

AbstractAquaculture provides an important and expanding source of protein rich and healthy food to the world. However, to minimize environmental harm from aquaculture, interactions with wild fish communities need to be thoroughly assessed. Here, we characterize the existing knowledge pertaining to such interactions, exemplified with Atlantic salmon (Salmo salar) farming in open net pens along the Norwegian coast and potential consequences for wild Atlantic cod (Gadus morhua) populations. Importantly, the wild cod fishery also provides a protein rich, high quality food source with high economic value. We identify seven risk sources that may affect behaviour, physiology, and survival in wild cod. Of particular importance is the large amount of waste feed that causes wild fish to aggregate around farms, thereby altering a multitude of ecological interactions including predation and disease transmission. Moreover, altered food quality in pellets may alter physiological processes and cause mortality to vulnerable life‐stages in wild cod. More research is needed on mechanisms and thresholds for harm. As the most important cod fisheries are found in northern Norway, where climate change also is rapid, we expect stronger and potentially more harmful interactions between fish farming and wild cod fisheries as aquaculture continues to expand. We hope that our analysis will inspire further research, on farmed salmon and wild cod interactions, but also on aquaculture and wild fish interactions in general. Such research is fundamental for the development of management systems that can reduce the impact of aquaculture on fisheries and the environment.

Swimming behaviour of Atlantic salmon kelts migrating past a hydropower plant dam: Effects of hydraulics and dam operations

Hydropower plants commonly impede the downstream migration of Atlantic salmon (Salmo salar) kelts. Thus, understanding the effects of hydraulic conditions on kelt behaviour and passage performance at dams is crucial for developing effective mitigation measures. In this study, we investigated the influence of hydraulic conditions on kelt passage performance and swimming behaviour at a Norwegian hydropower plant. We combined biological data from 48 kelts collected via acoustic telemetry with hydraulic data modelled using computational fluid dynamics. We assessed kelt passage performance using metrics such as time-to-pass, total number of detections, and total number of detections per day. Additionally, we analysed swimming depths and speeds in relation to the hydraulic conditions created by different dam operating conditions. We found that the dam operation schedule impacted the kelts' ability to find a route past the dam. Though kelts could have passed the dam throughout the study period via a submerged pipe at the dam (which had seemingly sufficient discharge for the kelts to find), 98 % of the kelts instead waited for a spill gate to open partway through the study period. The swimming depth analysis indicated diel variation, with kelts swimming nearer to the water surface during the night. We found that swimming speed increased with increasing kelt body length, particularly under high turbulence kinetic energy and during the day. Furthermore, kelts swam faster as water velocity increased, but slowed down again as turbulence intensity increased. Our findings reveal the effects of hydraulic conditions and dam operations on the migration behaviour of Atlantic salmon kelts. This provides valuable insights for developing strategies to optimise dam operations and improve fish passage performance, including the need to spill enough water to increase passage success and will contribute to sustainable management of Atlantic salmon populations in regulated rivers.

No additional stress of sublethal gas supersaturation in a landlocked population of Atlantic salmon (Salmo salar) exposed to environmental acidification

The landlocked Atlantic salmon population “bleke” faces extinction due to environmental acidification (EA) and hydropower expansion in the Norwegian river Otra. Despite of restoration, unexpected mortality has been reported for this population, possibly due to gas bubble trauma (GBT) from gas supersaturation (GSS) downstream of hydroelectric plants, or EA induced aluminum toxicity. In this study, we applied the allostasis concept to investigate interactions between EA and GBT. This concept comprises additive effects of stressors, which can lead to allostatic overload. Stress coping mechanisms become maladaptive in such situations, which can be indicated by an inability to mount a proper cortisol response in fish. Fish were exposed to sublethal levels of simulated EA (SEA), GSS (a total gas pressure; TGP; of 110%) or a combination of these stressors for six days. Effects on allostatic load were subsequently investigated by assessing the cortisol response to an acute stress test. SEA increased cortisol responsiveness and GSS induced clinical signs of GBT, but no interacting effects between GSS and SEA were observed. This suggests that that 110% TGP did not have an additive effect on the allostatic load imposed by SEA.

Optimal timing of return migration in Atlantic salmon

AbstractIn many populations of Atlantic salmon, individuals return to rivers months or even a year prior to spawning. This premature arrival in fresh water by far exceeds the time needed for upstream migrations to spawning areas. Leaving the ocean early means forgoing substantial growth and incurring high metabolic costs of fasting in freshwater. Differences in timing of return migration has been shown to have a genetic basis, and different sea age classes return to rivers at different times. Previously suggested explanations regarding the cause for this behaviour have included both environmental factors and life history trade‐offs, but these hypotheses have not been tested. Here, we combine data on marine growth and mortality of Atlantic salmon with the calculations of energetic expenditures of fasting in freshwater to explore how timing of river entry affects the probability of survival and energy recourses available for spawning. Our results show that to maximize the product of survival until spawning and energy available at spawning, multi sea winter fish in general must enter rivers earlier than one sea winter fish. And that for a large range of sea survival rates, the optimum river entry date for multi sea winter fish is as early as possible. This strongly suggests that the phenomena of premature arrival in Atlantic salmon is adaptive behaviour.

Population genomics, life-history tactics, and mixed-stock subsistence fisheries in the northernmost American Atlantic salmon populations.

While Atlantic salmon (Salmo salar) of the northernmost American populations is alimentary, economically, and culturally important for Ungava Inuit communities (Nunavik, Canada) and might play a key role in the persistence of the species in a global warming context, many mysteries remain about those remote and atypical populations. Thus, our first aim was to document the genomic structure of the Nunavik populations. The second objective was to determine whether salmon only migrating to the estuary without reaching the sea, apparently unique to those populations, represent distinct populations from the typical anadromous salmons and subsequently explore the genetic basis of migratory life-history tactics in the species. Finally, the third goal was to quantify the contribution of each genetically distinct population and life-history tactic in the mixed-stock subsistence fishery of the Koksoak R. estuary. We used Genotyping-by-Sequencing to genotype 14,061 single nucleotide polymorphisms in the genome of 248 individuals from 8 source populations and 280 individuals from the Koksoak estuary mixed-stock fishery. Life-history tactics were identified by a visual assessment of scales. Results show a hierarchical structure mainly influenced by isolation-by-distance with 7 populations out of the 8 studied rivers. While no obvious structure was detected between marine and estuarine salmon within the population, we have identified genomic regions putatively associated with those migration tactics. Finally, all salmon captured in the Koksoak estuary originated from the Koksoak drainage and mostly from 2 tributaries, but no inter-annual variation in the contribution of these tributaries was found. Our results indicate, however, that both marine and estuarine salmon contribute substantially to estuarine fisheries and that there is inter-annual variation in this contribution. These findings provide crucial information for the conservation of salmon populations in a rapidly changing ecosystem, as well as for fishery management to improve the food security of Inuit communities.

Determining early marine survival and predation by endothermic predators on acoustically tagged Atlantic salmon (Salmo salar) post-smolts

Many Atlantic salmon ( Salmo salar) populations have experienced significant declines for decades throughout North America and Europe. Mortality due to marine mammal predation during their early marine life could be an important factor contributing to these declines and limiting their population recoveries. However, quantifying predation events, and particularly the extent of marine mammal predation on Atlantic salmon, remains a challenge. In this study, we estimated the contribution of mesothermic and endothermic species predation to the mortality of Atlantic salmon post-smolts during their early marine life using acoustic telemetry. Predation events were inferred from changes in temperatures and depths experienced by acoustically tagged hatchery-reared Atlantic salmon smolts. No salmon were consumed by mesothermic predators, with most endothermic predation events being classified as marine mammals. Post-smolt mortality during the study period was low overall in both years (13.1%–16.7%), with endothermic predation accounting for 33.1%–42.9% of all marine mortality events (5.2%–5.6% mortality). Our results suggest that the current low return of adult Atlantic salmon observed in this area in recent years was not heavily influenced by endothermic predation on post-smolts in the first weeks at sea.