Salmon Populations Research Articles

Experiences from targeted removal of farmed Atlantic salmon from Norwegian rivers

Abstract Farmed salmon escaping from aquaculture and interbreeding with wild conspecifics pose a significant threat to the genetic integrity of natural salmon populations. Despite advancements in aquaculture security, escape incidents persist, prompting the need for effective mitigation strategies. This study summarizes experiences from efforts to remove escaped farmed salmon over a 12-year period in 63 western Norwegian rivers, using either (1) spearfishing during snorkelling by trained personnel or (2) traditional fishing methods employed by local groups. Recaptured farmed salmon ranged widely in size and included both spawners as well as immature fish, demonstrating that farmed fish entering rivers comprise fish of different ages and escape histories. Traditional fishing by locals recaptured the highest number of farmed fish, while removal during snorkelling in general captured larger and mature fish. On average, 53% of the farmed salmon observed during snorkelling were recaptured. This efficacy was influenced by the number of farmed fish present and the size of the farmed fish. In addition, efficacy increased over time, indicating that the removal team became more efficient. The study underscores that active removal, when executed judiciously, contributes to reducing the ecological risks associated with escaped farmed fish, complementing broader strategies for sustainable aquaculture.

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.

Most of the escaped farmed salmon entering a river during a 5-year period were infected with one or more viruses.

Disease interactions between farmed and wild populations have been poorly documented for most aquaculture species, in part due to the complexities to study this. Here, we tested 567 farmed Atlantic salmon escapees, captured in a Norwegian river during 2014-2018, for five viral infections that are prevalent in global salmonid aquaculture. Over 90% of the escapees were infected with one or more viruses. Overall prevalences were: 75.7% for piscine orthoreovirus (PRV-1), 43.6% for salmonid alphavirus (SAV), 31.2% for piscine myocarditis virus (PMCV), 1.2% for infectious pancreatic necrosis virus (IPNV) and 0.4% for salmon anaemia virus (ISAV). A significantly higher prevalence of PMCV infection was observed in immature compared to mature individuals. The prevalence of both SAV and PMCV infections was higher in fish determined by fatty acid profiling to be 'recent' as opposed to 'early' escapees that had been in the wild for a longer period of time. This is the first study to establish a time-series of viral infection status of escapees entering a river with a native salmon population. Our results demonstrate that farmed escapees represent a continuous source of infectious agents which could potentially be transmitted to wild fish populations.

The combined effects of predation, fishing, and ocean productivity on salmon species targeted by marine mammals in the northeast Pacific.

Along the northeast Pacific coast, the salmon-eating southern resident killer whale population (SRKW, Orcinus orca) have been at very low levels since the 1970s. Previous research have suggested that reduction in food availability, especially of Chinook salmon (Oncorhynchus tshawytscha), could be the main limiting factor for the SRKW population. Using the ecosystem modelling platform Ecopath with Ecosim (EwE), this study evaluated if the decline of the Pacific salmon populations between 1979 and 2020 may have been impacted by a combination of factors, including marine mammal predation, fishing activities, and climatic patterns. We found that the total mortality of most Chinook salmon populations has been relatively stable for all mature returning fish despite strong reduction in fishing mortality since the 1990s. This mortality pattern was mainly driven by pinnipeds, with increases in predation between 1979 and 2020 mortality ranging by factors of 1.8 to 8.5 across the different Chinook salmon population groups. The predation mortality on fall-run Chinook salmon smolts originating from the Salish Sea increased 4.6 times from 1979 to 2020, whereas the predation mortality on coho salmon (Oncorhynchus kisutch) smolts increased by a factor of 7.3. The model also revealed that the north Pacific gyre oscillation (NPGO) was the most important large-scale climatic index affecting the stock productivity of Chinook salmon populations from California to northern British Columbia. Overall, the model provided evidence that multiple factors may have affected Chinook salmon populations between 1979 and 2020, and suggested that predation mortality by marine mammals could be an important driver of salmon population declines during that time.

Association of ectoparasite Lepeophtheirus salmonis counts on farmed Atlantic salmon and wild sea trout in Scotland.

Parasitic sea lice (Copepoda: Caligidae) colonising marine salmonid (Salmoniformes: Salmonidae) aquaculture production facilities have been implicated as a possible pressure on wild salmon and sea trout populations. This investigation uses monitoring data from the mainland west coast and Western Isles of Scotland to estimate the association of the abundance of adult female Lepeophtheirus salmonis (Krøyer) colonising farmed Atlantic salmon Salmo salar L. with the occurrence of juvenile and mobile L. salmonis on wild sea trout, anadromous S. trutta L. The associations were evaluated using generalised linear mixed models incorporating farmed adult female salmon louse abundances which are temporally lagged relative to dependent wild trout values. The pattern of lags, which is consistent with time for L. salmonis development between egg and infective stage, was evaluated using model deviances. A significant positive association is identified between adult female L. salmonis abundance on farms and juvenile L. salmonis on wild trout. This association is consistent with a causal relationship in which increases in the number of L. salmonis copepodids originating from lice colonising farmed Atlantic salmon cause an increase of L. salmonis abundance on wild sea trout.

Population genetic diversity of coho salmon (Oncorhynchus kisutch Walbaum) in the Asian part of its range based on the results of microsatellite loci analysis

Polymorphism of 10 nuclear microsatellite loci in coho salmon populations in the Asian part of the range was studied for the first time. Three genetically distinct regional stock complexes were identified: Kamchatka, northern part of the Sea of Okhotsk and Sakhalin. It was shown that all populations, regardless of their geographic location, are characterized by a high level of genetic polymorphism.

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.

Restoring freshwater habitat mosaics to promote resilience of vulnerable salmon populations

AbstractPhenotypic diversity and abundance drive salmon resilience in the face of increasing environmental variability. But what happens when human activities fundamentally alter the habitat complexity that drives this diversity? And how can we restore habitats to recover both diversity and abundance to support salmon persistence in a warming climate? Here, we looked at the impact of a large watershed restoration effort on the abundance and climate resilience of the three remaining core natural spring‐run Chinook Salmon populations in the California Central Valley (Butte, Mill, and Deer Creek). Butte Creek fish, which have floodplain access, had higher overall productivity and faster juvenile growth compared with Mill and Deer Creek populations, and the proportion of floodplain inundation was positively correlated with Butte Creek adult abundance two years later. While Butte Creek exhibited significant increases in abundance post‐restoration (~2000%), it generally exhibited lower phenotypic diversity and only a marginal increase in population stability after restoration based on the coefficient of variation (CV). In particular, Butte Creek salmon tended to exhibit larger drops in escapement following dry years (e.g., return years 2010, 2017) compared with Mill and Deer Creek populations, presumably due to limited inundation of its downstream floodplain. The late‐migrating juvenile strategy (i.e., yearling), which disproportionately supported Mill and Deer Creek populations during droughts, was uncommon among Butte Creek adults (averaging 60% of returns for Mill and Deer Creek vs. 0.3% for Butte Creek). Increased spring‐run stock complex stability was found, post‐restoration, when combining the three spring‐run populations (i.e., lower aggregate CV). However, among‐river pairwise correlations also suggested increased synchronization in population abundances post‐restoration, potentially due to increasing frequency and severity of extreme climatic events (e.g., droughts and ocean warming). This study underscores the importance of restoring a connected mosaic of aquatic habitats across modified landscapes, such as cold water refugia and floodplains, to preserve multiple (across‐population) life history pathways for increasing salmon stock complex stability and abundance. These landscape‐scale process‐based habitat restoration efforts are likely to be crucial for the successful long‐term recovery of vulnerable species in a rapidly changing climate.

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.

Incorporation of climate change into a multiple stressor risk assessment for the Chinook salmon (Oncorhynchus tshawytscha) population in the Yakima River, Washington, USA.

One outcome of the 2022 Society of Environmental Toxicology and Chemistry Pellston Workshop on incorporating climate change predictions into ecological risk assessments was the key question of how to integrate ecological risk assessments that focus on contaminants with the environmental alterations from climate projections. This article summarizes the results of integrating selected direct and indirect effects of climate change into an existing Bayesian network previously used for ecological risk assessment. The existing Bayesian Network Relative Risk Model integrated the effects of two organophosphate pesticides (malathion and diazinon), water temperature, and dissolved oxygen levels on the Chinook salmon population in the Yakima River Basin (YRB), Washington, USA. The endpoint was defined as the entity, Yakima River metapopulation, and the attribute was defined as no decline to a subpopulation or the overall metapopulation. In this manner, we addressed the management objective of no net loss of Chinook salmon, an iconic and protected species. Climate change-induced changes in water quality parameters (temperature and dissolved oxygen levels) used models based on projected climatic conditions in the 2050s and 2080s by the use of a probabilistic model. Pesticide concentrations in the original model were modified assuming different scenarios of pest control strategies in the future, because climate change may alter pest numbers and species. Our results predict that future direct and indirect changes to the YRB will result in a greater probability that the salmon population will continue to fail to meet the management objective of no net loss. As indicated by the sensitivity analysis, the key driver in salmon population risk was found to be current and future changes in temperature and dissolved oxygen, with pesticide concentrations being not as important. Integr Environ Assess Manag 2024;20:419-432. © 2023 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Expanded, compressed, or equal? Interactions between spawning window and stream thermal regime generate three responses in modeled juvenile emergence for Pacific salmon

Climate warming poses challenges to native fish, particularly at high latitudes. We used incubation models to explore how interactions between spawning timing and daily varying water temperature affected emergence timing for five species of Pacific salmon in 33 thermally diverse streams in south-central Alaska. Interactions between spawning timing and stream thermal regime led to three different emergence timing responses: 1) “expanded” by typically 2–3 times the duration of the spawning window for summer spawning salmon at streams with a large annual water temperature range; 2) “equal” in duration to the spawning window, regardless of spawning timing, at streams with upwelling groundwater; and 3) “compressed” for late-spawning salmon where water temperature was cooler at spawning than at emergence. Across all sites, a ±15-day range in spawning timing had influence similar to anomalously warm winters (+2 to +3 °C) on the emergence timing window. Differences among species, spawning timing, and thermal regimes suggest a range of adaptations in spawning behavior will likely enable Pacific salmon populations to accommodate shifting thermal regimes during their early life history.

Genomic evidence for domestication selection in three hatchery populations of Chinook salmon, Oncorhynchus tshawytscha.

Fish hatcheries are widely used to enhance fisheries and supplement declining wild populations. However, substantial evidence suggests that hatchery fish are subject to differential selection pressures compared to their wild counterparts. Domestication selection, or adaptation to the hatchery environment, poses a risk to wild populations if traits specific to success in the hatchery environment have a genetic component and there is subsequent introgression between hatchery and wild fish. Few studies have investigated domestication selection in hatcheries on a genomic level, and even fewer have done so in parallel across multiple hatchery-wild population pairs. In this study, we used low-coverage whole-genome sequencing to investigate signals of domestication selection in three separate hatchery populations of Chinook salmon, Oncorhynchus tshawytscha, after approximately seven generations of divergence from their corresponding wild progenitor populations. We sequenced 192 individuals from populations across Southeast Alaska and estimated genotype likelihoods at over six million loci. We discovered a total of 14 outlier peaks displaying high genetic differentiation (F ST) between hatchery-wild pairs, although no peaks were shared across the three comparisons. Peaks were small (53 kb on average) and often displayed elevated absolute genetic divergence (D xy) and linkage disequilibrium, suggesting some level of domestication selection has occurred. Our study provides evidence that domestication selection can lead to genetic differences between hatchery and wild populations in only a few generations. Additionally, our data suggest that population-specific adaptation to hatchery environments likely occurs through different genetic pathways, even for populations with similar standing genetic variation. These results highlight the need to collect paired genotype-phenotype data to understand how domestication may be affecting fitness and to identify potential management practices that may mitigate genetic risks despite multiple pathways of domestication.

Quantifying impacts of harbor seal Phoca vitulina predation on juvenile Coho Salmon in the Strait of Georgia, British Columbia

AbstractObjectiveCoho Salmon Oncorhynchus kisutch provide an important resource for recreational, commercial, and Indigenous fisheries in the Pacific Northwest. The goal of this study was to improve our understanding of how marine mammal predation may be impacting the survival and productivity of Coho Salmon in the Strait of Georgia, British Columbia. Specifically, we quantified the impact of harbor seal Phoca vitulina predation on juvenile Coho Salmon during their first several months at sea. Early marine survival is believed to be the limiting factor for the recovery of Coho Salmon populations in this region.MethodsTo estimate the number of juvenile Coho Salmon consumed by harbor seals, we developed a mathematical model that integrates predator diet data and salmon population and mortality dynamics.ResultOur analysis estimated that harbor seals consumed an annual average of 46−59% of juvenile Coho Salmon between 2004–2016, providing the first quantitative estimate of seal predation in the Strait of Georgia.ConclusionMarine mammal predation on juvenile Coho Salmon is potentially a very important factor limiting survival and recovery of Coho Salmon in the Strait of Georgia.

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.

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.

Louse‐induced mortality thresholds in Atlantic salmon of wild‐origin

AbstractWild salmonid fish are faced with the challenge of infections from the ectoparasitic salmon louse, which thus dictates the management of salmon aquaculture in areas where farms and wild populations co‐exist. The mortality risk of wild Atlantic salmon is used as an indicator of threat levels when monitoring wild populations, and therefore the aim of this study was to robustly investigate the effect of infection intensity on probability of mortality in salmon of wild origin. To assess critical infection levels, recently‐smoltified Atlantic salmon were infected with intensities ranging from 0 to 2.5 lice g−1 and exposed to a 48‐h simulated migration. The first mortalities occurred when preadults appeared and ceased as lice became adults. Infection intensity negatively affected mortality probability and survival time, whereas the simulated migration had no influence on the probability of mortality. Individual‐level effects of infection on host mortality is difficult to quantify in the field; however, the correlation between louse load and mortality probability obtained in this study can facilitate indirect estimates of mortality risk of wild salmon populations and contribute to conservation efforts associated with this parasite.