Salmon Populations Research Articles

Monitoring and predicting the presence and abundance of juvenile Atlantic salmon in tributaries according to habitat characteristics using environmental DNA

AbstractConservation of the Atlantic salmon Salmo salar requires to monitor the spatial distribution and abundance of juveniles at a local scale in tributaries. However, tributaries are rarely accounted for in monitoring programs despite their importance for juvenile life stages. This is mainly because inventories of young salmon populations in tributaries can be technically challenging with traditional methods, as the number of tributaries in a watershed can be important and their access limited compared to the main stem. In this study, we tested the use of environmental DNA (eDNA) to quantify the abundance of juvenile Atlantic salmon in tributaries. We successfully detected eDNA of juvenile Atlantic salmon in 19 tributaries of three main rivers of the Gaspé Peninsula (Québec, Canada) using quantitative real‐time PCR analyses. By comparing the eDNA approach with electrofishing surveys conducted in parallel to water sampling, we found that eDNA concentrations positively correlated with juvenile abundance, total biomass, and body surface area. The use of the allometrically scaled mass (ASM) instead of abundance improved the correlation. Furthermore, we demonstrated that the levels of eDNA molecules detected for juvenile Atlantic salmon were also correlated with water temperature and canopy cover measured in each tributary. Finally, we tested if eDNA concentrations measured in a tributary could be used as a reliable indicator of juvenile abundance or biomass in that tributary. We found that our models slightly better predicted juvenile biomass than juvenile abundance. The use of ASM did not improve model prediction, suggesting that further refinement would be required in the future. Our method will facilitate the implementation of conservation practices appropriate to the ecology of juvenile Atlantic salmon in tributaries.

A Review of Pacific Salmon Hatcheries in British Columbia, Canada, and Interactions With Natural Populations

Pacific salmon Oncorhynchus spp. hatcheries in British Columbia (BC) have been the major activity of the Salmonid Enhancement Program since 1977. However, the present diminished abundance of Pacific salmon and loss of fisheries in BC called for a review of hatchery effectiveness. The Pacific Salmon Foundation conducted a review resulting in 15 reports publicly available on the Pacific Salmon Foundation marine science website. The review includes evaluations of effectiveness of hatchery production, evidence of interactions with natural salmon populations (including rebuilding natural populations with hatchery‐produced salmon), and future opportunities via genomics. Beyond the estimation of juvenile production and contribution to catches and spawning escapements, the ability to assess effectiveness was limited. The assessments of interactions provided a few examples of positive outcomes, but most were negative. The lack of comparative assessments in purely wild populations seriously limits interpretations of hatchery–wild interactions. Future evaluations of the hatchery effectiveness require more quantitative and integrated assessments of hatchery and wild salmon, open data sharing for public review or research, and related studies could benefit from application of new genomic technologies. This paper presents recommendations to address these needs and calls for regularized reviews of the Salmonid Enhancement Program and its net value to sustainability of BC's Pacific salmon.

Insights from Hi-C data regarding the Pacific salmon louse (Lepeophtheirus salmonis) sex-chromosomes.

Salmon lice, Lepeophtheirus salmonis (family Caligidae), are ectoparasites that have negatively impacted the salmon aquaculture industry and vulnerable wild salmon populations. Researchers have studied salmon lice to better understand their biology to develop effective control strategies. In this study, we updated the chromosome-level reference genome assembly of the Pacific subspecies of L. salmonis using Hi-C data. The previous version placed contigs/scaffolds using an Atlantic salmon louse genetic map. By utilizing Hi-C data from Pacific salmon lice, we were able to properly assign locations to contigs/scaffolds previously unplaced or misplaced. This resulted in a more accurate genome assembly and a more comprehensive characterization of the sex-chromosome unique to females (W). We found evidence that the same ZW-ZZ mechanism is common in both Atlantic and Pacific subspecies of salmon lice using PCR assays. The W-chromosome was approximately 800 kbp in size, which is ∼30 times smaller than the Z-chromosome (24 Mbp). The W-chromosome contained 61 annotated genes, including 32 protein-coding genes, 27 long non-coding RNA (lncRNA) genes, and 2 pseudogenes. Among these 61 genes, 39 genes shared homology to genes found on other chromosomes, while 20 were unique to the W-chromosome. Two genes of interest on the W-chromosome, prohibitin-2 and kinase suppressor of ras-2, were previously identified as potential sex-linked markers in the salmon louse. However, we prioritized the 20 unique genes on the W-chromosome as sex-determining candidates. This information furthers our understanding of the biology of this ectoparasite and may help in the development of more effective management strategies.

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.

Reintroducing Atlantic salmon in the river Rhine for decades: Why did it not result in the return of a viable population?

AbstractFreshwater species biodiversity is under threat. The average global decline for migratory fish species is estimated to be more than 75% since 1970. Atlantic salmon is one of these species with a steep decline in north‐western Europe and it even went extinct in the river Rhine in the 1950s. The causes for this decline have been posted to habitat loss, pollution, climate change and overfishing. Annual stocking in the Rhine since the late 1980s resulted in an initial increase in the Atlantic salmon numbers after which numbers collapsed again. In this paper, we lay out the recent decline, estimate losses of smolts and adults at different sections in the freshwater habitat and elaborate on potential causes of the recent decline and these losses. We found that the salmon population of the river Rhine has declined rapidly over the past two decades, with a current estimated spawning population of only ~350–800 individuals. The percentage of salmon smolts returning as adults to spawning grounds is estimated at 0.5%–0.6%, well below the 3% supposedly needed to maintain a self‐sustaining population. Many individuals disappear during their migrations, with the highest percentage of smolts disappearing in the German tributaries (44%) and the Dutch lower Rhine (71%), while the percentage of disappearing adults is highest in both the Dutch (74%) and the German (78%) Rhine. Causes for the losses per river section remain unclear and possible threats, some specific to the river Rhine, are being discussed. The large losses of smolts and adults in inland waters, compared with open sea losses, indicate that restocking the river Rhine might only result in a self‐sustaining population with more ecological restoration than carried out so far along the intensively shipped and highly regulated river course and associated high levels of predation, and might be increasingly limited by future climate change.

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.

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.

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.

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.

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.

Opening the black box: New insights into the role of temperature in the marine distributions of Pacific salmon

AbstractPacific salmon (Oncorhynchus spp.) spend much of their life near the ocean surface where climatic and oceanographic conditions affect their habitat and survival. Despite decades of study, critical knowledge gaps persist regarding their ecology and distributions. Consequently, it has been difficult to assess how environmental conditions influence the high‐seas distribution and habitat use of these culturally and socioeconomically important fishes, presenting challenges to fisheries managers trying to evaluate how climate change and fishing activities may impact salmon populations. We used a recently compiled, comprehensive database of historical coastal and high‐seas salmon survey data (1953–2022) in the North Pacific to fit species distribution models that (1) characterize the marine spatial distribution of six species of Oncorhynchus, (2) evaluate species‐specific temperature preferences, and (3) investigate how species' temperature preferences influence distribution. Sea surface temperature, along with seasonal migrations associated with spawning and feeding, significantly affects the distribution of all species, where the warm limits of estimated preferred thermal ranges were more similar than the cold limits. Furthermore, the distributions of some species appear more responsive to temperature than others and recently observed warm conditions have likely impacted realized ranges. These models have expanded our understanding of salmon ocean distributions and thermal niches by providing a unique window into this often unobserved but important part of the life cycle. They also serve as a baseline for future investigations into the mechanisms influencing salmon spatial ecology, responses to climate change, and vulnerability to harvest across the North Pacific.

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.