Wild Salmon Populations Research Articles

Wild salmon migration routes influence sea lice infestations: An agent-based model predicting farm-related infestations on juvenile salmon.

This study presents an Agent-Based Model (ABM) simulation to assess the impact of varying migration routes on sea lice (Caligus clemensi) infestation levels in juvenile wild sockeye salmon (Oncorhynchus nerka) in the Discovery Islands, British Columbia, Canada. This research highlights the importance of migratory routes in determining the extent of exposure to sea lice originating from nearby salmon farms. Three northward out-migration routes were modelled, each exposing the fish to different levels of infestation pressure based on proximity to salmon farms. The ABM incorporates spatially explicit migration patterns of juvenile sockeye salmon using a detailed raster map of the Discovery Islands. Key variables such as swimming speed, progression rate, and infestation levels were integrated into the model, offering a comprehensive analysis of migration and infestation dynamics. The study revealed that infestation rate is highly variable, depending on migration routes. Specifically, salmon traveling longer migration routes with lower infestation pressure may experience higher sea lice loads compared to those on shorter routes with higher infestation pressure. This underscores the role of low infestation pressures and the critical influence of swimming speed, which affects exposure time, and thus infestation rates. Additionally, the study conducted a sensitivity analysis to understand the influence of various parameters on infestation rates. This analysis highlighted the importance of swimming speed and progression rate, particularly in routes closer to the farms. The findings suggest that slower swimming speeds and meandering routes increase exposure to lice, thereby elevating infestation levels. The research contributes to understanding the dynamics of sea lice transmission and its relationship with salmon migration patterns. It underscores the necessity of considering migratory routes and farm proximity in managing and mitigating the impact of sea lice infestation on wild salmon populations. This study's insights are crucial for developing strategies to balance aquaculture practices with the conservation of wild salmon.

Salmon lice biology, environmental factors, and smolt behaviour with implications for the Norwegian salmon farming management system: A critical review

AbstractIn 2017, a new regulatory management system, the traffic light system (TLS), was implemented to estimate the effects of salmon lice from Norwegian salmon aquaculture on marine survival of wild Atlantic salmon and forms the basis of aquaculture capacity regulation. The TLS relies on observational data and a set of models to estimate the risk for negative impact on wild salmon populations. This review of the literature that forms the basis for the TLS as well as other relevant studies is presented in the context of the currently practiced TLS and suggestions are made for immediate and long‐term improvements. The main findings of this review are that: (1) assumed timing and duration of smolt migration contribute to unreliable observational and modelled data and overestimates of infection pressure; (2) production of lice larvae from farmed salmon is overestimated; (3) TLS model systems rely on or are calibrated by the same potentially flawed data; (4) lice‐associated mortality in wild salmon smolts may be overestimated; and (5) lice infection levels on farms are not associated with measurable effects on wild salmon. Recommendations to improve the accuracy and reliability of the TLS, and hence its environmental efficiency include the more complete use of available biological and physical environmental variables, adjusting the time period that observational data are registered and modelled data are integrated, adjusting the interpretation of data including recognition of uncertainty in model outcomes, and use of more realistic assumptions concerning lice‐induced mortality thresholds.

A comparison of sex‐specific markers for two wild masu salmon populations in Hokkaido, Japan

AbstractWe evaluated the utility of three male‐specific molecular markers, sdY, sdY 227U and OtY2m, in two wild populations of masu salmon (Oncorhynchus masou) in southwestern Hokkaido, Japan. Male‐specific fragments amplified in all phenotypic males across the markers. Phenotypic females were genetically identified as males using sdY (57%) and sdY 227U (4%), but no phenotypic females were identified as males using OtY2m. We conclude that OtY2m was the most reliable sex marker, followed closely by sdY 227U, among those tested in our study populations. Additional research is warranted to test the applicability of these markers in other populations and Oncorhynchus species.

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.

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

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

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.

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 kb in size, which is ∼30 times smaller than the Z chromosome (24 Mb). The W chromosome contained 61 annotated genes, including 32 protein-coding genes, 27 long noncoding 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.

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.

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.

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.

Modelling assessment of how small-scale vertical movements of infectious sea lice larvae can affect their large-scale distribution in fjordic systems

Sea lice are ectoparasites that can be found in high numbers in and around salmon farms, where they are a threat to fish health and can induce high aquacultural costs. Large numbers of suitable hosts facilitate the infection and subsequent release of their planktonic larvae in the surrounding environment where they can potentially infect wild salmonids, including migrating juvenile fish (smolts). Investigating sea lice spatial distribution is generally done using coupled hydrodynamic and particle tracking models. The quality of these numerical tools is critical to identify areas of higher infection risk to valuable wild salmon populations and thus support sustainable salmon aquaculture. While the transport of salmon lice is mainly affected by physical processes, biological behaviours such as vertical swimming can also play an important role. However, a review of previous sea lice studies shows no clear consensus on their swimming abilities and the parameters implemented in sea lice dispersion modelling. Here, we focus on the Diel Vertical Migration (DVM) behaviour, a vertical migration that sea lice perform within a daily cycle. Our sensitivity study of the infectious copepodid phase of sea lice highlights how their retention potential and spatial distribution within a water body are affected by their vertical swimming velocity and maximum swimming depth. In a fjordic system (Loch Linnhe on the West Coast of Scotland), the vertical position of sea lice can affect their horizontal trajectory due to the two-layer exchange flow of the estuarine circulation. At the surface, transport is mainly due to the wind driven circulation, and the residual seaward current. Lower in the water column, the saltier shelf water is drawn into the sea loch. This can potentially increase the retention of sea lice if they dive deep enough to reach those opposing subtidal currents. Therefore, lack of confidence in sea lice DVM parameterisation may introduce inaccuracy in modelled sea lice distribution. Effective sea lice management in aquaculture would benefit from more observational data like farm sea lice count, sea lice swimming laboratory observations, field observation of sea lice vertical distribution and accurate sea lice quantification in the field. This would help to reduce uncertainties derived from sea lice vertical swimming behaviour parameterisation in lice dispersal models.

Occurrence of salmonid alphavirus and piscine orthoreovirus-1 infections in migrating salmon (Salmo salar L.) post-smolt in western Norway.

Viral diseases are a serious problem in Atlantic salmon (Salmo salar L.) farming in Norway, often leading to reduced fish welfare and increased mortality. Disease outbreaks in salmon farms may lead to spread of viruses to the surrounding environment. There is a public concern that viral diseases may negatively affect the wild salmon populations. Pancreas disease (PD) caused by salmonid alphavirus (SAV) and heart and skeletal muscle inflammation (HSMI) caused by piscine orthoreovirus-1 (PRV-1) are common viral diseases in salmon farms in western Norway. In the current study, we investigated the occurrence of SAV and PRV-1 infections in 651 migrating salmon post-smolt collected from three fjord systems (Sognefjorden, Osterfjorden and Hardangerfjorden) located in western Norway in 2013 and 2014 by real-time RT-PCR. Of the collected post-smolts, 303 were of wild origin and 348 were hatchery-released. SAV was not detected in any of the tested post-smolt, but PRV-1 was detected in 4.6% of them. The Ct values of PRV-1 positive fish were usually high (mean 32.0; range: 20.1-36.8). PRV-1 prevalence in post-smolts from the three fjords was 6.1% in Sognefjorden followed by 4.8% in Osterfjorden and 2.3% in Hardangerfjorden. The prevalence PRV-1 was significantly higher in wild (6.9%) compared to hatchery-released post-smolt (2.6%). The occurrence of PRV-1 infection in the fish was lowest in the Hardangerfjorden which has the highest fish farming intensity. Our results suggest that SAV infection are uncommon in migrating smolt while PRV-1 infection can be detected at low level. These findings suggest that migrating smolts were at low risk from SAV or PRV-1 released from salmon farms located in their migration routes in 2013 and 2014.

Sea-lice regulation in salmon-farming countries: how science shape policies for protecting wild salmon

The proliferation of sea lice from aquaculture may substantially aggravate the decline in marine survival of wild salmons. In some countries, this risk has motivated regulators to adopt more precautionary policies; in other countries, however, regulators have disputed the need for stricter regulation. This article compares the sea-lice regulations of Norway, Scotland, Ireland, and Canada (British Columbia), showing how varying interpretations of the science on farm–wild interactions have shaped efforts to scale up regulatory measures for mitigating health hazards and mortality risks for wild salmon. In Norway and Scotland, scientific consensus has expedited cooperation between research and governing institutions and facilitated ambitious policy reforms. In Ireland and Canada, by contrast, scientific controversy around the scale of farm-lice impacts on wild salmon populations has led to conflict and disagreement between researchers and policymakers, and to failure of reform attempts desired by wild salmon stakeholders.

Using systematic conservation planning to inform restoration of freshwater habitat and connectivity for salmon

AbstractInstream barriers remain ubiquitous threats to freshwater species and their habitats. Decisions regarding barrier removal are often aimed at maximizing habitat area and connectivity for freshwater fish; yet can be challenging due to the sheer number of barriers, uncertainty in species presence, abundance, and habitat quality, as well as limited budgets alongside high costs of restoration. Here, we apply systematic conservation planning to prioritize in‐stream barrier removal aimed at restoring habitat connectivity for 14 populations of wild Pacific salmon in the lower Fraser River, Canada's most productive salmon‐bearing river. To understand how priorities change when stream quality is considered, we contrast scenarios that maximize habitat extent with scenarios that include four indicators of habitat quality. Region‐wide, approximately 64% of naturally accessible stream length is currently blocked by barriers. We estimate approximately 75% of this alienated habitat (over 1600 km of stream), could have full access restored with an investment of $200 million CAD, whereas 60% could be restored for half this amount. When stream quality was considered within the optimization, priorities for barriers removal shifted away from urbanized floodplain valleys towards less developed areas. The spatial shift in priorities meant that species like chum salmon (Oncorhynchus keta) would see less restored habitat. To inform barrier removal strategies using these model scenarios, an iterative and adaptive approach will be required that includes the values and priorities of rights and titleholders. Continuous improvement in data quality, accuracy, and feedback from monitoring as barriers are restored is also crucial.

Divergent RNA viruses infecting sea lice, major ectoparasites of fish.

Sea lice, the major ectoparasites of fish, have significant economic impacts on wild and farmed finfish, and have been implicated in the decline of wild salmon populations. As blood-feeding arthropods, sea lice may also be reservoirs for viruses infecting fish. However, except for two groups of negative-strand RNA viruses within the order Mononegavirales, nothing is known about viruses of sea lice. Here, we used transcriptomic data from three key species of sea lice (Lepeophtheirus salmonis, Caligus clemensi, and Caligus rogercresseyi) to identify 32 previously unknown RNA viruses. The viruses encompassed all the existing phyla of RNA viruses, with many placed in deeply branching lineages that likely represent new families and genera. Importantly, the presence of canonical virus-derived small interfering RNAs (viRNAs) indicates that most of these viruses infect sea lice, even though in some cases their closest classified relatives are only known to infect plants or fungi. We also identified both viRNAs and PIWI-interacting RNAs (piRNAs) from sequences of a bunya-like and two qin-like viruses in C. rogercresseyi. Our analyses showed that most of the viruses found in C. rogercresseyi occurred in multiple life stages, spanning from planktonic to parasitic stages. Phylogenetic analysis revealed that many of the viruses infecting sea lice were closely related to those that infect a wide array of eukaryotes with which arthropods associate, including fungi and parasitic tapeworms, implying that over evolutionary time there has been cross-phylum and cross-kingdom switching of viruses between arthropods and other eukaryotes. Overall, this study greatly expands our view of virus diversity in crustaceans, identifies viruses that infect and replicate in sea lice, and provides evidence that over evolutionary time, viruses have switched between arthropods and eukaryotic hosts in other phyla and kingdoms.

Reproductive success of jack and full-size males in a wild coho salmon population.

Despite the wealth of research on Pacific salmon Oncorhynchus spp. life histories there is limited understanding of the lifetime reproductive success of males that spend less time at sea and mature at a smaller size (jacks) than full-size males. Over half of returning male spawners can be jacks in some populations, so it is crucial to understand their contribution to population productivity. We quantified adult-to-adult reproductive success (RS) of jacks and their relative reproductive success (RRS) compared to full-size males in a wild population of coho salmon in the Auke Creek watershed, Juneau, Alaska. We used genetic data from nearly all individuals (approx. 8000) returning to spawn over a decade (2009-2019) to conduct parentage analysis and calculate individual RS. The average adult-to-adult RS of jacks (mean = 0.7 and s.e. = 0.1) was less than that of full-size males (mean = 1.1 and s.e. = 0.1). Jack RRS was consistently below 1.0 but ranged widely (0.23 to 0.96). Despite their lower average success, jacks contributed substantially to the population by siring 23% of the total returning adult offspring (1033 of 4456) produced between 2009 and 2015. Our results imply that jacks can affect evolutionary and population dynamics, and are relevant to the conservation and management of Pacific salmon.

Direct evidence of increased natural mortality of a wild fish caused by parasite spillback from domestic conspecifics.

Parasite spillback from domestic animals can distort the balance between host and parasites in surrounding wildlife, with potential detrimental effects on wild populations. In aquatic environments, parasite spillback from aquaculture to wild salmon is one of the most contentious sustainability debates. In a 19 year time series of release group studies of Atlantic salmon, we demonstrated that (i) the effect of subjecting out-migrating salmon smolts to parasite treatment on marine survival has been reduced over a time, (ii) the relation between salmon lice levels in the out-migration route of the salmon and effect of treatment against the parasite is weak, but also (iii) the return rates in both treated and untreated groups of salmon are negatively correlated with salmon lice levels, and (iv) returns of wild salmon to the region are similarly negatively correlated with salmon lice levels during the out-migration year. Our study suggests that salmon lice can have a large effect on wild salmon populations that is not revealed with randomized control trials using antiparasitic drugs. This should be better accounted for when considering the impacts of farms on wild salmon populations.

Detection and phylogenetic assessment of PRV-1 via sampling of biological materials released from salmon farms in British Columbia

The growth of the net pen salmon farming industry and the concurrent decline of many wild salmon populations have generated an ongoing call for research into the potential role of infectious agents associated with salmon farming. Here, we describe a method to screen for the presence of viral nucleic acids by sampling biological waste in the vicinity of farms. We collected biological samples adjacent to 56 marine net pens from five different companies, and two farm salmon processing plants ( n = 230), 70% of samples were positive for Piscine orthoreovirus-1 (PRV-1). Viral genome segments S1 ( n = 68) and M2 ( n = 39) were sequenced and subjected to phylogenetic analysis. Sequences were all monophyletic to the clade of PRV-1 routinely found in the region. Consistent with previous studies, samples collected near Atlantic salmon ( Salmo salar) farms were related to a lineage of PRV-1a commonly detected in both farmed and wild salmon in British Columbia, while a related lineage of PRV-1a was detected near Chinook salmon ( Oncorhynchus tshawytscha) farms. Similarity in sequence within companies suggests that Atlantic salmon freshwater hatcheries are a probable source of this virus to the marine environment, concordant with recent detections of PRV-1 within those hatcheries.

Links between host genetics, metabolism, gut microbiome and amoebic gill disease (AGD) in Atlantic salmon

BackgroundRapidly spreading parasitic infections like amoebic gill disease (AGD) are increasingly problematic for Atlantic salmon reared in aquaculture facilities and potentially pose a risk to wild fish species in surrounding waters. Currently, it is not known whether susceptibility to AGD differs between wild and farmed salmon. Wild Atlantic salmon populations are declining and this emerging disease could represent an additional threat to their long-term viability. A better understanding of how AGD affects fish health is therefore relevant for the accurate assessment of the associated risk, both to farming and to the well-being of wild populations. In this study, we assessed the impact of natural exposure to AGD on wild, hybrid and farmed post-smolt Atlantic salmon reared in a sea farm together under common garden conditions.ResultsWild fish showed substantially higher mortality levels (64%) than farmed fish (25%), with intermediate levels for hybrid fish (39%) suggesting that AGD susceptibility has an additive genetic basis. Metabolic rate measures representing physiological performance were similar among the genetic groups but were significantly lower in AGD-symptomatic fish than healthy fish. Gut microbial diversity was significantly lower in infected fish. We observed major shifts in gut microbial community composition in response to AGD infections. In symptomatic fish the relative abundance of key taxa Aliivibrio, Marinomonas and Pseudoalteromonas declined, whereas the abundance of Polaribacter and Vibrio increased compared to healthy fish.ConclusionsOur results highlight the stress AGD imposes on fish physiology and suggest that low metabolic-rate fish phenotypes may be associated with better infection outcomes. We consider the role increased AGD outbreak events and a warmer future may have in driving secondary bacterial infections and in reducing performance in farmed and wild fish.

Identifying a pathway towards recovery for depleted wild Pacific salmon populations in a large watershed under multiple stressors

Abstract Pacific salmon (Oncorhynchus spp.) support coastal and freshwater ecosystems, economies and cultures, but many populations have declined. We used priority threat management (PTM), a decision‐support framework for prioritizing conservation investments, to identify management strategies that could support thriving populations of wild salmon over 25 years. We evaluated the potential benefits of 14 strategies spanning fisheries, habitat, pollution, pathogens, hatcheries and predation management dimensions on 19 conservation units (CUs)—genetically and ecologically distinct populations—of the five Pacific salmon species in the lower Fraser River, British Columbia, Canada. The PTM assessment indicated that under the current trajectory of ‘business as usual’, zero CUs were predicted to have >50% chance of thriving in 25 years. Implementation of all management strategies at an annual investment between 45 and 110 million CAD was, however, predicted to achieve >50% chance of thriving for most CUs (n = 16), with nearly half (seven CUs) having a > 60% chance, indicating there is a pathway towards recovery for most populations if we invest now. In fact, substantial gains could be made by investing in five combined habitat strategies, costing 20M CAD annually. These habitat strategies were estimated to bring 14 of 19 salmon CUs above this 50% threshold. Co‐governance between First Nation and provincial and federal Canadian governments to manage salmon populations and harvest, and improved CU‐level monitoring emerged from the expert elicitation as critical ‘enabling’ strategies. By improving the feasibility of different management options, co‐governance brought an additional five CUs above the 60% threshold. Synthesis and applications. Supporting wild salmon in the face of cumulative threats will require strategic investment in effective management strategies, as identified by this priority threat management (PTM) assessment. PTM uses the best available data to objectively assess the potential outcomes of management alternatives. With renewed commitments from provincial and federal Canadian governments to protect and restore salmon populations and their habitats, positive conservation outcomes following implementation of targeted management strategies may be within reach.