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During spawning migrations, adult Pacific salmon ( Onco rhynchus spp.) must undergo a suite of morphological and physiological changes to prepare for spawning. Modern genomics approaches can be used to conduct nonlethal assessments of physiology and infectious agent presence in migrating salmon. We investigated gene expression changes and shifts in the prevalence and load of 18 infectious agents in the gill tissue of adult sockeye salmon ( Oncorhynchus nerka) during the final 50 km of their freshwater migration. We found 77% of fish successfully migrated to spawning grounds. Fish exhibited a decrease in thermal stress gene expression following lake migration, consistent with the hypothesized benefits of thermal refugia during spawning migrations. We also found evidence of cooler water selection (∼1.5 °C) during lake migration for fish with higher infection burden, suggesting behavioural changes for fish suffering higher infection burdens and potential benefits of thermal refuges for reducing the negative impacts of infection for migrating salmon. Collectively, our findings provide further evidence that fish behaviourally regulate exposure to stressful conditions such as high temperature that may undermine survival.

Substantial, acute mortality was observed in wild-caught Chinook salmon (Oncorhynchus tshawytscha) of various ages and sizes, from sub-adults to returning adults, held in tanks during two holding studies carried out in August and September 2022 at the Bamfield Marine Sciences Centre (BMSC), in Bamfield, British Columbia, Canada. Within days of capture, a substantial number of fish began presenting lethargy, loss of balance, abnormal swimming behavior, and skin ulcers involving the caudal peduncle, fins, belly, trunk and mouth. Molecular testing revealed high levels ofTenacibaculum dicentrarchiin skin swabs and gills, without appreciable consistent detections of other infectious agents.T. dicentrarchiwas also isolated from the skin ulcers. Histological analysis confirmed the presence of ulcerative dermatitis and myositis, associated with mats of filamentous, rod-shaped bacteria. In two individuals, the infection became systemic, with a bacterial colony (identified asT. dicentrarchi) observed in the liver of one individual. In-situ hybridization againstT. dicentrarchiandT. maritimumconfirmed the presence of only the former agent in the gills and skin ulcers of the affected fish. This clinical report represents the first diagnosed case of tenacibaculosis in wild-caught (captive) Chinook salmon in British Columbia.CONFLICT OF INTERESTThe authors have no conflicts of interest to report.DATA AVAILABILITY STATEMENTThe data that support the findings of this study are available from the corresponding author upon reasonable request.

Effective management of freshwater fish habitat is essential to supporting healthy aquatic ecosystems and sustainable fisheries. In Canada, recent changes to the Fisheries Act enhanced the protection of fish habitat, but application of those provisions relies on sound scientific evidence. We employed collaborative research prioritization methods to identify scientific research questions that, if addressed, would significantly advance the management of freshwater fish habitat in Canada. This list was generated by a diverse group of freshwater fish experts, including substantial contributions from practitioners who administer provisions of the Fisheries Act. The research questions generated in this study identify priority topics for future research, while highlighting issues that could be addressed with different funding models. As a result, this study should support evidence-based management of Canada’s aquatic resources by identifying scientific knowledge gaps faced by practitioners, and suggesting mechanisms to address them. Given the important contribution of Canadian freshwater systems to global ecosystem values, and the similar scientific challenges facing fish habitat managers in other jurisdictions, this study is likely to have broad applicability.

The early marine life of Pacific salmon is believed to be a critical period limiting population-level survival. Recent evidence suggests that some infectious agents are associated with survival but linkages with underlying physiological mechanisms are lacking. While challenge studies can demonstrate cause and effect relationships between infection and pathological change or mortality, in some cases pathological change may only manifest in the presence of environmental stressors; thus, it is important to gain context from field observations. Herein, we examined physiological correlates with infectious agent loads in Chinook salmon during their first ocean year. We measured physiology at the molecular (gene expression), metabolic (plasma chemistry) and cellular (histopathology) levels. Of 46 assayed infectious agents, 27 were detected, including viruses, bacteria and parasites. This exploratory study identified: Importantly, our study provides the first evidence that the molecular activation of viral disease response and the lesions observed during the development of the PRV-related disease jaundice/anemia in farmed Chinook salmon are also observed in wild juvenile Chinook salmon.

Climate change is causing large declines in many Pacific salmon populations. In particular, warm rivers are associated with high levels of premature mortality in migrating adults. The Fraser River watershed in British Columbia, Canada, supports some of the largest Chinook salmon (Oncorhynchus tshawytscha) runs in the world. However, the Fraser River is warming at a rate that threatens these populations at critical freshwater life stages. A growing body of literature suggests salmonids are locally adapted to their thermal migratory experience, and thus, population-specific thermal performance information can aid in management decisions. We compared the thermal performance of pre-spawning adult Chinook salmon from two populations, a coastal fall-run from the Chilliwack River (125 km cooler migration) and an interior summer-run from the Shuswap River (565 km warmer migration). We acutely exposed fish to temperatures reflecting current (12°C, 18°C) and future projected temperatures (21°C, 24°C) in the Fraser River and assessed survival, aerobic capacity (resting and maximum metabolic rates, absolute aerobic scope (AAS), muscle and ventricle citrate synthase), anaerobic capacity (muscle and ventricle lactate dehydrogenase) and recovery capacity (post-exercise metabolism, blood physiology, tissue lactate). Chilliwack Chinook salmon performed worse at high temperatures, indicated by elevated mortality, reduced breadth in AAS, enhanced plasma lactate and potassium levels and elevated tissue lactate concentrations compared with Shuswap Chinook salmon. At water temperatures exceeding the upper pejus temperatures (Tpejus, defined here as 80% of maximum AAS) of Chilliwack (18.7°C) and Shuswap (20.2°C) Chinook salmon populations, physiological performance will decline and affect migration and survival to spawn. Our results reveal population differences in pre-spawning Chinook salmon performance across scales of biological organization at ecologically relevant temperatures. Given the rapid warming of rivers, we show that it is critical to consider the intra-specific variation in thermal physiology to assist in the conservation and management of Pacific salmon.

Incorporating host-pathogen(s)-environment axes into management and conservation planning is critical to preserving species in a warming climate. However, the role pathogens play in host stress resilience remains largely unexplored in wild animal populations. We experimentally characterized how independent and cumulative stressors (fisheries handling, high water temperature) and natural infections affected the health and longevity of released wild adult sockeye salmon (Oncorhynchus nerka) in British Columbia, Canada. Returning adults were collected before and after entering the Fraser River, yielding marine- and river-collected groups, respectively (N = 185). Fish were exposed to a mild (seine) or severe (gill net) fishery treatment at collection, and then held in flow-through freshwater tanks for up to four weeks at historical (14°C) or projected migration temperatures (18°C). Using weekly nonlethal gill biopsies and high-throughput qPCR, we quantified loads of up to 46 pathogens with host stress and immune gene expression. Marine-collected fish had less severe infections than river-collected fish, a short migration distance (100 km, 5-7 days) that produced profound infection differences. At 14°C, river-collected fish survived 1-2 weeks less than marine-collected fish. All fish held at 18°C died within 4 weeks unless they experienced minimal handling. Gene expression correlated with infections in river-collected fish, while marine-collected fish were more stressor-responsive. Cumulative stressors were detrimental regardless of infections or collection location, probably due to extreme physiological disturbance. Because river-derived infections correlated with single stressor responses, river entry probably decreases stressor resilience of adult salmon by altering both physiology and pathogen burdens, which redirect host responses toward disease resistance.

Dead animals may be an important or the only source of tissues to analyze for stable isotopes, with the goal of making inferences about an animal’s past ecological history. However, in nature, stable isotope values may be affected by myriad decomposition processes, such as abiotic environmental conditions and bacterial and fungal decay, potentially reducing the accuracy of derived ecological conclusions. We used Pacific salmon carcasses left in air or submerged under water to test whether stable isotope values of metabolically active (skin, muscle, and adipose fin) and inactive (scale) tissues changed over time. We found that the δ13C values of active tissues were all affected by decomposition but not in a predictable direction, and hard scale tissue was not. In contrast, there was no effect on δ15N values for any tissue up to 4 days under water or 8 days in air. This suggests that tissues can be analyzed for nitrogen stable isotope values even after several days in water and even if covered in fungus on the surface. For populations within which dead animals are frequently encountered, e.g., salmonid carcass surveys, hard tissues of fish (scales, otoliths) and other animals (baleen, bone, hair, feathers) will likely yield relevant biological information even if soft tissue is rotting, providing another avenue to collect important data about the life history of those animals.

In recent decades, the relative proportion of female sockeye salmon (Oncorhynchus nerka) on spawning grounds of several British Columbia populations has declined. Coincident with the decline has been large changes to oceanic, estuarine, and river migration environments. Over the past 30 years, numerous telemetry tracking and laboratory studies have examined mortality of adult Fraser River sockeye salmon during ocean and freshwater migrations. We reviewed 19 studies that provided 40 situations where male and female mortality could be directly compared. Female mortality averaged 2.1 times greater than that of males and up to eightfold higher. High female mortality was also evident in migrating coho salmon (Oncorhynchus kisutch) and Chinook salmon (Oncorhynchus tshawytscha) and for sockeye salmon in other systems. Female mortality was highest when migration conditions were challenging (e.g., high or turbulent flows, high temperatures, confinement, or handling) and towards end of river migration. We review mechanisms for differential mortality, including energy exhaustion, cardiac performance, physiological stress, and immune factors. Female-specific mortality will become even more pronounced in coming years as ocean and riverine conditions continue to change.

Although telemetry is commonly used to study fishes, researchers rarely design experiments that facilitate in situ quantification of tagging-related impacts to survival. We experimentally applied high (mean burden = 9.6%) and low (2.6%) acoustic tag burdens and gill clip biopsies to migrating juvenile sockeye salmon (Oncorhynchus nerka). Mortality from release to the last marine receiver array was 1.51 times greater for the high tag burden group (25% surviving) compared with the low burden group (40% surviving). A biopsy effect was limited to the first migration segment (14 km), where mortality was 1.86 times greater for biopsied fish. These results demonstrate the importance of quantifying biopsy and tagging effects when survival estimates are prioritized.

Numerous laboratory and field studies have found that female Pacific salmon have higher mortality than males during their once-in-a-lifetime upriver spawning migration. However, the proximate cause(s) of this increased mortality are poorly understood. This study exposed sockeye salmon (Oncorhynchus nerka) to a mild capture and tagging stressor and evaluated physiological recovery and movement behaviour at 1 and 4 h postrelease. Female sockeye salmon did not expend more anaerobic energy in response to the stressor but did have higher plasma lactate levels 4 h after the stressor, indicating that females took longer to physiologically recover compared with males. In addition, female salmon had lower plasma glucose but higher plasma cortisol, plasma K+, and cardiac lactate levels compared with males. Male and female salmon had markedly different postrelease behaviours within the first hour of release; males were more likely to hold position within the staging area. Two potential mechanisms leading to increased mortality in female salmon were identified in this study: (a) prolonged recovery duration (possibly mediated by elevated plasma cortisol levels) and (b) insufficient oxygen delivery to the heart.

Many of the world’s rivers are dammed, altering the physiology, behaviour, ecology and survival of fish. Integrative research has the potential to improve our understanding of these impacts and could enable environmental managers to develop effective solutions for population conservation. Such approaches, however, are not yet prevalent. We use a case study on Pacific salmon (Oncorhynchus spp.) in British Columbia, Canada, to demonstrate how regulated rivers may be used as experimental systems, allowing for applied research that can advance our understanding of the biology of migratory fish as well as our ability to manage them. Through the integration of multiple research approaches (i.e. biotelemetry, behavioural tests, physiological and molecular analyses, and hydraulic monitoring), we characterized the effects of natal water dilution and dam flow releases on upstream navigation, passage success and post-passage survival of returning adult salmon. Our findings confirmed previously established operational guidelines for natal water dilution and informed the adoption of new operational conditions for dam flow releases, providing an example of the successful application of integrative research to the management of a fisheries resource in a regulated river. We encourage researchers to consider using an experimental approach that integrates multiple research disciplines to inform science-based management action.

In some salmonid populations, multiple smolt age classes co-emigrate owing to variation in the duration of freshwater residence. While it is assumed that smolts prolong freshwater residence to maximize survival, infectious agent profiles and host gene expression (GE) have not been compared between concurrently migrating age classes. We coupled molecular assays of gill samples from nonlethally biopsied Chilko Lake sockeye salmon smolts with acoustic telemetry to study variation in infectious agent profiles and GE between age classes and survival groups. Although neither infectious agent profiles or GE were associated with survival, age-2 smolts exhibited higher mortality in the first 14 km of the downstream migration. There were measurable differences between the age classes in GE and the prevalence and load of “Candidatus Branchiomonas cysticola”, a bacterium commonly found in British Columbia salmonids. Relative to age-1 smolts, age-2 smolts displayed elevated GE related to inflammation and a molecular-based mortality-related signature. Although not associated with migration failure in this study, these patterns of GE are suggestive of mortality and could have implications for smolt survival.

Multiple stressors are commonly encountered by wild animals, but their cumulative effects are poorly understood, especially regarding infection development. We conducted a holding study with repeated gill and blood sampling to characterize the effects of cumulative stressors on infection development in adult coho salmon. Treatments included chronic thermal stress (15°C vs. 10°C) and acute gill net entanglement with an air exposure (simulating fisheries bycatch release). The potential loadings of 35 infectious agents and the expression of 17 host immune genes were quantified using high-throughput quantitative polymerase chain reaction, while host physiology was characterized with chemical analysis of blood. Temporal increases in infectious agent richness and loads were concurrent with decreased expression of immune genes in fish sampled in the river. In the laboratory, mortality was minimal in cool water regardless of fishery treatment ( 1 wk) and enhanced mortality associated with handling and biopsy (∼40% both sexes). Experimental gillnetting at high temperature further enhanced female mortality (73%). Fish held at high temperature demonstrated heavier infectious agent loads, osmoregulatory impairment, suppressed female maturation, and upregulation of inflammatory and extracellular immune genes. At high temperature, heavy Parvicapsula minibicornis loads were associated with premature mortality. Females exhibited physiological impairment from both stressors after 1 wk, and infection burdens correlated poorly with immune gene regulation compared with males. Cumulative effects of multiple stressors on female mortality are likely a function of physiological impairment and enhanced infections at high temperature.

Biotelemetry data have been successfully incorporated into aspects of fishery and fish habitat management; however, the processes of knowledge mobilization are rarely published in peer-reviewed literature but are valuable and of interest to conservation scientists. Here, we explore case examples from the Ocean Tracking Network (OTN), including Pacific salmon (Oncorhynchus spp.) in British Columbia, Canada; Greenland halibut (Reinhardtius hippoglossoides) in Cumberland Sound, Canada; and lemon sharks (Negaprion brevirostris) in Florida, USA, to document key processes for science integration. Typical recommendations documented in the literature (e.g., co-production of knowledge, transdisciplinary methodologies, applied research questions) were recorded to have had successful fisheries management integration, although we documented some exceptions. In each case, it was early, active, and ongoing communication outside of traditional science communication and the visual evidence of fish movement that were critical in engaging all parties with a vested interest. Networks offer forums for knowledge sharing on lessons learned and development of skills to engage in active communication. Greater investments and attention to develop these skills are needed to foster positive and active relationships that can impart real change in management and conservation.

White sturgeon (Acipenser transmontanus) are anadromous and the largest fish occurring in fresh-water habitats in North America. The largest population is found in the lower Fraser River (LFR), British Columbia, Canada where anglers target the species in a catch-and-release (C&R) recreational fishery. Yet, little is known about the consequences of C&R on these wild fish. Sixty-three angled sturgeon had blood samples taken to assess the physiological stress response relative to fight times. Seven sturgeon were also fitted with acoustic transmitters equipped with accelerometer sensors to assess immediate post-release locomotor behaviour. To understand the relationship between accelerometry and fish behaviour, we calibrated the tags in a lab before deploying them in the field. A physiological stress response was apparent (i.e., increased whole-blood lactate and reduced plasma potassium) and was influenced by fight time. Post-release activity profiles showed a general decrease in activity over time. Post-release displacement was 2–75 m from the release site and all 7 sturgeon were relocated closer to shore. The possible preference we identified for nearshore areas after release should be examined in greater detail in the future as this may lend insight into optimal release locations for white sturgeon. Although C&R mortality rates are low for this species, there is some evidence of transient sub-lethal effects emphasizing the need to refine C&R practices to further improve fish welfare.

Understanding the perspectives of knowledge users and the demands of their decision-making environment would benefit researchers looking to enhance the utility of the knowledge they generate. Using the Fraser River Pacific salmon fishery as a case study, we investigate the views of 49 government employees and stakeholders regarding the barriers to incorporating new knowledge into fisheries management. Our study uses analysis of qualitative data structured by a knowledge–action framework, which revealed that 90% of respondents perceived the contextual dimension (e.g., institutional structures and norms) as a barrier for incorporating new knowledge, followed by barriers related to the characteristics of knowledge actors (52% of respondents), characteristics of the knowledge (27%), time and timing (27%), knowledge transfer strategies (17%), and relational dimension (8%). The identified barriers have indirect–direct relationship with knowledge producers and appear hierarchical in nature. We note that informal relationships can enable conditions whereby knowledge users can access new knowledge, and knowledge producers can gain insights on users’ needs. We discuss lessons learned from the case, which we believe can be applied more beyond fisheries.

Throughout history, humans have settled in areas of high biodiversity. Today these areas are home to our biggest urban centers with biodiversity at increasing risk from escalating cumulative threats. Identifying the management strategies to conserve species within such regions, and ensuring effective governance to oversee their implementation, presents enormous challenges. Using a novel Priority Threat Management (PTM) approach that calculates the cost‐effectiveness of conservation action and co‐governance, we discover that the 102 species at risk of local extinction within Canada's most diverse, heavily urbanized coastal region, the Fraser River estuary, require urgent investment in management strategies costing an estimated CAD$381 M over 25 years. Our study also suggests that co‐governance underpins conservation success in urban areas, by increasing the feasibility of management strategies. This study underscores that biodiversity conservation in heavily urbanized areas is not a lost cause but does require strategic planning, attention to governance, and large‐scale investment.

We used acoustic telemetry to investigate survival of age-2 sockeye salmon (Oncorhynchus nerka) as they emigrated from Chilko Lake, British Columbia, Canada, to northeastern Vancouver Island (NEVI) from 2010 to 2014. We built on our previously reported results by including an additional year of data and by converting survival estimates into rates (distance and time) to compare across disproportionate habitats. We also refined our survival estimates by including individual covariates in our survival models and by re-investigating the detection efficiency of the final detection site. There was a tag burden effect in 2012 and a body size effect in 2013. Excluding 2010, survival during the 35- to 47-day migration to NEVI (range of annual mean travel time; 1044 km) ranged between 8% and 14%. Weekly survival rate (S·week−1) during downstream migration to the Fraser River estuary, through the central Strait of Georgia (CSOG), and NEVI was 25%–46%, 75%–90%, and 34%–64%, respectively. In addition to marked losses in freshwater tributaries, sockeye also experienced high losses north of the CSOG consistent with earlier results for Cultus Lake sockeye.

We show that cardiac sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) activity differs considerably among sockeye salmon (Oncorhynchus nerka) populations. Variability in SERCA activity was significantly correlated with elevation gain and temperature during migration, as well as maximum cardiac stroke volume. Furthermore, because SERCA activity was not lowered during the spawning migration, this aspect of the cardiac contraction machinery is apparently spared during the senescence of these semelparous salmon, likely because it is essential for these fish to complete spawning. Only when spawning had been completed was there a significant reduction in SERCA activity, which was detectable in males at a 25 °C and in females at a 15 °C assay temperature. Hence, we propose that migration conditions act as a strong selective force that has resulted in local adaptation of myocardial SERCA activity among sockeye salmon populations.

Following interactions with fisheries gear, fishes may experience delayed mortality or display modified behavior. The physiological status of fish at the time of capture, including the presence of infectious agents, can also influence survival outcomes. To explore the relationship between capture, infectious agents and fate, we simulated gillnet capture on adult salmon returning to a hatchery, used quantitative PCR to quantify infectious agents in non-lethal gill biopsies, and determined longevity, migratory fate, and migration rate using radio telemetry. An accompanying holding experiment investigated the relationship between infectious agents and longevity. Gillnetted fish took longer to migrate than biopsy-only fish (median 3.8 versus 2.5 days), but there was no difference in survival or migratory success among treatment groups. Longevity for fish infected with a parasite, Cryptobia salmositica, was similar between the holding (median = 7.0 days) and telemetry (7.4 days) experiments and significantly lower than that of uninfected fish (17.4 days in telemetry experiment). Males were 5.1 times more likely to arrive at spawning grounds compared to females and also migrated faster. The impact of C. salmositica on adult Chinook salmon in our study was demonstrated at the molecular (genes), physiological (plasma variables), and organism (migratory success) levels. These results demonstrate an instance where sex and infection were better predictors of migratory fate than an experimentally applied capture experience.

Both laboratory and field respirometry are rapidly growing techniques to determine animal performance thresholds. However, replicating protocols to estimate maximum metabolic rate (MMR) between species, populations, and individuals can be difficult, especially in the field. We therefore evaluated seven different exercise treatments-four laboratory methods involving a swim tunnel (critical swim speed [Ucrit], Ucrit postswim fatigue, maximum swim speed [Umax], and Umax postswim fatigue) and three field-based chasing methods (3-min chase with 1-min air exposure, 3-min chase with no air exposure, and chase to exhaustion)-in adult coho salmon (Oncorhynchus kisutch) as a case study to determine best general practices for measuring and quantifying MMR in fish. We found that all seven methods were highly comparable and that chase treatments represent a valuable field alternative to swim tunnels. Moreover, we caution that the type of test and duration of measurement windows used to calculate MMR can have significant effects on estimates of MMR and statistical power for each approach.

Impoundments and diversions in freshwater corridors can alter the availability and concentration of natal water cues that migratory salmon rely on to guide homing during spawning migrations, although this has rarely been examined. By combining radiotelemetry and noninvasive biopsy, we provide the first detailed account of the effects of varying natal water concentrations, temperature, and individual physiology on the homing behaviour of wild adult Pacific salmon migrating through a regulated river. Most (89%) of the 346 sockeye salmon (Oncorhynchus nerka) from the two distinct populations tracked in this study in southwestern British Columbia (Canada) delayed their migration in the outlet of a powerhouse that discharges strong concentrations of natal lake water and subsequently wandered in the Fraser River before continuing upstream into the Seton River, where natal water cues can also vary. There were few associations between metabolic stress indices and reproductive hormone levels with this behaviour in either population; however, higher temperatures and elevated natal water concentrations in the Seton River were associated with shorter powerhouse delays and less wandering in late-run migrants.

Animal migrations act to couple ecosystems and are undertaken by some of the world's most endangered taxa. Predators often exploit migrant prey, but the movements taken by these consumers are rarely studied or understood. We define such movements, where migrant prey induce large-scale movements of predators, as migratory coupling. Migratory coupling can have ecological consequences for the participating prey, predators and the communities they traverse across the landscape. We review examples of migratory coupling in the literature and provide hypotheses regarding conditions favourable for their occurrence. We also provide a framework for interactions induced by migratory coupling and demonstrate their potential community-level impacts by examining other forms of spatial shifts in predators. Migratory coupling integrates the fields of landscape, movement, food web and community ecologies, and represents an understudied frontier in ecology.