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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.

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.

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.

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 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.

Electronic tags are significantly improving our understanding of aquatic animal behavior and are emerging as key sources of information forconservation and management practices. Future aquatic integrative biology and ecology studies will increasingly rely on data from electronictagging. Continued advances in tracking hardware and software are needed to provide the knowledge required by managers and policymakersto address the challenges posed by the world’s changing aquatic ecosystems. We foresee multiplatform tracking systems for simultaneouslymonitoring the position, activity, and physiology of animals and the environment through which they are moving. Improved data collection willbe accompanied by greater data accessibility and analytical tools for processing data, enabled by new infrastructure and cyberinfrastructure. Tooperationalize advances and facilitate integration into policy, there must be parallel developments in the accessibility of education and training,as well as solutions to key governance and legal issues

Coastal commercial fisheries targeting Pacific salmon inevitably capture a mix of co-migrating species and genetically distinct populations within each species, only some of which are sufficiently abundant to sustain exploitation. Species-specific release measures are implemented as a conservation measure, but there remains little understanding of the resulting mortality. A purse seine fishery for Pacific salmon in British Columbia, Canada, was simulated with the goal of estimating post-release mortality for coho salmon, a species commonly released from commercial fisheries. Landed coho salmon (n = 220) were tagged with acoustic transmitters and tracked along their coastal approach and into freshwater. Survival analyses accounting for variable migration pathways among populations revealed population-specific survival, with the population of greatest conservation concern having the best survival. Condition assessments revealed scale loss to be the strongest predictor of success. Physically exhausted fish, identified via reflex impairment tests, also experienced higher mortality. Results highlight the complexity of estimating release mortality in mixed-population commercial fisheries and are discussed in the context of management implications.

Pacific salmon encounter widely varying environmental conditions across populations. Performance traits and environmental tolerance limits are predicted to be related to the typical abiotic and biotic conditions encountered by each population. Endurance swim performance at three different temperatures (8, 12, 22 °C) was compared across nine populations of sockeye salmon (Oncorhynchus nerka (Walbaum, 1792)) parr from British Columbia, Canada, reared in a common laboratory environment. In addition, relative ventricular mass (RVM) was compared between good and poor performers from each population. Populations significantly differed in endurance swim performance and these differences were related to the natal lake environment. Specifically, parr populations that reside in warm, shallow lakes (Okanagan, Scotch, and Stellako) had superior swim performance at 12 °C compared with 8 °C. All other populations from deeper, cooler lakes had equivalent swim performance at 8 and 12 °C. Individual variability in swim performance within a population was not due to differences in cardiac size. Similarly, RVM did not vary across parr populations, suggesting that population differences in swim performance were not associated with cardiac size. This study provides further support that sockeye salmon parr are locally adapted to their environmental conditions.

Adult female Pacific salmon can have higher migration mortality rates than males, particularly at warm temperatures. However, the mechanisms underlying this phenomenon remain a mystery. Given the importance of swimming energetics on fitness, we measured critical swim speed, swimming metabolism, cost of transport, aerobic scope (absolute and factorial) and exercise recovery in adult female and male coho salmon (Oncorhynchus kisutch) held for 2 days at 3 environmentally relevant temperatures (9°C, 14°C, 18°C) in fresh water. Critical swimming performance (Ucrit) was equivalent between sexes and maximal at 14°C. Absolute aerobic scope was sex- and temperature-independent, whereas factorial aerobic scope decreased with increasing temperature in both sexes. The full cost of recovery from exhaustive exercise (excess post-exercise oxygen consumption) was higher in males compared to females. Immediately following exhaustive exercise (i.e. 1 h), recovery was impaired at 18°C for both sexes. At an intermediate time scale (i.e. 5 h), recovery in males was compromised at 14°C and 18°C compared to females. Overall, swimming, aerobic metabolism, and recovery energetics do not appear to explain the phenomenon of increased mortality rates in female coho salmon. However, our results suggest that warming temperatures compromise recovery following exhaustive exercise in both male and female salmon, which may delay migration progression and could contribute to en route mortality.

Co-management is widely seen as a way of improving environmental governance and empowering communities. When successful, co-management enhances the validity and legitimacy of decision-making, while providing stakeholders with influence over processes and outcomes that directly impact them. However, our research with participants in co-management across several cases leads us to argue that many of the individuals who contribute to co-management are subject to significant personal stress arising from both the logistical and social/emotional demands of participation in these processes. We argue that the literature on co-management has touched on this only indirectly, and that personal stress is a major challenge for participants that ought to be integrated into research agendas and addressed by policy-makers. In this article, we review the contours of the personal stress issue as it has appeared in our observations of co-management events and interviews with participants. While these findings are partial and preliminary, we argue that personal stress has theoretical and practical significance to the broader literature and process design. We conclude the article with recommendations for participants, researchers and policy-makers about how to consider and respond to problems of personal stress. “Consulted to death”: Personal stress as a major barrier to environmental co-management

Early marine survival of juvenile salmon is intimately associated with their physiological condition during ocean entry and especially smoltification. Smoltification is a developmental parr–smolt transformation allowing salmon to acquire the trait of seawater tolerance in preparation for marine living. Traditionally, this developmental process has been monitored using gill Na+/K+ATPase (NKA) activity or plasma hormones, but gill gene expression can be reliably used. Here, we describe the discovery of candidate genes from gill tissue for staging smoltification using comparisons of microarray studies with particular focus on the commonalities between anadromous Rainbow trout and Sockeye salmon datasets, as well as literature comparison encompassing more species. A subset of 37 candidate genes mainly from the microarray analyses was used for Taq-Man qPCR assay design and their monthly expression patterns were validated using gill samples from four groups, representing three species and two ecotypes: Coho salmon, Sockeye salmon, stream-type Chinook salmon, and ocean-type Chinook salmon. The best smoltification biomarkers, as measured by consistent changes across these four groups, were genes involved in ion regulation, oxygen transport, and immunity. Smoltification gene expression patterns (using the top 10 biomarkers) were confirmed by significant correlations with NKA activity and were associated with changes in body brightness, caudal fin darkness, and caudal peduncle length. We incorporate gene expression patterns of pre-smolt, smolt, and de-smolt trials from acute seawater transfers using a companion study to develop a preliminary seawater tolerance classification model for ocean-type Chinook salmon. This work demonstrates the potential of gene expression biomarkers to stage smoltification and classify juveniles as pre-smolt, smolt, or de-smolt.

For Pacific salmon captured and released by fisheries, post-release behaviour and survival may be influenced by their health and condition at time of capture. We sought to characterize the interactions between infectious agent burden, fish immune and stress physiology and fisheries stressors to investigate the potential for capture-mediated pathogen-induced mortality in adult coho salmon Oncorhynchus kisutch. We used radio-telemetry paired with high-throughput qPCR of non-lethal gill biopsies for infectious agents and host biomarkers from 200 tagged fish experimentally displaced and exposed to various experimental fisheries treatments (gill net entanglement, recreational angling and recreational angling with air exposure vs. non-sampled control). We characterized relationships among post-release behaviour and survival, infectious agent presence and loads, physiological parameters and transcription profiles of stress and immune genes. All infectious agents detected were endemic and in loads consistent with previous adult Pacific salmon monitoring. Individuals exposed to fisheries treatments were less likely to reach spawning habitat compared to controls, and handling duration independent of fisheries gear had a negative effect on survival. High infectious agent burden was associated with accelerated migration initiation post-release, revealing behavioural plasticity in response to deteriorating condition in this semelparous species. Prevalence and load of infectious agents increased post-migration as well as transcription signatures reflected changes in immune and stress profiles consistent with senescence. Results from this study further our understanding of factors associated with fisheries that increase risk of post-release mortality and characterize some physiological mechanisms that underpin migratory behaviour.

Female-biased mortality has been repeatedly reported in Pacific salmon during their upriver migration in both field studies and laboratory-holding experiments, especially in the presence of multiple environmental stressors, including thermal stress. Here we used coho salmon (Oncorhynchus kisutch) to test whether females exposed to elevated water temperatures (18°C) i) suppress circulating sex hormones (testosterone, 11-ketotestosterone, and estradiol), owing to elevated cortisol levels, ii) have higher activities of enzymes supporting anaerobic metabolism (e.g., lactate dehydrogenase), iii) lower activities of enzymes driving oxidative metabolism (e.g., citrate synthase; CS), in skeletal and cardiac muscle, and iv) have more oxidative stress damage and reduced capacity for antioxidant defense (lower catalase activity; CAT). We found no evidence that a higher susceptibility to oxidative stress contributes to female-biased mortality at warm temperatures. We did, however, find that females had significantly lower cardiac LDH and that 18°C significantly reduced plasma levels of testosterone and estradiol, especially in females. We also found that relative gonad size was significantly lower in the 18°C treatment regardless of sex, whereas relative liver size was significantly lower in females held at 18°C. Further, relative spleen size was significantly elevated in the 18°C treatments across both sexes, with larger warm-induced increases in females. Our results suggest that males may better tolerate bouts of cardiac hypoxia at high temperature, and that thermal stress may also disrupt testosterone- and estradiol-mediated protein catabolism, and the immune response (larger spleens) in migratory female salmon.

Environmental scientists have long been frustrated by the difficulties involved in transferring their research findings into policy-making, management, and public spheres. Despite increases in scientific knowledge about social-ecological systems, research has consistently shown that regulators and stakeholders draw on tacit, informal, and experiential knowledge far more than scientific knowledge in their decision-making. Social science research in the fields of knowledge exchange (KE) and knowledge mobilization (KMb) suggest that one of the major barriers to moving knowledge into practice is that scientists fail to align their communication strategies with the information-seeking behaviours and preferences of potential knowledge users. This article presents findings from in-depth qualitative research with government employees and stakeholders involved in co-managing Pacific salmon fisheries in Canada’s Fraser River. We investigate how members of these groups access, view, and use scientific information, finding both similarities and differences. Members of both groups express a strong interest in academic science, and self-report using scientific information regularly in their work and advocacy. However, the two groups engage in different information-seeking behaviours, and provide notably different advice to academic scientists about how to make research and communication more relevant to potential users. For example, government employees focus on the immediate applications of research to known problems, while stakeholders express greater concern for the political context and implications of scientific findings. We argue that scientists need to “go where the users are” in the behavioural and intellectual sense, and tailor their communications and engagement activities to match the habits, preferences, and expectations of multiple potential user groups. We conclude with recommendations on how this may be done.

Few estimates of migration rates or descriptions of behavior or survival exist for wild populations of out-migrating Pacific salmon smolts from natal freshwater rearing areas to the ocean. Using acoustic transmitters and fixed receiver arrays across four years (2010-2013), we tracked the migration of > 1850 wild sockeye salmon (Oncorhynchus nerka) smolts from Chilko Lake, British Columbia, to the coastal Pacific Ocean (> 1000 km distance). Cumulative survival to the ocean ranged 3-10% among years, although this may be slightly underestimated due to technical limitations at the final receiver array. Distinct spatial patterns in both behavior and survival were observed through all years. In small, clear, upper-river reaches, downstream migration largely occurred at night at speeds up to 50 km/d and coincided with poor survival. Among years, only 57-78% of smolts survived the first 80 km. Parallel laboratory experiments revealed excellent short-term survival and unhindered swimming performance of dummy-tagged smolts, suggesting that predators rather than tagging effects were responsible for the initial high mortality of acoustic-tagged smolts. Migration speeds increased in the Fraser River mainstem (~220 km/d in some years), diel movement patterns ceased, and smolt survival generally exceeded 90% in this segment. Marine movement rates and survival were variable across years, with among-year segment-specific survival being the most variable and lowest (19-61%) during the final (and longest, 240 km) marine migration segment. Osmoregulatory preparedness was not expected to influence marine survival, as smolts could maintain normal levels of plasma chloride when experimentally exposed to saltwater (30 ppt) immediately upon commencing their migration from Chilko Lake. Transportation of smolts downstream generally increased survival to the farthest marine array. The act of tagging may have affected smolts in the marine environment in some years as dummy-tagged fish had poorer survival than control fish when transitioned to saltwater in laboratory-based experiments. Current fisheries models for forecasting the number of adult sockeye returning to spawn have been inaccurate in recent years and generally do not incorporate juvenile or smolt survival information. Our results highlight significant potential for early migration conditions to influence adult recruitment.

The environment females experience during sexual maturation can have cascading effects on offspring. For free-swimming populations of wild fish, ecological factors including predation and competition are known to alter offspring phenotype. For wild-caught fish targeted for stock enhancement, logistical factors, such as the widespread practice of holding fish in captivity/confinement, also have the potential to modify offspring phenotype. Understanding how maternal captivity affects offspring, in comparison to offspring reared from fish that have matured in the wild, is an important but relatively understudied aspect of fish culture. We examined egg and offspring traits for wild-caught female sockeye salmon reared in captivity during the final stages of sexual maturation or captured on spawning grounds following in-river maturation. Compared to females that matured in-river, captive females had smaller eggs and offspring in poorer body condition. These same offspring did however swim for longer durations. These results suggest that maternal captivity prior to spawning elicits intergenerational phenotypic change. Whether captivity-induced maternal effects are maladaptive/reduce offspring fitness will be dependent upon the environment in which offspring are being released into (e.g. captive or wild). Intergenerational effects of short-term captivity of wild fish may be a contributing mechanism mediating the success of fisheries supplementation programmes.

This article examines threat perception as a potential dimension of inter-group conflict over salmon fisheries in Canada’s Fraser River watershed. Environmental changes and the entry of new user groups are putting pressure on both the resource and regulators, as well as threatening to exacerbate conflicts, notably between First Nation (indigenous) fishers and non-indigenous recreational anglers. While resource conflicts are often superficially conceptualized as cases of competing interests, we build on recent studies suggesting that conflicts are associated with deeper cognitive and perceptual differences among user groups. We report findings from 422 riverbank interviews with First Nation fishers and recreational anglers focusing on perceptions of threat to the fisheries. Responses reveal both substantial agreement and disagreement in threat perceptions between the two groups. These patterns provide a potential roadmap for consensus building, and suggest possible avenues for policy-makers to defuse the “blame game” that often dominates this type of conflict.

Aquatic animals are integral to ocean and freshwater ecosystems and their resilience, are depended upon globally for food sustainability, and support coastal communities and Indigenous peoples. However, global aquatic environments are changing profoundly due to anthropogenic actions and environmental change. These changes are altering distributions, movements, and survival of aquatic animals in ways that are not well understood. The Ocean Tracking Network (OTN) is a global partnership that is filling this knowledge gap. OTN Canada, a pan-Canadian (and beyond) research network, was launched in 2010 with visionary funding by the Canadian government. In our introduction to this special issue, we briefly overview how this interdisciplinary network has used state-of-the-art technologies, infrastructure, electronic tags and sensors, and associated cutting-edge research and training programs to better understand changing marine and freshwater dynamics and their impact on ecosystems, resources, and animal ecology. These studies have provided unprecedented insights into animal ecology and resource management at a range of spatial and temporal scales and by interfacing animal movements with novel measures of environment, physiology, disease, genetics–genomics, and anthropogenic stressors.

Pacific salmon routinely encounter stressors during their upriver spawning migration, which have the potential to influence offspring through hormonally-mediated maternal effects. To disentangle genetic vs. hormonal effects on offspring swimming performance, we collected gametes from three species of Pacific salmon (Chinook, pink and sockeye) at the end of migration and exposed a subset of eggs from each female to cortisol baths to simulate high levels of maternal stress. Fertilised eggs were reared to fry and put through a series of aerobic swim trials. Results show that exposure to cortisol early in development reduces maximum oxygen consumption while swimming, and decreases aerobic scope in all three species. Resting oxygen consumption did not differ between cortisol and control treatment groups. We also examined several metrics that could influence aerobic performance, and found no differences between treatment groups in haematocrit%, haemoglobin concentration, heart mass, citrate synthase activity or lactate dehydrogenase activity. Though it was not the focus of this study, an interesting discovery was that pink salmon had a higher MO2max and aerobic scope relative to the other species, which was supported by a greater haematocrit, haemoglobin, a larger heart and higher CS activity. Some management and conservation practices for Pacific salmon focus efforts primarily on facilitating adult spawning. However, if deleterious effects of maternal stress acquired prior to spawning persist into the next generation, consideration will need to be given to sub-lethal effects that could be imparted onto offspring from maternal stress., Lay summaries We investigated whether maternal stress in Pacific salmon can influence aerobic swimming performance of offspring, through stress hormones deposited into the eggs. We found that offspring exposed to higher levels of the stress hormone cortisol at fertilisation had poorer aerobic swimming performance, which may reduce survival in the wild.

An organism's ability to respond effectively to environmental change is critical to its survival. Yet, life stage and overall condition can dictate tolerance thresholds to heightened environmental stressors, such that stress may not be equally felt across individuals and at all times. Also, the transcriptional responses induced by environmental changes can reflect both generalized responses as well as others that are highly specific to the type of change being experienced. Thus, if transcriptional biomarkers specific to a stressor, even under multi-stressor conditions, can be identified, the biomarkers could then be applied in natural environments to determine when and where an individual experiences such a stressor. Here, we experimentally challenged juvenile Chinook salmon (Oncorhynchus tshawytscha) to validate candidate gill gene expression biomarkers. A sophisticated experimental design manipulated salinity (freshwater, brackish water and seawater), temperature (10, 14 and 18°C) and dissolved oxygen (normoxia and hypoxia) in all 18 possible combinations for 6 days using separate trials for three smolt statuses (pre-smolt, smolt and de-smolt). In addition, changes in juvenile behaviour, plasma variables, gill Na+/K+-ATPase activity, body size, body morphology and skin pigmentation supplemented the gene expression responses. We identified biomarkers specific to salinity and temperature that transcended the multiple stressors, smolt status and mortality (live, dead and moribund). Similar biomarkers for dissolved oxygen were not identified. This work demonstrates the unique power of gene expression biomarkers to identify a specific stressor even under multi-stressor conditions, and we discuss our next steps for hypoxia biomarkers using an RNA-seq study., Summary: Gene expression biomarkers associated with salinity stress and thermal stress, but not hypoxic stress, exist in salmon gill tissue. Biomarkers were also associated with mortality.

Background Pacific salmon (Oncorhynchus spp.) serve as good biological indicators of the breadth of climate warming effects on fish because their anadromous life cycle exposes them to environmental challenges in both marine and freshwater environments. Our study sought to mine the extensive functional genomic studies in fishes to identify robust thermally-responsive biomarkers that could monitor molecular physiological signatures of chronic thermal stress in fish using non-lethal sampling of gill tissue. Results Candidate thermal stress biomarkers for gill tissue were identified using comparisons among microarray datasets produced in the Molecular Genetics Laboratory, Pacific Biological Station, Nanaimo, BC, six external, published microarray studies on chronic and acute temperature stress in salmon, and a comparison of significant genes across published studies in multiple fishes using deep literature mining. Eighty-two microarray features related to 39 unique gene IDs were selected as candidate chronic thermal stress biomarkers. Most of these genes were identified both in the meta-analysis of salmon microarray data and in the literature mining for thermal stress markers in salmonids and other fishes. Quantitative reverse transcription PCR (qRT-PCR) assays for 32 unique genes with good efficiencies across salmon species were developed, and their activity in response to thermally challenged sockeye salmon (O. nerka) and Chinook salmon (O. tshawytscha) (cool, 13–14 °C and warm temperatures 18–19 °C) over 5–7 days was assessed. Eight genes, including two transcripts of each SERPINH1 and HSP90AA1, FKBP10, MAP3K14, SFRS2, and EEF2 showed strong and robust chronic temperature stress response consistently in the discovery analysis and both sockeye and Chinook salmon validation studies. Conclusions The results of both discovery analysis and gene expression showed that a panel of genes involved in chaperoning and protein rescue, oxidative stress, and protein biosynthesis were differentially activated in gill tissue of Pacific salmon in response to elevated temperatures. While individually, some of these biomarkers may also respond to other stressors or biological processes, when expressed in concert, we argue that a biomarker panel comprised of some or all of these genes could provide a reliable means to specifically detect thermal stress in field-caught salmon. Electronic supplementary material The online version of this article (10.1186/s12864-018-5108-9) contains supplementary material, which is available to authorized users.

There is a paucity of information on the physiological changes that occur over the course of salmon early marine migration. Here we aim to provide insight on juvenile Coho salmon (Oncorhynchus kisutch) physiology using the changes in gene expression (cGRASP 44K microarray) of four tissues (brain, gill, muscle, and liver) across the parr to smolt transition in freshwater and through the first eight months of ocean residence. We also examined transcriptome changes with body size as a covariate. The strongest shift in the transcriptome for brain, gill, and muscle occurred between summer and fall in the ocean, representing physiological changes that we speculate may be associated with migration preparation to feeding areas. Metabolic processes in the liver were positively associated with body length, generally consistent with enhanced feeding opportunities. However, a notable exception to this metabolic pattern was for spring post-smolts sampled soon after entry into the ocean, which showed a pattern of gene expression more likely associated with depressed feeding or recent fasting. Overall, this study has revealed life stages that may be the most critical developmentally (fall post-smolt) and for survival (spring post-smolt) in the early marine environment. These life stages may warrant further investigation.

Research on fisheries bycatch and discards frequently involves the assessment of reflex impairment, injury, or blood physiology as means of quantifying vitality and predicting post-release mortality, but exceptionally few studies have used all three metrics concurrently. We conducted an experimental purse seine fishery for Pacific salmon in the Juan de Fuca Strait, with a focus on understanding the relationships between different sublethal indicators and whether mortality could be predicted in coho salmon (Oncorhynchus kisutch) bycatch. We monitored mortality using a ~24-h net pen experiment (N = 118) and acoustic telemetry (N = 50), two approaches commonly used to assess bycatch mortality that have rarely been directly compared. Short-term mortality was 21% in the net pen experiment (~24 h) and estimated at 20% for telemetry-tagged fish (~48-96 h). Mortality was predicted by injury and reflex impairment, but only in the net pen experiment. Higher reflex impairment was mirrored by perturbations to plasma ions and lactate, supporting the notion that reflex impairment can be used as a proxy for departure from physiological homeostasis. Reflex impairment also significantly correlated with injury scores, while injury scores were significantly correlated with plasma ion concentrations. The higher time-specific mortality rate in the net pen and the fact that reflexes and injury corresponded with mortality in that experiment, but not in the telemetry-tagged fish released into the wild could be explained partly by confinement stress. While holding experiments offer the potential to provide insights into the underlying causes of mortality, chronic confinement stress can complicate the interpretation of patterns and ultimately affect mortality rates. Collectively, these results help refine our understanding of the different sublethal metrics used to assess bycatch and the mechanisms that can lead to mortality.

Acute stressors are commonly experienced by wild animals but their effects on fitness rarely are studied in the natural environment. Billions of fish are captured and released annually around the globe across all fishing sectors (e.g., recreational, commercial, subsistence). Whatever the motivation, release often occurs under the assumption of post-release survival. Yet, capture by fisheries (hereafter "fisheries-capture") is likely the most severe acute stressor experienced in the animal's lifetime, which makes the problem of physiological recovery and survival of relevance to biology and conservation. Indeed, fisheries managers require accurate estimates of mortality to better account for total mortality from fishing, while fishers desire guidance on strategies for reducing mortality and maintaining the welfare of released fish, to maximize current and future opportunities for fishing. In partnership with stakeholders, our team has extensively studied the effects of catch-and-release on Pacific salmon in both marine and freshwater environments, using biotelemetry and physiological assessments in a combined laboratory-based and field-based approach. The emergent theme is that post-release rates of mortality are consistently context-specific and can be affected by a suite of interacting biotic and abiotic factors. The fishing gear used, location of a fishery, water temperature, and handling techniques employed by fishers each can dramatically affect survival of the salmon they release. Variation among individuals, co-migrating populations, and between sexes all seem to play a role in the response of fish to capture and in their subsequent survival, potentially driven by pre-capture pathogen-load, maturation states, and inter-individual variation in responsiveness to stress. Although some of these findings are fascinating from a biological perspective, they all create unresolved challenges for managers. We summarize our findings by highlighting the patterns that have emerged most consistently, and point to areas of uncertainty that require further research.

The reproductive migration of anadromous salmonids through estuarine waters is one of the most challenging stages of their life cycle, yet little is known about the environmental and physiological conditions that influence migratory behaviour. We captured, sampled tissues, tagged and released 365 sockeye salmon (Oncorhynchus nerka) homing through inner coastal waters towards the Fraser River, British Columbia, Canada. Biotelemetry was used to assess the behaviour of individual sockeye salmon approaching estuarine waters and at river entry, which were related to both fish physiological condition at release and to prevailing environmental conditions. Sockeye salmon tended to stay close to the shore, migrated during the day, and movements were related to tide. Sockeye salmon migration rate was linked to wind-induced currents, salinity and an individual's physiological state, but these factors were specific to location and stock. We propose that wind-induced currents exposed sockeye salmon entering the estuary to stronger olfactory cues associated with Fraser River water, which in turn resulted in faster migration rates presumably due to either an increased ability for olfactory navigation and/or advanced reproductive schedule through a neuroendocrine response to olfactory cues. However, once the migration had progressed further into more concentrated freshwater of the river plume, sockeye salmon presumably used wind-induced currents to aid in movements towards the river, which may be associated with energy conservation. Results from this study improve our biological understanding of the movements of Fraser River sockeye salmon and are also broadly relevant to other anadromous salmonids homing in marine environments.

Directed animal movement, which drives behaviors such as natal philopatry or dispersal, is guided by the input of sensory information. Anadromous salmonids are philopatric (they return to their natal habitat to reproduce), and their upstream movements during the spawning migration are directed by olfactory cues. Two main sources of olfactory cues have been identified—imprinted natal cues and pheromones—although the relative importance of these cues is unresolved. We tested the response of migratory adult sockeye salmon (Oncorhynchus nerka) to conspecific odors in the presence of, and in the absence of, imprinted natal cues. The results indicate that sockeye salmon are attracted to conspecifics when imprinted natal cues are absent, but not when they are present. This suggests that pheromones may provide a directional cue that is secondary to the primary cue of imprinted chemicals. The finding follows the hierarchical navigation hypothesis and is supported by previous findings in salmonid research. There are several potential benefits to this method of navigation that could increase the reproductive success of stray migrants, which could promote dispersal and increase genetic diversity within populations.

SYNOPSIS Wild animals maximize fitness through certain behaviors (e.g., foraging, mating, predator avoidance) that incur metabolic costs and often require high levels of locomotor activity. Consequently, the ability of animals to achieve high fitness often relies on their physiological capacity for exercise (aerobic scope) and/or their ability to acquire and utilize energy judiciously. Here, we explore how environmental factors and physiological limitations influence exercise and metabolism in fish while foraging, migrating to spawning grounds, and providing parental care. We do so with three case studies that use a number of approaches to studying exercise in wild fish using biologging and biotelemetry platforms. Bonefish (Albula vulpes) selectively use shallow water tropical marine environments to forage when temperatures are near optimal for aerobic scope and exercise capacity. Bonefish energy expenditure at upper thermal extremes is maximal while activity levels diminish, likely caused by reduced aerobic scope. Pacific salmon (Oncorhynchus spp.) reproductive migrations frequently involve passage through hydraulically challenging areas, and their ability to successfully pass these regions is constrained by their physiological capacity for exercise. Aerobic scope and swim performance are correlated with migration difficulty among sockeye salmon (O. nerka) populations; however, depletion of endogenous energy stores can also limit migration success. In another example, male smallmouth bass (Micropterus dolomieu) allocate a significant amount of energy to nest-guarding behaviors to protect their developing brood. Smallmouth bass body size, endogenous energy reserves, and physiological state influence nest-guarding behaviors and reproductive success. We suggest that in some scenarios (e.g., bonefish foraging, Pacific salmon dam passage) metabolic capacity for exercise may be the strongest determinant of biological fitness, while in others (e.g., long distance salmon migration, smallmouth bass parental care) energy stores may be more important. Interactions among environmental and ecological factors, fish behavior, and fish physiology offer important avenues of mechanistic inquiry to explain ecological dynamics and demonstrate how exercise is fundamental to the ecology of fish.

This study describes sockeye salmon heart rate recovery profiles after a fisheries catch-and-release simulation in 16°C, 19°C and 21°C water. Warmer temperatures increased the peak heart rate, scope for heart rate, factorial heart rate and the initial rate of energy expenditure, though the overall recovery duration was consistent across treatments., Selective harvest policies have been implemented in North America to enhance the conservation of Pacific salmon (Oncorhynchus spp.) stocks, which has led to an increase in the capture and release of fish by all fishing sectors. Despite the immediate survival benefits, catch-and-release results in capture stress, particularly at high water temperatures, and this can result in delayed post-release mortality minutes to days later. The objective of this study was to evaluate how different water temperatures influenced heart rate disturbance and recovery of wild sockeye salmon (Oncorhynchus nerka) following fisheries interactions (i.e. exhaustive exercise). Heart rate loggers were implanted into Fraser River sockeye salmon prior to simulated catch-and-release events conducted at three water temperatures (16°C, 19°C and 21°C). The fisheries simulation involved chasing logger-implanted fish in tanks for 3 min, followed by a 1 min air exposure. Neither resting nor routine heart rate differed among temperature treatments. In response to the fisheries simulation, peak heart rate increased with temperature (16°C = 91.3 ± 1.3 beats min−1; 19°C = 104.9 ± 2.0 beats min−1 and 21°C = 117 ± 1.3 beats min−1). Factorial heart rate and scope for heart rate were highest at 21°C and lowest at 16°C, but did not differ between 19°C and 21°C. Temperature affected the initial rate of cardiac recovery but not the overall duration (~10 h) such that the rate of energy expenditure during recovery increased with temperature. These findings support the notion that in the face of climate change, efforts to reduce stress at warmer temperatures will be necessary if catch-and-release practices are to be an effective conservation strategy.

Autonomous acoustic telemetry monitoring systems have been deployed in aquatic ecosystems around the globe - from under ice sheets in the Arctic to coral reefs in Australia - to track animals. With tens of thousands of tagged aquatic animals from a range of taxa, vast amounts of data have been generated. As data accumulate, it is useful to reflect on how this information has advanced our understanding of aquatic animals and improved management and conservation. Here we identify knowledge gaps and discuss opportunities to advance aquatic animal science and management using acoustic telemetry monitoring. Current technological and analytical shortfalls still need to be addressed to fully realize the potential of acoustic monitoring. Future interdisciplinary research that relies on transmitter-borne sensors and emphasizes hypothesis testing will amplify the benefits of this technology.

We used biotelemetry and human dimensions surveys to explore potential solutions to migration mortality of an endangered population of coho salmon caught as bycatch in an aboriginal beach seine fishery. From 2009 to 2011, 182 wild coho salmon caught as bycatch in the lower Fraser River (Canada) were radio-tagged and tracked as they attempted to complete their migrations to natal spawning areas over 300 km upstream. Failure to survive to reach terminal radio receiving stations averaged 39% over three years. This mortality estimate is low compared to those obtained from telemetry studies on other salmon fisheries in the Fraser River. However, this value is markedly higher than the mortality estimate currently used to manage the fishery's impact. It is also in contrast to the perceptions of the majority of aboriginal fishers, who did not think survival of coho salmon is affected by capture and release from their fishery. Increased probability of survival was associated with lower reflex impairment, which is consistent with previous findings. Reflex impairment was positively correlated with entanglement time, suggesting that greater efforts by the fishers to release bycatch from their nets quickly would minimize post-release mortality. Survey responses by aboriginal fishers also suggested that they are receptive to employing new bycatch handling methods if they are shown to increase post-release survival. However, attempts to facilitate revival of a subset of captured fish using cylindrical in-river recovery bags did not improve migration success. Fisheries managers could use the new information from this study to better quantify impacts and evaluate different harvest options. Since aboriginal fishers were receptive to using alternate handling methods, efforts to improve knowledge on minimizing reflex impairment through reductions in handling time could help increase bycatch survival. Such a direct integration of social science and applied ecology is a novel approach to understanding conservation issues that can better inform meaningful actions to promote species recovery.

Emerging diseases are impacting animals under high-density culture, yet few studies assess their importance to wild populations. Microparasites selected for enhanced virulence in culture settings should be less successful maintaining infectivity in wild populations, as once the host dies, there are limited opportunities to infect new individuals. Instead, moderately virulent microparasites persisting for long periods across multiple environments are of greatest concern. Evolved resistance to endemic microparasites may reduce susceptibilities, but as barriers to microparasite distributions are weakened, and environments become more stressful, unexposed populations may be impacted and pathogenicity enhanced. We provide an overview of the evolutionary and ecological impacts of infectious diseases in wild salmon and suggest ways in which modern technologies can elucidate the microparasites of greatest potential import. We present four case studies that resolve microparasite impacts on adult salmon migration success, impact of river warming on microparasite replication, and infection status on susceptibility to predation. Future health of wild salmon must be considered in a holistic context that includes the cumulative or synergistic impacts of multiple stressors. These approaches will identify populations at greatest risk, critically needed to manage and potentially ameliorate the shifts in current or future trajectories of wild populations.

Although behaviour and physiology of the reproductive migration of Pacific salmon Oncorhynchus spp. have been studied for the upriver migration, equivalent information for the coastal marine migratory phase has been difficult to obtain. Acoustic acceleration transmitters equipped with pressure sensors provide a tool to study swimming activity and migration depth of salmon in both marine and fresh water. Ocean migrating sockeye salmon O. nerka bound for the Fraser River, British Columbia (Canada), were intercepted approximately 200 km from the river entrance, tagged and tracked as they crossed several acoustic receiver lines in coastal waters and the lower Fraser River. Acceleration data were converted to swim speed using an existing statisti- cal model. Data from 55 tagged fish revealed that swim speed and depth varied among migratory locales. Migration difficulty (freshwater migration distance and elevation to natal stream) was related to swim speed in the marine environment. Some of the variability in swim speed and depth was explained by diel and tidal cycles. In the marine environment, average (±SEM) swim speed estimate was ~1.23 body lengths (BL) s �1 at an average depth of 13 ± 0.058 m (range = 0�171 m), whereas the average swim speed in the river was significantly higher at ~1.57 BL s �1 at an average (±SEM) depth of ~9 ± 0.018 m (range = 0�21 m). Consistent with the physiological literature, coastal migrating fish were swimming near metabolically optimal speeds (0.9�1.2 BL s �1 ). Overall this study demonstrates that using acoustic accelerometer transmitters can provide valuable insights into behaviour of homing sockeye salmon in both marine and freshwater environments.

Temperature is recognized as a key factor influencing physiology, behaviour and survival of anadromous salmonids, yet little is known about their thermal experience, nor factors affecting it, during marine homeward migrations. In 2006 and 2010, approximately 1000 Fraser River sockeye salmon Oncorhynchus nerka were captured and tagged in coastal marine waters, ~215 km from the river mouth, during their spawning migration. Individual salmon were blood sampled, gastrically implanted with temperature loggers fixed to radio or acoustic tags, and released. We recovered 50 loggers from freshwater locales containing 14690 hourly temperature readings. Mixed-effects models were used to characterize marine thermal experience, and examine the association of thermal experience with initial physiological status as well as oceanographic and meteorological conditions. Sockeye salmon thermal experience was highly variable (8.4°C to 20.5°C), and we detected opposite diel patterns between study years that could be associated with moon phase, behavioural thermoregulation, olfactory/celestial navigation or predator avoidance. We were unable to find any relationships between thermal experience and environmental conditions or fish physiological state. Nonetheless, we found that the greatest variability in thermal experience was attributed to within-individual variation, suggesting that environmental and physiological variables need to be examined at different temporal and spatial scales, and/or additional environmental and physiological variables need to be assessed. Overall, the factors associated with the thermal experience of homing sockeye salmon in coastal marine environments are more complex than previously thought, and multiple year studies are needed before generalizing behavioural patterns observed from single year studies.