Physiological condition infers habitat choice in juvenile sockeye salmon

The amount of time that juvenile salmon remain in an estuary varies among and within populations, with some individuals passing through their estuary in hours while others remain in the estuary for several months. Underlying differences in individual physiological condition, such as body size, stored energy and osmoregulatory function, could drive individual variation in the selection of estuary habitat. Here we investigated the role of variation in physiological condition on the selection of estuarine and ocean habitat by sockeye salmon (Oncorhynchus nerka) smolts intercepted at the initiation of their 650-km downstream migration from Chilko Lake, Fraser River, British Columbia (BC). Behavioural salinity preference experiments were conducted on unfed smolts held in fresh water at three time intervals during their downstream migration period, representing the stage of migration at lake-exit, and the expected timing for estuary-entry and ocean-entry (0, 1 and 3 weeks after lake-exit, respectively). In general, salinity preference behaviour varied across the three time periods consistent with expected transition from river to estuary to ocean. Further, individual physiological condition did influence habitat choice. Smolt condition factor (K) and energy density were positively correlated with salinity preference behaviour in the estuary and ocean outmigration stages, but not at lake-exit. Our results suggest that smolt physiological condition upon reaching the estuary could influence migratory behaviour and habitat selection. This provides evidence on the temporally dependent interplay of physiology, behaviour and migration in wild juvenile Pacific salmon, with juvenile rearing conditions influencing smolt energetic status, which in turn influences habitat choice during downstream migration. The implication for the conservation of migratory species is that the relative importance of stopover habitats may vary as a function of initial condition.

Adult Neurogenesis of Teleost Fish Determines High Neuronal Plasticity and Regeneration

Studying the properties of neural stem progenitor cells (NSPCs) in a fish model will provide new information about the organization of neurogenic niches containing embryonic and adult neural stem cells, reflecting their development, origin cell lines and proliferative dynamics. Currently, the molecular signatures of these populations in homeostasis and repair in the vertebrate forebrain are being intensively studied. Outside the telencephalon, the regenerative plasticity of NSPCs and their biological significance have not yet been practically studied. The impressive capacity of juvenile salmon to regenerate brain suggests that most NSPCs are likely multipotent, as they are capable of replacing virtually all cell lineages lost during injury, including neuroepithelial cells, radial glia, oligodendrocytes, and neurons. However, the unique regenerative profile of individual cell phenotypes in the diverse niches of brain stem cells remains unclear. Various types of neuronal precursors, as previously shown, are contained in sufficient numbers in different parts of the brain in juvenile Pacific salmon. This review article aims to provide an update on NSPCs in the brain of common models of zebrafish and other fish species, including Pacific salmon, and the involvement of these cells in homeostatic brain growth as well as reparative processes during the postraumatic period. Additionally, new data are presented on the participation of astrocytic glia in the functioning of neural circuits and animal behavior. Thus, from a molecular aspect, zebrafish radial glia cells are seen to be similar to mammalian astrocytes, and can therefore also be referred to as astroglia. However, a question exists as to if zebrafish astroglia cells interact functionally with neurons, in a similar way to their mammalian counterparts. Future studies of this fish will complement those on rodents and provide important information about the cellular and physiological processes underlying astroglial function that modulate neural activity and behavior in animals.

Efficient species identification for Pacific salmon genetic monitoring programs

Genetic monitoring of Pacific salmon in the Columbia River basin provides crucial information to fisheries managers that is otherwise challenging to obtain using traditional methods. Monitoring programs such as genetic stock identification (GSI) and parentage-based tagging (PBT) involve genotyping tens of thousands of individuals annually. Although rare, these large sample collections inevitably include misidentified species, which exhibit low genotyping success on species-specific Genotyping-in-Thousands by sequencing (GT-seq) panels. For laboratories involved in large-scale genotyping efforts, diagnosing non-target species and reassigning them to the appropriate monitoring program can be costly and time-consuming. To address this problem, we identified 19 primer pairs that exhibit consistent cross-species amplification among salmonids and contain 51 species informative variants. These genetic markers reliably discriminate among 11 salmonid species and two subspecies of Cutthroat Trout and have been included in species-specific GT-seq panels for Chinook Salmon, Coho Salmon, Sockeye Salmon, and Rainbow Trout commonly used for Pacific salmon genetic monitoring. The majority of species-informative amplicons (16) were newly identified from the four existing GT-seq panels, thus demonstrating a low-cost approach to species identification when using targeted sequencing methods. A species-calling script was developed that is tailored for routine GT-seq genotyping pipelines and automates the identification of non-target species. Following extensive testing with empirical and simulated data, we demonstrated that the genetic markers and accompanying script accurately identified species and are robust to missing genotypic data and low-frequency, shared polymorphisms among species. Finally, we used these tools to identify Coho Salmon incidentally caught in the Columbia River Chinook Salmon sport fishery and used PBT to determine their hatchery of origin. These molecular and computing resources provide a valuable tool for Pacific salmon conservation in the Columbia River basin and demonstrate a cost-effective approach to species identification for genetic monitoring programs.

An interdisciplinary synthesis of floodplain ecosystem dynamics in a rapidly deglaciating watershed

Glacier retreat is rapidly transforming some watersheds, with ramifications for water supply, ecological succession, important species such as Pacific salmon (Oncorhynchus spp.), and cultural uses of landscapes. To advance a more holistic understanding of the evolution of proglacial landscapes, we integrate multiple lines of knowledge starting in the early 1900s with contemporary data from the Taaltsux̱éi (Tulsequah) Watershed in British Columbia, Canada. Our objectives were to: 1) synthesize recent historical geography and Indigenous Knowledge, including glacier dynamics, and hydrology; 2) describe the limnology of a proglacial lake; 3) quantify decadal-scale downstream physical floodplain change; and 4) characterize riverine physical, chemical, and biological differences relative to distance from the proglacial lake. Since 1982, the Tulsequah Glacier has receded 0.07 km/yr, exposing a cold, deep, and growing proglacial lake. The downstream floodplain is rapidly changing; satellite imagery analysis revealed a 14 % increase in vegetation from 2003 to 2017 and Indigenous Knowledge described increases in vegetation and wildlife habitat over the last century. Contemporary measurements of physical-chemical water properties differed across sites representing the upper and lower watershed, and mainstem and off-channel habitats. Catches of juvenile salmonids in the upper watershed (closer to the glacier) were mostly limited to warmer, clearer groundwater-fed channels, whereas in the lower watershed there were salmonids in both groundwater-fed and mainstem habitats. There was limited zooplankton taxa diversity from the proglacial lake and benthic macroinvertebrates in the river. Collectively, our synthesis suggests that the transformation of proglacial landscapes experiencing rapid ice loss can be influenced by interlinked abiotic processes of glacier retreat, lake formation, and altered hydrology, as well as corresponding biological processes such as beaver repopulation, wetland formation, and riparian vegetation growth. These factors, along with expected increases to proglacial lake productivity and salmon habitat suitability, are an important consideration for forward-looking watershed management of glacier-fed rivers.

Reliability of trans-generational genetic mark-recapture (tGMR) for enumerating Pacific salmon

As Pacific salmon (Oncorhynchus spp.) decline across much of their range, it is imperative to further develop minimally invasive tools to quantify population abundance. One such advancement, trans-generational genetic mark-recapture (tGMR), uses parentage analysis to estimate the size of wild populations. Our study examined the precision and accuracy of tGMR through a comparison to a traditional mark-recapture estimate for Chilkat River Chinook salmon (O. tshawytscha) in Southeast Alaska. We examined how adult sampling location and timing impact tGMR by comparing estimates derived using samples collected in the lower river mainstem to those using samples obtained in upriver spawning tributaries. Results indicated that tGMR estimates using a representative sample of mainstem adults were most concordant with, and 3% more precise than, the traditional mark-recapture estimate for this stock. Importantly, the timing and location of adult sampling were found to impact abundance estimates, depending on what proportion of the population dies or moves to unsampled areas between downriver and upriver sampling events. Additionally, we identified potential sources of bias in tGMR arising from violations of key assumptions using a novel individual-based modeling framework, parameterized with empirical values from the Chilkat River. Simulations demonstrated that increased reproductive success and sampling selectivity of older, larger individuals, introduced negative bias into tGMR estimates. Our individual-based model offers a customizable and accessible method to identify and quantify these biases in tGMR applications (https://github.com/swrosenbaum/tGMR_simulations). We underscore the critical role of system-specific sampling design considerations in ensuring the precision and accuracy of tGMR projects. This study validates tGMR as a potentially useful tool for improved population enumeration in semelparous species.

Habitat modulates population-level responses of freshwater salmon growth to a century of change in climate and competition

The impacts of climate change are widespread and threaten natural systems globally. Yet, within regions, heterogeneous physical landscapes can differentially filter climate, leading to local response diversity. For example, it is possible that while freshwater lakes are sensitive to climate change, they may exhibit a diversity of thermal responses owing to their unique morphology, which in turn can differentially affect the growth and survival of vulnerable biota such as fishes. In particular, salmonids are cold-water fishes with complex life histories shaped by diverse freshwater habitats that are sensitive to warming temperatures. Here we examine the influence of habitat on the growth of sockeye salmon (Oncorhynchus nerka) in nursery lakes of Canada's Skeena River watershed over a century of change in regional temperature and intraspecific competition. We found that freshwater growth has generally increased over the last century. While growth tended to be higher in years with relatively higher summer air temperatures (a proxy for lake temperature), long-term increases in growth appear largely influenced by reduced competition. However, habitat played an important role in modulating the effect of high temperature. Specifically, growth was positively associated with rising temperatures in relatively deep (>50 m) nursery lakes, whereas warmer temperatures were not associated with a change in growth for fish among shallow lakes. The influence of temperature on growth also was modulated by glacier extent whereby the growth of fish from lakes situated in watersheds with little (i.e., <5%) glacier cover increased with rising temperatures, but decreased with rising temperatures for fish in lakes within more glaciated watersheds. Maintaining the integrity of an array of freshwater habitats-and the processes that generate and maintain them-will help foster a diverse climate-response portfolio for important fish species, which in turn can ensure that salmon watersheds are resilient to future environmental change.

Stream hydrology and a pulse subsidy shape patterns of fish foraging

Pulsed subsidy events create ephemeral fluxes of hyper-abundant resources that can shape annual patterns of consumption and growth for recipient consumers. However, environmental conditions strongly affect local resource availability for much of the year, and can heavily impact consumer foraging and growth patterns prior to pulsed subsidy events. Thus, a consumer's capacity to exploit pulse subsidy resources may be influenced by antecedent environmental conditions, but this has rarely been shown in nature and is unknown in aquatic ecosystems. Here, we sought to understand the importance of hydrologic variation and a salmon pulse subsidy on the foraging and growth patterns of two stream salmonids in a coastal southeast Alaska drainage. To do this, we sampled fish stomach contents at a high temporal frequency (daily-weekly measurements) and analyzed fish consumption rates in relation to streamflow and pulse subsidy resource availability. We then explored the influence of interannual hydrologic variation on access to pulse subsidy resources (i.e. whether fish exceeded an egg consumption gape limit) in a bioenergetic simulation. Prior to Pink Salmon spawning, Dolly Varden and Coho Salmon displayed distinct and nonlinear flow-foraging relationships, where forage for both species consisted primarily of macroinvertebrates. During this time period, consumption maxima coincided with baseflow and the highest observed flow conditions, and consumption minima were observed at severe low-water and intermediate flow values. After salmon spawning began, forage was not significantly related to flow and consisted primarily of salmon eggs. Further, consumption rates increased overall, and foraging patterns did not appear to be affected by flow in either species. Bioenergetic simulations revealed that patterns of interannual hydrologic variation may shift Coho Salmon growth trajectories among years. Together, our results suggest that access to marine pulse subsidy resources may depend on whether antecedent hydrologic conditions are suitable for juvenile salmonids to grow large enough to consume salmon eggs by the onset of spawning.

Pacific salmon as vectors of environmental contaminants: An experimental test confirms synoptic surveys in natural streams

Pacific salmon transfer large quantities of material to tributaries during their spawning migrations, including carcass tissue and labile nutrients but also persistent organic pollutants (POPs) and heavy metals. We conducted a Before-After-Control-Intervention experiment by adding salmon carcasses and eggs to a Michigan (USA) stream that had never received inputs from non-native salmon to understand the bioaccumulation and persistence of biotransported contaminants. Our experimental outcomes were compared to previous studies using meta-analysis. Coincident with the introduction of salmon, the PCB and DDE burden of resident trout significantly increased. However, we did not observe changes in total mercury (Hg). Two years after the salmon addition experiment concluded, resident trout POP concentrations had returned to pre-addition levels, with no difference between the treatment and control reaches. Analysis of effect sizes suggested that the contaminant response observed in our experiment is consistent with field survey observations. Our study suggested that the consumption of salmon eggs drove the increase in POP burden of resident trout while Hg bioaccumulation was influenced by watershed sources. Critically, our study suggests that ecosystems are capable of quickly recovering from POP inputs from species migrations if contaminant sources are removed.

Hypoxia vulnerability in the salmon watersheds of Southeast Alaska

The frequency of dissolved oxygen depletion events (hypoxia) in coastal aquatic ecosystems has risen dramatically since the late 20th century, yet the causes and consequences of hypoxia for some culturally and economically important species remain poorly understood. In rivers, oxygen depletion can be caused by high densities of spawning Pacific salmon (Oncorhynchus spp.) consuming oxygen faster than can be replaced by reaeration. This process may be exacerbated when salmon densities are artificially inflated, such as when hatchery-origin salmon stray into rivers instead of returning to hatcheries. In Southeast Alaska, hatchery salmon production has increased rapidly since the 1970s, with over 553 million chum salmon (O. keta) and 64 million pink salmon (O. gorbuscha) released in 2021 alone. Straying is pervasive in streams with outlets <25 km from nearshore marine hatchery release sites. Using a previously ground-truthed mechanistic model of dissolved oxygen dynamics, we examined how water temperature and low-flow channel hydraulics contribute to hypoxia vulnerability. We then applied the model to predict hypoxia vulnerability for watersheds within 25 km of hatchery salmon release points, where straying salmon spawner densities are expected to be higher and promote dissolved oxygen depletion. Our model predicted that low-gradient stream reaches, regardless of water temperature, are the most prone to hypoxia due to low reaeration rates. Our spatial analysis determined that nearly 17,000 km of anadromous-accessible stream reaches are vulnerable to high densities of hatchery-origin salmon based on 2021 release sites. To our knowledge, this study is the first to map the spatial variation of hypoxia vulnerability in anadromous watersheds, identify habitat conditions most likely to promote hypoxia, and provide a repeatable analytical approach to identify hypoxia-prone stream reaches that can be updated as empirical data sets improve.

Sex-specific heritabilities for length at maturity among Pacific salmonids and their consequences for evolution in response to artificial selection

Artificial selection, whether intentional or coincidental, is a common result of conservation policies and natural resource management. To reduce unintended consequences of artificial selection, conservation practitioners must understand both artificial selection gradients on traits of interest and how those traits are correlated with others that may affect population growth and resilience. We investigate how artificial selection on male body size in Pacific salmon (Oncorhynchus spp.) may influence the evolution of female body size and female fitness. While salmon hatchery managers often assume that selection for large males will also produce large females, this may not be the case-in fact, because the fastest-growing males mature earliest and at the smallest size, and because female age at maturity varies little, small males may produce larger females if the genetic architecture of growth rate is the same in both sexes. We explored this possibility by estimating sex-specific heritability values of and natural and artificial selection gradients on length at maturity in four populations representing three species of Pacific salmon. We then used the multivariate breeder's equation to project how artificial selection against small males may affect the evolution of female length and fecundity. Our results indicate that the heritability of length at maturity is greater within than between the sexes and that sire-daughter heritability values are especially small. Salmon hatchery policies should consider these sex-specific quantitative genetic parameters to avoid potential unintended consequences of artificial selection.

Metabolic constraints and individual variation shape the trade-off between physiological recovery and anti-predator responses in adult sockeye salmon

Metabolic scope represents the aerobic energy budget available to an organism to perform non-maintenance activities (e.g., escape a predator, recover from a fisheries interaction, compete for a mate). Conflicting energetic requirements can give rise to ecologically relevant metabolic trade-offs when energy budgeting is constrained. The objective of this study was to investigate how aerobic energy is utilized when individual sockeye salmon (Oncorhynchus nerka) are exposed to multiple acute stressors. To indirectly assess metabolic changes in free-swimming individuals, salmon were implanted with heart rate biologgers. The animals were then exercised to exhaustion or briefly handled as a control, and allowed to recover from this stressor for 48 h. During the first 2 h of the recovery period, individual salmon were exposed to 90 ml of conspecific alarm cues or water as a control. Heart rate was recorded throughout the recovery period. Recovery effort and time was higher in exercised fish, relative to control fish, whereas exposure to an alarm cue had no effect on either of these metrics. Individual routine heart rate was negatively correlated with recovery time and effort. Together, these findings suggest that metabolic energy allocation towards exercise recovery (i.e., an acute stressor; handling, chase, etc.) trumps anti-predator responses in salmon, although individual variation may mediate this effect at the population level.

Population-size history inferences from the coho salmon (Oncorhynchus kisutch) genome

Coho salmon (Oncorhynchus kisutch) are a culturally and economically important species that return from multiyear ocean migrations to spawn in rivers that flow to the Northern Pacific Ocean. Southern stocks of coho salmon in Canada and the United States have significantly declined over the past quarter century, and unfortunately, conservation efforts have not reversed this trend. To assist in stock management and conservation efforts, we generated a chromosome-level genome assembly. We also resequenced the genomes of 83 coho salmon across their North American range to identify nucleotide variants, and understand the demographic histories of these salmon by modeling effective population size from genome-wide data. From demographic history modeling, we observed reductions in effective population sizes between 3750-8000 years ago for several northern sampling sites, which may correspond to bottleneck events during recolonization after glacial retreat.

Relationship between salmon egg subsidy and the distribution of an avian predator

As a spatial subsidy, which is the phenomenon of transferring resources from a donor system to a recipient system, anadromous salmonids contribute to the supply of marine-derived nutrients to freshwater and terrestrial systems. Live salmon and salmon carcasses and eggs are utilized by various organisms and affect their abundance and distribution. However, the evaluation of the effect of salmon subsidies on the abundance and distribution of terrestrial animals is biased toward predators or scavengers that utilize spawning adults and carcasses, and few studies have focused on the effect of salmon eggs as a subsidy. To avoid underestimating the function of salmon subsidies, the response to the availability of salmon eggs in various systems should be investigated. Here, we investigated the abundance and feeding behavior of the brown dipper Cinclus pallasii, as a consumer of salmon eggs, based on the hypothesis that the availability of salmon eggs affects the diet composition and stream distribution of this small predator. In addition, to test whether changes in the abundance of brown dippers are determined by salmon spawning, their abundance was compared upstream and downstream of the check dams in three streams during the peak spawning period. Brown dippers used salmon eggs during the spawning season (53.7% of diet composition), and their abundance increased as the number of spawning redds increased. In contrast, this pattern was not observed upstream of the check dam. These results suggested that the abundance and stream distribution of brown dippers vary according to the variation in the spatiotemporal availability of salmon eggs.

Species distributions and the recognition of risk in restoration planning: A case study of salmonid fishes

One of the risks faced by habitat restoration practitioners is whether habitats included in restoration planning will be used by the target species or, conversely, whether habitats excluded from restoration planning would have benefited the target species. With the goal of providing a quantitative decision-making approach that represented varying levels of risk tolerance, we used multiple probability decision thresholds (PDT) to predict the range of occurrence for three anadromous fishes (Oncorhynchus spp.) in a watershed in southwestern Washington, USA. For each species, we compared the predicted range of occurrence to the distribution used for restoration planning and quantified the amount of habitat blocked by anthropogenic barriers. Coho salmon (O. kisutch) had the broadest predicted range of occurrence (3061.6-6357.9 km; 0.75-0.25 PDT), followed by steelhead trout (O. mykiss; 1828.8-2836.8 km) and chum salmon (O. keta; 1373.9-1629.1 km). For each species, the predicted range of occurrence was similar or greater than the distribution used for restoration planning, suggesting that the current plan may exclude habitats that would benefit each species. Coho salmon had the greatest percentage of habitat blocked by anthropogenic barriers, followed by steelhead trout and chum salmon, respectively. Modeling species distributions at multiple risk-tolerance scenarios acknowledges uncertainty in restoration planning and allows practitioners to weigh the ecological benefits and budgetary constraints when considering locations for restoration. To effectively communicate restoration science to support practitioners in decision-making, we developed an R Shiny application online user interface available at: https://shiny.wdfw-fish.us/ChehalisRiverBasinSalmonidRangeOfOccurence/.

Temporal trends of persistent organic pollutants biotransport by Pacific salmon in the Northwest Pacific (2008-2018)

The present study aimed to assess the biotransport of POPs, including OCPs and PCBs, by Pacific salmon (genus Oncorhynchus) on the northwestern Pacific Ocean. In 2008-2012, the Amur River basin, the eastern Kamchatka, and the mainland coast of the Sea of Okhotsk received the largest amounts of pesticides. In 2018, the transport of OCPs to the Russian northwestern Pacific reached only 1 kg, and the total OCP levels in muscles of fish from this region were significantly lower than in previous years. The average concentration of PCBs for all species under study differed from that of OCPs, with the highest concentration recorded from sockeye salmon. In 2018, pink salmon brought the largest amount of PCBs to the Russian northwestern Pacific. Coastal water pollution has decreased significantly in recent years due to the ban on the use of POPs in the Northwest Pacific (according to the measurements in 2010 and 2018).

A melting cryosphere constrains fish growth by synchronizing the seasonal phenology of river food webs

Mountain watersheds often contain a mosaic of glacier-, snow-, and rain-fed streams that have distinct hydrologic, temperature, and biogeochemical regimes. However, as glaciers diminish and precipitation shifts from snow to rain, the physical and chemical characteristics that make glacial or snowmelt streams distinct from rain-fed streams will fade. Among the unforeseen consequences of this hydrologic homogenization could be the loss of unique food webs that sustain aquatic consumers. To explore the impacts of a melting cryosphere on stream food webs, we parameterized an aquatic food web model with empirical physicochemical data from glacier-, snow-, and rain-fed streams in southeast Alaska and used the model to simulate the seasonal biomass dynamics of aquatic primary producers and consumers and the growth of juvenile salmon. Model results suggest that glacier-, snow-, and rain-fed streams exhibit seasonal asynchronies in the timing of biofilm and aquatic invertebrate abundance. Although warmer rain-fed streams were more productive during the summer (June through September), colder glacial and snowmelt streams provided enhanced foraging and growth opportunities throughout the remainder of the year. For juvenile salmon that can track peaks in resource abundance within river networks, the loss of meltwater streams strongly constrained modeled growth opportunities by removing spatially and temporally distinct foraging habitats within a watershed. These findings suggest that climate change induced homogenization of high latitude river networks may result in the loss of unique food web dynamics, which could diminish the capacity of watersheds to sustain mobile consumers.

Olfactory behavioural and neural responses of planktivorous lacustrine sockeye salmon (Oncorhynchus nerka) to prey odours

Fish use a variety of sensory systems when foraging. Salmonids are generally considered visual feeders. However, some species feed on zooplanktons under dark conditions, suggesting they also detect prey using nonvisual cues. Under experimental conditions, hatchery-reared rainbow trout (Oncorhynchus mykiss) have been shown to use olfaction when searching for food pellets, but olfactory foraging has not been documented in wild salmonids. In the present study, to examine their behavioural response and neural activity in the olfactory nervous system using c-fos expression as a neural molecular marker, immature wild-caught lacustrine sockeye salmon (Oncorhynchus nerka) in a flow-through aquarium were exposed to zooplanktons (Daphnia spp.) extract including zooplanktons odorant and to dimethyl sulfide. The salmon exposed to zooplanktons odour increased their total swimming distance and time, numbers of turns and ascents, and c-fos expression in the olfactory bulb, suggesting that they can detect zooplanktons extract to locate prey in the laboratory experiments. However, no response was seen in those exposed to dimethyl sulfide. The results of this study suggest that prey odour may serve as a chemosensory cue for wild immature salmonids.

Implications of Large-Effect Loci for Conservation: A Review and Case Study with Pacific Salmon

The increasing feasibility of assembling large genomic datasets for non-model species presents both opportunities and challenges for applied conservation and management. A popular theme in recent studies is the search for large-effect loci that explain substantial portions of phenotypic variance for a key trait(s). If such loci can be linked to adaptations, 2 important questions arise: 1) Should information from these loci be used to reconfigure conservation units (CUs), even if this conflicts with overall patterns of genetic differentiation? 2) How should this information be used in viability assessments of populations and larger CUs? In this review, we address these questions in the context of recent studies of Chinook salmon and steelhead (anadromous form of rainbow trout) that show strong associations between adult migration timing and specific alleles in one small genomic region. Based on the polygenic paradigm (most traits are controlled by many genes of small effect) and genetic data available at the time showing that early-migrating populations are most closely related to nearby late-migrating populations, adult migration differences in Pacific salmon and steelhead were considered to reflect diversity within CUs rather than separate CUs. Recent data, however, suggest that specific alleles are required for early migration, and that these alleles are lost in populations where conditions do not support early-migrating phenotypes. Contrasting determinations under the US Endangered Species Act and the State of California's equivalent legislation illustrate the complexities of incorporating genomics data into CU configuration decisions. Regardless how CUs are defined, viability assessments should consider that 1) early-migrating phenotypes experience disproportionate risks across large geographic areas, so it becomes important to identify early-migrating populations that can serve as reliable sources for these valuable genetic resources; and 2) genetic architecture, especially the existence of large-effect loci, can affect evolutionary potential and adaptability.

High egg retention in Chinook Salmon Oncorhynchus tshawytscha carcasses sampled downstream of a migratory barrier

Barriers in rivers have the potential to severely decrease functional connectivity between habitats. Failure to pass barriers and reach natal spawning habitat may compromise individual reproductive success, particularly for semelparous, philopatric species that rely on free-flowing rivers to reach natal habitat during their once-in-a-lifetime spawning migrations. To investigate the consequences of in-river barriers on fish spawning success, we quantified egg retention and spawning effort (caudal fin wear) in female Chinook Salmon Oncorhynchus tshawytscha carcasses collected downstream of the Whitehorse Hydro Plant on the upper Yukon River and at a nearby free-flowing tributary (Teslin River) from 2018 to 2020 (~2900 km migrations). Previous studies have demonstrated that a large proportion of fish attempting to reach spawning locations upstream of the hydro plant fail to pass the associated fishway. We estimated nearly all female salmon failing to pass the hydro plant attempted spawning in non-natal habitat downstream, but that these females retained ~34% of their total fecundity compared to ~6% in females from the free-flowing river. Females downstream of the hydro plant also had lower wear on their caudal fin, a characteristic that was correlated with increased egg deposition. Egg retention did not vary across years with different run sizes, and we propose that egg retention downstream of the hydro plant was not driven by density-dependent mechanisms. Findings from this work indicate that female Chinook Salmon can still deposit eggs following failed fish passage and failure to reach natal spawning sites, though egg retention rates are considerably higher and uncertainties remain about reproductive success. We encourage researchers to incorporate carcass surveys into fish passage evaluations for semelparous species to fully account for consequences of failed passage.

Genome-Wide Investigation of the Multiple Origins Hypothesis for Deep-Spawning Kokanee Salmon (Oncorhynchus nerka) across its Pan-Pacific Distribution

Salmonids have emerged as important study systems for investigating molecular processes underlying parallel evolution given their tremendous life history variation. Kokanee, the resident form of anadromous sockeye salmon (Oncorhynchus nerka), have evolved multiple times across the species' pan-Pacific distribution, exhibiting multiple reproductive ecotypes including those that spawn in streams, on lake-shores, and at lake depths >50 m. The latter has only been detected in 5 locations in Japan and British Columbia, Canada. Here, we investigated the multiple origins hypothesis for deep-spawning kokanee, using 9721 single nucleotide polymorphisms distributed across the genome analyzed for the vast majority of known populations in Japan (Saiko Lake) and Canada (Anderson, Seton, East Barrière Lakes) relative to stream-spawning populations in both regions. We detected 397 outlier loci, none of which were robustly identified in paired-ecotype comparisons in Japan and Canada independently. Bayesian clustering and principal components analyses based on neutral loci revealed 6 distinct clusters, largely associated with geography or translocation history, rather than ecotype. Moreover, a high level of divergence between Canadian and Japanese populations, and between deep- and stream-spawning populations regionally, suggests the deep-spawning ecotype independently evolved on the 2 continents. On a finer level, Japanese kokanee populations exhibited low estimates of heterozygosity, significant levels of inbreeding, and reduced effective population sizes relative to Canadian populations, likely associated with transplantation history. Along with preliminary evidence for hybridization between deep- and stream-spawning ecotypes in Saiko Lake, these findings should be considered within the context of on-going kokanee fisheries management in Japan.

Effects of spawning Pacific salmon on terrestrial invertebrates: Insects near spawning habitat are isotopically enriched with nitrogen-15 but display no differences in body size

When Pacific salmon (Oncorhynchus spp.) spawn and die, they deliver marine-derived nutrient subsidies to freshwater and riparian ecosystems. These subsidies can alter the behavior, productivity, and abundance of recipient species and their habitats. Isotopes, such as nitrogen-15 (15N), are often used to trace the destination of marine-derived nutrients in riparian habitats. However, few studies have tested for correlations between stable isotopes and physiological responses of riparian organisms. We examined whether increases in δ 15N in terrestrial insect bodies adjacent to salmon spawning habitat translate to changes in percent nitrogen content and body size. This involved comparisons between distance from a salmon-bearing river, marine-derived nutrients in soils and insects, soil moisture content, and body size and nitrogen content in two common beetle families (Coleoptera: Curculionidae, Carabidae). As predicted, δ15N in riparian soils attenuated with distance from the river but was unaffected by soil moisture. This gradient was mirrored by δ15N in the herbivorous curculionid beetles, whereas carabid beetles, which feed at a higher trophic level and are more mobile, did not show discernable patterns in their δ15N content. Additionally, neither distance from the river nor body δ15N content was related to beetle body size. We also found that nitrogen-15 was not correlated with total percent nitrogen in insect bodies, meaning that the presence of spawning salmon did not increase the percent nitrogen content of these insects. We conclude that while salmon-derived nutrients had entered terrestrial food webs, the presence of δ15N alone did not indicate meaningful physiological changes in these insects in terms of percent nitrogen nor body size. While stable isotopes may be useful tracers of marine-derived nutrients, they cannot necessarily be used as a proxy for physiologically important response variables.

Distribution and Pathogenicity of Two Cutthroat Trout Virus (CTV) Genotypes in Canada

The sole member of the Piscihepevirus genus (family Hepeviridae) is cutthroat trout virus (CTV) but recent metatranscriptomic studies have identified numerous fish hepevirus sequences including CTV-2. In the current study, viruses with sequences resembling both CTV and CTV-2 were isolated from salmonids in eastern and western Canada. Phylogenetic analysis of eight full genomes delineated the Canadian CTV isolates into two genotypes (CTV-1 and CTV-2) within the Piscihepevirus genus. Hepevirus genomes typically have three open reading frames but an ORF3 counterpart was not predicted in the Canadian CTV isolates. In vitro replication of a CTV-2 isolate produced cytopathic effects in the CHSE-214 cell line with similar amplification efficiency as CTV. Likewise, the morphology of the CTV-2 isolate resembled CTV, yet viral replication caused dilation of the endoplasmic reticulum lumen which was not previously observed. Controlled laboratory studies exposing sockeye (Oncorhynchus nerka), pink (O. gorbuscha), and chinook salmon (O. tshawytscha) to CTV-2 resulted in persistent infections without disease and mortality. Infected Atlantic salmon (Salmo salar) and chinook salmon served as hosts and potential reservoirs of CTV-2. The data presented herein provides the first in vitro and in vivo characterization of CTV-2 and reveals greater diversity of piscihepeviruses extending the known host range and geographic distribution of CTV viruses.

Organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) in Pacific salmon from the Kamchatka Peninsula and Sakhalin Island, Northwest Pacific

The purpose of the present study was to determine levels of POPs (dieldrin, endrin, HCH isomers, DDT metabolites, and PCB congeners) in organs of chum (Oncorhynchus keta), pink (O. gorbuscha), sockeye (O. nerka), masu (O. masou), and Chinook salmon (O. tshawytscha), and to identify the patterns of toxicants' distribution in organisms and the environment of the northwestern Pacific. Principal component factor analysis showed that all the salmon species typically exhibit relationships between the PCB congeners and are characterized by a similar pattern of entry of PCBs 101, 118, and 153. The OCPs levels in the organs of Pacific salmon are decreasing from 2012 to 2018, which suggests the elimination of these toxicants from the northwestern Pacific Ocean.

A fast HRMA tool to authenticate eight salmonid species in commercial food products

Atlantic and Pacific salmon are frequently consumed species with very different economic values: farmed Atlantic salmon is cheaper than wild-caught Pacific salmons. Species replacements occur with the high valued Pacific species (Oncorhynchus keta, O. gorbuscha, O. kisutch, O. nerka and O. tshawytscha) substituted by cheaper farmed Atlantic salmon (Salmo salar) and Atlantic salmon by rainbow trout (Oncorhynchus mykiss) and brown trout (Salmo trutta). Here we use High-Resolution Melting Analysis (HRMA) to identify eight salmonid species. We designed primers to generate short amplicons of 72 and 116 bp from the fish barcode genes CO1 and CYTB. The time of analysis was under 70 min, after DNA extraction. Food processing of Atlantic salmon (fresh, "Bellevue", "gravadlax", frozen and smoked) did not impact the HRMA profiles allowing reliable identification. A blind test was conducted by three different institutes, showing correct species identifications irrespective of the laboratory conducting the analysis. Finally, a total of 82 retail samples from three European countries were analyzed and a low substitution rate of 1.2% was found. The developed tool provides a quick way to investigate salmon fraud and contributes to safeguard consumers.

Modelling entanglement rates to estimate mortality of marine birds in British Columbia commercial salmon gillnet fisheries

Incidental mortality of marine birds in fisheries is an international conservation concern, including in Canada where globally significant populations of vulnerable diving species overlap with coastal gillnet fisheries. In British Columbia (BC), commercial salmon gillnet fishing effort was historically very high (>200,000 days fished annually in the early 1950's), and although this fishery has declined, over 6,400 days were fished annually in the 2006-2016 decade. Observations of seabird bycatch within the commercial fishery, however, are limited in both scope (comprising <2% of cumulative effort 2001-2016) and in time (being available only from 1995 onwards and only for a small number of areas). Using onboard fishery observer data from commercial, test and experimental fisheries (1995-2016), we developed two models to estimate the number of marine birds captured per set in sockeye (Oncorhynchus nerka) and chum (O. keta) salmon gillnet fisheries employing a Generalized Linear Mixed Modeling (GLMM) approach in a hierarchical Bayesian framework, with observer data post-stratified by fisheries management area and year. Using estimates of total commercial fishing effort (estimated number of sets, 2001-2016) we applied the models to extrapolate annual take for the main bird species (or groups) of interest. Multinomial probability estimates of species composition were calculated based upon a sample of 852 birds identified to species that were associated with sockeye or chum fisheries, enabling estimates (with CIs) of potential numbers of the mostly commonly observed species (common murres (Uria aalge), rhinoceros auklets (Cerorhinca monocerata), and marbled murrelets (Brachyramphus marmoratus)) entangled annually in commercial sockeye and chum salmon gillnet fisheries throughout BC. Conservative estimates of annual losses to entanglement were greatest for common murres (2,846, 95% CI: 2,628-3,047), followed by rhinoceros auklets (641, CI: 549-770) and marbled murrelets (228 CI: 156-346). Populations of all three of these alcids species are currently in decline in BC and entanglement mortality is a conservation concern. Gillnet mortality has been identified as a longstanding threat to marbled murrelet populations, which are recognized as Threatened in the Canada and the United States of America (USA). In addition, 622 (CI: 458-827) birds from 12 other species were estimated to be entangled annually. We conclude that cumulative mortality from incidental take in salmon gillnet fisheries is one of the largest sources of human-induced mortality for marine birds in BC waters, a conservation concern impacting both breeders and visiting migrants.

Bias in self-reported parasite data from the salmon farming industry

Many industries are required to monitor themselves in meeting regulatory policies intended to protect the environment. Self-reporting of environmental performance can place the cost of monitoring on companies rather than taxpayers, but there are obvious risks of bias, often addressed through external audits or inspections. Surprisingly, there have been relatively few empirical analyses of bias in industry self-reported data. Here, we test for bias in reporting of environmental compliance data using a unique data set from Canadian salmon farms, where companies monitor the number of parasitic sea lice on fish in open sea pens, in order to minimize impacts on wild fish in surrounding waters. We fit a hierarchical population-dynamics model to these sea-louse count data using a Bayesian approach. We found that the industry's monthly counts of two sea-louse species, Caligus clemensi and Lepeophtheirus salmonis, increased by a factor of 1.95 (95% credible interval: 1.57, 2.42) and 1.18 (1.06, 1.31), respectively, in months when counts were audited by the federal fisheries department. Consequently, industry sea-louse counts are less likely to trigger costly but mandated delousing treatments intended to avoid sea-louse epidemics in wild juvenile salmon. These results highlight the potential for combining external audits of industry self-reported data with analyses of their reporting to maintain compliance with regulations, achieve intended conservation goals, and build public confidence in the process.

Relationships between Pacific salmon and aquatic and terrestrial ecosystems: implications for ecosystem-based management

Pacific salmon influence temperate terrestrial and freshwater ecosystems through the dispersal of marine‐derived nutrients and ecosystem engineering of stream beds when spawning. They also support large fisheries, particularly along the west coast of North America. We provide a comprehensive synthesis of relationships between the densities of Pacific salmon and terrestrial and aquatic ecosystems, summarize the direction, shape, and magnitude of these relationships, and identify possible ecosystem‐based management indicators and benchmarks. We found 31 studies that provided 172 relationships between salmon density (or salmon abundance) and species abundance, species diversity, food provisioning, individual growth, concentration of marine‐derived isotopes, nutrient enhancement, phenology, and several other ecological responses. The most common published relationship was between salmon density and marine‐derived isotopes (40%), whereas very few relationships quantified ecosystem‐level responses (5%). Only 13% of all relationships tended to reach an asymptote (i.e., a saturating response) as salmon densities increased. The number of salmon killed by bears and the change in biomass of different stream invertebrate taxa between spawning and nonspawning seasons were relationships that usually reached saturation. Approximately 46% of all relationships were best described with linear or curved nonasymptotic models, indicating a lack of saturation. In contrast, 41% of data sets showed no relationship with salmon density or abundance, including many of the relationships with stream invertebrate and biofilm biomass density, marine‐derived isotope concentrations, or vegetation density. Bears required the highest densities of salmon to reach their maximum observed food consumption (i.e., 9.2 kg/m² to reach the 90% threshold of the relationship’s asymptote), followed by freshwater fish abundance (90% threshold = 7.3 kg/m² of salmon). Although the effects of salmon density on ecosystems are highly varied, it appears that several of these relationships, such as bear food consumption, could be used to develop indicators and benchmarks for ecosystem‐based fisheries management.

Genomes reveal genetic diversity of Piscine orthoreovirus in farmed and free-ranging salmonids from Canada and USA

Piscine orthoreovirus (PRV-1) is a segmented RNA virus, which is commonly found in salmonids in the Atlantic and Pacific Oceans. PRV-1 causes the heart and skeletal muscle inflammation disease in Atlantic salmon and is associated with several other disease conditions. Previous phylogenetic studies of genome segment 1 (S1) identified four main genogroups of PRV-1 (S1 genogroups I–IV). The goal of the present study was to use Bayesian phylogenetic inference to expand our understanding of the spatial, temporal, and host patterns of PRV-1 from the waters of the northeast Pacific. To that end, we determined the coding genome sequences of fourteen PRV-1 samples that were selected to improve our knowledge of genetic diversity across a broader temporal, geographic, and host range, including the first reported genome sequences from the northwest Atlantic (Eastern Canada). Nucleotide and amino acid sequences of the concatenated genomes and their individual segments revealed that established sequences from the northeast Pacific were monophyletic in all analyses. Bayesian inference phylogenetic trees of S1 sequences using BEAST and MrBayes also found that sequences from the northeast Pacific grouped separately from sequences from other areas. One PRV-1 sample (WCAN_BC17_AS_2017) from an escaped Atlantic salmon, collected in British Columbia but derived from Icelandic broodstock, grouped with other S1 sequences from Iceland. Our concatenated genome and S1 analysis demonstrated that PRV-1 from the northeast Pacific is genetically distinct but descended from PRV-1 from the North Atlantic. However, the analyses were inconclusive as to the timing and exact source of introduction into the northeast Pacific, either from eastern North America or from European waters of the North Atlantic. There was no evidence that PRV-1 was evolving differently between free-ranging Pacific Salmon and farmed Atlantic Salmon. The northeast Pacific PRV-1 sequences fall within genogroup II based on the classification of Garseth, Ekrem, and Biering (Garseth, A. H., Ekrem, T., and Biering, E. (2013) ‘Phylogenetic Evidence of Long Distance Dispersal and Transmission of Piscine Reovirus (PRV) between Farmed and Wild Atlantic Salmon’, PLoS One, 8: e82202.), which also includes North Atlantic sequences from Eastern Canada, Iceland, and Norway. The additional full-genome sequences herein strengthen our understanding of phylogeographical patterns related to the northeast Pacific, but a more balanced representation of full PRV-1 genomes from across its range, as well additional sequencing of archived samples, is still needed to better understand global relationships including potential transmission links among regions.

Refuges and ecological traps: Extreme drought threatens persistence of an endangered fish in intermittent streams

Recent droughts raise global concern over potential biodiversity loss and mitigating impacts to vulnerable species has become a management priority. However, drought impacts on populations are difficult to predict, in part, because habitat refuges can buffer organisms from harsh environmental conditions. In a global change context, more extreme droughts may turn previously suitable habitats into ecological traps, where vulnerable species can no longer persist. Here, we explore the impacts of California's recent record-breaking drought on endangered juvenile Coho salmon. We estimated the variability of cumulative salmon survival using mark-recapture of nearly 20,000 tagged fish in intermittent stream pools during a 7-year period encompassing drought and non-drought conditions. We then determined the relative importance of physical habitat, streamflow, precipitation, landscape, and biological characteristics that may limit survival during drought. Our most striking result was an increase in the number of pools with reduced or zero survival during drought years and a coincident increase in spatial variability in survival among study reaches. In nearly half of the stream pools, salmon survival during drought was similar to mean survival of pools assessed during non-drought years, indicating some pools had remarkable resistance (ability to withstand disturbance) to extreme drought. Lower survival was most attributable to longer duration of disconnection between upstream and downstream habitats, a consequence of increasing drought severity. Our results not only suggest that many pools sustain juvenile salmon in non-drought years transition into ecological traps during drought but also highlight that some pools serve as refuges even under extreme drought conditions. Projected increases in drought severity that lead to longer droughts and greater habitat fragmentation could transform an increasing proportion of suitable habitats into ecological traps. Predicting future impacts of drought on Coho salmon and other sensitive species will require identification and protection of drought refuges and management strategies that prevent further habitat fragmentation.

Ontogenetic niche shifts as a driver of seasonal migration

Ontogenetic niche shifts have helped to understand population dynamics. Here we show that ontogenetic niche shifts also offer an explanation, complementary to traditional concepts, as to why certain species show seasonal migration. We describe how demographic processes (survival, reproduction and migration) and associated ecological requirements of species may change with ontogenetic stage (juvenile, adult) and across the migratory range (breeding, non-breeding). We apply this concept to widely different species (dark-bellied brent geese (Branta b. bernicla), humpback whales (Megaptera novaeangliae) and migratory Pacific salmon (Oncorhynchus gorbuscha) to check the generality of this hypothesis. Consistent with the idea that ontogenetic niche shifts are an important driver of seasonal migration, we find that growth and survival of juvenile life stages profit most from ecological conditions that are specific to breeding areas. We suggest that matrix population modelling techniques are promising to detect the importance of the ontogenetic niche shifts in maintaining migratory strategies. As a proof of concept, we applied a first analysis to resident, partial migratory and fully migratory populations of barnacle geese (Branta leucopsis). We argue that recognition of the costs and benefits of migration, and how these vary with life stages, is important to understand and conserve migration under global environmental change.

Proliferative kidney disease in Alaskan salmonids with evidence that pathogenic myxozoans may be emerging north

Proliferative kidney disease (PKD) of salmonids, a chronic immunopathology caused by the myxozoan parasite Tetracapsuloides bryosalmonae, is exacerbated by increased water temperatures. PKD causes economic concerns to trout farmers and contributes to the decline of wild salmonid populations in North America and Europe. The parasite occurs as far north as Norway and Iceland in Europe and was confirmed from California to southern British Columbia in the American continent. In mid-September 2011 adult chum salmon (Oncorhynchus keta) were sampled from Kantishna River, a tributary to Yukon River in Alaska. Clinical PKD was diagnosed based on the macroscopic appearance of mottled kidneys that were uniformly swollen and by the detection of tumultuous histozoic extrasporogonic and coelozoic sporogonic stages of T. bryosalmonae in renal tissue by histopathology. Archived samples provided the molecular confirmation and local strain identification, representing the first confirmed case of PKD in wild adult chum salmon, also co-infected with Parvicapsula minibicornis that represents another novel myxozoan detection in Alaska. Our investigation was extended to another case from August/September 1997, with mortality following furunculosis and ectoparasite co-infections, in sockeye salmon (Oncorhynchus nerka) pre-smolts net-pen reared in English Bay Lakes, Alaska. Immunohistochemistry on archived histological preparations confirmed T. bryosalmonae sporogonic and extrasporogonic stages, indicating a severe to resolving PKD, with concomitant Chloromyxum spp. infection. Those cases provide the first documentation that this parasite is present in Alaska and causes PKD in wild and cultured salmonids in the region. The known geographic range of T. bryosalmonae can be extended to ~267 km south of the Arctic Circle, representing the northernmost detection in America. Given the vast size of Alaska and small resident population, it is likely that T. bryosalmonae remained undetected, but more recently became evident due to the clinical manifestation of PKD, possibly linked to increasing water temperatures reported at the sample locations.

Glacier Retreat and Pacific Salmon

Glaciers have shaped past and present habitats for Pacific salmon (Oncorhynchus spp.) in North America. During the last glacial maximum, approximately 45% of the current North American range of Pacific salmon was covered in ice. Currently, most salmon habitat occurs in watersheds in which glacier ice is present and retreating. This synthesis examines the multiple ways that glacier retreat can influence aquatic ecosystems through the lens of Pacific salmon life cycles. We predict that the coming decades will result in areas in which salmon populations will be challenged by diminished water flows and elevated water temperatures, areas in which salmon productivity will be enhanced as downstream habitat suitability increases, and areas in which new river and lake habitat will be formed that can be colonized by anadromous salmon. Effective conservation and management of salmon habitat and populations should consider the impacts of glacier retreat and other sources of ecosystem change.

Exposure to exogenous egg cortisol does not rescue juvenile Chinook salmon body size, condition, or survival from the effects of elevated water temperatures

Climate change is leading to altered temperature regimes which are impacting aquatic life, particularly for ectothermic fish. The impacts of environmental stress can be translated across generations through maternally derived glucocorticoids, leading to altered offspring phenotypes. Although these maternal stress effects are often considered negative, recent studies suggest this maternal stress signal may prepare offspring for a similarly stressful environment (environmental match). We applied the environmental match hypothesis to examine whether a prenatal stress signal can dampen the effects of elevated water temperatures on body size, condition, and survival during early development in Chinook salmon Oncorhynchus tshawytscha from Lake Ontario, Canada. We exposed fertilized eggs to prenatal exogenous egg cortisol (1,000 ng/ml cortisol or 0 ng/ml control) and then reared these dosed groups at temperatures indicative of current (+0°C) and future (+3°C) temperature conditions. Offspring reared in elevated temperatures were smaller and had a lower survival at the hatchling developmental stage. Overall, we found that our exogenous cortisol dose did not dampen effects of elevated rearing temperatures (environmental match) on body size or early survival. Instead, our eyed stage survival indicates that our prenatal cortisol dose may be detrimental, as cortisol-dosed offspring raised in elevated temperatures had lower survival than cortisol-dosed and control reared in current temperatures. Our results suggest that a maternal stress signal may not be able to ameliorate the effects of thermal stress during early development. However, we highlight the importance of interpreting the fitness impacts of maternal stress within an environmentally relevant context.

Cumulative Effects of Thermal and Fisheries Stressors Reveal Sex-Specific Effects on Infection Development and Early Mortality of Adult Coho Salmon (Oncorhynchus kisutch)

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 (<15%). Elevated water temperature under laboratory conditions increased mortality of males and females (8% and 28% mortality, respectively, delayed by >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.

Simulated maternal stress reduces offspring aerobic swimming performance in Pacific salmon

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 MO_2max 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.

Evolutionary dynamics of Ceratonova species (Cnidaria: Myxozoa) reveal different host adaptation strategies

The myxozoan parasite Ceratonova shasta is an important pathogen that infects multiple species of Pacific salmonids. Ongoing genetic surveillance has revealed stable host-parasite relationships throughout the parasite's endemic range. We applied Bayesian phylogenetics to test specific hypotheses about the evolution of these host-parasite relationships within the well-studied Klamath River watershed in Oregon and California, USA. The results provide statistical support that different genotypes of C. shasta are distinct lineages of one species, which is related to two other Ceratonova species in the same ecosystems; Ceratonova X in speckled dace and C. gasterostea in threespine stickleback. Furthermore, we found strong support for the hypothesis that C. shasta type 0 in native steelhead trout and type I in Chinook salmon each evolved with a specialist host adaptation strategy, while C. shasta type II in coho salmon resulted from a generalist host adaptation strategy. Inferred date and host species of the most recent common ancestor of extant Klamath basin types indicate that it occurred between 14,000 and 21,000 years ago, and most likely infected a native steelhead or rainbow trout host.

Artificial selection on reproductive timing in hatchery salmon drives a phenological shift and potential maladaptation to climate change

The timing of breeding migration and reproduction links generations and substantially influences individual fitness. In salmonid fishes, such phenological events (seasonal return to freshwater and spawning) vary among populations but are consistent among years, indicating local adaptation in these traits to prevailing environmental conditions. Changing reproductive phenology has been observed in many populations of Atlantic and Pacific salmon and is sometimes attributed to adaptive responses to climate change. The sockeye salmon spawning in the Cedar River near Seattle, Washington, USA, have displayed dramatic changes in spawning timing over the past 50 years, trending later through the early 1990s, and becoming earlier since then. We explored the patterns and drivers of these changes using generalized linear models and mathematical simulations to identify possible environmental correlates of the changes, and test the alternative hypothesis that hatchery propagation caused inadvertent selection on timing. The trend toward later spawning prior to 1993 was partially explained by environmental changes, but the rapid advance in spawning since was not. Instead, since its initiation in 1991, the hatchery has, on average, selected for earlier spawning, and, depending on trait heritability, could have advanced spawning by 1-3 weeks over this period. We estimated heritability of spawning date to be high (h 2 ~0.8; 95% CI: 0.5-1.1), so the upper end of this range is not improbable, though at lower heritabilities a smaller effect would be expected. The lower reproductive success of early spawners and relatively low survival of early emerging juveniles observed in recent years suggest that artificial and natural selection are acting in opposite directions. The fitness costs of early spawning may be exacerbated by future warming; thus, the artificially advanced phenology could reduce the population's productivity. Such artificial selection is known in many salmon hatcheries, so there are broad consequences for the productivity of wild populations comingled with hatchery-produced fish.

Distribution and Phylogeny of Erythrocytic Necrosis Virus (ENV) in Salmon Suggests Marine Origin

Viral erythrocytic necrosis (VEN) affects over 20 species of marine and anadromous fishes in the North Atlantic and North Pacific Oceans. However, the distribution and strain variation of its viral causative agent, erythrocytic necrosis virus (ENV), has not been well characterized within Pacific salmon. Here, metatranscriptomic sequencing of Chinook salmon revealed that ENV infecting salmon was closely related to ENV from Pacific herring, with inferred amino-acid sequences from Chinook salmon being 99% identical to those reported for herring. Sequence analysis also revealed 89 protein-encoding sequences attributed to ENV, greatly expanding the amount of genetic information available for this virus. High-throughput PCR of over 19,000 fish showed that ENV is widely distributed in the NE Pacific Ocean and was detected in 12 of 16 tested species, including in 27% of herring, 38% of anchovy, 17% of pollock, and 13% of sand lance. Despite frequent detection in marine fish, ENV prevalence was significantly lower in fish from freshwater (0.03%), as assessed with a generalized linear mixed effects model (p = 5.5 × 10⁻⁸). Thus, marine fish are likely a reservoir for the virus. High genetic similarity between ENV obtained from salmon and herring also suggests that transmission between these hosts is likely.

Using a dynamic bioenergetics-bioaccumulation model to understand mechanisms of uptake and bioaccumulation of salmon-derived contaminants by stream-resident fish

Ecosystem linkages created by migratory organisms such as Pacific salmon (Oncorhynchus spp.) facilitate the transfer of ecologically beneficial resource subsidies and environmentally damaging contaminants to recipient food webs. In the Laurentian Great Lakes, introduced Pacific salmon accumulate large contaminant burdens that they disperse to streams during spawning in the form of carcass and gametic tissue, with uncertain consequences for stream food webs. Here, we describe a coupled bioenergetics-bioaccumulation model parameterized using empirical and literature-sourced data to predict the dual effect of Pacific salmon on stream-resident brook trout (Salvelinus fontinalis) growth and contaminant bioaccumulation. Within the model, we developed four unique scenarios to ascertain how the (1) trophic pathway to contamination, (2) level of salmon egg consumption, (3) intensity and duration of salmon exposure, and (4) age of first exposure to salmon, affected growth and contaminant bioaccumulation in brook trout. Our model demonstrated that salmon egg consumption increased brook trout growth and PCB bioaccumulation while reducing Hg tissue concentrations. Other trophic pathways, including direct carcass consumption and an indirect food web pathway, did not strongly influence growth or contaminant bioaccumulation. Our model also demonstrated that variation in the magnitude and temporal duration of salmon egg consumption mostly strongly influenced the growth and contaminant concentration of younger brook trout. Overall, our model highlighted that Pacific salmon transfer energy and contaminants but this balance is dictated by the food web pathway and plasticity in the diet of stream-resident fish. Our mechanistic, model-based evaluation of salmon contaminant biotransport can be extended to predict the impact of other migratory fishes on recipient food webs.

Otolith microchemistry and diadromy in Patagonian river fishes

Coastal habitats in Chile are hypothesized to support a number of diadromous fish species. The objective of this study was to document migratory life histories of native galaxiids and introduced salmonids from a wide latitudinal range in Chilean Patagonia (39–48°S). Otolith microchemistry data were analysed using a recursive partitioning approach to test for diadromy. Based on annular analysis of Sr:Ca ratios, a diadromous life history was suggested for populations of native Aplochiton taeniatus, A. marinus, and Galaxias maculatus. Lifetime residency in freshwater was suggested for populations of A. zebra and G. platei. Among introduced salmonids, populations of Oncorhynchus tshawytscha and O. kisutch exhibited patterns consistent with anadromy, whereas the screened population of O. mykiss appeared restricted to freshwater. Salmo trutta exhibited variable patterns suggesting freshwater residency and possibly anadromy in one case. The capacity and geographic scope of hydropower development is increasing and may disrupt migratory routes of diadromous fishes. Identification of diadromous species is a critical first step for preventing their loss due to hydropower development.

Non-stationary climate-salmon relationships in the Gulf of Alaska

Studies of climate effects on ecology often account for non-stationarity in individual physical and biological variables, but rarely allow for non-stationary relationships among variables. Here, we show that non-stationary relationships among physical and biological variables are central to understanding climate effects on salmon (Onchorynchus spp.) in the Gulf of Alaska during 1965-2012. The relative importance of two leading patterns in North Pacific climate, the Pacific Decadal Oscillation (PDO) and North Pacific Gyre Oscillation (NPGO), changed around 1988/1989 as reflected by changing correlations with leading axes of sea surface temperature variability. Simultaneously, relationships between the PDO and Gulf of Alaska environmental variables weakened, and long-standing temperature-salmon and PDO-salmon covariance declined to zero. We propose a mechanistic explanation for changing climate-salmon relationships in terms of non-stationary atmosphere-ocean interactions coinciding with changing PDO-NPGO relative importance. We also show that regression models assuming stationary climate-salmon relationships are inappropriate over the multidecadal time scale we consider. Relaxing assumptions of stationary relationships markedly improved modelling of climate effects on salmon catches and productivity. Attempts to understand the implications of changing climate patterns in other ecosystems might also be aided by the application of models that allow associations among environmental and biological variables to change over time.

Developing specific molecular biomarkers for thermal stress in salmonids

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.

Interspecies variation in the susceptibility of adult Pacific salmon to toxic urban stormwater runoff

Adult coho salmon (Oncorhynchus kisutch) prematurely die when they return from the ocean to spawn in urban watersheds throughout northwestern North America. The available evidence suggests the annual mortality events are caused by toxic stormwater runoff. The underlying pathophysiology of the urban spawner mortality syndrome is not known, and it is unclear whether closely related species of Pacific salmon are similarly at risk. The present study co-exposed adult coho and chum (O. keta) salmon to runoff from a high traffic volume urban arterial roadway. The spawners were monitored for the familiar symptoms of the mortality syndrome, including surface swimming, loss of orientation, and loss of equilibrium. Moreover, the hematology of both species was profiled by measuring arterial pH, blood gases, lactate, plasma electrolytes, hematocrit, and glucose. Adult coho developed behavioral symptoms within a few hours of exposure to stormwater. Various measured hematological parameters were significantly altered compared to coho controls, indicating a blood acidosis and ionoregulatory disturbance. By contrast, runoff-exposed chum spawners showed essentially no indications of the mortality syndrome, and measured blood hematological parameters were similar to unexposed chum controls. We conclude that contaminant(s) in urban runoff are the likely cause of the disruption of ion balance and pH in coho but not chum salmon. Among the thousands of chemicals in stormwater, future forensic analyses should focus on the gill or cardiovascular system of coho salmon. Because of their distinctive sensitivity to urban runoff, adult coho remain an important vertebrate indicator species for degraded water quality in freshwater habitats under pressure from human population growth and urbanization.

Individual variation, population-specific behaviours and stochastic processes shape marine migration phenologies

The phenology of long-distance migrations can influence individual fitness, moderate population dynamics and regulate the availability of ecosystem services to other trophic levels. Phenology varies within and among populations, and can be influenced by conditions individuals experience both prior to departure and encounter en route. Assessing how intrinsic and extrinsic factors (e.g., individual physical condition vs. environmental conditions) interact to influence variation in migratory phenologies across ecological scales is often limited due to logistical constraints associated with tracking large numbers of individuals from multiple populations simultaneously. We used two natural tags, DNA and otolith microstructure analysis, to estimate the relative influence of individual traits (life-history strategy, body size at departure and growth during migration), population-specific behaviours and interannual variability on the phenology of marine migrations in juvenile sockeye salmon Oncorhynchus nerka. We show that the timing and duration of juvenile sockeye salmon migrations were correlated with both life-history strategy and body size, while migration duration was also correlated with departure timing and growth rates during migration. Even after accounting for the effect of individual traits, several populations exhibited distinct migration phenologies. Finally, we observed substantial interannual and residual variation, suggesting stochastic environmental conditions moderate the influence of carry-over effects that develop prior to departure, as well as population-specific strategies. Migratory phenologies are shaped by complex interactions between drivers acting at multiple ecological and temporal scales. Given evidence that intraspecific diversity can stabilize ecological systems, conservation efforts should seek to maintain migratory variation among populations and preserve locally adapted phenotypes; however, variation within populations, which may buffer systems from environmental stochasticity, should also be regularly assessed and preserved.

Genetic signals of artificial and natural dispersal linked to colonization of South America by non-native Chinook salmon (Oncorhynchus tshawytscha)

Genetics data have provided unprecedented insights into evolutionary aspects of colonization by non-native populations. Yet, our understanding of how artificial (human-mediated) and natural dispersal pathways of non-native individuals influence genetic metrics, evolution of genetic structure, and admixture remains elusive. We capitalize on the widespread colonization of Chinook salmon Oncorhynchus tshawytscha in South America, mediated by both dispersal pathways, to address these issues using data from a panel of polymorphic SNPs. First, genetic diversity and the number of effective breeders (Nb) were higher among artificial than natural populations. Contemporary gene flow was common between adjacent artificial and natural and adjacent natural populations, but uncommon between geographically distant populations. Second, genetic structure revealed four distinct clusters throughout the Chinook salmon distributional range with varying levels of genetic connectivity. Isolation by distance resulted from weak differentiation between adjacent artificial and natural and between natural populations, with strong differentiation between distant Pacific Ocean and Atlantic Ocean populations, which experienced strong genetic drift. Third, genetic mixture analyses revealed the presence of at least six donor geographic regions from North America, some of which likely hybridized as a result of multiple introductions. Relative propagule pressure or the proportion of Chinook salmon propagules introduced from various geographic regions according to government records significantly influenced genetic mixtures for two of three artificial populations. Our findings support a model of colonization in which high-diversity artificial populations established first; some of these populations exhibited significant admixture resulting from propagule pressure. Low-diversity natural populations were likely subsequently founded from a reduced number of individuals.

Olfactory gene expression in migrating adult sockeye salmon Oncorhynchus nerka

Expression of 12 olfactory genes was analysed in adult sockeye salmon Oncorhynchus nerka nearing spawning grounds and O. nerka that had strayed from their natal migration route. Variation was found in six of these genes, all of which were olfc olfactory receptors and had lower expression levels in salmon nearing spawning grounds. The results may reflect decreased sensitivity to natal water olfactory cues as these fish are no longer seeking the correct migratory route. The expression of olfactory genes during the olfactory-mediated spawning migration of Pacific salmon Oncorhynchus spp. is largely unexplored and these findings demonstrate a link between migratory behaviours and olfactory plasticity that provides a basis for future molecular research on salmon homing.

The energetic consequences of habitat structure for forest stream salmonids

Increasing habitat availability (i.e. habitat suitable for occupancy) is often assumed to elevate the abundance or production of mobile consumers; however, this relationship is often nonlinear (threshold or unimodal). Identifying the mechanisms underlying these nonlinearities is essential for predicting the ecological impacts of habitat change, yet the functional forms and ultimate causation of consumer-habitat relationships are often poorly understood. Nonlinear effects of habitat on animal abundance may manifest through physical constraints on foraging that restrict consumers from accessing their resources. Subsequent spatial incongruence between consumers and resources should lead to unimodal or saturating effects of habitat availability on consumer production if increasing the area of habitat suitable for consumer occupancy comes at the expense of habitats that generate resources. However, the shape of this relationship could be sensitive to cross-ecosystem prey subsidies, which may be unrelated to recipient habitat structure and result in more linear habitat effects on consumer production. We investigated habitat-production relationships for juveniles of stream-rearing Pacific salmon and trout (Oncorhynchus spp.), which typically forage in low-velocity pool habitats, while their prey (drifting benthic invertebrates) are produced upstream in high-velocity riffles. However, juvenile salmonids also consume subsidies of terrestrial invertebrates that may be independent of pool-riffle structure. We measured salmonid biomass production in 13 experimental enclosures each containing a downstream pool and upstream riffle, spanning a gradient of relative pool area (14%-80% pool). Increasing pool relative to riffle habitat area decreased prey abundance, leading to a nonlinear saturating effect on fish production. We then used bioenergetics model simulations to examine how the relationship between pool area and salmonid biomass is affected by varying levels of terrestrial subsidy. Simulations indicated that increasing terrestrial prey inputs linearized the effect of habitat availability on salmonid biomass, while decreasing terrestrial inputs exaggerated a "hump-shaped" effect. Our results imply that nonlinear effects of habitat availability on consumer production can arise from trade-offs between habitat suitable for consumer occupancy and habitat that generates prey. However, cross-ecosystem prey subsidies can effectively decouple this trade-off and modify consumer-habitat relationships in recipient systems.

Roads to ruin: conservation threats to a sentinel species across an urban gradient

Urbanization poses a global challenge to species conservation. This is primarily understood in terms of physical habitat loss, as agricultural and forested lands are replaced with urban infrastructure. However, aquatic habitats are also chemically degraded by urban development, often in the form of toxic stormwater runoff. Here we assess threats of urbanization to coho salmon throughout developed areas of the Puget Sound Basin in Washington, USA. Puget Sound coho are a sentinel species for freshwater communities and also a species of concern under the U.S. Endangered Species Act. Previous studies have demonstrated that stormwater runoff is unusually lethal to adult coho that return to spawn each year in urban watersheds. To further explore the relationship between land use and recurrent coho die-offs, we measured mortality rates in field surveys of 51 spawning sites across an urban gradient. We then used spatial analyses to measure landscape attributes (land use and land cover, human population density, roadways, traffic intensity, etc.) and climatic variables (annual summer and fall precipitation) associated with each site. Structural equation modeling revealed a latent urbanization gradient that was associated with road density and traffic intensity, among other variables, and positively related to coho mortality. Across years within sites, mortality increased with summer and fall precipitation, but the effect of rainfall was strongest in the least developed areas and was essentially neutral in the most urbanized streams. We used the best-supported structural equation model to generate a predictive mortality risk map for the entire Puget Sound Basin. This map indicates an ongoing and widespread loss of spawners across much of the Puget Sound population segment, particularly within the major regional north-south corridor for transportation and development. Our findings identify current and future urbanization-related threats to wild coho, and show where green infrastructure and similar clean water strategies could prove most useful for promoting species conservation and recovery.

Epizootiology of the ectoparasitic protozoans Ichthyobodo salmonis and Trichodina truttae on wild chum salmon Oncorhynchus keta

Infestations of the ectoparasitic flagellate Ichthyobodo salmonis and the ciliate Trichodina truttae have caused acute mortalities of hatchery-reared juvenile chum salmon Oncorhynchus keta in Hokkaido, northern Japan. This study examined the epizootiology of I. salmonis and T. truttae on wild chum salmon as a possible infection source of the 2 parasitic protozoans in hatcheries. Infestations by both ectoparasites were detected on freshwater-adapted adult and juvenile chum salmon in all 4 rivers examined. This is the first study of an anadromous Pacific salmonid to report infestation of I. salmonis and T. truttae in adults returning for spawning. Among the marine-inhabiting phase of chum salmon, infestation with I. salmonis, but not T. truttae, was observed on adults and juveniles. The 2 protozoans were experimentally transmitted at the same time from wild to hatchery-reared chum salmon juveniles, and caused a high rate of mortality in the hatchery fish. In freshwater, the proliferation rate of T. truttae was greater than that of I. salmonis. These observations show that the euryhaline ectoparasite I. salmonis can infest chum salmon throughout their life cycle, in both river and ocean habitats, whereas T. truttae is able to infest these salmonids only in freshwater. Furthermore, wild chum salmon were shown to be a potential infestation source for both T. truttae and I. salmonis in hatchery fish.

Reduced growth in wild juvenile sockeye salmon Oncorhynchus nerka infected with sea lice

Daily growth rings were examined in the otoliths of wild juvenile sockeye salmon Oncorhynchus nerka to determine whether infection by ectoparasitic sea lice Caligus clemensi and Lepeophtheirus salmonis was associated with reduced host body growth, an important determinant of survival. Over 98% of the sea lice proved to be C. clemensi and the fish that were highly infected grew more slowly than uninfected individuals. Larger fish also grew faster than smaller fish. Finally, there was evidence of an interaction between body size and infection status, indicating the potential for parasite-mediated growth divergence.