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.

Pacific salmon in the Canadian Arctic highlight a range-expansion pathway for sub-Arctic fishes.

Rapid climate change is altering Arctic ecosystems at unprecedented rates. These changes in the physical environment may open new corridors for species range expansions, with substantial implications for subsistence-dependent communities and sensitive ecosystems. Over the past 20 years, rising incidental harvest of Pacific salmon by subsistence fishers has been monitored across a widening range spanning multiple land claim jurisdictions in Arctic Canada. In this study, we connect Indigenous and scientific knowledges to explore potential oceanographic mechanisms facilitating this ongoing northward expansion of Pacific salmon into the western Canadian Arctic. A regression analysis was used to reveal and characterize a two-part mechanism related to thermal and sea-ice conditions in the Chukchi and Beaufort seas that explains nearly all of the variation in the relative abundance of salmon observed within this region. The results indicate that warmer late-spring temperatures in a Chukchi Sea watch-zone and persistent, suitable summer thermal conditions in a Beaufort Sea watch-zone together create a range-expansion corridor and are associated with higher salmon occurrences in subsistence harvests. Furthermore, there is a body of knowledge to suggest that these conditions, and consequently the presence and abundance of Pacific salmon, will become more persistent in the coming decades. Our collaborative approach positions us to document, explore, and explain mechanisms driving changes in fish biodiversity that have the potential to, or are already affecting, Indigenous rights-holders in a rapidly warming Arctic.

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.

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.

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.

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.

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/.

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.

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.

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.

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.

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.

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.

Reverberating effects of resource exchanges in stream-riparian food webs.

Fluxes of materials or organisms across ecological boundaries, often termed "resource subsidies," directly affect recipient food webs. Few studies have addressed how such direct responses in one ecosystem may, in turn, influence the fluxes of materials or organisms to other habitats or the potential for feedback relationships to occur among ecosystems. As part of a large-scale, multi-year experiment, we evaluated the hypothesis that the input of a marine-derived subsidy results in a complex array of resource exchanges (i.e., inputs, outputs, feedbacks) between stream and riparian ecosystems as responses disperse across ecological boundaries. Moreover, we evaluated how the physical properties of resource subsidies mediated complex responses by contrasting carcasses with a pelletized salmon treatment. We found that salmon carcasses altered stream-riparian food webs by directly subsidizing multiple aquatic and terrestrial organisms (e.g., benthic insect larvae, fishes, and terrestrial flies). Such responses further influenced food webs along indirect pathways, some of which spanned land and water (e.g., subsidized fishes reduced aquatic insect emergence, with consequences for spiders and bats). Subsidy-mediated feedbacks manifested when carcasses were removed to riparian habitats where they were colonized by carrion flies, some of which fell into the stream and acted as another prey subsidy for fishes. As the effects of salmon subsidies propagated through the stream-riparian food web, the sign of consumer responses was not always positive and appeared to be determined by the outcome of trophic interactions, such that localized trophic interactions within one ecosystem mediated the export of organisms to others.

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.

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.

Difficulties for cost-benefit analysis in the 2020 environmental impact statement to recover the endangered wild salmon and steelhead in the Columbia River Basin.

Runs of the endangered wild salmon/steelhead in the Columbia River basin may be only two to seven percent of historic levels. These fish are a common-pool resource, where stakeholders over-consume, pollute rivers and oceans, block passage with dams and culverts, operate net pen fish farms, and plant huge numbers of hatchery fish that compete with and hybridize wild fish. Rivers provide free or subsidized services that stakeholders covet, however recovery of the endangered wild fish requires that peoples utilizing the rivers and the ocean must constrain their behavior, often reducing their profit. A new Environmental Impact Statement (EIS) and cost-benefit analysis are in progress for recovery of the endangered wild salmon/steelhead in the Columbia River basin. New regulations require surveys of U.S. households to measure the non-use benefits of salmon/steelhead recovery that can be important for endangered species. We review the 2002 EIS for juvenile salmon migration on the lower Snake River tributary to find mistakes to avoid in the new EIS and in other recovery studies.

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.

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.