Climate vulnerability assessment for Pacific salmon and steelhead in the California Current Large Marine Ecosystem

A Weight-of-Evidence Approach for Understanding the Recovery of Okanagan Sockeye Salmon

The productivity of Pacific Sockeye salmon (Oncorhynchus nerka) in the Columbia River has been declining over the past century. Yet, the Okanagan River Sockeye salmon population, which spawns in the Okanagan River, a Canadian tributary of the Columbia River, has seen a remarkable turnaround in abundance. Different hypotheses and lines of evidence covering multiple spatial scales have been proposed to explain this recovery; but they have never been comprehensively assessed. We adopted a weight-of-evidence approach to systematically assess the relative likelihood that each of these causal hypotheses contributed to the observed recovery. Our analysis disentangles the relative consequences of a set of environmental management actions that have been implemented to augment the Sockeye salmon freshwater productivity, while accounting for changes in freshwater and marine environmental conditions. Our list of potentially explanatory causal factors (anthropogenic and natural) included: (1) changes in escapement concurrent with improving local fish passage, (2) the implementation of fish-friendly flows in the Okanagan River, (3) initiating a hatchery restocking program, (4) potential improvements to Columbia dam operations to support higher relative survival of out-migrating juvenile fish, (5) possible shifts in survival-favorable conditions in the coastal marine environment for ocean-going life stages, and (6) broader changes to multi-stock harvest regimes in the Columbia River. Our assessment leveraged comparisons with the population dynamics of another Sockeye salmon stock in the Columbia River basin to differentiate between the impacts of management actions taken within the Okanagan watershed (our focus) from those occurring over the broader basin and marine scale. The results suggest that while shifts towards survival-favorable conditions in the coastal marine environment in 2007 played an important role in the upturn of the Okanagan population, alone it cannot explain the rate at which the Okanagan River Sockeye salmon recovered. Strong evidence supports the combined effect of increased escapement in conjunction with establishing and securing fish-friendly flows during spawning, incubation, and alevin emergence. Additionally, Sockeye salmon restocking improved the resilience of the stock against density-independent mortality events. These combined basin-level management actions played a pivotal role in magnifying the recovery trajectory afforded by improved marine survivorship. The spectacular response of the Okanagan River Sockeye salmon to the holistic perspectives and management interventions of Indigenous and other caretakers provides hope that other Pacific salmon stocks can be stabilized and recovered.

Integrating otolith and genetic tools to reveal intraspecific biodiversity in a highly impacted salmon population

Intraspecific biodiversity is vital for species persistence in an increasingly volatile world. By embracing methods that integrate information at different spatiotemporal scales, we can directly monitor and reconstruct changes in intraspecific biodiversity. Here we combined genetics and otolith biochronologies to describe the genotypic and phenotypic diversity of Chinook salmon (Oncorhynchus tshawytscha) in the Yuba River, California, comparing cohorts that experienced a range of hydroclimatic conditions. Yuba River salmon have been heavily impacted by habitat loss and degradation, and large influxes of unmarked hatchery fish each year have led to concern about introgression and uncertainty around the viability of its wild populations, particularly the rarer spring-run salmon. Otolith strontium isotopes showed that Yuba River origin fish represented, on average, 42% (range 7%-73%) of spawners across six return years (2009-2011, 2018-2020), with large interannual variability. The remainder of adult Chinook salmon in the river were primarily strays from the nearby Feather River hatchery, and since 2018 from the Mokelumne River hatchery. Among the Yuba-origin spawners, on average, 30% (range 14%-50%) exhibited the spring-run genotype. The Yuba-origin fish also displayed a variety of outmigration phenotypes that differed in the timing and size at which they left the Yuba river. Early-migrating fry dominated the returns (mean 59%, range 33%-89%), and their contribution rates were negatively correlated with freshwater flows. It is unlikely that fry survival rates are elevated during droughts, suggesting that this trend reflects disproportionately low survival of larger later migrating parr, smolts, and yearlings along the migratory corridor in drier years. Otolith daily increments indicated generally faster growth rates in non-natal habitats, emphasizing the importance of continuing upstream restoration efforts to improve in-river growing conditions. Together, these findings show that, despite a long history of habitat degradation and hatchery introgression, the Yuba River maintains intraspecific biodiversity that should be taken into account in future management, restoration, and reintroduction plans. The finding that genotypic spring-run are reproducing, surviving, and returning to the Yuba River every year suggests that re-establishment of an independent population is possible, although hatchery-wild interactions would need to be carefully considered. Integrating methods is critical to monitor changes in key genetic, physiological, and behavioral traits to assess population viability and resilience.

Salmon hatchery strays can demographically boost wild populations at the cost of diversity: quantitative genetic modelling of Alaska pink salmon

Hatcheries are vital to many salmon fisheries, with inherent risks and rewards. While hatcheries can increase the returns of adult fish, the demographic and evolutionary consequences for natural populations interacting with hatchery fish on spawning grounds remain unclear. This study examined the impacts of stray hatchery-origin pink salmon on natural population productivity and resilience. We explored temporal assortative mating dynamics using a quantitative genetic model that assumed the only difference between hatchery- and natural-origin adults was their return timing to natural spawning grounds. This model was parameterized with empirical data from an intensive multi-generational study of hatchery-wild interactions in the world's largest pink salmon fisheries enhancement program located in Prince William Sound, Alaska. Across scenarios of increasing hatchery fish presence on spawning grounds, our findings underscore a trade-off between demographic enhancement and preservation of natural population diversity. While enhancement bolstered natural population sizes towards local carrying capacities, hatchery introgression reduced variation in adult return timing by up to 20%. Results indicated that hatchery-origin alleles can rapidly assimilate into natural populations, despite the reduced fitness of hatchery fish attributable to phenotypic mismatches. These findings elucidate the potential for long-term demographic and evolutionary consequences arising from specific hatchery-wild interactions, emphasizing the need for management strategies that balance demographic enhancement with the conservation of natural diversity.

Remnant salmon life history diversity rediscovered in a highly compressed habitat

Chinook salmon (Oncorhynchus tshawytscha) display remarkable life history diversity, underpinning their ability to adapt to environmental change. Maintaining life history diversity is vital to the resilience and stability of Chinook salmon metapopulations, particularly under changing climates. However, the conditions that promote life history diversity are rapidly disappearing, as anthropogenic forces promote homogenization of habitats and genetic lineages. In this study, we use the highly modified Yuba River in California to understand if distinct genetic lineages and life histories still exist, despite reductions in spawning habitat and hatchery practices that have promoted introgression. There is currently a concerted effort to protect federally listed Central Valley spring-run Chinook salmon populations, given that few wild populations still exist. Despite this, we lack a comprehensive understanding of the genetic and life history diversity of Chinook salmon present in the Yuba River. To understand this diversity, we collected migration timing data and GREB1L genotypes from hook-and-line, acoustic tagging, and carcass surveys of Chinook salmon in the Yuba River between 2009 and 2011. Variation in the GREB1L region of the genome is tightly linked with run timing in Chinook salmon throughout their range, but the relationship between this variation and entry on spawning grounds is little explored in California's Central Valley. We found that the date Chinook salmon crossed the lowest barrier to Yuba River spawning habitat (Daguerre Point Dam) was tightly correlated with their GREB1L genotype. Importantly, our study confirms that ESA-listed spring-run Chinook salmon are spawning in the Yuba River, promoting a portfolio of life history and genetic diversity, despite the highly compressed habitat. This work highlights the need to identify and protect this life history diversity, especially in heavily impacted systems, to maintain healthy Chinook salmon metapopulations. Without protection, we run the risk of losing the last vestiges of important genetic variation.

Spatial and Temporal Variability in Stream Thermal Regime Drivers for Three River Networks During the Summer Growing Season

Many cold-water dependent aquatic organisms are experiencing habitat and population declines from increasing water temperatures. Identifying mechanisms which drive local and regional stream thermal regimes facilitates restoration at ecologically relevant scales. Stream temperatures vary spatially and temporally both within and among river basins. We developed a modeling process to identify statistical relationships between drivers of stream temperature and covariates representing landscape, climate, and management-related processes. The modeling process was tested in 3 study areas of the Pacific Northwest USA during the growing season (May [start], August [warmest], September [end]). Across all months and study systems, covariates with the highest relative importance represented the physical landscape (elevation [1st], catchment area [3rd], main channel slope [5th]) and climate covariates (mean monthly air temperature [2nd] and discharge [4th]). Two management covariates (ground water use [6th] and riparian shade [7th]) also had high relative importance. Across the growing season (for all basins) local reach slope had high relative importance in May, but transitioned to a regional main channel slope covariate in August and September. This modeling process identified regionally similar and locally unique relationships among drivers of stream temperature. High relative importance of management-related covariates suggested potential restoration actions for each system.

An updated end-to-end ecosystem model of the Northern California Current reflecting ecosystem changes due to recent marine heatwaves

The Northern California Current is a highly productive marine upwelling ecosystem that is economically and ecologically important. It is home to both commercially harvested species and those that are federally listed under the U.S. Endangered Species Act. Recently, there has been a global shift from single-species fisheries management to ecosystem-based fisheries management, which acknowledges that more complex dynamics can reverberate through a food web. Here, we have integrated new research into an end-to-end ecosystem model (i.e., physics to fisheries) using data from long-term ocean surveys, phytoplankton satellite imagery paired with a vertically generalized production model, a recently assembled diet database, fishery catch information, species distribution models, and existing literature. This spatially-explicit model includes 90 living and detrital functional groups ranging from phytoplankton, krill, and forage fish to salmon, seabirds, and marine mammals, and nine fisheries that occur off the coast of Washington, Oregon, and Northern California. This model was updated from previous regional models to account for more recent changes in the Northern California Current (e.g., increases in market squid and some gelatinous zooplankton such as pyrosomes and salps), to expand the previous domain to increase the spatial resolution, to include data from previously unincorporated surveys, and to add improved characterization of endangered species, such as Chinook salmon (Oncorhynchus tshawytscha) and southern resident killer whales (Orcinus orca). Our model is mass-balanced, ecologically plausible, without extinctions, and stable over 150-year simulations. Ammonium and nitrate availability, total primary production rates, and model-derived phytoplankton time series are within realistic ranges. As we move towards holistic ecosystem-based fisheries management, we must continue to openly and collaboratively integrate our disparate datasets and collective knowledge to solve the intricate problems we face. As a tool for future research, we provide the data and code to use our ecosystem model.

A global synthesis of climate vulnerability assessments on marine fisheries: Methods, scales, and knowledge co-production

Undertaking climate vulnerability assessments (CVAs) on marine fisheries is instrumental to the identification of regions, species, and stakeholders at risk of impacts from climate change, and the development of effective and targeted responses for fisheries adaptation. In this global literature review, we addressed three important questions to characterize fisheries CVAs: (i) what are the available approaches to develop CVAs in various social-ecological contexts, (ii) are different geographic scales and regions adequately represented, and (iii) how do diverse knowledge systems contribute to current understanding of vulnerability? As part of these general research efforts, we identified and characterized an inventory of frameworks and indicators that encompass a wide range of foci on ecological and socioeconomic dimensions of climate vulnerability on fisheries. Our analysis highlighted a large gap between countries with top research inputs and the most urgent adaptation needs. More research and resources are needed in low-income tropical countries to ensure existing inequities are not exacerbated. We also identified an uneven research focus across spatial scales and cautioned a possible scale mismatch between assessment and management needs. Drawing on this information, we catalog (1) a suite of research directions that could improve the utility and applicability of CVAs, particularly the examination of barriers and enabling conditions that influence the uptake of CVA results into management responses at multiple levels, (2) the lessons that have been learned from applications in data-limited regions, particularly the use of proxy indicators and knowledge co-production to overcome the problem of data deficiency, and (3) opportunities for wider applications, for example diversifying the use of vulnerability indicators in broader monitoring and management schemes. This information is used to provide a set of recommendations that could advance meaningful CVA practices for fisheries management and promote effective translation of climate vulnerability into adaptation actions.

Adult spawners: A critical period for subarctic Chinook salmon in a changing climate

Concurrent, distribution-wide abundance declines of some Pacific salmon species, including Chinook salmon (Oncorhynchus tshawytscha), highlights the need to understand how vulnerability at different life stages to climate stressors affects population dynamics and fisheries sustainability. Yukon River Chinook salmon stocks are among the largest subarctic populations, near the northernmost extent of the species range. Existing research suggests that Yukon River Chinook salmon population dynamics are largely driven by factors occurring between the adult spawner life stage and their offspring's first summer at sea (second year post-hatching). However, specific mechanisms sustaining chronic poor productivity are unknown, and there is a tremendous sense of urgency to understand causes, as declines of these stocks have taken a serious toll on commercial, recreational, and indigenous subsistence fisheries. Therefore, we leveraged multiple existing datasets spanning parent and juvenile stages of life history in freshwater and marine habitats. We analyzed environmental data in association with the production of offspring that survive to the marine juvenile stage (juveniles per spawner). These analyses suggest more than 45% of the variability in the production of juvenile Chinook salmon is associated with river temperatures or water discharge levels during the parent spawning migration. Over the past two decades, parents that experienced warmer water temperatures and lower discharge in the mainstem Yukon River produced fewer juveniles per spawning adult. We propose the adult spawner life stage as a critical period regulating population dynamics. We also propose a conceptual model that can explain associations between population dynamics and climate stressors using independent data focused on marine nutrition and freshwater heat stress. It is sobering to consider that some of the northernmost Pacific salmon habitats may already be unfavorable to these cold-water species. Our findings have immediate implications, given the common assumption that northern ranges of Pacific salmon offer refugia from climate stressors.

Thiamine Supplementation Improves Survival and Body Condition of Hatchery-Reared Steelhead (Oncorhynchus mykiss) in Oregon

Early rearing of steelhead (Oncorhynchus mykiss) in Oregon hatcheries is often problematic; fry can become emaciated and die during the period between hatch and first feed. Thiamine (vitamin B1) deficiency has caused early mortality in salmonids; however, the thiamine status of Oregon's steelhead populations is unknown, to date. Of the 26 egg samples from three Oregon hatcheries in 2019, 20 (77%) had thiamine levels < 10 nmol/g, and 13 of those samples (50%) had levels <6.5 nmol/g, suggesting the thiamine deficiency of adult, female steelhead. To investigate if thiamine deficiency was causally related to fry survival, females were injected with buffered thiamine HCl 50 mg/kg prior to spawning; additionally, a subset of eggs were supplemented via bath treatment with thiamine mononitrate (1000 ppm) at spawning. Cumulative fry mortality at 8 weeks post-hatch from thiamine-injected females was 2.9% compared to 13.8% mortality of fry without thiamine supplementation. Fry treated only with the thiamine via bath as eggs had a mortality rate of 6.9%. There were no additional improvements for the survival of fry from injected females that also received a thiamine bath. Furthermore, condition factors were greater in thiamine-supplemented fry than in those that received no thiamine. These data identify thiamine deficiency in Oregon steelhead and suggest supplementation with thiamine can mitigate early rearing mortality.

Has the IPCC's revised vulnerability concept been well adopted?

In the Third and Fourth Assessment Reports (TAR and AR4, respectively) by the Intergovernmental Panel on Climate Change (IPCC), vulnerability is conceived as a function of exposure, sensitivity, and adaptive capacity. However, in its Special Report on Managing the Risks of Extreme Events and Disasters to Advance Climate Change Adaptation (SREX) and Fifth Assessment Report (AR5), the IPCC redefined and separated exposure, and it reconceptualized vulnerability to be a function of sensitivity and capacity to cope and adapt. In this review, we found that the IPCC's revised vulnerability concept has not been well adopted and that researchers' preference, possible misinterpretation, possible confusion, and possible unawareness are among the possible technical and practical reasons. Among the issues that need further clarification from the IPCC is whether or not such a reconceptualization of vulnerability in the SREX/AR5 necessarily implies nullification of the TAR/AR4 vulnerability concept as far as the IPCC is concerned.

Tough places and safe spaces: Can refuges save salmon from a warming climate?

The importance of thermal refuges in a rapidly warming world is particularly evident for migratory species, where individuals encounter a wide range of conditions throughout their lives. In this study, we used a spatially explicit, individual-based simulation model to evaluate the buffering potential of cold-water thermal refuges for anadromous salmon and trout (Oncorhynchus spp.) migrating upstream through a warm river corridor that can expose individuals to physiologically stressful temperatures. We considered upstream migration in relation to migratory phenotypes that were defined in terms of migration timing, spawn timing, swim speed, and use of cold-water thermal refuges. Individuals with different migratory phenotypes migrated upstream through riverine corridors with variable availability of cold-water thermal refuges and mainstem temperatures. Use of cold-water refuges (CWRs) decreased accumulated sublethal exposures to physiologically stressful temperatures when measured in degree-days above 20, 21, and 22°C. The availability of CWRs was an order of magnitude more effective in lowering accumulated sublethal exposures under current and future mainstem temperatures for summer steelhead than fall Chinook Salmon. We considered two emergent model outcomes, survival and percent of available energy used, in relation to thermal heterogeneity and migratory phenotype. Mean percent energy loss attributed to future warmer mainstem temperatures was at least two times larger than the difference in energy used in simulations without CWRs for steelhead and salmon. We also found that loss of CWRs reduced the diversity of energy-conserving migratory phenotypes when we examined the variability in entry timing and travel time outside of CWRs in relation to energy loss. Energy-conserving phenotypic space contracted by 7%-23% when CWRs were unavailable under the current thermal regime. Our simulations suggest that, while CWRs do not entirely mitigate for stressful thermal exposures in mainstem rivers, these features are important for maintaining a diversity of migration phenotypes. Our study suggests that the maintenance of diverse portfolios of migratory phenotypes and cool- and cold-water refuges might be added to the suite of policies and management actions presently being deployed to improve the likelihood of Pacific salmonid persistence into a future characterized by climate change.

The diadromous watersheds-ocean continuum: Managing diadromous fish as a community for ecosystem resilience

Diadromous fishes play important ecological roles by delivering ecosystem services and making crucial connections along the watersheds-ocean continuum. However, it is difficult to fully understand the community-level impacts and cumulative benefits of diadromous fish migrations, as these species are most often considered individually or in small groups. Their interactions at a community level (e.g., interdependencies such as predation, co-migration, and habitat conditioning) and the connections between their ecosystem roles and functions (e.g., cumulative marine-derived nutrient contributions, impacts on stream geomorphology) are yet to be fully understood. Similarly, freshwater, estuarine, and marine ecosystems are often considered as independent parts, limiting understanding of the importance of connections across systems. We argue that not considering the ecosystem interdependence and importance of diadromous fish as a community currently hinders the implementation of the large-scale management required to increase ecosystem resilience and fish productivity across the full range of these species. We developed a conceptual model, the Diadromous Watersheds-Ocean Continuum (DWOC), that uses ecosystem services to promote a more holistic approach to the management of the diadromous community and encourages an integrated understanding of the ecosystem connections made by these species. DWOC provides a framework for discussions that can help identify research and management needs, discuss the trade-offs of different management options, and analyze what pressing questions impede the implementation of large-scale management solutions toward a more ecosystem-based management approach.

Recommendations for quantifying and reducing uncertainty in climate projections of species distributions

Projecting the future distributions of commercially and ecologically important species has become a critical approach for ecosystem managers to strategically anticipate change, but large uncertainties in projections limit climate adaptation planning. Although distribution projections are primarily used to understand the scope of potential change-rather than accurately predict specific outcomes-it is nonetheless essential to understand where and why projections can give implausible results and to identify which processes contribute to uncertainty. Here, we use a series of simulated species distributions, an ensemble of 252 species distribution models, and an ensemble of three regional ocean climate projections, to isolate the influences of uncertainty from earth system model spread and from ecological modeling. The simulations encompass marine species with different functional traits and ecological preferences to more broadly address resource manager and fishery stakeholder needs, and provide a simulated true state with which to evaluate projections. We present our results relative to the degree of environmental extrapolation from historical conditions, which helps facilitate interpretation by ecological modelers working in diverse systems. We found uncertainty associated with species distribution models can exceed uncertainty generated from diverging earth system models (up to 70% of total uncertainty by 2100), and that this result was consistent across species traits. Species distribution model uncertainty increased through time and was primarily related to the degree to which models extrapolated into novel environmental conditions but moderated by how well models captured the underlying dynamics driving species distributions. The predictive power of simulated species distribution models remained relatively high in the first 30 years of projections, in alignment with the time period in which stakeholders make strategic decisions based on climate information. By understanding sources of uncertainty, and how they change at different forecast horizons, we provide recommendations for projecting species distribution models under global climate change.

Social-ecological vulnerability of fishing communities to climate change: A U.S. West Coast case study

Climate change is already impacting coastal communities, and ongoing and future shifts in fisheries species productivity from climate change have implications for the livelihoods and cultures of coastal communities. Harvested marine species in the California Current Large Marine Ecosystem support U.S. West Coast communities economically, socially, and culturally. Ecological vulnerability assessments exist for individual species in the California Current but ecological and human vulnerability are linked and vulnerability is expected to vary by community. Here, we present automatable, reproducible methods for assessing the vulnerability of U.S. West Coast fishing dependent communities to climate change within a social-ecological vulnerability framework. We first assessed the ecological risk of marine resources, on which fishing communities rely, to 50 years of climate change projections. We then combined this with the adaptive capacity of fishing communities, based on social indicators, to assess the potential ability of communities to cope with future changes. Specific communities (particularly in Washington state) were determined to be at risk to climate change mainly due to economic reliance on at risk marine fisheries species, like salmon, hake, or sea urchins. But, due to higher social adaptive capacity, these communities were often not found to be the most vulnerable overall. Conversely, certain communities that were not the most at risk, ecologically and economically, ranked in the category of highly vulnerable communities due to low adaptive capacity based on social indicators (particularly in Southern California). Certain communities were both ecologically at risk due to catch composition and socially vulnerable (low adaptive capacity) leading to the highest tier of vulnerability. The integration of climatic, ecological, economic, and societal data reveals that factors underlying vulnerability are variable across fishing communities on the U.S West Coast, and suggests the need to develop a variety of well-aligned strategies to adapt to the ecological impacts of climate change.

Risks of mining to salmonid-bearing watersheds

Mining provides resources for people but can pose risks to ecosystems that support cultural keystone species. Our synthesis reviews relevant aspects of mining operations, describes the ecology of salmonid-bearing watersheds in northwestern North America, and compiles the impacts of metal and coal extraction on salmonids and their habitat. We conservatively estimate that this region encompasses nearly 4000 past producing mines, with present-day operations ranging from small placer sites to massive open-pit projects that annually mine more than 118 million metric tons of earth. Despite impact assessments that are intended to evaluate risk and inform mitigation, mines continue to harm salmonid-bearing watersheds via pathways such as toxic contaminants, stream channel burial, and flow regime alteration. To better maintain watershed processes that benefit salmonids, we highlight key windows during the mining governance life cycle for science to guide policy by more accurately accounting for stressor complexity, cumulative effects, and future environmental change.

How riparian and floodplain restoration modify the effects of increasing temperature on adult salmon spawner abundance in the Chehalis River, WA

Stream temperatures in the Pacific Northwest are projected to increase with climate change, placing additional stress on cold-water salmonids. We modeled the potential impact of increased stream temperatures on four anadromous salmonid populations in the Chehalis River Basin (spring-run and fall-run Chinook salmon Oncorhynchus tshawytscha, coho salmon O. kisutch, and steelhead O. mykiss), as well as the potential for floodplain reconnection and stream shade restoration to offset the effects of future temperature increases. In the Chehalis River Basin, peak summer stream temperatures are predicted to increase by as much as 3°C by late-century, but restoration actions can locally decrease temperatures by as much as 6°C. On average, however, basin-wide average stream temperatures are expected to increase because most reaches have low temperature reduction potential for either restoration action relative to climate change. Results from the life cycle models indicated that, without restoration actions, increased summer temperatures are likely to produce significant declines in spawner abundance by late-century for coho (-29%), steelhead (-34%), and spring-run Chinook salmon (-95%), and smaller decreases for fall-run Chinook salmon (-17%). Restoration actions reduced these declines in all cases, although model results suggest that temperature restoration alone may not fully mitigate effects of future temperature increases. Notably, floodplain reconnection provided a greater benefit than riparian restoration for steelhead and both Chinook salmon populations, but riparian restoration provided a greater benefit for coho. This pattern emerged because coho salmon tend to spawn and rear in smaller streams where shade restoration has a larger effect on stream temperature, whereas Chinook and steelhead tend to occupy larger rivers where temperatures are more influenced by floodplain connectivity. Spring-run Chinook salmon are the only population for which peak temperatures affect adult prespawn survival in addition to rearing survival, making them the most sensitive species to increasing stream temperatures.

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.

Quantification of thermal impacts across freshwater life stages to improve temperature management for anadromous salmonids

Water temperature is the major controlling factor that shapes the physiology, behaviour and, ultimately, survival of aquatic ectotherms. Here we examine temperature effects on the survival of Chinook salmon (Oncorhynchus tshawytscha), a species of high economic and conservation importance. We implement a framework to assess how incremental changes in temperature impact survival across populations that is based on thermal performance models for three freshwater life stages of Chinook salmon. These temperature-dependent models were combined with local spatial distribution and phenology data to translate spatial-temporal stream temperature data into maps of life stage-specific physiological performance in space and time. Specifically, we converted temperature-dependent performance (i.e. energy used by pre-spawned adults, mortality of incubating embryos and juvenile growth rate) into a common currency that measures survival in order to compare thermal effects across life stages. Based on temperature data from two abnormally warm and dry years for three managed rivers in the Central Valley, California, temperature-dependent mortality during pre-spawning holding was higher than embryonic mortality or juvenile mortality prior to smolting. However, we found that local phenology and spatial distribution helped to mitigate negative thermal impacts. In a theoretical application, we showed that high temperatures may inhibit successful reintroduction of threatened Central Valley spring-run Chinook salmon to two rivers where they have been extirpated. To increase Chinook salmon population sizes, especially for the threatened and declining spring-run, our results indicate that adults may need more cold-water holding habitat than currently available in order to reduce pre-spawning mortality stemming from high temperatures. To conclude, our framework is an effective way to calculate thermal impacts on multiple salmonid populations and life stages within a river over time, providing local managers the information to minimize negative thermal impacts on salmonid populations, particularly important during years when cold-water resources are scarce.

Contribution of Glacier Runoff during Heat Waves in the Nooksack River Basin USA

The thirty-eight-year record (1984–2021) of glacier mass balance measurement indicates a significant glacier response to climate change in the North Cascades, Washington that has led to declining glacier runoff in the Nooksack Basin. Glacier runoff in the Nooksack Basin is a major source of streamflow during the summer low-flow season and mitigates both low flow and warm water temperatures; this is particularly true during summer heat waves. Synchronous observations of glacier ablation and stream discharge immediately below Sholes Glacier from 2013–2017, independently identify daily discharge during the ablation season. The identified ablation rate is applied to glaciers across the North Fork Nooksack watershed, providing daily glacier runoff discharge to the North Fork Nooksack River. This is compared to observed daily discharge and temperature data of the North Fork Nooksack River and the unglaciated South Fork Nooksack River from the USGS. The ameliorating role of glacier runoff on discharge and water temperature is examined during 24 late summer heat wave events from 2010–2021. The primary response to these events is increased discharge in the heavily glaciated North Fork, and increased stream temperature in the unglaciated South Fork. During the 24 heat events, the discharge increased an average of +24% (±17%) in the North Fork and decreased an average of 20% (±8%) in the South Fork. For water temperature the mean increase was 0.7 °C (±0.4 °C) in the North Fork and 2.1 °C (±1.2 °C) in the South Fork. For the North Fork glacier runoff production was equivalent to 34% of the total discharge during the 24 events. Ongoing climate change will likely cause further decreases in summer baseflow and summer baseflow, along with an increase in water temperature potentially exceeding tolerance levels of several Pacific salmonid species that would further stress this population.

One hundred-seventy years of stressors erode salmon fishery climate resilience in California's warming landscape

People seek reliable natural resources despite climate change. Diverse habitats and biologies stabilize productivity against disturbances like climate, prompting arguments to promote climate-resilient resources by prioritizing complex, less-modified ecosystems. These arguments hinge on the hypothesis that simplifying and degrading ecosystems will reduce resources' climate resilience, a process liable to be cryptically evolving across landscapes and human generations, but rarely documented. Here, we examined the industrial era (post 1848) of California's Central Valley, chronicling the decline of a diversified, functional portfolio of salmon habitats and life histories and investigating for empirical evidence of lost climate resilience in its fishery. Present perspectives indicate that California's dynamic, warming climate overlaid onto its truncated, degraded habitat mosaic severely constrains its salmon fishery. We indeed found substantial climate constraints on today's fishery, but this reflected a shifted ecological baseline. During the early stages of a stressor legacy that transformed the landscape and -- often consequently -- compressed salmon life history expression, the fishery diffused impacts of dry years across a greater number of fishing years and depended less on cool spring-summer transitions. The latter are important given today's salmon habitats, salmon life histories, and resource management practices, but are vanishing with climate change while year-to-year variation in fishery performance is rising. These findings give empirical weight to the idea that human legacies influence ecosystems' climate resilience across landscapes and boundaries (e.g., land/sea). They also raise the question of whether some contemporary climate effects are recent and attributable not only to increasing climate stress, but to past and present human actions that erode resilience. In general, it is thus worth considering that management approaches that prioritize complex, less-modified ecosystems may stabilize productivity despite increasing climate stress and such protective actions may be required for some ecological services to persist into uncertain climate futures.

Perspectives on managing fisheries for community wellbeing in the face of climate change

Coastal communities are being impacted by climate change, affecting the livelihoods, food security, and wellbeing of residents. Human wellbeing is influenced by the heath of the environment through numerous pathways and is increasingly being included as a desired outcome in environmental management. However, the contributors to wellbeing can be subjective and the values and perspectives of decision-makers can affect the aspects of wellbeing that are included in planning. We used Q methodology to examine how a group of individuals in fisheries management prioritize components of wellbeing that may be important to coastal communities in the California Current social-ecological system (SES). The California Current SES is an integrated system of ecological and human communities with complex linkages and connections where commercial fishing is part of the culture and an important livelihood. We asked individuals that sit on advisory bodies to the Pacific Fisheries Management Council to rank 36 statements about coastal community wellbeing, ultimately revealing three discourses about how we can best support or improve wellbeing in those communities. We examine how the priorities differ between the discourses, identify areas of consensus, and discuss how these perspectives may influence decision-making when it comes to tradeoffs inherent in climate adaptation in fisheries. Lastly, we consider if and how thoughts about priorities have been affected by the COVID-19 pandemic.

An assessment of marine, estuarine, and riverine habitat vulnerability to climate change in the Northeast U.S

Climate change is impacting the function and distribution of habitats used by marine, coastal, and diadromous species. These impacts often exacerbate the anthropogenic stressors that habitats face, particularly in the coastal environment. We conducted a climate vulnerability assessment of 52 marine, estuarine, and riverine habitats in the Northeast U.S. to develop an ecosystem-scale understanding of the impact of climate change on these habitats. The trait-based assessment considers the overall vulnerability of a habitat to climate change to be a function of two main components, sensitivity and exposure, and relies on a process of expert elicitation. The climate vulnerability ranks ranged from low to very high, with living habitats identified as the most vulnerable. Over half of the habitats examined in this study are expected to be impacted negatively by climate change, while four habitats are expected to have positive effects. Coastal habitats were also identified as highly vulnerable, in part due to the influence of non-climate anthropogenic stressors. The results of this assessment provide regional managers and scientists with a tool to inform habitat conservation, restoration, and research priorities, fisheries and protected species management, and coastal and ocean planning.

Glacier retreat creating new Pacific salmon habitat in western North America

Glacier retreat poses risks and benefits for species of cultural and economic importance. One example is Pacific salmon (Oncorhynchus spp.), supporting subsistence harvests, and commercial and recreational fisheries worth billions of dollars annually. Although decreases in summer streamflow and warming freshwater is reducing salmon habitat quality in parts of their range, glacier retreat is creating new streams and lakes that salmon can colonize. However, potential gains in future salmon habitat associated with glacier loss have yet to be quantified across the range of Pacific salmon. Here we project future gains in Pacific salmon freshwater habitat by linking a model of glacier mass change for 315 glaciers, forced by five different Global Climate Models, with a simple model of salmon stream habitat potential throughout the Pacific Mountain ranges of western North America. We project that by the year 2100 glacier retreat will create 6,146 (±1,619) km of new streams accessible for colonization by Pacific salmon, of which 1,930 (±569) km have the potential to be used for spawning and juvenile rearing, representing 0 to 27% gains within the 18 sub-regions we studied. These findings can inform proactive management and conservation of Pacific salmon in this era of rapid climate change.

Climate change vulnerability of cetaceans in Macaronesia: Insights from a trait-based assessment

Over the last decades global warming has caused an increase in ocean temperature, acidification and oxygen loss which has led to changes in nutrient cycling and primary production affecting marine species at multiple trophic levels. While knowledge about the impacts of climate change in cetacean's species is still scarce, practitioners and policymakers need information about the species at risk to guide the implementation of conservation measures. To assess cetacean's vulnerability to climate change in the biogeographic region of Macaronesia, we adapted the Marine Mammal Climate Vulnerability Assessment (MMCVA) method and applied it to 21 species management units using an expert elicitation approach. Results showed that over half (62%) of the units assessed presented Very High (5 units) or High (8 units) vulnerability scores. Very High vulnerability scores were found in archipelago associated units of short-finned pilot whales (Globicephala macrorhynchus) and common bottlenose dolphins (Tursiops truncatus), namely in the Canary Islands and Madeira, as well as Risso's dolphins (Grampus griseus) in the Canary Islands. Overall, certainty scores ranged from Very High to Moderate for 67% of units. Over 50% of units showed a high potential for distribution, abundance and phenology changes as a response to climate change. With this study we target current and future information needs of conservation managers in the region, and guide research and monitoring efforts, while contributing to the improvement and validation of trait-based vulnerability approaches under a changing climate.

Estimating the genetic diversity of Pacific salmon and trout using multigene eDNA metabarcoding

Genetic diversity underpins species conservation and management goals, and ultimately determines a species' ability to adapt. Using freshwater environmental DNA (eDNA) samples, we examined mitochondrial genetic diversity using multigene metabarcode sequence data from four Oncorhynchus species across 16 sites in Oregon and northern California. Our multigene metabarcode panel included targets commonly used in population genetic NADH dehydrogenase 2 (ND2), phylogenetic cytochrome c oxidase subunit 1 (COI) and eDNA (12S ribosomal DNA) screening. The ND2 locus showed the greatest within-species haplotype diversity for all species, followed by COI and then 12S rDNA for all species except Oncorhynchus kisutch. Sequences recovered for O. clarkii clarkii were either identical to, or one mutation different from, previously characterized haplotypes (95.3% and 4.5% of reads, respectively). The greatest diversity in O. c. clarkii was among coastal watersheds, and subsets of this diversity were shared with fish in inland watersheds. However, coastal streams and the Umpqua River watershed appear to harbour unique haplotypes. Sequences from O. mykiss revealed a disjunction between the Willamette watershed and southern watersheds suggesting divergent histories. We also identified similarities between populations in the northern Deschutes and southern Klamath watersheds, consistent with previously hypothesized connections between the two via inland basins. Oncorhynchus kisutch was only identified in coastal streams and the Klamath River watershed, with most diversity concentrated in the coastal Coquille watershed. Oncorhynchus tshawytscha was only observed at one site, but contained multiple haplotypes at each locus. The characterization of genetic diversity at multiple loci expands the knowledge gained from eDNA sampling and provides crucial information for conservation actions and genetic management.

Direct and size-mediated effects of temperature and ration-dependent growth rates on energy reserves in juvenile anadromous alewives (Alosa pseudoharengus)

Growth rate and energy reserves are important determinants of fitness and are governed by endogenous and exogenous factors. Thus, examining the influence of individual and multiple stressors on growth and energy reserves can help estimate population health under current and future conditions. In young anadromous fishes, freshwater habitat quality determines physiological state and fitness of juveniles emigrating to marine habitats. In this study, the authors tested how temperature and food availability affect survival, growth and energy reserves in juvenile anadromous alewives (Alosa pseudoharengus), a forage fish distributed along the eastern North American continent. Field-collected juvenile anadromous A. pseudoharengus were exposed for 21 days to one of two temperatures (21°C and 25°C) and one of two levels of food rations (1% or 2% tank biomass daily) and compared for differences in final size, fat mass-at-length, lean mass-at-length and energy density. Increased temperature and reduced ration both led to lower growth rates, and the effect of reduced ration was greater at higher temperature. Fat mass-at-length decreased with dry mass, and energy density increased with total length, suggesting size-based endogenous influences on energy reserves. Lower ration also directly decreased fat mass-at-length, lean mass-at-length and energy density. Given the fitness implications of size and energy reserves, temperature and food availability should be considered important indicators of nursery habitat quality and incorporated in A. pseudoharengus life-history models to improve forecasting of population health under climate change.

Integrating thermal infrared stream temperature imagery and spatial stream network models to understand natural spatial thermal variability in streams

Under a warmer future climate, thermal refuges could facilitate the persistence of species relying on cold-water habitat. Often these refuges are small and easily missed or smoothed out by averaging in models. Thermal infrared (TIR) imagery can provide empirical water surface temperatures that capture these features at a high spatial resolution (<1 m) and over tens of kilometers. Our study examined how TIR data could be used along with spatial stream network (SSN) models to characterize thermal regimes spatially in the Middle Fork John Day (MFJD) River mainstem (Oregon, USA). We characterized thermal variation in seven TIR longitudinal temperature profiles along the MFJD mainstem and compared them with SSN model predictions of stream temperature (for the same time periods as the TIR profiles). TIR profiles identified reaches of the MFJD mainstem with consistently cooler temperatures across years that were not consistently captured by the SSN prediction models. SSN predictions along the mainstem identified ~80% of the 1-km reach scale temperature warming or cooling trends observed in the TIR profiles. We assessed whether landscape features (e.g., tributary junctions, valley confinement, geomorphic reach classifications) could explain the fine-scale thermal heterogeneity in the TIR profiles (after accounting for the reach-scale temperature variability predicted by the SSN model) by fitting SSN models using the TIR profile observation points. Only the distance to the nearest upstream tributary was identified as a statistically significant landscape feature for explaining some of the thermal variability in the TIR profile data. When combined, TIR data and SSN models provide a data-rich evaluation of stream temperature captured in TIR imagery and a spatially extensive prediction of the network thermal diversity from the outlet to the headwaters.

Coldwater fish in a warm water world: Implications for predation of salmon smolts during estuary transit

Predator-prey systems face intensifying pressure from human exploitation and a warming climate with implications for where and how natural resource management can successfully intervene. We hypothesized young salmon migrating to the Pacific Ocean face a seasonally intensifying predator gauntlet when warming water temperature intensifies a multiple predator effect (MPE) from Striped Bass Morone saxatilis and Largemouth Bass Micropterus salmoides. We evaluated this hypothesis using data synthesis and simulation modeling.Contemporary studies based on acoustically tagged fish reaffirmed older observations that Chinook Salmon smolts must transit the Delta before water temperature reaches 20°C or mortality will be nearly 100%. Striped Bass attack rates on tethered smolts were insensitive to distance from shore and water temperature, whereas Largemouth Bass attack rates were highest near shorelines in warm water, supporting the temporal aspect of the hypothesis. Whether the combined effects of the two predators produce an MPE remains unconfirmed due to limitations on quantifying salmon behavior.We used multiple simulation models to try to reconstruct the empirical relationship between smolt survival and water temperature. Simulations reinforced attack rate results, but could not recreate the temperature dependence in smolt survival except at higher than observed temperatures. We propose three hypotheses for why and recommend discerning among them should be a focus of research.We found significant linear relationships between monthly mean inflow to the Delta from each of its two largest tributaries and monthly mean water temperatures along associated salmon migration routes, but these relationships can be nonlinear, with most of the correlation occurring at low inflows when water temperature is largely controlled by air temperature and day length. As the global climate warms, changed circumstances in predator-prey relationships may present important challenges when managing species vulnerable to extinction in addition to presently more abundant species.

Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem

DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. Here we evaluate the performance of MiFish 12S taxonomic assignments using a case study of California Current Large Marine Ecosystem fishes to determine best practices for metabarcoding. Specifically, we use a taxonomy cross-validation by identity framework to compare classification performance between a global database comprised of all available sequences and a curated database that only includes sequences of fishes from the California Current Large Marine Ecosystem. We demonstrate that the regional database provides higher assignment accuracy than the comprehensive global database. We also document a tradeoff between accuracy and misclassification across a range of taxonomic cutoff scores, highlighting the importance of parameter selection for taxonomic classification. Furthermore, we compared assignment accuracy with and without the inclusion of additionally generated reference sequences. To this end, we sequenced tissue from 597 species using the MiFish 12S primers, adding 252 species to GenBank's existing 550 California Current Large Marine Ecosystem fish sequences. We then compared species and reads identified from seawater environmental DNA samples using global databases with and without our generated references, and the regional database. The addition of new references allowed for the identification of 16 additional native taxa representing 17.0% of total reads from eDNA samples, including species with vast ecological and economic value. Together these results demonstrate the importance of comprehensive and curated reference databases for effective metabarcoding and the need for locus-specific validation efforts.

Thermal effects in rainbow trout (Oncorhynchus mykiss) F1 embryos (farmed female × wild thermal-resistant male)

The aim of this work was to investigate the response of rainbow trout embryos (Oncorhynchus mykiss) (i.e., survival, size at hatching, time to hatching, malformations) to four incubation temperatures (5.8, 8.9, 14.0 and 16.8°C), taking into account the origin of the male parental genome and comparing pure farmed and F1 embryos (farmed female × wild thermal-resistant male). Several consequences of thermal stress were observed: lower accumulated thermal units (ATU) at hatching at high temperatures, and lower survival, shorter hatched free embryos and less-consumed yolk sac at extreme temperatures. The effect of the thermal-adapted male parental genome was shown only in the lower percentage of incompletely hatched free embryos in the F1 families. It appears that to obtain greater modification of thermal performance during early development, the adapted genome of the wild thermal-resistant population has to be included through maternal inheritance, thus producing a stabilized strain selected for domesticity, growth and thermal adaptation.

Environmentally triggered shifts in steelhead migration behavior and consequences for survival in the mid-Columbia River

The majority of Columbia River summer-run steelhead encounter high river temperatures (near or > 20°C) during their spawning migration. While some steelhead pass through the mid-Columbia River in a matter of days, others use tributary habitats as temperature refuges for periods that can last months. Using PIT tag detection data from adult return years 2004-2016, we fit 3-component mixture models to differentiate between "fast", "slow", and "overwintering" migration behaviors in five aggregated population groups. Fast fish migrated straight through the reach on average in ~7-9 days while slow fish delayed their migration for weeks to months, and overwintering fish generally took ~150-250 days. We then fit covariate models to examine what factors contributed to the probability of migration delay during summer months (slow or overwintering behaviors), and to explore how migration delay related to mortality. Finally, to account for the impact of extended residence times in the reach for fish that delayed, we compared patterns in estimated average daily rates of mortality between migration behaviors and across population groups. Results suggest that migration delay was primarily triggered by high river temperatures but temperature thresholds for delay were lowest just before the seasonal peak in river temperatures. While all populations groups demonstrated these general patterns, we documented substantial variability in temperature thresholds and length of average delays across population groups. Although migration delay was related to higher reach mortality, it was also related to lower average daily mortality rates due to the proportional increase in reach passage duration being larger than the associated increase in mortality. Lower daily mortality rates suggest that migration delay could help mitigate the impacts of harsh migration conditions, presumably through the use of thermal refuges, despite prolonged exposure to local fisheries. Future studies tracking individual populations from their migration through reproduction could help illuminate the full extent of the tradeoffs between different migration behaviors.

Endangered predators and endangered prey: Seasonal diet of Southern Resident killer whales

Understanding diet is critical for conservation of endangered predators. Southern Resident killer whales (SRKW) (Orcinus orca) are an endangered population occurring primarily along the outer coast and inland waters of Washington and British Columbia. Insufficient prey has been identified as a factor limiting their recovery, so a clear understanding of their seasonal diet is a high conservation priority. Previous studies have shown that their summer diet in inland waters consists primarily of Chinook salmon (Oncorhynchus tshawytscha), despite that species' rarity compared to some other salmonids. During other times of the year, when occurrence patterns include other portions of their range, their diet remains largely unknown. To address this data gap, we collected feces and prey remains from October to May 2004-2017 in both the Salish Sea and outer coast waters. Using visual and genetic species identification for prey remains and genetic approaches for fecal samples, we characterized the diet of the SRKWs in fall, winter, and spring. Chinook salmon were identified as an important prey item year-round, averaging ~50% of their diet in the fall, increasing to 70-80% in the mid-winter/early spring, and increasing to nearly 100% in the spring. Other salmon species and non-salmonid fishes, also made substantial dietary contributions. The relatively high species diversity in winter suggested a possible lack of Chinook salmon, probably due to seasonally lower densities, based on SRKW's proclivity to selectively consume this species in other seasons. A wide diversity of Chinook salmon stocks were consumed, many of which are also at risk. Although outer coast Chinook samples included 14 stocks, four rivers systems accounted for over 90% of samples, predominantly the Columbia River. Increasing the abundance of Chinook salmon stocks that inhabit the whales' winter range may be an effective conservation strategy for this population.

Climate change threatens Chinook salmon throughout their life cycle

Widespread declines in Atlantic and Pacific salmon (Salmo salar and Oncorhynchus spp.) have tracked recent climate changes, but managers still lack quantitative projections of the viability of any individual population in response to future climate change. To address this gap, we assembled a vast database of survival and other data for eight wild populations of threatened Chinook salmon (O. tshawytscha). For each population, we evaluated climate impacts at all life stages and modeled future trajectories forced by global climate model projections. Populations rapidly declined in response to increasing sea surface temperatures and other factors across diverse model assumptions and climate scenarios. Strong density dependence limited the number of salmon that survived early life stages, suggesting a potentially efficacious target for conservation effort. Other solutions require a better understanding of the factors that limit survival at sea. We conclude that dramatic increases in smolt survival are needed to overcome the negative impacts of climate change for this threatened species.

Differential impacts of freshwater and marine covariates on wild and hatchery Chinook salmon marine survival

Large-scale atmospheric conditions in the Northeast Pacific Ocean affect both the freshwater environment in the Columbia River Basin and marine conditions along the coasts of Oregon, Washington, and British Columbia, resulting in correlated conditions in the two environments. For migrating species, such as salmonids that move through multiple habitats, these correlations can amplify the impact of good or poor physical conditions on growth and survival, as movements among habitats may not alleviate effects of anomalous conditions. Unfortunately, identifying the mechanistic drivers of salmon survival in space and time is hindered by these cross-habitat correlations. To address this issue, we modeled the marine survival of Snake River spring/summer Chinook salmon with multiple indices of the marine environment and an explicit treatment of the effect of arrival timing from freshwater to the ocean, and found that both habitats contribute to marine survival rates. We show how this particular carryover effect of freshwater conditions on marine survival varies by year and rearing type (hatchery or wild), with a larger effect for wild fish. As environmental conditions change, incorporating effects from both freshwater and marine habitats into salmon survival models will become more important, and has the additional benefit of highlighting how management actions that affect arrival timing may improve marine survival.

Climate change vulnerability assessment of the main marine commercial fish and invertebrates of Portugal

This is the first attempt to apply an expert-based ecological vulnerability assessment of the effects of climate change on the main marine resources of Portugal. The vulnerability, exposure, sensitivity, adaptive capacity, and expected directional effects of 74 species of fish and invertebrates of commercial interest is estimated based on criteria related to their life-history and level of conservation or exploitation. This analysis is performed separately for three regions of Portugal and two scenarios of climate change (RCP 4.5 and RCP 8.5). To do that, the fourth assessment report IPCC framework for vulnerability assessments was coupled to the outputs of a physical-biogeochemical model allowing to weight the exposure of the species by the expected variability of the environmental variables in the future. The highest vulnerabilities were found for some migratory and elasmobranch species, although overall vulnerability scores were low probably due to the high adaptive capacity of species from temperate ecosystems. Among regions, the highest average vulnerability was estimated for the species in the Central region while higher vulnerabilities were identified under climate change scenario RCP 8.5 in the three regions, due to higher expected climatic variability. This work establishes the basis for the assessment of the vulnerability of the human activities relying on marine resources in the context of climate change.

Quantifying thermal exposure for migratory riverine species: Phenology of Chinook salmon populations predicts thermal stress

Migratory species are particularly vulnerable to climate change because habitat throughout their entire migration cycle must be suitable for the species to persist. For migratory species in rivers, predicting climate change impacts is especially difficult because there is a lack of spatially continuous and seasonally varying stream temperature data, habitat conditions can vary for an individual throughout its life cycle, and vulnerability can vary by life stage and season. To predict thermal impacts on migratory riverine populations, we first expanded a spatial stream network model to predict mean monthly temperature for 465,775 river km in the western U.S., and then applied simple yet plausible future stream temperature change scenarios. We then joined stream temperature predictions to 44,396 spatial observations and life-stage-specific phenology (timing) for 26 ecotypes (i.e., geographically distinct population groups expressing one of the four distinct seasonal migration patterns) of Chinook salmon (Oncorhynchus tshawytscha), a phenotypically diverse anadromous salmonid that is ecologically and economically important but declining throughout its range. Thermal stress, assessed for each life stage and ecotype based on federal criteria, was influenced by migration timing rather than latitude, elevation, or migration distance such that sympatric ecotypes often showed differential thermal exposure. Early-migration phenotypes were especially vulnerable due to prolonged residency in inland streams during the summer. We evaluated the thermal suitability of 31,699 stream km which are currently blocked by dams to explore reintroduction above dams as an option to mitigate the negative effects of our warmer stream temperature scenarios. Our results showed that negative impacts of stream temperature warming can be offset for almost all ecotypes if formerly occupied habitat above dams is made available. Our approach of combining spatial distribution and phenology data with spatially explicit and temporally explicit temperature predictions enables researchers to examine thermal exposure of migrating populations that use seasonally varying habitats.

Differential sensitivity to warming and hypoxia during development and long-term effects of developmental exposure in early life stage Chinook salmon

Warming and hypoxia are two stressors commonly found within natural salmon redds that are likely to co-occur. Warming and hypoxia can interact physiologically, but their combined effects during fish development remain poorly studied, particularly stage-specific effects and potential carry-over effects. To test the impacts of warm water temperature and hypoxia as individual and combined developmental stressors, late fall-run Chinook salmon embryos were reared in 10 treatments from fertilization through hatching with two temperatures [10°C (ambient) and 14°C (warm)], two dissolved oxygen saturation levels [normoxia (100% air saturation, 10.4-11.4 mg O₂/l) and hypoxia (50% saturation, 5.5 mg O₂/l)] and three exposure times (early [eyed stage], late [silver-eyed stage] and chronic [fertilization through hatching]). After hatching, all treatments were transferred to control conditions (10°C and 100% air saturation) through the fry stage. To study stage-specific effects of stressor exposure we measured routine metabolic rate (RMR) at two embryonic stages, hatching success and growth. To evaluate carry-over effects, where conditions during one life stage influence performance in a later stage, RMR of all treatments was measured in control conditions at two post-hatch stages and acute stress tolerance was measured at the fry stage. We found evidence of stage-specific effects of both stressors during exposure and carry-over effects on physiological performance. Both individual stressors affected RMR, growth and developmental rate while multiple stressors late in development reduced hatching success. RMR post-hatch showed persistent effects of embryonic stressor exposure that may underlie differences observed in developmental timing and acute stress tolerance. The responses to stressors that varied by stage during development suggest that stage-specific management efforts could support salmon embryo survival. The persistent carry-over effects also indicate that considering sub-lethal effects of developmental stressor exposure may be important to understanding how climate change influences the performance of salmon across life stages.

Thermal sensitivity and flow-mediated migratory delays drive climate risk for coastal sockeye salmon

Climate change is subjecting aquatic species to increasing temperatures and shifting hydrologic conditions. Understanding how these changes affect individual survival can help guide conservation and management actions. Anadromous Pacific salmon ( Oncorhynchus spp.) in some large river systems are acutely impacted by the river temperatures and flows encountered during their spawning migrations. However, comparatively little is known about drivers of en route mortality for salmon in smaller coastal watersheds, and climate impacts may differ across watersheds and locally adapted salmon populations. To understand the effects of climate on the survival of coastal sockeye salmon ( Oncorhynchus nerka; hísn in Haíɫzaqv), we tagged 1785 individual fish with passive integrated transponders across four migration seasons in the Koeye River—a low-elevation watershed in coastal British Columbia—and tracked them during their relatively short migration (∼13 km) from river entry to spawning grounds. Overall, 64.7% of sockeye survived to enter the spawning grounds, and survival decreased rapidly when water temperatures exceeded 15 °C. The best-fitting model included an interaction between river flow and temperature, such that temperature effects were worse when flows were low, and river entry ceased at the lowest flows. Results revealed temperature-mediated mortality and migration delays from low water that may synergistically reduce survival among sockeye salmon returning to coastal watersheds.

Can the creation of new freshwater habitat demographically offset losses of Pacific salmon from chronic anthropogenic mortality?

Over 1 billion USD are devoted annually to rehabilitating freshwater habitats to improve survival for the recovery of endangered salmon populations. Mitigation often requires the creation of new habitat (e.g. habitat offsetting) to compensate population losses from human activities, however offsetting schemes are rarely evaluated. Anadromous Pacific salmon are ecologically, culturally, and economically important in the US and Canada, and face numerous threats from degradation of freshwater habitats. Here we used a matrix population model of coho salmon (Oncorhynchus kisutch) to determine the amount of habitat offsetting needed to compensate mortality (2–20% per year) caused by a range of development activities. We simulated chronic mortality to three different life stages (egg, parr, smolt/adult), individually and simultaneously, to mimic impacts from development, and evaluated if the number of smolts produced from constructed side-channels demographically offset losses. We show that under ideal conditions, the typical size of a constructed side-channel in the Pacific Northwest (PNW) (3405 m²) is sufficient to compensate for only relatively low levels of chronic mortality to either the parr or smolt/adult stages (2–7% per year), but populations do not recover if mortality is >10% per year. When we assumed lower productivity (e.g.; 25^th percentile), we found that constructed channels would need to be 2.5–4.5 fold larger as compared to the typical size built in the PNW, respectively, to maintain population sizes. Moreover, when we imposed mortality to parr and smolt/adult stages simultaneously, we found that constructed side-channels would need to be between 1.8- and 2.3- fold larger that if the extra chronic mortality was imposed to one life stage only. We conclude that habitat offsetting has the potential to mitigate chronic mortality to early life stages, but that realistic assumptions about productivity of constructed side-channels and cumulative effects of anthropogenic disturbances on multiple life stages need to be considered.

Assessing contributions of cold-water refuges to reproductive migration corridor conditions for adult Chinook Salmon and steelhead trout in the Columbia River, USA

Diadromous fish populations face multiple challenges along their migratory routes. These challenges include suboptimal water quality, harvest, and barriers to longitudinal and lateral connectivity. Interactions among factors influencing migration success make it challenging to assess management options for improving migratory fish conditions along riverine migration corridors. We describe a spatially explicit simulation model that integrates complex individual behaviors of fall-run Chinook Salmon (Oncorhynchus tshawytscha) and summer-run steelhead trout (O. mykiss) during migration, responds to variable habitat conditions over a large extent of the Columbia River, and links migration corridor conditions to fish condition outcomes. The model is built around a mechanistic behavioral decision tree that drives individual interactions of fish within their simulated environments. By simulating several thermalscapes with alternative scenarios of thermal refuge availability, we examined how behavioral thermoregulation in cold-water refuges influenced migrating fish conditions. Outcomes of the migration corridor simulation model show that cold-water refuges can provide relief from exposure to high water temperatures, but do not substantially contribute to energy conservation by migrating adults. Simulated cooling of the Columbia River decreased reliance on cold-water refuges and there were slight reductions in migratory energy expenditure. This modeling of simulated thermalscapes provides a framework for assessing the contribution of cold-water refuges to the success of migrating fishes, but any final determination will depend on analyzing fish survival and health for their entire migration, water temperature management goals and species recovery targets.

Snake River sockeye and Chinook salmon in a changing climate: Implications for upstream migration survival during recent extreme and future climates

In 2015, the Pacific marine heat wave, low river flows, and record high water temperatures in the Columbia River Basin contributed to a near-complete failure of the adult migration of endangered Snake River sockeye salmon (Oncorhynchus nerka, NOAA Fisheries 2016). These extreme weather events may become the new normal due to anthropogenic climate change, with catastrophic consequences for endangered species. Existing anthropogenic pressures may amplify vulnerability to climate change, but these potential synergies have rarely been quantified. We examined factors affecting survival of endangered sockeye (Oncorhynchus nerka) and threatened Chinook salmon (O. tshawytscha) as they migrated upstream through eight dams and reservoirs to spawning areas in the Snake River Basin. Our extensive database included histories of 17,279 individual fish that migrated since 2004. A comparison between conditions in 2015 and daily temperatures and flows in a regulated basin forced by output from global climate models showed that 2015 did have many characteristics of projected future mean conditions. To evaluate potential salmon responses, we modeled migration timing and apparent survival under historical and future climate scenarios (2040s). For Chinook salmon, adult survival from the first dam encountered to spawning grounds dropped by 4-15%, depending on the climate scenario. For sockeye, survival dropped by ~80% from their already low levels. Through sensitivity analyses, we observed that the adult sockeye migration would need to shift more than 2 weeks earlier than predicted to maintain survival rates typical of those seen during 2008-2017. Overall, the greater impacts of climate change on adult sockeye compared with adult Chinook salmon reflected differences in life history and environmental sensitivities, which were compounded for sockeye by larger effect sizes from other anthropogenic factors. Compared with Chinook, sockeye was more negatively affected by a history of juvenile transportation and by similar temperatures and flows. The largest changes in temperature and flow were projected to be upstream from the hydrosystem, where direct mitigation through hydrosystem management is not an option. Unfortunately, Snake River sockeye have likely lost much of their adaptive capacity with the loss of the wild population. Further work exploring habitat restoration or additional mitigation actions is urgently needed.

Climate change effects on biodiversity, ecosystems, ecosystem services, and natural resource management in the United States

Climate change is a pervasive and growing global threat to biodiversity and ecosystems. Here, we present the most up-to-date assessment of climate change impacts on biodiversity, ecosystems, and ecosystem services in the U.S. and implications for natural resource management. We draw from the 4th National Climate Assessment to summarize observed and projected changes to ecosystems and biodiversity, explore linkages to important ecosystem services, and discuss associated challenges and opportunities for natural resource management. We find that species are responding to climate change through changes in morphology and behavior, phenology, and geographic range shifts, and these changes are mediated by plastic and evolutionary responses. Responses by species and populations, combined with direct effects of climate change on ecosystems (including more extreme events), are resulting in widespread changes in productivity, species interactions, vulnerability to biological invasions, and other emergent properties. Collectively, these impacts alter the benefits and services that natural ecosystems can provide to society. Although not all impacts are negative, even positive changes can require costly societal adjustments. Natural resource managers need proactive, flexible adaptation strategies that consider historical and future outlooks to minimize costs over the long term. Many organizations are beginning to explore these approaches, but implementation is not yet prevalent or systematic across the nation.