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Claire E. Couch

Publications and source records attributed to Claire E. Couch.

14 recordsLinked to original sources
USGS2026

Estimating habitat availability for Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) to inform reintroduction planning in the middle Snake River basin, USA

Anadromous fishes have been blocked from the middle Snake River basin since the construction of flood control, irrigation, and hydroelectric projects during the 19 th and 20 th centuries, culminating with the construction of Hells Canyon Dam (river kilometer [rkm] 398) in 1967. Seven large watersheds in the blocked area of the basin are under consideration for Pacific salmon reintroduction. The primary objective of this study was to identify and characterize potential reintroduction sites with high-quality rearing and spawning habitat for Chinook salmon ( Oncorhynchus tshawytscha ) and steelhead ( O. mykiss ) upstream of the Hells Canyon Complex in Idaho, Oregon, and Nevada, USA. We created and tested habitat models to predict rearing presence/absence, rearing abundance, and spawning presence/absence using channel morphology, hydrology, and stream temperature variables obtained from regional peer-reviewed datasets. Habitat models were trained with salmonid presence and abundance records collected in the lower Snake River basin (downstream of Hells Canyon Dam), where anadromous fish can currently access, from 1993 to 2011. Model performance was tested with set-aside data comprised of randomly selected reaches and independent environmental DNA data. An index model was created in the middle Snake River basin for each species by combining results from the habitat models. Modeling covariates differed by species and life stage and included different combinations of August stream temperature, summer flow, channel slope, and quadratic terms for temperature and slope. The habitat models predicted high versus low Chinook salmon and steelhead probability and abundance with 66% to 85% accuracy depending on species and life stage. The index models predicted a total of 2,887 km of Chinook salmon habitat and 2,434 km of steelhead habitat in the blocked area. The three basins in the blocked area with the greatest amount of predicted habitat were the Powder River, South Fork Payette River, and North Fork Payette River for Chinook salmon, and the Powder River, South Fork Boise River, and South Fork Payette River for steelhead. The modeling approach presented here is complementary to other planning efforts for Chinook salmon and steelhead reintroduction in the blocked area of the Snake River basin, and similar approaches may be useful for reintroduction planning in other systems.

Idaho, Nevada, Oregon, Utah, Washington, Wyoming↗
USGS2026

Navigating uncertainty and competing objectives: Spring chinook salmon recovery in the upper Willamette river

Globally, anadromous fish populations are threatened with extinction due to multiple factors, including river impoundments that block migration, widespread alteration of physical habitat, temperature, and flow regimes, commercial and recreational harvest, changes in biological communities, and long-term climate trends. In this synthesis, we describe how physical and biological factors, policy and law, and public resource allocation affect management of spring-run Chinook Salmon ( Oncorhynchus tshawytscha ) in the Upper Willamette River (UWR), Oregon, USA. Efforts to restore salmon populations often involve trade-offs, for example, water management decisions must account for flood control, agricultural and municipal water use, and management of other species. UWR Chinook Salmon recovery efforts are also governed by multiple laws, policies, and action agencies that in some cases have incongruent objectives. Competing and conflicting objectives, combined with uncertainty regarding the outcomes of proposed management actions, create significant challenges for decision makers. Resource limitations, regulatory constraints, and incongruent objectives have created challenges for managers in the UWR, but opportunities exist for improved adaptive management and collaboration, which could build trust and engagement among stakeholders and ultimately support the successful implementation of decision tools. A suite of decision support tools that have been used in the Willamette River basin and elsewhere across the range of Pacific salmon have the potential to enhance decision processes. These tools can be effective when decision makers and stakeholders commit to long-term, collaborative utilization of the tools for decision making, and when available resources and regulatory environments are conducive to implementation and adaptive refinement of both the decision-support tools and management plans. The general biological and institutional principles discussed for UWR Chinook Salmon in this work apply more generally to populations of anadromous fishes across their range, especially to populations in highly regulated river systems.

Oregon↗
USGS2026

Seasonal trophic dynamics drive growth potential and predation risk for reintroduced Chinook salmon in Shasta Reservoir

Reservoir ecosystems can significantly affect anadromous salmon populations reintroduced upstream of impassable high-head dams. In this study, we examine how a novel reservoir food web created by an impoundment can limit juvenile growth or survival through the seasonal production or access to food, promote competition for available resources, and affect risk of the food supply or predation mortality, all of which can be strongly influenced by the thermal regime. Shasta Reservoir, the largest impoundment in California’s Central Valley Project, presents opportunities and risks for winter-run Chinook salmon ( Oncorhynchus tshawytscha ), a federally endangered population targeted for reintroduction into the McCloud River, which flows into the reservoir. We integrated field sampling, stable isotope analysis, hydroacoustic surveys, and bioenergetics modeling to characterize Shasta Reservoir’s food web and evaluate seasonal growth potential and predation risk for juvenile salmon. Zooplankton, dominated by Daphnia , provided favorable foraging conditions in spring but declined sharply by late summer, coinciding with high consumption demand from abundant threadfin shad ( Dorosoma petenense ). Bioenergetics simulations indicated that fry that would ordinarily enter the reservoir in autumn would face poor growth opportunities. They would also be exposed to elevated predation risk driven by warm temperatures and high metabolic demand, particularly from piscivorous salmonids and Sacramento pikeminnow ( Ptychocheilus grandis ). Limited information on predator abundances precludes the ability to quantify total predation demand. Alternatively, juveniles entering the reservoir the following spring would encounter greater prey availability and reduced predation pressure. These findings highlight the strong influence of seasonal thermal structure and food web dynamics on reservoir constraints and underscore the need to incorporate the dynamics of key habitats into reintroduction management and decisions. Our framework provides a quantitative, mechanistically-based approach for evaluating the role of reservoirs in salmon reintroductions above high-head dams.

California↗
USGS2026

Effects of a low-lipid diet on the gut microbiome and head kidney transcriptome of juvenile Chinook Salmon

Objective Pacific salmon Oncorhynchus spp. reared in production hatcheries are typically fed high-lipid, energy-dense diets to achieve large size and high body condition prior to release. In contrast, juveniles in natural environments tend to consume low-lipid, high-protein diets, and fish reared for research or conservation purposes are sometimes fed diets that are formulated to mimic natural diets and promote wild-like phenotypes. Understanding how these alternative diets affect fish health beyond growth and body condition could ultimately contribute to improving hatchery fish fitness. Methods In this work, we evaluated changes in the fecal microbiome and gene expression of juvenile Chinook Salmon O. tshawytscha on a standard high-lipid hatchery diet versus a low-lipid diet formulated to mimic the nutrition profile of natural-origin fish. To evaluate the time scale at which diet alters the fecal microbiome, we collected longitudinal samples over a 12-week period and switched the diets of a subset of fish twice during the experiment. We used 16S ribosomal RNA gene amplicon sequencing to characterize fecal microbiome differences between fish on the two diets as well as hatchery-reared fish at a production hatchery, hatchery fish that had been captured after release into a stream, and natural-origin, stream-reared fish of similar ages. Additionally, we conducted RNA sequencing on head kidney samples from laboratory-reared fish to evaluate changes in gene expression in this important immune organ. Results We found that the low-lipid diet and the hatchery diet resulted in microbiomes that differed from the microbiome of natural-origin fish and from each other and that diet-driven changes to the microbiome could occur in under 14 d. The low-lipid diet did not result in a microbiome that resembled the microbiome of naturally produced fish. Instead, the low-lipid diet resulted in a microbiome community that was distinct from those of fish reared on the hatchery diet and fish sampled from the wild. The RNA sequencing results indicated differential enrichment of pathways related to immunity, metabolism, and hormone synthesis between fish that were fed the two experimental diets. Conclusions The results suggest that additional environmental factors influence the microbiome more strongly than diet formulation or that the low-lipid diet has a smaller effect on the microbiome than a natural, ­invertebrate-based diet. Given that the gut microbiome and systemic immune function contribute significantly to disease resistance, our findings highlight the importance of understanding how diets fed to fish in captivity may affect fish health beyond growth and body condition metrics.

Journal of Aquatic Animal Health↗
USGS2026

Response of juvenile Chinook Salmon to an experimental reservoir operation to facilitate downstream migration

Objectives High-head dams and storage reservoirs impact ecological processes, impeding recovery efforts of Pacific salmon Oncorhynchus spp. in the western United States. These projects can delay migration, increase risks of predation and disease, and induce mortality for juvenile Pacific salmon during downstream passage. To mitigate these negative effects, large-scale changes to dam operations have been proposed as interim measures or alternatives to engineered fish passage solutions. A novel deep drawdown operation of the Lookout Point Project (two dams and reservoirs) in Oregon serves as a case study for learning from a large-scale management experiment. Beginning in July 2024, Lookout Point Reservoir was slowly lowered to attain minimal levels from mid-November to mid-December with the intent of expediting downstream passage through the project for juvenile Chinook Salmon Oncorhynchus tshawytscha . We evaluated the impacts of the months-long operation on two life histories of juvenile Chinook Salmon with different rearing environments and growth rates. Methods Acoustic telemetry was used to monitor juvenile Chinook Salmon in the Lookout Point Project. Environmental data, including water temperature and hydrological conditions, were collected. We fitted a time-integrated migration survival model to these data to estimate the effects of management-influenced covariates and fish length on apparent survival and residence time in each reach of the Lookout Point Project. Results Larger fish had higher survival than smaller fish in each reach of the Lookout Point Project. Apparent survival through each dam of the Lookout Point Project was highest and forebay residence times lowest during the latter part of the drawdown (late November). However, early periods of the drawdown (September) were associated with a transition from a thermally stratified reservoir to a warm isothermal reservoir that negatively impacted reservoir survival. Conclusions The deep drawdown of the Lookout Point Project achieved the management intent to improve downstream passage for juvenile Chinook Salmon at the lowest reservoir elevations but also caused unintended changes in the reservoir rearing environment prior to full drawdown. Further research could resolve remaining uncertainties regarding the overall effectiveness of drawdown operations with respect to the population dynamics of different juvenile life history strategies. Understanding these factors would help optimize future management actions aimed at Pacific salmon recovery above the Lookout Point Project.

Oregon↗
USGS2026

Evaluating reservoir passage and survival of juvenile Chinook Salmon to support reintroduction upstream of Shasta Dam, California

Objective Juvenile Chinook Salmon Oncorhynchus tshawytscha that are released upstream of Shasta Reservoir migrate more than 35 km to reach Shasta Dam, although survival through this system is poorly understood. We conducted a reservoir-scale acoustic telemetry study to quantify downstream movement and survival under seasonally variable environmental conditions to inform decisions about juvenile collection strategies for Chinook Salmon reintroduction above Shasta Dam. Methods A total of 656 hatchery-origin juvenile Chinook Salmon were acoustic-tagged, released near the mouth of the McCloud River, and monitored in Shasta Reservoir and the Sacramento River from September 2024 through March 2025 using an array of telemetry receivers. Results Most tagged fish failed to move downstream through the McCloud River Arm of Shasta Reservoir and arrive at Shasta Dam. Survival probabilities were estimated at 0.268 to the downstream end of the McCloud River Arm and 0.119 to Shasta Dam. For fish that did reach the dam, elapsed time from release to arrival was 66.4 d, and fish typically arrived and departed during daylight hours. Nine tagged juveniles were detected downstream of the dam, and three were later detected more than 500 km downstream. Conclusions The consistently low survival and restricted downstream movement provide important information indicating that downstream collection of juvenile Chinook Salmon should be focused in the lower McCloud River and the upper portion of the McCloud River Arm of Shasta Reservoir rather than at Shasta Dam.

California↗
USGS2026

Evaluation of pathogen risks and testing considerations for Chinook salmon egg movements between New Zealand and California

Executive Summary Oncorhynchus tshawytscha (Walbaum in Artedi, 1792; Chinook salmon) were historically abundant in the McCloud River but are now extirpated from this tributary owing to dam construction and lack of passage. Planning efforts to restore populations above Shasta and Keswick Dams are currently underway, including an evaluation of potential source populations. One potential source is New Zealand Chinook salmon, which are believed to have originated from tributaries of the Sacramento River. These fish could be returned to California if reintroduction risks, including risks of pathogen introduction, could be sufficiently mitigated. The U.S. Geological Survey was contracted to provide scientific support for reintroduction efforts, including evaluating the risks of pathogen transmission via the movement of Chinook salmon eggs from New Zealand to the McCloud River. This report estimates pathogen risks associated with egg movement and considers epidemiological and biosecurity measures to minimize these risks. Pathogen risks associated with the movement of Chinook salmon eggs from New Zealand were evaluated based on pathogen virulence, transmission route, and geographic distribution. These criteria identified 14 moderate- and high-risk pathogens out of the 30 pathogens evaluated. Pathogen species and strains were considered high risk if they have the potential for vertical transmission (that is, transmission from parent to offspring), are moderately or highly virulent, and are exotic to the Sacramento River Basin. According to these criteria, we identified the following pathogens as high risk: New Zealand rickettsia-like organisms 1 and 2. —These bacterial pathogens have been associated with mortality events in farmed Chinook salmon from the South Island of New Zealand but have not been detected in other regions. Pilchard orthomyxovirus (POMV). —POMV has been detected in Sardina pilchardus (Walbaum, 1792; pilchards) and Salmo salar (Linnaeus, 1758; Atlantic salmon) from the coasts of southern Australia and Tasmania. POMV can cause relatively high mortality rates and may be indirectly transmitted via contaminated water sources. Infectious pancreatic necrosis virus (IPNV). —IPNV has a wide geographic distribution and is present in the Sacramento River Basin, but the IPNV-like viruses detected in Australia and New Zealand are unique from those found in the United States. Yersinia ruckeri . —This bacterial pathogen is the causative agent of enteric redmouth disease and has a widespread geographic distribution. However, the strains that are present in Australia and New Zealand are unique from those found in North America. Strategic use of testing and biosecurity measures can minimize pathogen risks associated with the movement of eggs. The most effective measures include iodophor treatment of eggs to remove external pathogens, testing of all the adult fish from which gametes are obtained, and a quarantine period after transport to confirm pathogen testing results. Additional measures to enhance biosecurity could include testing the quarantined fish following emergence and (or) developing a fish health history of the source population through pathogen monitoring.

California↗
USGS2025

Laboratory transmission of adult salmon enteritis and associated pathogens in juvenile Chinook salmon ( Oncorhynchus tshawytscha )

Adult salmon enteritis (ASE), characterised by severe ulcerative enteritis, has been linked to prespawn mortality (PSM) in spring Chinook salmon ( Oncorhynchus tshawytscha ) in certain rivers in Oregon, USA. Catastrophic losses of spring Chinook salmon have resulted from PSM, a significant threat to their population stability. Understanding the causes of ASE is therefore critical for mitigating PSM and supporting conservation. This study investigates the potential infectious aetiology of ASE using a juvenile Chinook salmon model. Fish were immunocompromised with dexamethasone implants, fasted, and exposed to intestinal tissues from ASE-affected adult Chinook. Histopathology of recipient fish revealed mid-intestinal lesions consistent with ASE. The microsporidium Enterocytozoon schreckii , which is observed in ASE-affected adults from rivers, was transmitted for the first time to juvenile Chinook Salmon, making E. schreckii a potential new pathogen of juvenile salmon. Additionally, intranuclear inclusions were identified in enterocytes by histopathology and viral particles were detected by electron microscopy in recipient fish. The study demonstrates that intestinal lesions consistent with ASE can be experimentally induced in juvenile Chinook salmon through oral exposure to infected tissues, supporting an infectious aetiology. Further research is needed to isolate specific pathogens, including viruses and E. schreckii , and to elucidate their roles in ASE development.

Oregon↗
USGS2024

Influence of stream temperature and human disturbance on prespawn mortality of Chinook Salmon in the Willamette River basin

Objective Premature mortality of adult female Chinook Salmon Oncorhynchus tshawytscha is a major barrier to population recovery. The Willamette River basin, Oregon, typifies the problems that are faced by fishery managers in the Pacific Northwest (USA). Adult salmon are trapped and transported upstream of dams to access historical spawning grounds, but annual rates of prespawn mortality (PSM) are high (often >40%) and may limit the recovery of natural populations. The purpose of this study was to identify potential factors related to PSM of female Chinook Salmon that are outplanted above dams and incorporate them into a modeling framework to facilitate adaptive management of outplanting operations. Methods We evaluated PSM in Fall Creek of the Willamette River basin prior to transport facility improvements in summer and fall of 2010–2017 and postimprovement during 2020–2021. We estimated PSM and conducted exploratory analyses to identify possible nontransport sources of stress that may contribute to the observed high PSM rates. Candidate factors included long‐term elevated temperature exposure, elevated temperature exposure below the trap, total number of outplanted fish, and monthly human disturbance of outplanted fish. We then developed and fit three models, each representing a hypothesis of a factor influencing PSM, incorporated them into a single alternative decision model, and conducted sensitivity analyses. Result Prespawn mortality averaged 0.66 (ranging from 0.37 to 0.94) over the study period. According to the simulation results, the top two management actions were to exclude human activities—swimming and fishing—from Fall Creek in July and August. Conclusion Expected PSM rates were predicted to be 0.38 when human activity was excluded in July and 0.37 for August. Sensitivity analyses indicated that the most influential decision model component was the choice of the alternative model.

Oregon↗
USGS2024

Unique diet and Philonema sp. infections in reservoir-rearing juvenile Chinook Salmon

Objective Dams and reservoirs can alter juvenile growth and survival of migratory salmonids through several physical and biological mechanisms. Juvenile Chinook Salmon Oncorhynchus tshawytscha that are produced upstream of large hydropower dams may have associated passage mortality, but the reservoirs created by these dams can support rapid growth. Characterizing the biotic drivers of growth and mortality in reservoirs may aid in understanding the cumulative effects of river impoundments on migratory salmonid populations. The purpose of this study was to understand how reservoirs facilitate rapid growth in juvenile Chinook Salmon. Methods We analyzed stomach contents to determine diet composition throughout the summer and fall. We also recorded prevalence of the parasitic nematode Philonema sp. in the coeloms of fish. Result We found that juvenile Chinook Salmon frequently consumed young-of-year centrarchids, which likely contributed to rapid growth. Piscivory was highest from July through October and decreased with surface temperature from November through December. Correspondingly, zooplankton and arthropod consumption increased in November and December. Prevalence of visible Philonema sp. infections in the coelom was high (34.6%), negatively associated with time, and nonlinearly associated with fork length. Conclusion These findings reveal unique diet patterns and suggest potential parasite-associated mortality in reservoir-rearing Chinook Salmon, but more detailed studies across a longer time scale are needed to robustly assess the population-level effects of this parasite.

Transaction of the American Fisheries Society↗
USGS2023

Gut microbiome composition associates with corticosteroid treatment, morbidity, and senescence in Chinook salmon (Oncorhynchus tshawytscha)

Pacific salmon experience prolonged elevation in corticosteroid hormones during important life history events including migration, reproduction, and senescence. These periods of elevated corticosteroids correspond with changes to immunity and energy metabolism; therefore, fish may be particularly vulnerable to mortality at these times. Recent studies found that stress-induced cortisol release associated with microbial community shifts in salmonids, raising the question of how longer-term corticosteroid dynamics that accompany life history transitions affect salmonid microbiomes. In this work, we experimentally evaluated the relationships between gut microbiome composition, chronically elevated corticosteroids, and mortality in juvenile Chinook salmon ( Oncorhynchus tshawytscha) . We found that treatment with slow-release implants of the corticosteroids cortisol or dexamethasone resulted in persistent changes to the gut microbiome. Morbidity was also associated with microbiome composition, suggesting that the gut microbiome reflects individual differences in susceptibility to opportunistic pathogens. Additionally, we analyzed a small number of samples from adult fish at various stages of senescence. Results from these samples suggest that microbiome composition associated with gut integrity, and that the microbial communities of corticosteroid treated juveniles shift in composition toward those of senescent adults. Overall, findings from this work suggest that the gut microbiome associates with mortality risk during periods of chronic corticosteroid elevation.

Scientific Reports↗
USGS2023

Evaluating the institutional and ecological effects of invasive species prevention policy: A case study from the U.S. Fish and Wildlife Service

Wildlife and natural resource institutions play key roles in invasive species monitoring and management. Paradoxically, the extensive fieldwork undertaken by these institutions and their partners may result in the inadvertent movement and spread of invasive species within and between sensitive ecosystems. In this work, we consider the potential effects of internal guidelines and policies designed to prevent the spread of invasive species by the field activities of management institutions and their partners. Such policies could be high-leverage tools for invasive species prevention, however, as large, complex organizations seek to implement policies to limit the spread of invasive species, it may be challenging to accommodate the wide diversity of potential invasion pathways and mitigation efforts facilitated via the programs, activities, and ecosystems they manage. Prevention policies may also be met with resistance due to the costs of implementation unless concrete benefits can be demonstrated. Assessing and communicating the effects of prevention policies could motivate improved implementation and adherence by institutional units and partners and could help inform adaptive policy changes. However, assessing the effectiveness of invasive species prevention presents a unique set of challenges, including incomplete data on invasive species distribution and pathways, that make it difficult to measure the effects of prevention efforts. In this work, we present a conceptual framework for evaluating institutional policies for invasive species prevention. We describe a flexible, multifaceted approach that considers policy implementation and adherence as well as ecological outcomes. We discuss potential application of this framework using a policy recently implemented by the Pacific Region of the U.S. Fish and Wildlife Service to prevent the introduction and spread of invasive species by service personnel and partners during field activities as a case study.

Management of Biological Invasions↗
USGS2022

Scope of the cortisol stress response in Chinook salmon during maturation

In semelparous Pacific salmon, increased cortisol levels accompany sexual maturation and may be related to the rapid senescence and death that occur after spawning. In fish with extremely high cortisol, pre-spawning mortality is more likely. This may be because elevated cortisol is accompanied by energy depletion and reduces the immune capacity of sexually maturing individuals, thus increasing their susceptibility to parasites and pathogens. Several studies have measured cortisol levels in Pacific salmon during the last few weeks prior to spawning, but there is a lack of information regarding longer-term changes in resting and stressed cortisol levels of migrating adult Pacific salmon. A better understanding of the scope of the cortisol response during sexual maturation could contribute to understanding the extremely high pre-spawning mortality experienced by some threatened populations of Pacific salmon. The objective of this study was to determine the scope of the cortisol stress response in spring Chinook salmon as well as the dynamics of resting cortisol during maturation. We conducted a laboratory experiment in which plasma cortisol in adult Chinook salmon was measured before and after application of a standardized stressor applied at monthly intervals during the last three months prior to spawning. We found that resting and stressed cortisol levels increased during the last three months prior to spawning. We also found that sexually maturing Chinook salmon are able to mount a cortisol response to acute stressors when resting levels are elevated during maturation. Additionally, the effects of stress and time on cortisol dynamics differed between males and females as well as between individuals, which has implications for population resilience to anthropogenic stressors in wild populations.

Oregon↗