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Recovery of endangered salmon species in the Central Valley of California amidst prolonged drought and climate change necessitates innovative water management actions that balance species recovery and California's water demands. We describe an individual-based ecological particle tracking model (ECO-PTM) that can be used to assess the efficacy of proposed actions. Based on a random walk theory, the model tracks individual particles’ travel time, routing and survival in a flow field simulated by the Delta Simulation Model 2 hydrodynamic module (DSM2 HYDRO). The random walk particles are parameterized to have fish-like swimming behaviors, including upstream/downstream swimming, probabilistic holding behaviors, and stochastic swimming velocities. Particle routing at key junctions is based on well-established statistical models, and route-specific survival is calculated using the XT mean free-path length model. Behavioral parameters were estimated by fitting several competing models to a multiyear dataset of travel times from acoustic tagged juvenile salmon. The model’s baseline simulations under historical flow conditions from 1991 to 2016 successfully replicated essential relationships between salmon outmigration survival and hydrodynamic conditions, consistent with previous studies and the STARS (Survival Travel Time and Routing Simulation) statistical simulation model. Simulation results for management scenarios revealed multifaceted influences on fish survival, including Delta flow, flow at key junctions, route alterations, seasons, and water availability characteristics. Importantly, these results highlight ECO-PTM’s potential to predict fish survival outcomes of proposed actions, serving as a foundation for informed future research, decision-making, and effective management strategies to enhance the survival prospects of outmigrating salmonids within the Sacramento-San Joaquin Delta ecosystem.

Tidal wetland restoration to benefit at-risk fish species in the Sacramento-San Joaquin Delta and Suisun marsh has gained momentum over the past decade, much of it in response to mitigation requirements for the State Water Project and Central Valley Project. In fall 2023, the Department of Water Resources and the State Water Contractors convened a symposium, entitled Delta-Suisun Tidal Wetland Restoration Symposium: State of the Science and Future Directions, to discuss the latest wetland restoration research and future directions. The symposium was held 10 years after the 2013 symposium “Tidal Marshes and Native Fishes in the Delta: Will Restoration Make a Difference?”, so served as an opportunity to follow up on the progress that has been made over the past decade. This paper synthesizes the key findings from the 2023 workshop.The paper begins with the historical context of wetland restoration in the Delta and Suisun marsh, then outlines the restoration process as it is currently implemented. It then describes the monitoring of tidal wetlands in terms of their capacity to support fish (capacity), the opportunity fish have to use the habitat (opportunity), and the realized functions provided when fish are actually using the site.Finally, the paper identifies priority science actions to advance our understanding and management of tidal wetland restoration sites. These actions include further research into fish habitat utilization, improved monitoring techniques, and enhanced adaptive management strategies. This list of information needs is intended to inform future monitoring of restoration sites, scientific studies, funding, and prioritization of wetland research.

Green sturgeon (Acipenser medirostris) are an anadromous threatened species of sturgeon found along the Pacific coast of North America. The southern distinct population segment only spawns in the Sacramento River and is exposed to water temperatures kept artificially cold for the conservation and management of winter-run Chinook salmon (Oncorhynchus tshawytscha). Past research has demonstrated costs of cold-water rearing including reduced growth rates, condition and survivorship of juvenile green sturgeon. Our research investigates how the stressors of water temperature and food limitation influence the metabolic performance of green sturgeon. We reared green sturgeon at two acclimation temperatures (13 and 19°C) and two ration amounts (100% and 40% of optimal feed). We then measured the routine and maximum metabolic rates (RMR and MMR, respectively) of sturgeon acclimated to these rearing conditions across a range of acute temperature exposures (11 to 31°C). Among both temperature acclimation treatments (13 or 19°C), we found that feed restriction reduced RMR across a range of acute temperatures. The influence of feed restriction on RMR and MMR interacted with acclimation temperature. Fish reared at 13°C preserved their MMR and aerobic scope (AS) despite feed restriction, while fish fed reduced rations and acclimated to 19°C showed reduced MMR and AS capacity primarily at temperatures below 16°C. The sympatry of threatened green sturgeon with endangered salmonids produces a conservation conflict, such that cold-water releases for the conservation of at-risk salmonids may constrain the metabolic performance of juvenile green sturgeon. Understanding the impacts of environmental conditions (e.g. temperature, dissolved oxygen) on ecological interactions of green sturgeon will be necessary to determine the influence of salmonid-focused management.

Climate change is affecting freshwater systems, leading to increased water temperatures, which is posing a threat to freshwater ecological communities. In the Nechako River, British Columbia, a water management program has been in place since the 1980s to maintain water temperatures at 20 °C during the migration of adult Sockeye salmon. However, the program's effectiveness in mitigating the impacts of climate change on resident species like Chinook salmon's thermal exposure is uncertain. In this study, we utilised the CEQUEAU hydrological model and life stage-specific physiological data to evaluate the consequences of the current program on Chinook salmon's thermal exposure under two contrasting climate change and socio-economic scenarios (SSP2-4.5 and SSP5-8.5). The results indicate that the thermal exposure risk is projected to be above the optimal threshold for parr (intermediate juvenile) and adult life stages under both scenarios relative to the 1980s. Under the SSP5-8.5 scenario, these life stages could experience an increase in thermal exposure ranging from two to five times higher by the 2090s compared to the 1980s. This exposure is projected to occur during the months in which these life stages emerge, including the period when the program is active (July 20th to August 20th). Additionally, our study shows that climate change will result in a substantial rise in cumulative heat degree days, ranging from 1.9 to 5.8 times (2050s) and 2.9 to 12.9 times (2090s) in comparison to the 1980s under SSP5-8.5. Our study highlights the need for a holistic approach to reviewing the current Nechako management plan, ensuring that all species in the Nechako River system are considered especially in the face of climate change. [ABSTRACT FROM AUTHOR]

Habitat selection theory enables inferences about species habitat choice across a range of observed population densities. However, it is relatively uncommon to use habitat selection theory in studies of habitat restoration efficacy to understand the effect of restoration on habitat competition. We combined observational density data and resource selection functions to analyze habitat correlations with both habitat selection theory and a mark–recapture experiment to show how habitat restoration can mitigate competition between species with similar habitat preferences. To restore degraded and channelized riverine habitat for juvenile Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (Oncorhynchus mykiss) engineered log jams (ELJs) have been installed to create pools to enhance growth and rearing. Application of habitat selection theory first showed that both species share a preference for ELJ‐treated habitat over unrestored habitat. Linear models showed that steelhead are generalists with respect to depth in unrestored habitat, whereas both species' abundance varies along a depth gradient in ELJ‐treated habitat. Selective versus opportunistic use of deep and shallow ELJ pools was density‐dependent. We found a range of densities at which a "ghost of competition" exists, where Chinook are selective on deep ELJ‐treated pools and steelhead are selective on shallow pools. A mark–recapture experiment confirmed that steelhead limit Chinook movement into unrestored habitat, but this competitive effect vanished in ELJ‐treated habitat where selection occurred with respect to pool depth. The experiment, combined with theory, enabled (1) the identification of a mechanism allowing for shared preference of restored habitat and (2) the description of how restoration can mitigate competition. [ABSTRACT FROM AUTHOR]

Recovery of endangered salmon species in the Central Valley of California amidst prolonged drought and climate change necessitates innovative water-management actions that balance species recovery and California's water demands. We describe an individual-based ecological particle-tracking model (ECO-PTM) that can be used to assess the efficacy of proposed actions. Based on a "random walk" theory, the model tracks the travel time, routing, and survival of individual particles in a flow field simulated by the Delta Simulation Model 2 hydrodynamic module (DSM2 HYDRO). The random walk particles are parameterized to have fish-like swimming behaviors, including upstream and downstream swimming, probabilistic holding behaviors, and stochastic swimming velocities. Particle routing at key junctions is based on wellestablished statistical models, and route-specific survival is calculated using the XT mean freepath length model. Behavioral parameters were estimated by fitting several competing models to a multi-year dataset of travel times from acoustictagged juvenile salmon. The model's baseline simulations under historical flow conditions from 1991 to 2016 successfully replicated essential relationships between salmon outmigration survival and hydrodynamic conditions, consistent with previous studies and the STARS (Survival Travel Time and Routing Simulation) statistical simulation model. Simulation results for management scenarios revealed multi-faceted influences on fish survival, including Delta flow, flow at key junctions, route alterations, seasons, and water-availability characteristics. Importantly, these results highlight ECO-PTM's potential to predict improvements in fish survival from proposed actions, serving as a foundation for informed future research, decision-making, and effective management strategies to enhance the survival prospects of outmigrating salmonids within the Sacramento-San Joaquin Delta ecosystem. [ABSTRACT FROM AUTHOR]

Trade‐offs among objectives in natural resource management can be exacerbated in altered ecosystems and when there is uncertainty in predicted management outcomes. Multi‐criteria decision analysis and value of information (VOI) are underutilized decision tools that can assist fisheries managers in handling trade‐offs and evaluating the importance of uncertainty. We demonstrate the use of these tools using a case study in the Sacramento River, California, USA, where two imperiled species with different temperature requirements, winter‐run Chinook Salmon Oncorhynchus tshawytscha and Green Sturgeon Acipenser medirostris, spawn and rear in the artificially cold Shasta Dam tailwater. A temperature‐control device installed on Shasta Dam maintains cool water for Chinook Salmon; however, uncertainties exist related to the effects of temperatures on the spawning and rearing of both species. We consider four alternative hypotheses in models of early life‐stage dynamics to evaluate the effects of alternative temperature management strategies on Chinook Salmon and Green Sturgeon management objectives. We used VOI to quantify the increase in management performance that can be expected by resolving hypothesis‐based uncertainties as a function of the weight assigned to species‐specific objectives. We found the decision was hindered by uncertainty; the best performing alternative depends on which hypothesis is true, with warmer or cooler alternative management strategies recommended when weights favor Green Sturgeon or Chinook Salmon objectives, respectively. The value of reducing uncertainty was highest when Green Sturgeon was slightly favored, highlighting the interaction between scientific uncertainty and decision makers' values. Our demonstration features multi‐criteria decision analysis and VOI as transparent, deliberative tools that can assist fisheries managers in confronting value conflicts, prioritizing resolution of uncertainty, and optimally managing aquatic ecosystems. [ABSTRACT FROM AUTHOR]

Type III secretion system (T3SS) is an important virulence system in Gram‐negative bacteria. In this investigation, different environmental conditions that regulate the expression of T3SS genes in Yersinia ruckeri were investigated aimed at obtaining a better understanding about its modulation after various environmental challenges. Four isolates of Y. ruckeri CSF007‐82, ATCC29473, A7959‐11 and YRNC10 were cultivated under the diverse in vitro challenges iron depletion, high salt, low pH and in the presence of fish serum or in the fish cell culture (Chinook Salmon Embryo – CHSE). The transcriptional modulation of the chromosomal genes ysaV, ysaC, ysaJ and prgH of ysa were investigated using quantitative real‐time PCR. The expression of prgH, ysaV, ysaC and ysaJ was differentially expressed in all four strains under evaluation. The highest gene expression levels were observed for Y. ruckeri YRNC10 AN after addition of 0.3 M NaCl in Luria Bertani broth. The results obtained from this study provide initial insights into T3SS responses in Y. ruckeri, which pave the way for further studies aimed at expanding our knowledge on the functional roles of the T3SS genes in Y. ruckeri. [ABSTRACT FROM AUTHOR]

Exposure to temperatures outside of a fish's optimal range results in suppression of the immune system, ultimately leaving aquaculture stocks susceptible to disease outbreaks. This effect is exacerbated in triploid fishes, which demonstrate greater susceptibility to stress than their diploid counterparts. This study investigates the impacts of acute heat stress on the abundance of immune transcripts and proteins in diploid and triploid Chinook salmon (Oncorhynchus tshawytscha), an important finfish crop. This study also demonstrates that acute heat stress induces significant increases in the abundance hsp70, hsp90 and il1b transcripts in the head kidneys, gills and heart ventricles of both diploid and triploid Chinook salmon. Widespread dysregulation of antigen‐presentation transcripts was also observed in fish of both ploidies. These results suggest that acute heat stress activates acute‐phase responses in Chinook salmon and dysregulates antigen presentation, potentially leaving fish more susceptible to infection. At the protein level, IL‐1β was differentially expressed in the head kidney and ventricles of diploid and triploid salmon following heat shock. Differential expression of two tapasin‐like proteins in diploid and triploid salmon subjected to heat shock was also observed. Altogether, these data indicate that diploid and triploid Chinook salmon respond differently to acute thermal stressors. [ABSTRACT FROM AUTHOR]

Many species exhibit alternative mating tactics (ARTs), with larger socially dominant males competing for females and smaller males adopting "sneaker" strategies to exploit fertilisation opportunities without competition or courtship. Females typically prefer larger socially dominant males, but their ability to manipulate mating or fertilisation outcomes is largely unknown. Here, using chinook salmon Oncorhynchus tshawytscha, we examined whether the female's ovarian fluid (OF) differentially influences the temporal patterns of sperm swimming traits in ejaculates from non-preferred sneaker ('parr') and preferred (dominant) males. Results demonstrate that OF improves sperm swimming speed and linearity compared to river water, regardless of male mating tactic. We report a novel tactic-specific difference in sperm linearity in which parr male sperm initially maintain straighter trajectories in river water, compared to dominant males, but then rapidly change to less linear and more circular paths over time. Intriguingly, we show that OF counteracts this change in sperm linearity in parr males so that patterns become indistinguishable from dominants when parr sperm swim in OF. Together, these results show that male chinook salmon exhibit differential sperm trait investment strategies depending on reproductive tactic. [ABSTRACT FROM AUTHOR]

The mitochondrial anti-viral signaling (MAVS) protein is an intermediary adaptor protein of retinoic acid-inducible gene-1 (RIG-I) like receptor (RLR) signaling, which activates the transcription factor interferon (IFN) regulatory factor 3 (IRF3) and NF-kB to produce type I IFNs. MAVS expression has been reported in different fish species, but few studies have shown its functional role in anti-viral responses to fish viruses. In this study, we used the transcription activator-like effector nuclease (TALEN) as a gene editing tool to disrupt the function of MAVS in Chinook salmon (Oncorhynchus tshawytscha) embryonic cells (CHSE) to understand its role in induction of interferon I responses to infections with the (+) RNA virus salmonid alphavirus subtype 3 (SAV-3), and the dsRNA virus infectious pancreatic necrosis virus (IPNV) infection. A MAVS-disrupted CHSE clone with a 7-aa polypeptide (GVFVSRV) deletion mutation at the N-terminal of the CARD domain infected with SAV-3 resulted in significantly lower expression of IRF3, IFNa, and ISGs and increased viral titer (1.5 log10) compared to wild-type. In contrast, the IPNV titer in MAVS-disrupted cells was not different from the wild-type. Furthermore, overexpression of salmon MAVS in MAVS-disrupted CHSE cells rescued the impaired type I IFN-mediated anti-viral effect against SAV-3. [ABSTRACT FROM AUTHOR]

Cells are equipped with intracellular RIG-like Receptors (RLRs) detecting double stranded (ds)RNA, a molecule with Pathogen-Associated Molecular Pattern (PAMPs) generated during the life cycle of many viruses. Melanoma Differentiation-Associated protein 5 (MDA5), a helicase enzyme member of the RLRs encoded by the ifih1 gene, binds to long dsRNA molecules during a viral infection and initiates production of type I interferon (IFN1) which orchestrates the antiviral response. In order to understand the contribution of MDA5 to viral resistance in fish cells, we have isolated a clonal Chinook salmon Oncorhynchus tshawytscha epithelial-like cell line invalidated for the ifih1 gene by CRISPR/Cas9 genome editing. We demonstrated that IFN1 induction is impaired in this cell line after infection with the Snakehead Rhabdovirus (SHRV), the Salmon Alphavirus (SAV) or Nervous Necrosis Virus (NNV). The cell line, however, did not show any increase in cytopathic effect when infected with SHRV or SAV. Similarly, no cytopathic effect was observed in the ifih1-/- cell line when infected with Infectious Pancreatic Necrosis Virus (IPNV), Infectious Haemorrhagic Necrotic Virus (IHNV). These results indicate the redundancy of the antiviral innate defence system in CHSE-derived cells, which helps with circumventing viral evasion strategies. [ABSTRACT FROM AUTHOR]

Differences in the availability of prey may explain the low numbers of southern resident killer whales and the increase in northern resident killer whales in British Columbia and Washington State. However, in-situ data on the availability of their preferred prey (Chinook salmon, Oncorhynchus tshawytscha) in the core feeding areas used by these two populations of fish-eating killer whales have been lacking to test this hypothesis. We used multi-frequency echosounders (38, 70, 120, and 200 kHz) to estimate densities of adult Chinook (age-4+, > 81 cm) within 16 hot-spot feeding areas used by resident killer whales during summer 2020 in the Salish Sea and North Island Waters. We found Chinook were generally concentrated within 50 m from the bottom in the deep waters, and tended to be absent near the surface in the shallow waters (< 50 m). In general, the densities of Chinook we encountered were highest as the fish entered the Salish Sea (from Swiftsure Bank in the south) and Johnstone Strait (from Queen Charlotte Strait to the north)—and declined as fish migrated eastward along the shoreline of Vancouver Island. Median densities of Chinook for all sampled areas combined were 0.4 ind.·1000 m−2 in northern resident foraging areas, and 0.9 ind.·1000 m−2 in southern resident killer whale areas (p < 0.05, Mann–Whitney U test). Thus, Chinook salmon were twice as prevalent within the hot-spot feeding areas of southern versus northern resident killer whales. This implies that southern resident killer whales have greater access to Chinook salmon compared to northern residents during summer—and that any food shortage southern residents may be encountering is occurring at other times of year, or elsewhere in their range. [ABSTRACT FROM AUTHOR]

Dispersal is a ubiquitous ecological process that has been extensively studied in many plants and animals. Anadromous salmonids are an interesting system for examining dispersal, in part because of their well‐known philopatric behaviour, but also because of the conservation challenges related to the dispersal of hatchery‐origin fish. Building on earlier work, we provide an updated systematic review of dispersal and gene flow in anadromous salmonids. In particular, we compared studies on the dispersal of anadromous salmonids from wild and hatchery origins, including studies providing estimates of dispersal rates, observations of dispersal and results from modelling studies. We reviewed 228 studies and found these were unevenly distributed among species, with Atlantic salmon, Chinook salmon and sea trout being well‐represented. Our results showcase considerable variability in estimated dispersal rates within and across studies, which is likely related to the different methodologies, dispersal propensities across species and populations, and spatial extents considered. Overall, our results confirmed a higher tendency of hatchery fish to disperse relative to wild fish, but we also found some variation across species that warrants further study. Moreover, we found that dispersal propensity tended to decline exponentially with distance and that the drivers of dispersal varied considerably among studies. Additionally, we highlight various facets of dispersal captured across this suite of studies, including variation in terminology, methods and metrics for characterising dispersal, and the spatio‐temporal scales considered. Finally, our review revealed that few studies considered, and even fewer assessed, the implications of dispersal for the conservation and management of anadromous salmonids. [ABSTRACT FROM AUTHOR]

Disentangling the influences of climate change from other stressors affecting the population dynamics of aquatic species is particularly pressing for northern latitude ecosystems, where climate‐driven warming is occurring faster than the global average. Chinook salmon (Oncorhynchus tshawytscha) in the Yukon‐Kuskokwim (YK) region occupy the northern extent of their species' range and are experiencing prolonged declines in abundance resulting in fisheries closures and impacts to the well‐being of Indigenous people and local communities. These declines have been associated with physical (e.g., temperature, streamflow) and biological (e.g., body size, competition) conditions, but uncertainty remains about the relative influence of these drivers on productivity across populations and how salmon–environment relationships vary across watersheds. To fill these knowledge gaps, we estimated the effects of marine and freshwater environmental indicators, body size, and indices of competition, on the productivity (adult returns‐per‐spawner) of 26 Chinook salmon populations in the YK region using a Bayesian hierarchical stock‐recruitment model. Across most populations, productivity declined with smaller spawner body size and sea surface temperatures that were colder in the winter and warmer in the summer during the first year at sea. Decreased productivity was also associated with above average fall maximum daily streamflow, increased sea ice cover prior to juvenile outmigration, and abundance of marine competitors, but the strength of these effects varied among populations. Maximum daily stream temperature during spawning migration had a nonlinear relationship with productivity, with reduced productivity in years when temperatures exceeded thresholds in main stem rivers. These results demonstrate for the first time that well‐documented declines in body size of YK Chinook salmon were associated with declining population productivity, while taking climate into account. [ABSTRACT FROM AUTHOR]

The Fraser River once supported massive salmon returns. However, over the last century, the largest returns have consistently been less than half of the recorded historical maximum. There is substantial interest from surrounding communities and governments to increase salmon returns for both human use and functional ecosystems. To generate resources for this endeavor, we resequenced genomes of Chinook (Oncorhynchus tshawytscha), coho (Oncorhynchus kisutch), and sockeye salmon (Oncorhynchus nerka) from the Fraser River at moderate coverage (∼16×). A total of 954 resequenced genomes were analyzed, with 681 collected specifically for this study from tissues sampled between 1997 and 2021. An additional 273 were collected from previous studies. At the species level, Chinook salmon appeared to have 1.6–2.1× more SNPs than coho or sockeye salmon, respectively. This difference may be attributable to large historical declines of coho and sockeye salmon. At the population level, 3 Fraser River genetic groups were identified for each species using principal component and admixture analyses. These were consistent with previous research and supports the continued use of these groups in conservation and management efforts. Environmental factors and a migration barrier were identified as major factors influencing the boundaries of these genetic groups. Additionally, 20 potentially adaptive loci were identified among the genetic groups. This information may be valuable in new management and conservation efforts. Furthermore, the resequenced genomes are an important resource for contemporary genomics research on Fraser River salmon and have been made publicly available. [ABSTRACT FROM AUTHOR]

Current procedures to establish vertebral column regionalization (e.g., histology) in fish are time consuming and difficult to apply. The aim of this study was to develop a more rapid and accurate radiology‐based method for Atlantic salmon (Salmo salar). A detailed analysis of 90 animals (4 kg) led to the establishment of region‐specific radiographic hallmarks. To elucidate its transferability to other salmonid species, radiography was carried out in brown trout (Salmo trutta), Arctic char (Salvelinus alpinus), rainbow trout (Oncorhynchus mykiss), pink salmon (Oncorhynchus gorbuscha), and Chinook salmon (Oncorhynchus tshawytscha). This method was also evaluated for whole ungutted fish. The vertebral column of Atlantic salmon can be subdivided into five regions (R1–R5) based on anatomy: postcranial (R1, V1, and V2), abdominal (R2, V3–V26), transitional (R3, V27–V36), caudal (R4, V37–V53), and ural (R5, V54–V59). The following specific radiographic hallmarks allow the identification of regions: (i) lack of ribs in R1, (ii) modified parapophysis of the first vertebra of R3, (iii) prominent hemal spine of the first vertebra of R4, and (iv) the separated hemal spine of the most cranial pre‐ural vertebra of R5. These hallmarks were all transferable to the other salmonid species assessed. The results include a further description of various region‐specific characteristics in Atlantic salmon. The method was found applicable for sedated/whole ungutted fish, verifying it as quick and easy compared to other regionalization methods. The regions defined by radiology in this study agree with the vertebral column regions recently defined for Chinook salmon (O. tshawytscha). Thus, and considering the results of this study on various salmonid species, the currently developed regionalization protocol can be generally used for salmonids. [ABSTRACT FROM AUTHOR]

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. Impact StatementAlthough trap and haul operations allow wild salmon populations to access historical spawning grounds, despite impoundment structures, populations are hindered by high prespawn mortality rates and recovery efforts may benefit from an adaptive management plan. [ABSTRACT FROM AUTHOR]

Anthropogenic disturbance of stream ecosystems, often chronic in nature, has been studied extensively. However, when disturbance is driven by more than one resource policy over many decades, feedback between habitat evolution and biological adaptation can be disrupted and ecological function affected in unforeseen ways. We analyzed over 100 years of Chinook salmon (Oncorhynchus tshawytscha) length frequency trends associated with fisheries management and changes in available spawning substrate (habitat) linked to flow regulation in a highly altered California river. Over time, salmon lengths generally decreased, fluctuating with exploitation (ocean harvest) and hatchery production rates. Female size reduction, coupled with a degrading and coarsening channel, and perching peripheral habitat related to past mining activity, indicates available spawning substrate may be too large to support the current salmon population. Assuming a salmon can move material ~10% of her body length, length frequency data and current substrate size distribution suggest that increasing salmon sizes to historic distributions could increase available spawning habitat by as much as 13%. Alternatively, decreasing spawning substrate size could support a greater portion of the current population. To test the latter hypothesis and inform future management actions, we monitored two spawning riffles where large and small gravel was placed on top of a cobble. We observed an immediate spawning activity increase that was more pronounced where smaller gravel was deposited. Following a decade of habitat decline, the two sites were both replenished with medium gravel. Elevated spawning use occurred immediately at both sites, commensurate with this intermediate size, further supporting our hypotheses. Sediment coarsening and habitat disconnect below dams, combined with reduced salmon size, indicate the natural spawning process may be decoupled from available habitat below dams in the foreseeable future without continuous intervention. Actively managing salmon population demographics through modified hatchery and size‐selective harvest practices and developing a coarse sediment budget with size‐appropriate material for regulated anadromous rivers could produce immediate benefits for ecosystem services, including salmon populations. However, these management actions will require continued maintenance and informed socio‐ecological goals to remain successful. [ABSTRACT FROM AUTHOR]

King (Chinook) salmon is the only salmon species farmed in Aotearoa New Zealand and accounts for over half of the world's production of king salmon. Determining the health status of king salmon effectively is important for farming. However, it is a challenging task due to the complex biotic and abiotic factors that influence health. Evolutionary machine learning algorithms have shown their superiority in learning models for challenging tasks. However, they have not been investigated for health prediction in king salmon farming. This paper focuses on data processing and machine learning algorithm design to develop king salmon health prediction models in Aotearoa New Zealand. Particularly, this paper proposes a king salmon health prediction method based on genetic programming which is an evolutionary machine learning algorithm. The results show that genetic programming achieves the best overall performance among all examined typical machine learning algorithms for most trials. Further analyses show that genetic programming can automatically detect important features for learning classifiers for king salmon health classification tasks effectively, and can also learn potentially interpretable models. Our results are an important step forward in developing health prediction tools to automatically assess health status of farmed king salmon in Aotearoa New Zealand. [ABSTRACT FROM AUTHOR]

Ectotherms have peculiar relationships with microorganisms. For instance, bacteria are recovered from the blood and internal organs of healthy teleosts. However, the presence of microbial communities in the healthy teleost brain has not been proposed. Here, we report a living bacterial community in the brain of healthy salmonids with bacterial loads comparable to those of the spleen and 1000-fold lower than in the gut. Brain bacterial communities share >50% of their diversity with gut and blood bacterial communities. Using culturomics, we obtained 54 bacterial isolates from the brains of healthy trout. Comparative genomics suggests that brain bacteria may have adaptations for niche colonization and polyamine biosynthesis. In a natural system, Chinook salmon brain microbiomes shift from juveniles to reproductively mature adults. Our study redefines the physiological relationships between the brain and bacteria in teleosts. This symbiosis may endow salmonids with a direct mechanism to sense and respond to environmental microbes. [ABSTRACT FROM AUTHOR]

Background: A genotype-by-environment (G × E) interaction is defined as genotypes responding differently to different environments. In salmonids, G × E interactions can occur in different rearing conditions, including changes in salinity or temperature. However, water flow, an important variable that can influence metabolism, has yet to be considered for potential G × E interactions, although water flows differ across production stages. The salmonid industry is now manipulating flow in tanks to improve welfare and production performance, and expanding sea pen farming offshore, where flow dynamics are substantially greater. Therefore, there is a need to test whether G × E interactions occur under low and higher flow regimes to determine if industry should consider modifying their performance evaluation and selection criteria to account for different flow environments. Here, we used genotype-by-sequencing to create a genomic-relationship matrix of 37 Chinook salmon, Oncorhynchus tshawytscha, families to assess possible G × E interactions for production performance under two flow environments: a low flow regime (0.3 body lengths per second; bl s−1) and a moderate flow regime (0.8 bl s−1). Results: Genetic correlations for the same production performance trait between flow regimes suggest there is minimal evidence of a G × E interaction between the low and moderate flow regimes tested in this study, for Chinook salmon reared from 82.9 ± 16.8 g ( x ¯ ± s.d.) to 583.2 ± 117.1 g ( x ¯ ± s.d.). Estimates of genetic and phenotypic correlations between traits did not reveal any unfavorable trait correlations for size- (weight and condition factor) and growth-related traits, regardless of the flow regime, but did suggest measuring feed intake would be the preferred approach to improve feed efficiency because of the strong correlations between feed intake and feed efficiency, consistent with previous studies. Conclusion: This new information suggests that Chinook salmon families do not need to be selected separately for performance across different flow regimes. However, further studies are needed to confirm this across a wider range of fish sizes and flows. This information is key for breeding programs to determine if separate evaluation groups are required for different flow regimes that are used for production (e.g., hatchery, post smolt recirculating aquaculture system, or offshore). [ABSTRACT FROM AUTHOR]

Captive‐breeding programs are increasingly implemented to curb population declines but can have unintended negative effects on genetic diversity and phenotypes. Through an analysis of ~10 years of genetic monitoring, pedigree information, and phenotypic data, we evaluated a captive‐breeding program that uses adaptive management to reduce inbreeding and improve captive broodstock performance. A captive‐breeding program was established in 2012 to reintroduce spring‐run Chinook salmon to the southern edge of their range in California's San Joaquin River (SJR), using fish produced each year at the nearby Feather River Hatchery (FRH). We found that the SJR program adequately captured the genetic diversity of the FRH source population and that mate pairings guided by genetic relatedness reduced inbreeding. However, the SJR broodstock reared in captivity had smaller body size at maturity in comparison to the FRH source broodstock which matures at sea, but this effect disappeared when SJR juveniles were released from captivity to mature at sea. Phenotypic traits of SJR female parents also influenced reproductive performance; older mothers and those with smaller eggs had offspring with lower survival. These findings demonstrate that adaptive genetic monitoring and pedigree information can be powerful tools for reducing risks of captive breeding and evaluating program effectiveness. [ABSTRACT FROM AUTHOR]

Evaluation of goals is crucial for effective management to conserve viable and diverse fish populations and to support harvest. Management of wild Chinook Salmon Oncorhynchus tshawytscha in the Snake River basin exemplifies the struggle to meet fisheries goals. Considering contemporary production of juvenile emigrants, it is imperative to determine the survival from emigration to adult (Se‐a) required to meet abundance goals. Increased anthropogenic impact on spawning and rearing habitats leads to higher Se‐a required to attain goals. Wilderness populations exhibit viability and could sustain fisheries with Se‐a lower than required elsewhere. Conversely, populations targeted for habitat restoration demand higher Se‐a to fulfill goals, indicating a need to enhance egg‐to‐smolt survival. However, Se‐a has fallen below the threshold needed for replacement in all populations, even at current low abundances. Despite these challenges, most populations still possess the potential to achieve abundance goals, emphasizing the importance of strategic interventions to bolster their resilience. [ABSTRACT FROM AUTHOR]

Many river systems within the Central Valley of California have been disconnected from their floodplains, hypothesized to be partially responsible for declining Chinook salmon populations (Oncorhynchus tshawytscha). The primary floodplain of the system, Yolo By‐Pass (known regionally as "Yolo Bypass"), offered an opportunity to examine whether improved connectivity between the floodplain and river could limit negative climate change effects on salmon populations. Specifically, the top of the floodplain (Fremont Weir) is being modified to provide Sacramento River Chinook salmon better access to floodplain rearing habitat. We estimated restoration effects on the Yolo By‐Pass flood regime now and under future climate scenarios using flow rating curves. Additionally, we used temperature and flow‐specific effects on Chinook salmon population dynamics within the Yolo By‐Pass and Sacramento River complex to describe how the restoration project and climate change may interact to affect juvenile Chinook salmon biomass production. Our results indicate that the Fremont Weir restoration project will extend the frequency, timing, and duration of Yolo By‐Pass flooding. Our production model indicates that the modification will result in greater salmon entrainment rates into the Yolo By‐Pass, where salmon growth rates, survival rates, and biomass production were higher when compared to the Sacramento River main stem. The project appears to benefit all regional runs of Chinook salmon, which should help support life history diversity. Our results suggest that the weir modification should benefit native fish from the Central Valley that use floodplain habitat and that these benefits may be resilient to challenges created by a changing climate. [ABSTRACT FROM AUTHOR]

Concern over rising water temperatures for freshwater ectotherms has led to application of experimentally derived thermal thresholds to stream temperature models for estimation of streams at high risk of exceeding thermal thresholds under current and future climate conditions. We optimised an approach that links field‐relevant thermal maxima experiments to corresponding stream temperature models and identifies opportunities to reduce stream temperatures through riparian tree growth.We conducted a thermal maxima experiment on cold‐water adapted juvenile Chinook (Oncorhynchus tshawytscha) and coho salmon (Oncorhynchus kisutch) that reflected natural temperatures by using incremental temperature ramping with diel fluctuations (IT‐Dmax) and refit a regionally specific stream temperature model for British Columbia, Canada to directly relate to lab‐derived thresholds. Salmon‐bearing streams across British Columbia were categorised by threshold exceedance risk (i.e., low, moderate, high, severe) based on risk tolerance scenarios for management decision making (i.e., considering a range of prediction intervals [PIs] and stream thermal sensitivities to air temperature). We linked these results directly to riparian management and restoration actions by estimating the potential for riparian tree growth to reduce threshold exceedance risk.Lab‐derived IT‐Dmax endpoints were consistently 24°C (based on the median value between the 7‐day average of the daily maximum and the mean weekly average temperature) across acclimation treatments for both species. Under current conditions, most stream reaches (99.6% using an intermediate risk tolerance scenario) were below the thermal threshold; streams with moderate to high risk of threshold exceedance were projected to increase from 0.4% to 1.5% (total linear stream length of 6,929 km) by end of century. The risk‐averse (high sensitivity, 75% PI) and risk‐tolerant (low sensitivity, 95% PI) scenarios differed by 1,107 km of streams predicted to have a moderate to severe risk of exceeding thresholds by end of century. Maximal riparian tree growth was predicted to shift 670 km of streams from moderate to low exceedance risk under end‐of‐century conditions and intermediate risk tolerance, showing the potential for mitigation from thermal impacts.Our integrative approach tackled several key considerations in identifying streams at high temperature risk for freshwater ectotherms that to date have not been addressed. Furthermore, we showcased the delineation of spatially comprehensive estimates that identify where management mitigation and a specific restoration activity may be most needed to reduce impacts of rising temperatures on rearing salmonids across an extensive region. [ABSTRACT FROM AUTHOR]

Juvenile Pacific salmon (Oncorhynchus spp.) use estuary habitats to varying degrees with some species and populations thought to rely heavily on these areas for early growth. In the Fraser River, British Columbia, there are 18 distinct conservation units of Chinook salmon (O. tshawytscha), and all but one is of conservation concern. Our study compares the outmigration timing, size, and habitat use of juvenile Chinook salmon in the Fraser River estuary. Over 5 years (2016–2020), we captured 6493 juvenile Chinook salmon, with 3318 sampled for stock identification. Fraser River Chinook salmon extensively used estuary habitats, but patterns varied considerably by population. Juvenile Chinook salmon from the Lower Fraser River were most abundant and present the longest, arriving the smallest in late March and early April, and captured until July. South Thompson ocean-type Chinook salmon entered the estuary later, starting to arrive in late May or early June and remaining present until mid-August. Overall, juvenile Chinook salmon varied considerably in their estuary use across populations. Understanding this variation can inform differences in productivity and guide recovery actions. [ABSTRACT FROM AUTHOR]

Striped Bass (Morone saxatilis) monitoring and research in California's Central Valley primarily occurs in the Sacramento River basin and the Sacramento-San Joaquin Delta. A relatively under-studied contingent of the Striped Bass population is present in the San Joaquin River and its tributaries. One such tributary, the Stanislaus River, is an important source of natural production of native anadromous fishes, including fall-run Chinook Salmon (Oncorhynchus tshawytscha), Steelhead (O. mykiss), and Pacific Lamprey (Entosphenus tridentatus). Because Striped Bass are a non-native piscivore, characterizing when and where their distribution overlaps with native fishes is a first step to assessing the potential for negative inter-specific interactions. We compiled incidental observations of Striped Bass made during long-term (1996 to 2021) salmonid monitoring programs performed at different times of the year, and found that Striped Bass were present at monitoring locations throughout most of the year, although not detected in every year. We also used data on Striped Bass captured during boat electrofishing surveys conducted during the 2019, 2020, and 2021 juvenile salmonid emigration season (February to June), for a more detailed evaluation of Striped Bass occupancy within the lower 65 kilometers of the Stanislaus River. Median fork length (FL) of Striped Bass captured from February to April was significantly larger than those captured in May and June (p < 0.001). Using dynamic occupancy models, we showed that Striped Bass larger than 300 mm FL were present, and their occupancy increases earlier in the year than individuals under 300 mm FL. In all 3 years, occupancy estimates were greater than 80% of the lower Stanislaus River by May. Our results suggest a high degree of spatial and temporal overlap with native migratory fishes, which may have important implications for understanding and managing how predation affects juvenile salmon and other native species. [ABSTRACT FROM AUTHOR]

Variations in species distribution, population structure, and behavior can provide a portfolio effect that buffers populations against rapid environmental change. Although diversity has been identified as a goal for effective resource management and genetic and demographic tools have been developed, life history remains challenging to quantify. In this study, we demonstrate a novel metric of life history diversity using telemetry data from migratory fish. Here, we examined diversity in the outmigration behavior of juvenile Chinook salmon (Oncorhynchus tshawytscha) released in the Sacramento River, California, between 2007 and 2017. In this synthesis, we examined a wide variety of landscape and demographic drivers at high resolution by incorporating many individual telemetry studies, with variability in release location by year, environmental conditions, and all runs of salmon that are present in the watershed. When years were grouped by shared hydrologic conditions, variation in travel time was significantly higher in wet years. Further, our model showed a negative effect of warm temperatures at low flows on the variation in migration movements. This suggests that enhanced hydrologic connectivity increases the variation in migration time, a representation of habitat complexity and biocomplexity, despite the degraded state of this watershed and the weakened state of these populations. Variation in migration behavior could buffer species from current and future environmental changes, such as climate effects on precipitation and temperature. Hence, behavioral metrics generated from telemetry studies can be used to understand life history diversity and the potential effects of environmental fluctuations. [ABSTRACT FROM AUTHOR]

Current prophylactic and disease control measures in aquaculture highlight the need of alternative strategies to prevent disease and reduce antibiotic use. Mucus covered mucosal surfaces are the first barriers pathogens encounter. Mucus, which is mainly composed of highly glycosylated mucins, has the potential to contribute to disease prevention if we can strengthen this barrier. Therefore, aim of this study was to develop and characterize fish in vitro mucosal surface models based on commercially available cell lines that are functionally relevant for studies on mucin regulation and host-pathogen interactions. The rainbow trout (Oncorhynchus mykiss) gill epithelial cell line RTgill-W1 and the embryonic cell line from Chinook salmon (Oncorhynchus tshawytscha) CHSE-214 were grown on polycarbonate membrane inserts and chemically treated to differentiate the cells into mucus producing cells. RTGill-W1 and CHSE-214 formed an adherent layer at two weeks post-confluence, which further responded to treatment with the γ-secretase inhibitor DAPT and prolonged culture by increasing the mucin production. Mucins were metabolically labelled with N-azidoacetylgalactosamine 6 h post addition to the in vitro membranes. The level of incorporated label was relatively similar between membranes based on RTgill-W1, while larger interindividual variation was observed among the CHSE in vitro membranes. Furthermore, O-glycomics of RTgill-W1 cell lysates identified three sialylated O-glycans, namely Galβ1-3(NeuAcα2–6)GalNAcol, NeuAcα-Galβ1-3GalNAcol and NeuAcα-Galβ1-3(NeuAcα2–6)GalNAcol, resembling the glycosylation present in rainbow trout gill mucin. These glycans were also present in CHSE-214. Additionally, we demonstrated binding of the fish pathogen A. salmonicida to RTgill-W1 and CHSE-214 cell lysates. Thus, these models have similarities to in vivo mucosal surfaces and can be used to investigate the effect of pathogens and modulatory components on mucin production. [ABSTRACT FROM AUTHOR]

The Steelhead ecotype (Oncorhynchus mykiss) and chinook salmon (Oncorhynchus tshawytscha) have promoted a recreational fishery in the Santa Cruz river, the last large free flowing river of Patagonia. However, two dams are being built upstream in the middle course, potentially affecting the life cycle of these anadromous salmonids. The study describes the dynamics of the recreational fishing of the Santa Cruz river around Piedrabuena city and anglers perceptions, discussing its trends according to possible river connectivity scenarios. The fishery was assessed through a monthly year-round field sampling from April 2018 to April 2019, developing instantaneous angler counts, discriminating fishing methods, effort, and catch per unit effort; also, in situ interviews were used to collect information on anglers’ motivations and perceptions. In addition, information on fishing tournaments was used. Three fishing zones (FZ) were identified near Piedrabuena city: FZ-1, located downstream where anglers used baited hook and line to catch the native marine Patagonian blenny (Eleginops maclovinus); FZ-2, located in the town where baited hook and line, spinning, and fly-cast are used to catch Patagonian blenny and salmonids; FZ-3 located upstream the town, where fishing effort was mainly directed to salmonids employing spinning and fly-cast. Fishing effort showed a seasonal pattern with high values from March to May and September to October, agreeing with Steelhead and Chinook salmon runs, respectively. The most relevant motivations for anglers were nonoriented catch variables. Anglers preferred the capture of salmonids over native species, considering dams to be a major threat to fishery. Although a postdamming scenario could allow the adult salmonids to migrate upstream, the current reproduction grounds of Steelhead will be flooded, and juveniles and adults of both species will be hindered in their downstream migration to sea. These aspects seem to seriously compromise the future of these unique fisheries. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Southern Distinct Population Segment (sDPS) green sturgeon spawn solely in one stretch of the Sacramento River in California. Management of this spawning habitat is complicated by cold water temperature requirements for the conservation of winter-run Chinook salmon. This study assessed whether low incubation and rearing temperatures resulted in carryover effects across embryo to early juvenile life stages on scaling relationships in growth and metabolism in northern DPS green sturgeon used as a proxy for sDPS green sturgeon. Fish were incubated and reared at 11 °C and 15 °C, with a subset experiencing a reciprocal temperature transfer post-hatch, to assess recovery from cold incubation or to simulate a cold-water dam release which would chill rearing larvae. Growth and metabolic rate of embryos and larvae were measured to 118 days post hatch. Reciprocal temperature transfers revealed a greater effect of low temperature exposure during larval rearing rather than during egg incubation. While 11 °C eggs hatched at a smaller length, log-transformed length–weight relationships showed that these differences in developmental trajectory dissipated as individuals achieved juvenile morphology. However, considerable size-at-age differences persisted between rearing temperatures, with 15 °C fish requiring 60 days post-hatch to achieve 1 g in mass, whereas 11 °C fish required 120 days to achieve 1 g, resulting in fish of the same age at the completion of the experiment with a ca. 37-fold difference in weight. Consequently, our study suggests that cold rearing temperatures have far more consequential downstream effects than cold embryo incubation temperatures. Growth delays from 11 °C rearing temperatures would greatly increase the period of vulnerability to predation in larval green sturgeon. The scaling relationship between log-transformed whole-body metabolism and mass exhibited a steeper slope and thus an increased oxygen requirement with size in 11 °C reared fish, potentially indicating an energetically unsustainable situation. Understanding how cold temperatures affect green sturgeon ontogeny is necessary to refine our larval recruitment estimations for this threatened species. [ABSTRACT FROM AUTHOR]

Objective: Genetic stock identification (GSI) can be an effective tool for fisheries management, but development of reference baselines for species with broad geographic distributions can be challenging. Mixed‐stock fisheries for Chinook Salmon Oncorhynchus tshawytscha have utilized GSI analyses for decades with various genetic baselines, but these have largely become outdated with advances in technology that enable more efficient genotyping. Thus, our goals were to (1) create nested baselines of genotypic data for Chinook Salmon throughout their entire natural range using existing data from multiple sources and (2) evaluate the utility of those nested baselines to conduct accurate hierarchical GSI of mixture proportions or the stock identification of individual fish. Methods: In this study, we compiled a large genetic baseline of single‐nucleotide polymorphism (SNP) markers for 389 populations that encompass the entire geographic range of Chinook Salmon. We used cross validation and realistic mixture simulations to test the accuracy of the baseline in generating GSI estimates. Result: We demonstrated that a multi‐tiered assignment approach can provide high accuracy at both tier 1 (broadscale, with three coastwide reporting groups; 97.8% mean accuracy) and tier 2 (fine‐scale regional reporting groups; up to 97.7% mean accuracy) levels. Realistic mixture simulations showed that this multi‐tiered approach can provide highly effective GSI results for several common mixed‐stock fisheries applications in the Pacific Ocean. Conclusion: This new SNP baseline and the multi‐tiered assignment approach provide the most comprehensive rangewide GSI baseline for Chinook Salmon over any previous application and enable highly accurate estimates for GSI purposes. Impact statementA Chinook Salmon genetic stock identification baseline encompassing the species' entire range has broad applications in fishery management and harvest allocation as well as in basic research. [ABSTRACT FROM AUTHOR]

Adaptive management, a process of planning, implementing, and evaluating management strategies, is often recommended for monitoring ecological systems. However, few examples of successful implementation and retrospective case studies exist. We provide a case study of adaptively managing hatchery-assisted protection and recovery for Chinook salmon (Oncorhynchus tshawytscha) and winter steelhead trout (O. mykiss) during and after the removal of two large mainstem dams in the Elwha River, WA. We summarize key aspects of the monitoring and adaptive management plan over the last decade and highlight successes, challenges, and complications during the plan's implementation. The Elwha Monitoring and Adaptive Management Guidelines included a trigger-based system for moving through four phases of recovery that included preservation, recolonization, local adaptation, and viable natural population, each with differing levels of hatchery production as the management actions. The monitoring component of the plan has been very successful, providing critical data to guide management actions that otherwise may not have occurred and, opportunistically, provided data for other native species in the Elwha River. Implementing adaptive management provided mixed results and was at times hindered by divergent management goals among project partners, the inflexibility of the Endangered Species Act regulatory requirements as implemented for this project, and conflicting information among guidance documents. We learned that some metrics and triggers in the plan were ill-defined or too difficult to measure in the field. In some cases, the performance indicators and/or triggers were successfully modified to incorporate what was learned; however, in other cases, we were unable to revise the values due to differing opinions among partners. The ability to reach consensus on revised triggers appeared to be influenced by the recovery trajectory of the species involved. The implemented adaptive management strategy resulted in substantial collaboration and learning, which resulted in revised management strategies, but was imperfect. Sufficient long-term funding is necessary to implement a well-designed monitoring program and could benefit from including a defined leadership position to shepherd and facilitate a multi-stakeholder adaptive management program. Additionally, incorporating adaptive management into legally binding conditions under the Endangered Species Act is feasible, but requires substantial pre-planning in close coordination with regulatory agencies. [ABSTRACT FROM AUTHOR]

Large dam removal is being used to restore river systems, but questions remain regarding their outcomes. We examine how the removal of two large dams in the Elwha River, coupled with hatchery production and fishing closures, affected population attributes of Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss). Initial responses by returning adult Chinook salmon and steelhead was an increase in the number and spatial extent of natural and hatchery origin fish. Although few naturally produced juvenile Chinook salmon and steelhead outmigrants were observed prior to and during dam removal, abundances increased three years after adult fish passage was restored, suggesting that impacts due to downstream sedimentation after dam removal were reduced. The Chinook salmon population demographics remain dominated by hatchery production, while increases in winter steelhead abundance included both hatchery and natural-origin spawners. The spatial expansion of winter steelhead upstream of former dam sites was predominantly by natural-origin spawners. We also observed a natural "reawakening" of summer steelhead that were in part derived from an up-river resident population that returned to the Upper Elwha. Our results showed that a combination of habitat, hatchery, and harvest actions can result in positive responses for salmonid populations. [ABSTRACT FROM AUTHOR]

Introduction: Habitat loss and degradation pose significant threats to global fish and wildlife populations, prompting substantial investments in habitat creation and restoration efforts. Not all habitats provide equal benefits, leading to challenges in prioritizing restoration actions. For example, juvenile anadromous salmonids require high quality rearing aquatic habitats to achieve the physiological requirements needed to successfully migrate to the ocean. However, there are profound disagreements among anadromous salmon restoration managers whether it is best to focus efforts on restoring in-channel habitats that are available for the entire rearing period or floodplain habitats that, while facilitating greater growth and survival than in-channel habitats, are only available for a few weeks at a time and are typically only activated every two-to-three years. Methods: We used an existing fall-run Chinook salmon decision-support model to evaluate under what conditions floodplain restoration would provide greater benefits than in-channel habitat restoration. The simulations included a wide range of floodplain inundation frequencies and durations and floodplain benefits in the form of increased survival and growth relative to in-channel habitats. Results: The simulations results indicated that in-channel habitat restoration was always the best habitat restoration action when there was no existing in-channel habitat despite simulating a wide range of flood frequency, duration, and growth and survival benefits. Floodplain restoration was generally best when there was sufficient in-channel habitat available to successfully rear most of the juveniles produced by the returning adult salmon. Discussion: We hypothesize that in-channel and floodplain habitats have different roles in salmon population maintenance with in-channel habitats regulating the overall population size and floodplains acting as recurrent resource pulses. Our study provides a quantitative framework to evaluate the benefit of these two habitat types and provides generalizable rulesets that can be used by managers when implementing habitat restoration strategies for species that inhabit both in-channel and floodplain habitats. [ABSTRACT FROM AUTHOR]

The lack of recovery of Chinook salmon (Oncorhynchus tshawytscha) in the Pacific Northwest has been blamed in part on predation by pinnipeds, particularly the harbor seal (Phoca vitulina). Previous work at a limited number of locations has shown that male seal diet contains more salmon than that of female seals and that sex ratios at haul‐out sites differ spatiotemporally. This intrapopulation variation in predation may result in greater effects on salmon than suggested by models assuming equal spatial distribution and diet proportion. To address the generality of these patterns, we examined the sex ratios and diet of male and female harbor seals from 13 haul‐out sites in the inland waters of Washington State and the province of British Columbia during 2012–2018. DNA metabarcoding was conducted to determine prey species proportions of individual scat samples. The sex of harbor seals was then determined from each scat matrix sample with the use of quantitative polymerase chain reaction (qPCR). We analyzed 2405 harbor seal scat samples using generalized linear mixed models (GLMMs) to examine the factors influencing harbor seal sex ratio at haul‐out sites and permutational multivariate analysis of variance (PERMANOVA) to examine the influence of sex and haul‐out site on harbor seal diet composition. We found that the overall sex ratio was 1:1.02 (female:male) with notable spatiotemporal variation. Salmoniformes were about 2.6 times more abundant in the diet of males than in the diet of females, and Chinook salmon comprised ca. three times more of the average male harbor seal's diet than the average female's diet. Based on site‐specific sex ratios and diet data, we identified three haul‐out sites where Chinook salmon appear to be under high predation pressure by male harbor seals: Cowichan Bay, Cutts Area, and Fraser River. Our study indicates that combining sex‐specific pinniped diet data with the sex ratio of haul‐out sites can help identify priority sites of conservation concern. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Objective: Parentage analysis is a routine methodology in fisheries research, but study systems exist where it is impractical to sample both parents. The ability to reliably assign offspring to a single parent is beneficial in these situations. We applied single‐parentage assignments to a naturally spawning population of Chinook Salmon Oncorhynchus tshawytscha to quantify production of anadromous returns by unsampled precocial males. Methods: We used an approach that focused on two important aspects of parentage analyses: (1) addressing the presence of family structure within the set of sampled parents and (2) controlling for false‐positive and false‐negative assignments. Result: Results indicated that 30% of reproductively successful males were precocial males, which produced 20% of the returning anadromous offspring. Conclusion: This study provides a framework for applying single‐parent assignments in a salmonid study system while explicitly addressing sources of assignment errors. Impact statementApplication of single‐parent assignments revealed that a precocial resident population of Chinook Salmon contributed substantially to returns of anadromous adults. [ABSTRACT FROM AUTHOR]

Objectives: Annual migration monitoring can help to discern patterns and environmental factors that impact growth, survival, and movement timing in small fish. Mark–recapture methods form the basis for such monitoring, and the standard 12‐mm passive integrated transponder (PIT) tag has emerged as an essential tool for studies of juvenile salmonids. A smaller, 9‐mm PIT tag now provides the potential to conduct mark–recapture studies on smaller fish. We evaluated relative performance of the 9‐mm tag, which is similar in design to its 12‐mm predecessor. Methods: For this comparison, we tagged and released approximately 8400 wild spring Chinook Salmon Oncorhynchus tshawytscha parr in Valley Creek, Idaho, from 2011 to 2013. Tag‐size cohorts were of similar average body size and were tagged in equal numbers. We estimated survival and detection probability for each cohort over two river segments. Results: In both segments, survival varied among years, but we observed no significant differences between tag‐size groups. At Valley Creek, average detection rates of fish with 9‐mm tags were a little less than one‐half the rates of fish with 12‐mm tags and were significantly lower in all 3 years. At Lower Granite Dam, detection rates were again lower for 9‐mm tags, but the differences were much smaller (3%–12%) and were not statistically significant. Conclusion: We found that 9‐mm tags can be as effective as 12‐mm tags and may allow for better inference to smaller (<55‐mm) non‐tagged fish. However, the lower detection rates of the 9‐mm tags could lead to less precise estimates, and site‐specific detection rates should be considered for studies that rely on these tags. Impact statementFish tagging technology has evolved with a goal of having minimal tag burden on study fish. However, use of tags that are smaller than the standard size may result in performance trade‐offs and therefore requires careful consideration to address specific research inquiries effectively. [ABSTRACT FROM AUTHOR]

Research efforts focusing on salmonid populations have highlighted the need to better understand demographic parameters for the fry and parr life stages. Monitoring these small fish presents a challenge because negative effects from handling and tagging can bias subsequent parameter estimates. Removal models and associated sampling designs represent one class of mark-recapture models with potential to be applied to very small juvenile salmon, yet existing methods associated with removal studies are not well-suited for all study environments. For example, populations residing in large storage reservoirs may yield low capture probabilities when subjected to removal sampling, making unbiased estimation of survival using traditional removal models difficult. To address this limitation, we developed a sampling design and associated model using parentage-based tagging in hatchery-raised juvenile Chinook salmon (Oncorhynchus tshawytscha) to estimate survival over a 2-year study period in a large storage reservoir in western Oregon, USA. Individual fish were identified to family groups, serving as replicate batch marks in a robust design removal model framework. Results from a simulation suggested that parameter estimates were unbiased even at very low capture probabilities, although the use of model constraints (i.e., covariates or constant parameter values) was necessary to achieve this. Model fitting to field data supported a trend in survival over time, with survival increasing with time since release in the first study year but decreasing in the second. [ABSTRACT FROM AUTHOR]

Despite increased interest in Chinook salmon aquaculture, there is inadequate understanding regarding the bacterial immune defenses of this species. This study describes the establishment and characterization of a continuous stromal-like cell line derived from Chinook salmon spleen, CHST, and its response to a heat-killed bacterial exposure challenge. Optimal growth of CHST was seen at 18 °C when grown in Leibovitz's L15 media supplemented with 20 % fetal bovine serum. DNA analyses confirmed that CHST did originate from Chinook salmon tissue. Vibrio anguillarum, a common pathogen of marine aquaculture and the causative agent of an acute hemorrhagic septicaemia known as vibriosis was used for exposure studies. V. anguillarum was heat-killed and CHST was challenged so that pro-inflammatory (IL-1β, IL-6 and TNFα) as well as anti-inflammatory (IL-10) cytokine transcript levels could be measured at 1, 4, 12, 24 and 96 hour (h) post-exposure. The heat-killed bacteria were observed to significantly stimulate the expression of all three pro-inflammatory cytokines at 4, 12, 24 and 96 h post-exposure with the peak in expression occurring at 12 and 24 h. Meanwhile, IL-10 was not observed to significantly increase until 96 h post-stimulation, which was also the time when the inflammatory cytokine expression was decreasing. The establishment and characterization of CHST provides a valuable model for studying the immune response of Chinook salmon stromal-like cells in response to stimuli, including those of bacterial origin.