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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]

Maturation schedules shape the age structure of a population and influence productivity and exposure to fishing. Fish cultivated and raised in artificial environments such as hatcheries may mature at different ages compared to their natural-origin counterparts. We evaluated whether endangered Sacramento River winter-run Chinook salmon Oncorhynchus tshawytscha produced in a conservation hatchery had different maturation schedules compared to naturalorigin fish, and how any differences affected their exposure to, and impact from, the ocean salmon fishery. Using coded-wire tags collected from hatchery fish in the ocean and in-river fisheries and on the spawning grounds, and scales collected from natural-origin spawner carcasses, we reconstructed the life history of hatchery and natural-origin cohorts from 2002-2015 brood years. Hatchery fish had similar age-2 maturation rates but higher age-3 maturation rates compared to natural-origin fish, resulting in fewer age-4 individuals and an overall more truncated age structure. Because natural-origin winter-run Chinook salmon were more likely to remain at sea until age 4, they were exposed to fishing for an additional year and experienced greater reduction in escapement. Compared to natural-origin males, hatchery-origin males were much less likely to return at an older age, possibly because sexual selection that is occurring on the spawning grounds is not occurring to the same extent in the hatchery. Identifying how reproductive maturation differs across sources, sex, and life histories is critical to understanding how fisheries can disproportionately impact subsets of a population and affect its long-term population dynamics and sustainability.

Chinook salmon (Oncorhynchus tshawytscha, Salmonidae) are foundational to social-ecological systems of the Northeast Pacific Rim and exhibit a rich diversity of life histories including in their adult migration timing, age at critical life-history transitions and marine feeding distributions. In recent decades Chinook have experienced declines across much of their native range; however, changes in productivity and abundance have rarely been evaluated in relation to life-history variation. To understand trends in Chinook salmon production, and how they are related to life history, we compiled time series data from the Fraser River to the Sacramento River on total run size (pre-fishery abundance) and escapement (post-fishery spawner abundance) and fit time series models to estimate trends across this bioregion. Our analysis revealed that most Chinook populations are declining, with negative trends in escapement (57 of 79) and total run (16 of 23) size. Trends were most acutely negative for interior spring Chinook in the Fraser, Columbia and Snake Rivers and most populations in California. Summer and fall Chinook had mixed trends, with several summer and fall upriver bright populations in the interior Columbia and Fraser exhibiting increases in abundance from the 1990s to 2019. Our research reveals widespread declines of this important species, but local complexity in trends that are mediated by population-level life history, migratory behaviours and watershed-scale restoration actions. Understanding linkages between life histories and resilience should inform rebuilding efforts for Chinook salmon and highlight the need to conserve intraspecific biodiversity.

Fish in all the world’s oceans exhibit variable body size and growth over time, with some populations exhibiting long-term declines in size. These patterns can be caused by a range of biotic, abiotic, and anthropogenic factors and impact the productivity of harvested populations. Within a given species, individuals often exhibit a range of life history strategies that may cause some groups to be buffered against change. One of the most studied declines in size-at-age has been in populations of salmon; Chinook salmon in the Northeast Pacific Ocean are the largest-bodied salmon species and have experienced long-term declines in size. Using long-term monitoring data, we develop novel size and growth models to link observed changes in Chinook size to life history traits and environmental variability. Our results identify three distinct trends in size across the 48 stocks in our study. Differences among populations are correlated with ocean distribution, migration timing, and freshwater residence. We provide evidence that trends are driven by interannual variation in certain oceanographic processes and competition with pink salmon.

Snorkel surveys were conducted on the Sacramento River to investigate the relative importance of microhabitat and mesohabitat scales on the abundance of young of the year (YOY) Chinook salmon (Oncorhynchus tshawytscha), while taking into account temporal and segment-scale spatial variations. Sites, with 13 different mesohabitat types, were sampled nine times from April to September in 1996. Both the sites and cells within the sites were classified by cover type. The analyses revealed that the microhabitat scale, specifically woody cover, best explained YOY abundance, versus the mesohabitat scale. Temporal and large-scale spatial patterns reflect the timing and abundance of different runs of Chinook salmon, while microhabitat scale patterns reflect cover preference of YOY Chinook salmon.

Accurate taxonomic identification is foundational for effective species monitoring and management. When visual identifications are infeasible or inaccurate, genetic approaches provide a reliable alternative. However, these approaches are sometimes less viable (e.g., need for near real-time results, remote locations, funding concerns, molecular inexperience). In these situations, CRISPR-based genetic tools can fill an unoccupied niche between real-time, inexpensive, but error-prone visual identification and more expensive or time-consuming, but accurate genetic identification for taxonomic units that are difficult or impossible to visually identify. Herein, we use genomic data to develop CRISPR-based SHERLOCK assays capable of rapidly (

Central Valley Spring-run Chinook (CVSC) are listed as threatened under the California and federal Endangered Species Acts, but how ocean fisheries affect CVSC is not routinely monitored or managed , largely because of data limitations. Most tag data for CVSC are from a hatchery program that may not sufficiently represent natural-origin fish in ocean and inland fishery recovery data. However, a discontinued tagging program for Butte Creek Wild Spring-run Chinook (BCWSC) provides for estimation of fishery impacts and maturation schedules for a limited set of years, which we compared with estimates for hatchery-origin fish for common years, while extending the hatchery-origin estimates over a wider time-frame. Additional scale-age data from BCWSC allow inferences about more recent maturation rates, conditional on harvest-rate estimates borrowed from other stocks. Overall, CVSC appear to experience low age-3 ocean fishery impact rates, but age-4 impact rates can be comparable to ocean harvest rates estimated for Sacramento River Fall Chinook. Tagging data from the years available indicate that ocean fisheries may reduce spawning run sizes  (all ages combined) by 40% to 60% during periods of high fishing effort. Effects of ocean fishing on spawner abundance are weaker in years of reduced fishing or for cohorts displaying earlier maturation. It appears that maturation rates of hatchery-origin CVSC may have increased (i.e., earlier maturation) over the full time-period examined, and there may be indications of increasing maturation rates for BCWSC as well.

The escapement objective used to manage fisheries for Sacramento River Fall Chinook (SRFC) Salmon was established in 1984. Despite substantial changes to the system and multiple calls to re-evaluate the objective, data and analytical limitations have slowed progress. Synthesizing the available information is further complicated by the different measurement scales employed by relevant studies. Here, I offer a modeling framework for integrating consideration of established hatchery spawning goals, natural-area production or habitat capacities measured at varying spatial scales, and policy decisions about what fraction of potential natural production is desired along with risk tolerance. The model allows evaluating how likely a potential escapement goal (measured at the currently-used scale of fall-run adults returning to both hatcheries and natural areas throughout the Sacramento River basin) is both to meet hatchery goals and to produce at least a specified fraction of potential natural production. The framework also incorporates consideration of forecasting and ocean harvest planning error into identifying a pre-season planning target and its probability of resulting in escapement at least as high as the goal. The model indicates that the low end of the current escapement goal range of 122,000 to 180,000 adults, if achieved, would be more likely than not to achieve hatchery goals while achieving around 50% of potential natural production. Realized escapement equal to the high end is modeled to be very likely to achieve hatchery goals, and likely to achieve around 75% of potential basin-wide natural production or around 60% of upper Sacramento River potential production. The model indicates diminishing returns from total adult SRFC escapements higher than about 300,000 adults. However, past performance of forecast and harvest-planning models suggest that a pre-season target higher than the ultimate escapement goal is needed to have even a 50% chance of achieving the escapement goal.

Objective: Density‐related information for landlocked fall Chinook Salmon Oncorhynchus tshawytscha shortly after first feeding is poorly understood. This study was undertaken to determine the effects of a range of rearing densities (low, intermediate, and high) on rearing performance and survival of newly feed‐trained juvenile landlocked fall Chinook Salmon. Methods: The fish were reared for 66 days in 1.8‐m (diameter) tanks with approximate volume of 2036 L at one of three loadings of approximately 2500, 5000, or 10,000 fish/tank. Result: The initial and final densities for each of the three loadings were 0.73 and 8.93, 1.45 and 16.41, and 2.90 and 26.86 kg/m3, respectively. At the end of the study, the specific growth rates were significantly lower, total lengths were significantly shorter, and feed conversion ratios were significantly greater in the fish from the highest‐density treatment relative to the fish in the other treatments. Percentage of weight gain, final weights, and condition factor were significantly reduced in fish from the highest‐density treatment relative those at the lowest density. There were no significant differences in any growth metrics between fish that were reared at the lowest and intermediate densities. The intermediate density (5000 fish/tank) produced intermediate results that did not significantly differ from either the highest or lowest densities. Mortality was not significantly different among the density treatments. Conclusion: An initial loading of 5000 fish in 1.8‐m (diameter) circular tanks, corresponding to initial and final densities of 1.45 and 16.41 kg/m3, respectively, is recommended to minimize the detrimental effects of density on newly feeding Chinook Salmon while maximizing their production in often limited hatchery space. Impact statementThe use of intermediate tank loadings of fall Chinook Salmon in 1.8‐m (diameter) circular tanks (corresponding to initial and final densities of 1.45 and 16.41 kg/m3, respectively) minimized the detrimental effects of rearing density on newly feeding salmon while maximizing Chinook Salmon production in limited hatchery space. [ABSTRACT FROM AUTHOR]

The entrainment and impingement of fish into water diversion infrastructure is one of the several factors contributing to their decline. Here, controlled experiments assessed the potential for a behavioral guidance device [a light-emitting diode (LED) light array] strobing at various spectra to reduce the entrainment of juvenile Chinook salmon (Oncorhynchus tshawytscha) into a water diversion pipe. Fish were tested during the day and night, and under control conditions (light off) and red, blue, and white spectra strobing at 2 Hz. Fish entrainment into the diversion pipe was evaluated. Results indicated greater entrainment at night compared to day. All trials at night with the LED light strobing had higher entrainment than the control, with blue and white spectra corresponding to greater entrainment than red spectra. During the day, the white spectra treatment was different from the red treatment, with lower entrainment. LED lights employed to repel migratory juvenile salmon away from water intake structures may be ineffectual but there is potential for the light to be used as an attractant to guide fish towards desirable features such as “safe” areas (bypass channels or fishways).

Recent articles from the Agricultural Experiment Station campuses and UC ANR's county offices, institutes and research and extension centers.

Conservation and management of culturally and economically important species rely on monitoring programs to provide accurate and robust estimates of population size. Rotary screw traps (RSTs) are often used to monitor populations of anadromous fish, including fall-run Chinook Salmon (Oncorhynchus tshawytscha) in California’s Central Valley. Abundance estimates from RST data depend on estimating a trap's efficiency via mark-recapture releases. Because efficiency estimates are highly variable and influenced by many factors, abundance estimates can be highly uncertain. An additional complication is the multiple accepted methods for how to apply a limited number of trap efficiency estimates, each from discrete time-periods, to a population’s downstream migration, which can span months. Yet, few studies have evaluated these different methods, particularly with long-term monitoring programs. We used 21 years of mark-recapture data and RST catch of juvenile fall-run Chinook Salmon on the Stanislaus River, California, to investigate factors associated with trap efficiency variability across years and mark-recapture releases. We compared annual abundance estimates across five methods that differed in treatment of trap efficiency (stratified versus modeled) and statistical approach (frequentist versus Bayesian) to assess the variability of estimates across methods, and to evaluate whether method affected trends in estimated abundance. Consistent with short-term studies, we observed negative associations between estimated trap efficiency and river discharge as well as fish size. Abundance estimates were robust across all methods, frequently having overlapping confidence intervals. Abundance trends, for the number of increases and decreases from year to year, did not differ across methods. Estimated juvenile abundances were significantly related to adult escapement counts, and the relationship did not depend on estimation method. Understanding the sources of uncertainty related to abundance estimates is necessary to ensure that high-quality estimates are used in life cycle and stock-recruitment modeling.

Connectivity among populations can have counteracting effects on population stability. Demographically, connectivity can rescue local populations but increase the synchrony across populations. Genetically, connectivity can counteract drift locally but homogenize genotypes across populations. Population independence and diversity underlies system-level buffering against environmental variability, termed the portfolio effect. The portfolio effect has declined in California fall-run Chinook salmon, possibly in part because of the trucking of juvenile hatchery-reared fish for downstream release, which reduces juvenile mortality but increases the connectivity between rivers. We use a dynamical population model to test whether this increased connectivity can explain the loss of the portfolio effect and quantify the relative demographic and genetic contributions to portfolio effect erosion. In the model, populations experience different within-population environmental conditions and the same time-variable ocean conditions, the response to which can depend on a quantitative genetic trait. We find that increased trucking for one population's hatchery can lead to a loss of the portfolio effect, with a system-level trade-off between increased average abundance and increased variability in abundance. This trade-off is much stronger when we include the effects of genetic homogenization than when we consider demographic synchronization alone. Therefore, genetic homogenization can outweigh demographic synchrony in determining the system-level effect of connectivity.

Accurate taxonomic identification is foundational for effective species monitoring and management. When visual identifications are infeasible or inaccurate, genetic approaches provide a reliable alternative. However, these approaches are sometimes less viable (e.g., need for near real‐time results, remote locations, funding concerns, molecular inexperience). In these situations, CRISPR‐based genetic tools can fill an unoccupied niche between real‐time, inexpensive, but error‐prone visual identification and more expensive or time‐consuming, but accurate genetic identification for taxonomic units that are difficult or impossible to visually identify. Herein, we use genomic data to develop CRISPR‐based SHERLOCK assays capable of rapidly (<1 h), accurately (94%–98% concordance between phenotypic and genotypic assignments), and sensitively (detects 1–10 DNA copies/reaction) distinguishing ESA‐listed Chinook salmon runs (winter‐ and spring‐run) from each other and from unlisted runs (fall‐ and late fall‐run) in California's Central Valley. The assays can be field deployable with minimally invasive mucus swabbing negating the need for DNA extraction (decreasing costs and labour), minimal and inexpensive equipment needs, and minimal training to conduct following assay development. This study provides a powerful genetic approach for a species of conservation concern that benefits from near real‐time management decision‐making but also serves as a precedent for transforming how conservation scientists and managers view genetic identification going forward. Once developed, CRISPR‐based tools can provide accurate, sensitive, and rapid results, potentially without the prohibitive need for expensive specialty equipment or extensive molecular training. Further adoption of this technology will have widespread value for the monitoring and protection of our natural resources. [ABSTRACT FROM AUTHOR]

A study was carried out on two important recreational fishing rivers in southern Chile, the Petrohué and the Puelo, to assess the population structure of the salmonid species inhabiting both rivers. Five river sectors were surveyed on four dates between April 2016 and February 2017. In the Petrohué River, 2400 fish were sampled (42.9% rainbow trout Oncorhynchus mykiss; 23.8% brown trout Salmo trutta, and 33.3% Chinook salmon Oncorhynchus tshawytscha), while in the Puelo River, 1972 fish were examined (51.6% rainbow trout; 30.4% brown trout and 18% Chinook salmon). Fry and fingerling stages accounted for the highest proportion of fish collected by electrofishing. In the Petrohué and Puelo rivers, rainbow trout fry and fingerlings represented 96.3 and 99.2% of the fish sampled, respectively; 96.8 and 97.1% in the case of brown trout, while for Chinook salmon, parr and pre-smolts represented 97% of the fish examined in the Petrohué River and 98.3% in the Puelo River. Rainbow and brown trout shared the same habitats and food items in both rivers, and the two oldest trout recorded 5+ and 6 + years. Parr and pre-smolt Chinook salmon were present mainly in the winter and spring seasons and were aged 1+ and 2+, respectively. There were no differences in the food items recorded from the juvenile fish sampled in both rivers. The mature, returning adult Chinook salmon aged between 1.5+ and 1.6+ years were devoid of food and were recorded over the autumn season with the highest abundance in the Petrohué River. The study did not identify any adverse competition or negative interactions among the three main salmonid species sharing the same habitat. [ABSTRACT FROM AUTHOR]

Central Valley spring-run Chinook Salmon (CVSC) are designated threatened by state and federal authorities. Although CVSC are caught in ocean fisheries, their harvest is not actively managed, because it is assumed that measures currently in place to protect endangered Sacramento River winter-run Chinook Salmon (SWRC) will also sufficiently protect CVSC. Recoveries of tags and genetically-identified CVSC suggest these fish have a more northerly distribution than SRWC. Further, escapement data and cohort reconstructions suggest that CVSC mature later than SRWC. Thus, regulations (time/area restrictions and minimum size limits) crafted to protect SRWC alone may not adequately protect CVSC; on the other hand, regulations to constrain impacts on Klamath River and California coastal Chinook Salmon populations may also reduce impacts on CVSC. Trends in CVSC escapement were deemed acceptable in recent status updates, but concerns remain because of the negative effects caused by recent drought and ocean conditions. Should more active management of CVC be desired, current options are limited. The most promising approach is based on estimating age-specific ocean fishing mortality rates by using cohort reconstructions applied to tagged Chinook Salmon that originate from the Feather River Hatchery. At a minimum, ocean fishing mortality rates could be monitored and compared to proxy thresholds. If reference harvest rates were established, harvest models could be developed to predict how CVSC would be affected by fishing regulations, similar to the way fall-run Chinook Salmon fisheries are evaluated. Abundance forecasts would require improved juvenile production data (e.g., from genetic sampling of juvenile emigrants), since sibling-based forecasts commonly used for fall-run Chinook Salmon would not be available in time for pre-season planning. It is unclear if ocean fishing mortality rate estimates derived from hatchery proxies for natural-origin fish are truly representative, but existing data do not demonstrate obvious differences in ocean distribution or size-at-age fish. Substantial new investments in tagging or sampling would be needed to directly estimate ocean fishing mortality rates for natural-origin CVSC. Establishing specific harvest targets or limits for CVSC requires an improved understanding of production throughout their life cycle through juvenile production estimates and long-term information on spawner age structure.

Tag effect studies are paramount in interpreting the results of survival studies. The objective of this study was to analyze the influence of tag implantation and tag burden on the survival, tag retention, growth, and wound healing of juvenile Chinook Salmon 7.8 ± 0.9 g initial weight. Fish were obtained from the Merced River Hatchery, held for 7 d, and then surgically implanted with Juvenile Salmon Acoustic Telemetry System (JSATS) SS300 dummy tags (0.3 g in air). Tag burden ranged from 2.9–4.8% (3.86 ± 0.43%, mean ± standard deviation). Weight and fork length were taken immediately before tag implantation. All fish (i.e., control and dummy-tagged) were also implanted with a visible implant alpha tag next to the dorsal insertion. Control and dummy-tagged fish were held in a single tank for 30 d. Any fish that died during the 30-d period were noted. At the end of the holding period, all fish were euthanized, weighed, measured, and necropsied. All dummy-tagged fish retained their dummy tag, and survival rates between the two groups were similar. Wound healing was also similar across the range of tag burdens analyzed. Specific growth rates, however, differed significantly between the two groups, with control fish growing at a rate of 1.08 ± 0.38% d− 1 compared to 0.55 ± 0.48 % d− 1 in dummy-tagged fish (P < 0.001). Tag burdens and specific growth rates for dummy-tagged fish (P = 0.961) did not correlate, nor did initial weight and specific growth rate for control (P = 0.363) or dummy-tagged (P = 0.983) fish. The cause of the decreased growth rate in dummy-tagged fish remains unknown. Determining the cause of decreased growth in tagged juvenile Chinook Salmon, and how that decreased growth may influence survival in the wild, should be investigated further.

Fluctuations in aggressive behavior of group‐living species can reflect social conflict and competition for resources faced by individuals throughout their lifespan and can negatively impact survival and reproduction. In marine mammals, where social interactions are difficult to observe, tooth rake marks can be used as an indicator of received aggression. Using 38 years of photographic data, we quantified the occurrence of tooth rake marks on wild resident killer whales (Orcinus orca), examining the effects of age, sex, and prey abundance on rake density. Our analysis revealed sex and age effects, with males exhibiting higher rake density than females and rake density declining significantly with age. Contrary to predictions, we observed an increase in rake density across the population as the abundance of their primary food resource, Chinook salmon (Oncorhynchus tshawytscha), increased. These results provide indirect evidence of fluctuations in received aggression from conspecifics across the lifespan of an individual, possibly reflecting changes in patterns of social conflict which may be mediated by resource abundance. Our findings highlight the need for further research to examine the fitness consequences of aggression in killer whales and to understand the proximate mechanisms by which resource abundance influences rates of aggression in the population. [ABSTRACT FROM AUTHOR]

Fish disease surveillance methods can be complicated and time consuming, which limits their value for timely intervention strategies on aquaculture farms. Novel molecular-based assays using droplet digital Polymerase Chain Reaction (ddPCR) can produce immediate results and enable high sample throughput with the ability to multiplex several targets using different fluorescent dyes. A ddPCR tetraplex assay was developed for priority salmon diseases for farmers in New Zealand including New Zealand Rickettsia -like organism 1 (NZ-RLO1), NZ-RLO2, Tenacibaculum maritimum , and Yersinia ruckeri. The limit of detection in singleplex and tetraplex assays was reached for most targets at 10−9 ng/μl with, respectively, NZ-RLO1 = 0.931 and 0.14 copies/μl, NZ-RLO2 = 0.162 and 0.21 copies/μl, T. maritimum = 0.345 and 0.93 copies/μl, while the limit of detection for Y. ruckeri was 10−8 with 1.0 copies/μl and 0.7 copies/μl. While specificity of primers was demonstrated in previous studies, we detected cross-reactivity of T. maritimum with some strains of Tenacibaculum dicentrarchi and Y. ruckeri with Serratia liquefaciens , respectively. The tetraplex assay was applied as part of a commercial fish disease surveillance program in New Zealand for 1 year to demonstrate the applicability of tetraplex tools for the salmonid aquaculture industry. [ABSTRACT FROM AUTHOR]

Fish disease surveillance methods can be complicated and time consuming, which limits their value for timely intervention strategies on aquaculture farms. Novel molecular-based assays using droplet digital Polymerase Chain Reaction (ddPCR) can produce immediate results and enable high sample throughput with the ability to multiplex several targets using different fluorescent dyes. A ddPCR tetraplex assay was developed for priority salmon diseases for farmers in New Zealand including New Zealand Rickettsia-like organism 1 (NZ-RLO1), NZ-RLO2, Tenacibaculum maritimum, and Yersinia ruckeri. The limit of detection in singleplex and tetraplex assays was reached for most targets at 10−9 ng/μl with, respectively, NZ-RLO1 = 0.931 and 0.14 copies/μl, NZ-RLO2 = 0.162 and 0.21 copies/μl, T. maritimum = 0.345 and 0.93 copies/μl, while the limit of detection for Y. ruckeri was 10−8 with 1.0 copies/μl and 0.7 copies/μl. While specificity of primers was demonstrated in previous studies, we detected cross-reactivity of T. maritimum with some strains of Tenacibaculum dicentrarchi and Y. ruckeri with Serratia liquefaciens, respectively. The tetraplex assay was applied as part of a commercial fish disease surveillance program in New Zealand for 1 year to demonstrate the applicability of tetraplex tools for the salmonid aquaculture industry.

Thermal exposure is a serious and growing challenge facing fish species worldwide. Chinook salmon (Oncorhynchus tshawytscha) living in the southern portion of their native range are particularly likely to encounter warmer water due to a confluence of factors. River alterations have increased the likelihood that juveniles will be exposed to warm water temperatures during their freshwater life stage, which can negatively impact survival, growth, and development and pose a threat to dwindling salmon populations. To better understand how acute thermal exposure affects the biology of salmon, we performed a transcriptional analysis of gill tissue from Chinook salmon juveniles reared at 12° and exposed acutely to water temperatures ranging from ideal to potentially lethal (12° to 25°). Reverse-transcribed RNA libraries were sequenced on the Illumina HiSeq2000 platform and a de novo reference transcriptome was created. Differentially expressed transcripts were annotated using Blast2GO and relevant gene clusters were identified. In addition to a high degree of downregulation of a wide range of genes, we found upregulation of genes involved in protein folding/rescue, protein degradation, cell death, oxidative stress, metabolism, inflammation/immunity, transcription/translation, ion transport, cell cycle/growth, cell signaling, cellular trafficking, and structure/cytoskeleton. These results demonstrate the complex multi-modal cellular response to thermal stress in juvenile salmon.

The Central Valley fall-run Chinook salmon (Oncorhynchus tshawytscha) is the dominant population complex supporting the California and Southern Oregon commercial salmon fishery. The stock is largely dominated by hatchery productionand has shown high variability in adult returns, suggesting that hatchery practices are critical to thelong-term sustainability of the fishery. We compiled information from numerous sources to synthesizetrends in the number, location, size, and timingof fall-run Chinook salmon released from the five Central Valley hatcheries between 1946 and 2012. Approximately 2 billion fish were released duringthis period, nearly half of which were released from the single federally operated hatchery. Juveniles have been planted off-site in the estuary with increasing frequency since the early 1980s, particularly by state-operated hatcheries. Approximately 78% of all releases occurred between January and June, including ~25% in April and ~20% in May. Release timing and size trends differed among hatcheries,and were correlated. For example, the Coleman and Nimbus hatcheries tended to release small fish (10 g, on average) later in the year. Moreover, sizes-at-release (by month) haveincreased since the 1980s, leading to the emergence of a new life-history type that now comprises nearly all of the estuary releases: springtime releases of large ocean-ready “advanced smolts.” We collapsed release timing and size data into a single index of life-history diversity and our results indicate a reduction in juvenile life-history diversity, with decreased variability in release number, timing, and size through time. Together, these results indicate a reduction in the diversity of life-history types represented in the fall-run Chinook salmon hatchery releases, which may be a factor that contributes to the decreased stability of the Central Valley fall-run Chinook salmon stock complex.

Snorkel surveys were conducted on the Sacramento River to investigate the relative importance of microhabitat and mesohabitat scales on the abundance of young of the year (YOY) Chinook salmon (Oncorhynchus tshawytscha), while taking into account temporal and segment-scale spatial variations. Sites, with 13 different mesohabitat types, were sampled nine times from April to September in 1996. Both the sites and cells within the sites were classified by cover type. The analyses revealed that the microhabitat scale, specifically woody cover, best explained YOY abundance, versus the mesohabitat scale. Temporal and large-scale spatial patterns reflect the timing and abundance of different runs of Chinook salmon, while microhabitat scale patterns reflect cover preference of YOY Chinook salmon. [ABSTRACT FROM AUTHOR]

The habitat complexity of a riverine ecosystem influences the bioenergetics of drift feeding fish. We coupled hydrodynamic and bioenergetic models to assess the influence of habitat complexity generated by large woody debris (LWD) on the growth potential of juvenile Chinook salmon (Oncorhynchus tshawytscha) in a river that lacked large wood. Simulations indicated how LWD diversified the flow field, creating pronounced velocity gradients, which enhanced fish feeding and resting activities at the sub-meter scale. Fluid drag created by individual wood structures increased under higher wood loading amounts, leading to a 5-19% reduction in the reach-averaged velocity. The reach-scale growth potential was asymptotically related to wood loading, suggesting that the river became saturated with LWD and additional loading would produce minimal benefit for the configurations we simulated. In the scenario we analyzed for illustration, LWD additions could quadruple the potential growth area available before that limit was reached for the configurations selected for demonstration. Wood depletion in the world's rivers has been documented extensively, leading to widespread attempts by river managers to reverse this trend by adding wood to simplified aquatic habitats. However, systematic prediction of the effects of wood on fish growth has not been previously accomplished. We offer a quantitative approach for assessing the influence of wood on habitat potential for fish growth at the microhabitat and reach-scales. © 2014 Elsevier B.V.

The habitat complexity of a riverine ecosystem influences the bioenergetics of drift feeding fish. We coupled hydrodynamic and bioenergetic models to assess the influence of habitat complexity generated by large woody debris (LWD) on the growth potential of juvenile Chinook salmon (Oncorhynchus tshawytscha) in a river that lacked large wood. Simulations indicated how LWD diversified the flow field, creating pronounced velocity gradients, which enhanced fish feeding and resting activities at the sub-meter scale. Fluid drag created by individual wood structures increased under higher wood loading amounts, leading to a 5-19% reduction in the reach-averaged velocity. The reach-scale growth potential was asymptotically related to wood loading, suggesting that the river became saturated with LWD and additional loading would produce minimal benefit for the configurations we simulated. In the scenario we analyzed for illustration, LWD additions could quadruple the potential growth area available before that limit was reached for the configurations selected for demonstration. Wood depletion in the world's rivers has been documented extensively, leading to widespread attempts by river managers to reverse this trend by adding wood to simplified aquatic habitats. However, systematic prediction of the effects of wood on fish growth has not been previously accomplished. We offer a quantitative approach for assessing the influence of wood on habitat potential for fish growth at the microhabitat and reach-scales. © 2014 Elsevier B.V.

A primary goal of the Central Valley Project Improvement Act is to at least double natural production of Chinook salmon (Oncorhynchus tshawytscha), in California Central Valley (CV) streams on a sustainable basis. Achievement relies on restoration actions that involve both discharge (e.g., dam releases) and non-discharge (e.g., gravel augmentation, screening) components. Annual adult and juvenile abundance estimates for individual watersheds must be tracked to assess effectiveness of individual actions. However, to date, no substantial efforts have been taken to demonstrate success or deficiencies of their implementations. A major challenge in interpreting time series of counts at any one life stage is that they reflect the cumulative effects of both freshwater and marine factors over the full life cycle. To address this issue, we developed a conceptual framework based on ratios of the abundance of consecutive CV fall-run Chinook salmon life stages and how variation in these ratios tracks key independent variables during the freshwater portion of the life cycle. Model validation with several case studies shows that estimates of previous stage class production correlate well with estimated individuals produced in the next class, indicating that transition rates tend to vary within a constrained range, and that monitoring programs generate abundance estimates whose errors are small enough not to swamp out the underlying signal. When selected environmental parameters were added to demonstration models, abundance estimates were more closely modeled and several tested relationships between environmental drivers and life-stage transition rates proved consistent across watersheds where data were available. Results from this generalized life-stage conceptual model suggest a potential framework for tracking the success of actions meant to improve survival for a given life stage within an individual stream and for determining how successive stages respond to these changes. Though examples are provided for CV Chinook salmon, these concepts can be applied wherever migratory salmonid populations and associated environmental data are being adequately monitored.

Scientists have identified 117 new single nucleotide polymorphisms (SNPs) for detecting the genetic relatedness of Chinook salmon.The most basic genetic variation possible, a SNP (pronounced “snip”) refers to a single difference in one base pair of a nucleotide. The major outcome of this project is the identification of an optimal panel of 96 SNPs that is capable of detecting both the parentage of hatchery-born Chinook and the origin (i.e., stock) of Chinook caught off California and Oregon.SNPs are fast becoming the tool of choice for population genetics studies of nonmodel organisms such as Pacific salmon, because of their low rates of error (mutation) and high resolving power. The detailed resolution of SNPs is particularly well suited for studies of anadromous fishes such as Chinook salmon (Oncorhynchus tshawytscha), as their fidelity to their natal rivers leads to a hierarchical population structure. This project demonstrates applications and advantages of SNP markers for California’s most commercially important salmon species.

The state of the Chinook salmon (Oncorhynchus tshawytscha) fishery in California is imperiled. One of the proposed mechanisms for recent population declines and fisheries closures is environmental variation having deleterious effects on prey availability and the ocean survival of Sacramento River fall Chinook (Lindley et al. 2009). To address this hypothesis, we analyzed collaborative fisheries research data (stomach samples obtained from commercial and recreational fisherman) on Chinook salmon diet in central California during the early-mid 1980s and mid 2000s. We compared this information with historic diet records for this population from 1955. Salmon diet composition changed significantly through time, with a decline in diet diversity. Specifically, previously important prey groups including juvenile rockfish (Sebastes spp.), krill (Euphausiidae), Pacific herring (Clupea pallesi) and market squid (Loligo opalsecens) were either greatly reduced or disappeared from the diet altogether. Conversely, Pacific sardine (Sardinops sagax), conspicuously absent from the diet (and environment) since the 1950s, became the second most important prey item in the 2000s. Northern anchovy (Engraulis mordax) remains an important prey item. The strongest correlation between salmon diet and environmental conditions was for local SST for all years in the study between 1955-2007. In the early 1980s, SST best explained salmon diet composition. While relationships were not significant in the mid 2000s, likely due to the short time period sampled, upwelling or the NPGO were the best descriptors of salmon diet variation. These physical pressure-state indicators have exhibited increasing trends and increasing variability through time and are indicative of the changing climate. Finally, we decomposed multiple prey variables into a univariate annual index and thus compared diet variation with the Sacramento Index (SI) of Chinook ocean abundance. We found a relationship between diet and the SI lagged by 2 years, potentially an indication of prey availability experienced by smolts after ocean entry (Figure 5). Collaborative fisheries research offers a means to track variation in salmonid diet with implications for understanding the connections between environmental variation, salmon survival, and declining fisheries in California.

Considerable resources have been invested in ecological restoration projects across the globe to restore ecosystem integrity. Restoration strategies are often diverse and have been met with mixed success. In this article, we describe the Chinook salmon (Oncorhynchus tshawytscha) decision‐support models developed by the Central Valley Project Improvement Act Science Integration Team as part of a larger structured decision‐making effort aimed at maximizing natural adult production of Chinook salmon in California's Central Valley, the United States. We then describe the decision‐analytic tools the stakeholder group used to solve the models and explore model results, including stochastic dynamic programming, forward simulation, proportional scoring, relative loss, expected value of perfect information, response profile analyses, and indifference curves. Using these tools, the stakeholder group was able to develop and evaluate restoration strategies for multiple Chinook salmon runs simultaneously, a first for the restoration program. We found that actions targeted at one run were detrimental to others, which was unexpected. Furthermore, information uncovered during this process was used to direct efforts towards targeted research/monitoring to reduce critical uncertainties in salmon demographic rates and make better restoration decisions moving forward. The decision sciences have established a wide range of analytical tools and approaches to simplify complex problems into key components, and we believe the concepts described in this article are of great interest and can be applied by many restoration practitioners that undoubtedly face similar difficulties when implementing restoration strategies for complex systems. [ABSTRACT FROM AUTHOR]

Decline in size‐at‐age of Chinook Salmon (Oncorhynchus tshawytscha) has been observed for many populations across the entire Northeast Pacific Ocean, and identifying external drivers of this decline is important for sustainable management of these ecologically, economically, and culturally valuable resources. We assessed size‐at‐age of 96,939 Chinook Salmon sampled in the Fraser River watershed (Canada) from 1969 to 2017. A broad decline in size‐at‐age was confirmed across all population aggregates of Fraser River Chinook Salmon, in particular since year 2000. By developing a novel probability‐based approach to calculate age‐ and year‐specific growth rates for Fraser River Chinook Salmon and relating growth rates to environmental conditions in specific years through a machine learning method (boosted regression trees), we were able to disentangle multi‐year effects on size‐at‐age and thus identify environmental factors that were most related to the observed size‐at‐age of Chinook Salmon. Among 10 selected environmental variables, ocean salinity at Entrance Island in spring, the Aleutian Low Pressure Index and the North Pacific Current Bifurcation Index were consistently identified as important contributors for four of the seven age and population aggregate combinations. These top environmental contributors could be incorporated into future stock assessment and forecast models to improve Chinook Salmon fisheries management under climate change. [ABSTRACT FROM AUTHOR]

Astaxanthin (Ax), the main carotenoid responsible for the distinct red flesh color in salmonids (Oncorhynchus, Salvelinus, Salmo, and Parahucho), is added to the diet of farmed fish at a substantial cost. Despite the great economical value for the salmon industry, the key molecular mechanisms involved in the regulation of muscle coloration are poorly understood. Chinook salmon (Oncorhynchus tshawytscha) represent an ideal model to study flesh coloration because they exhibit a distinct color polymorphism responsible for two color morphs, white and red flesh pigmented fish. This study was designed to identify the molecular basis for the development of red and white coloration of fish reared under the same experimental conditions and to better understand the absorption mechanism of Ax in salmonids. Pyloric caeca, liver, and muscle of both groups (n = 6 each) were selected as the most likely critical target organs to be involved respectively in the intestinal uptake, metabolism, and retention of Ax. Difference in the transcriptome profile of each tissue using next-generation sequencing technology was conducted. Ten KEGG pathways were significantly enriched for differentially expressed genes between red and white salmon pylorus tissue, while none for the transcriptome profile in the other two tissues. Differential expressed gene (DE) analyses showed that there were relatively few differences in muscle (31 DE genes, p < 0.05) and liver (43 DE genes, p < 0.05) of white and red Chinook salmon compared approximately 1125 DE genes characterized in the pylorus tissue, with several linked to Ax binding ability, absorption, and metabolism. [ABSTRACT FROM AUTHOR]

Pumping at the water export facilities in the southern Sacramento-San Joaquin Delta kills fish at and near the associated fish-salvage facilities. Correlative analyses of salvage counts with population indices have failed to provide quantitative estimates of the magnitude of this mortality. I estimated the proportional losses of Sacramento River Chinook salmon (Oncorhynchus tshawytscha) and delta smelt (Hypomesus transpacificus) to place these losses in a population context. The estimate for salmon was based on recoveries of tagged smolts released in the upper Sacramento River basin, and recovered at the fish-salvage facilities in the south Delta and in a trawling program in the western Delta. The proportion of fish salvaged increased with export flow, with a mean value around 10% at the highest export flows recorded. Mortality was around 10% if pre-salvage losses were about 80%, but this value is nearly unconstrained. Losses of adult delta smelt in winter and young delta smelt in spring were estimated from salvage data (adults) corrected for estimated pre-salvage survival, or from trawl data in the southern Delta (young). These losses were divided by population size and accumulated over the respective seasons. Losses of adult delta smelt were 1–50% (median 15%) although the highest value may have been biased upward. Daily losses of larvae and juveniles were 0–8%, and seasonal losses accumulated were 0–25% (median 13%). The effect of these losses on population abundance was obscured by subsequent 50-fold variability in survival from summer to fall.

Protected evolutionarily significant units (ESUs) of salmonids require objective and measurable criteria for guiding their recovery. In this report, we develop a method for assessing population viability and two ways to integrate these population-level assessments into an assessment of ESU viability. Population viability is assessed with quantitative extinction models or criteria relating to population size, population growth rate, the occurrence of catastrophic declines, and the degree of hatchery influence. ESU viability is assessed by examining the number and distribution of viable populations across the landscape and their proximity to sources of catastrophic disturbance.Central Valley spring-run and winter-run Chinook salmon ESUs are not currently viable, according to the criteria-based assessment. In both ESUs, extant populations may be at low risk of extinction, but these populations represent a small portion of the historical ESUs, and are vulnerable to catastrophic disturbance. The winter-run Chinook salmon ESU, in the extreme case, is represented by a single population that spawns outside of its historical spawning range. We are unable to assess the status of the Central Valley steelhead ESU with our framework because almost all of its roughly 80 populations are classified as data deficient. The few exceptions are those populations with a closely associated hatchery, and the naturally-spawning fish in these streams are at high risk of extinction. Population monitoring in this ESU is urgently needed.Global and regional climate change poses an additional risk to the survival of salmonids in the Central Valley. A literature review suggests that by 2100, mean summer temperatures in the Central Valley region may increase by 2-8°C, precipitation will likely shift to more rain and less snow, with significant declines in total precipitation possible, and hydrographs will likely change, especially the the southern Sierra Nevada mountains. Warming at the lower end of the predicted range may allow spring-run Chinook salmon to persist in some streams, while making some currently utilized habitat inhospitable. At the upper end of the range of predicted warming, very little spring-run Chinook salmon habitat is expected to remain suitable.In spite of the precarious position of Central Valley salmonid ESUs, there are prospects for greatly improving their viability. Recovering Central Valley ESUs may require re-establishing populations where historical populations have been extirpated (e.g., upstream of major dams). Such major efforts should be focused on those watersheds that offer the best possibility of providing suitable habitat in a warmer future.

In the fall of 1980, a spawning escapement study was initiated on the West Branch Mill Creek, a major fall chinook salmon (Oncorhynchus tshawytscha) tributary of the Smith River, Del Norte County, California. The purpose of the study was to estimate the relative abundance of spawning fall chinook in a defined study section over a period of more than 20 years as habitat changed. An age composition of the spawning population was also determined. The 23-year analysis of the 2.7 kilometer (1.7 mile) study section of the West Branch Mill Creek provided “minimum” chinook spawning estimates from 1980—2002. The annual spawning chinook estimates ranged from 31–361 total chinook. The 23-year mean for chinook spawners was 151 fish (89 fish per mile). The spawner sampling verified that three distinct chinook runs exist for fall chinook entering the West Branch Mill Creek. Scale sample analysis was used to determine the age composition of West Branch Mill Creek chinook spawners. Age analysis for 22 years (1980 excluded) showed that the overall percentages for female spawners was 53% (4-year olds), 38% (3-year olds), and 9% (5-year olds). The age composition of male spawners showed a high degree of variability throughout the study. Male chinook of age 2, 3 and 4 were dominant annually, but 5- and 6-year-old fish were present in most spawning seasons. All chinook carcasses from which scales were collected were also measured for length (over 1240 samples in 22 years). Decreases in mean length were documented for all age classes for each of the El Niño episodes that occurred during the study (1982–84; 1992–93; 1997–98). The decreases in mean length appeared to carry forward for each cohort’s age class. The total number of chinook redds was tabulated by counting “fresh” redds during weekly spawning surveys. The mean number of redds was 117 for the 23-year period with a mean of 0.9 redds per adult salmon or 1.8 redds per female. The abundance of chinook spawners dramatically increased during the last three years of the study, probably a reflection of improved ocean survival during the recent Pacific Ocean Decadal Oscillation phenomenon.,

Wild juvenile chinook salmon appear to spend an extended period of time in the estuary of the Smith River, California. Based on recovery patterns of freeze-branded juveniles released from June through August, 2000, mean estuarine residence time ranged from 8.3-13.8 d during June and July, and increased to an estimated 38.3 d for fish marked and released in August.  Based on computer simulations of the process of estuarine entrance and exit, and on evidence of estuarine growth of juvenile Chinook salmon, it appears that these estimates of mean residence times were negatively biased. True mean residence times calculated in other studies may also be considerably longer than those estimated using existing published methods.Rowdy Creek Hatchery rears large numbers of chinook salmon and many are released as fingerlings into the Smith River estuary during May–June. In 1999, about 13% of Rowdy Creek fingerlings were marked with a left maxillary clip, whereas in 2000 about 22% of fingerlings were marked with an adipose fin clip and coded wire tag. Based on collection and examination of juvenile chinook salmon in the Smith River estuary, following release of these hatchery fish, it appears that the majority of chinook salmon juveniles are still produced by wild spawning fish rather than by Rowdy Creek Hatchery. Maximum estimated daily percentages of hatchery juveniles were 33% in 1999 and 31% during 2000. Within 30 days following releases in 1999 and 2000, the estimated percentages of hatchery fish present in the estuary had dropped to 15% and 9%, respectively. Together, these estimates of estuarine residence time and percentages of hatchery fish suggest that the Smith River estuary may be an important habitat for wild juvenile chinook salmon.

The collapse of iconic, keystone populations of sockeye (Oncorhynchus nerka) and Chinook (Oncorhynchus tshawytscha) salmon in the Northeast Pacific is of great concern. It is thought that infectious disease may contribute to declines, but little is known about viruses endemic to Pacific salmon. Metatranscriptomic sequencing and surveillance of dead and moribund cultured Chinook salmon revealed a novel arenavirus, reovirus and nidovirus. Sequencing revealed two different arenavirus variants which each infect wild Chinook and sockeye salmon. In situ hybridisation localised arenavirus mostly to blood cells. Population surveys of >6000 wild juvenile Chinook and sockeye salmon showed divergent distributions of viruses, implying different epidemiological processes. The discovery in dead and dying farmed salmon of previously unrecognised viruses that are also widely distributed in wild salmon, emphasizes the potential role that viral disease may play in the population dynamics of wild fish stocks, and the threat that these viruses may pose to aquaculture.

Sex-biased predation, a predator's bias for one prey sex over the other, can have important demographic impacts on prey species of conservation concern. Yet, it is difficult to measure in the wild. Molecular scatology has been used to indirectly determine the proportion of prey items consumed in the diet, and it may be possible to apply similar approaches to determine the sex-biased consumption of prey items. We developed a molecular method to indirectly examine sex-specific predation employing scat, focusing on predator–prey interactions between Chinook salmon (Oncorhynchus tshawytscha) and harbor seals (Phoca vitulina richardii). We established that the proportions of male and female Chinook DNA can be determined in a controlled sample by measuring a Y-linked marker, growth hormone pseudogene, using qPCR. We then applied the assay to harbor seal scat samples. Although the assay amplified in 83% of scat samples, 27% of samples quantified had an estimated male proportion > 1, which may have been due to a lack of robustness of the PCR assay in samples. Lastly, we constructed a biomass calibration curve to determine whether DNA measurements could estimate the proportions of male and female biomass consumed. The calibration curve was skewed by high male DNA density precluding our ability to quantify the relative amounts. We demonstrated that nuclear prey markers can be amplified in predator scat, however, contamination and extreme DNA density differences between the prey sexes may pose practical difficulties to estimate the relative amounts of male to female biomass consumed. [ABSTRACT FROM AUTHOR]

Estuaries provide a mosaic of vital nursery habitat types for threatened Chinook salmon (Oncorhynchus tshawytscha) by promoting an ecological portfolio effect, whereby multiple habitat types and networked environmental strata maximize foraging opportunities for out-migrating Chinook salmon by varying the abundance and composition of prey through space and time. To study this portfolio effect, the foraging capacity of five estuarine habitat types was evaluated within the Nisqually River Delta (Puget Sound, Washington, USA). Within each habitat type, invertebrate prey resources were sampled from the terrestrial, aquatic, benthic, and epifaunal environmental strata and compared with juvenile Chinook salmon diets from corresponding sampling events. The estuarine emergent salt marsh supplied twice as much aquatic prey biomass as any other habitat type (720–5523 mg/m3), followed by the mudflat (246–2543 mg/m3) and eelgrass (Zostera marina; 141–2694 mg/m3). Despite some evidence for selectivity, juvenile Chinook salmon diets exhibited substantial compositional overlap, especially when compared with among-habitat differences in available prey resources. Fish that were captured in the emergent salt marsh, mudflat, and eelgrass habitat types consumed aquatic crustaceans such as mysids, while fish captured upriver in freshwater tidal forest and transitional emergent marsh habitat types ate a higher proportion of adult and larval insects. The availability and consumption of greater quantities of energy-poor crustaceans in the salt marsh and lower quantities of energy-rich insects upriver highlights a quantity-for-quality trade-off among estuarine habitat types. Overall results indicate that the timing, productivity, and diversity of prey across multiple habitat types and environmental strata determine an estuary's capacity to support foraging for multiple life history strategies, size classes, and cohorts of juvenile Chinook salmon. [ABSTRACT FROM AUTHOR]

Colour vision is mediated by the expression of different visual pigments in photoreceptors of the vertebrate retina. Each visual pigment is a complex of a protein (opsin) and a vitamin A chromophore; alterations to either component affects visual pigment absorbance and, potentially, the visual capabilities of an animal. Many species of fish undergo changes in opsin expression during retinal development. In the case of salmonid fishes the single cone photoreceptors undergo a switch in opsin expression from SWS1 (ultraviolet sensitive) to SWS2 (blue‐light sensitive) starting at the yolk‐sac alevin stage, around the time when they first experience light. Whether light may initiate this event or produce a plastic response in the various photoreceptors is unknown. In this study, Chinook salmon Oncorhynchus tshawytscha were exposed to light from the embryonic (5 days prior to hatching) into the yolk sac alevin (25 days post hatching) stage and the spectral phenotype of photoreceptors assessed with respect to that of unexposed controls by in situ hybridization with opsin riboprobes. Light exposure did not change the spectral phenotype of photoreceptors, their overall morphology or spatial arrangement. These results concur with those from a variety of fish species and suggest that plasticity in photoreceptor spectral phenotype via changes in opsin expression may not be a widespread occurrence among teleosts. [ABSTRACT FROM AUTHOR]

Migration patterns of juvenile Columbia River Chinook salmon (Oncorhynchus tshawytscha) differ among stocks and life history types, creating diverse marine distributions of these fish. This results in different stocks being subject to different ocean conditions during their first summer of marine residence, a time that is critical for their survival. Understanding their early marine distributions, and the conditions that affect their survival, may enhance conservation efforts for these stocks, many of which are protected under the Endangered Species Act. We analyzed juvenile Chinook salmon samples collected in trawls made from 2011 to 2015 off the southeastern (SE) Alaskan panhandle, and off the coasts of Washington and Oregon. We used genetic stock identification techniques to estimate stock proportions of juvenile Chinook salmon in each of these areas. Results indicated that most juvenile Chinook salmon in our SE Alaska coast study area in July originate from Columbia River spring-run stocks. We found a significant relationship in catch per unit effort (CPUE) over all stocks between the SE Alaska and the Washington and Oregon coast samples. In 2011, CPUE for Columbia River spring-run stocks for the SE Alaska coast was lower than for the Washington and Oregon coast, suggesting a differing level of marine mortality that year. We also found a significant relationship between juvenile CPUE of interior Columbia River spring-run stocks off the SE Alaska coast and adult counts at Bonneville Dam two years later. Our results provide marine life history, performance and survival information that supports management and recovery efforts for Columbia River Chinook salmon. [ABSTRACT FROM AUTHOR]

Featured Application: Using autonomous underwater vehicles equipped with telemetry-based payload control to locate marine fish tagged with acoustic transmitters. An autonomous underwater vehicle (AUV) under payload control (PC) was used to map the movements of juvenile Chinook salmon (Oncorhynchus tshawytscha) tagged with acoustic transmitters. After detecting a tag, the AUV deviated from its pre-programmed route and performed a maneuver designed to enhance the location estimate of the fish and to move closer to collect proximal environmental data. Nineteen fish were released into marine waters of southeastern Alaska. Seven missions with concurrent AUV and vessel-based surveys were conducted with two to nine fish present in the area per mission. The AUV was able to repeatedly detect and estimate the location of the fish, even when multiple individuals were present. Although less effective at detecting the fish, location estimates from the vessel-based surveys helped verify the veracity of the AUV data. All of the fish left the area within 48 h of release. Most fish exhibited localized movements (milling behavior) before leaving the area. Dispersal rates calculated for the fish suggest that error associated with the location estimates was minimal. The average movement rate was 0.62 body length per second and was comparable to marine movement rates reported for other Chinook salmon stocks. These results suggest that AUV-based payload control can provide an effective method for mapping the movements of marine fish. [ABSTRACT FROM AUTHOR]

Abstract Understanding how rearing environments influence the stress response is relevant to many fish management practices. This is particularly relevant in aquaculture, where it is important to be able to minimize the effects of stress to enhance animal wellbeing. The stress response is also interesting from a basic science perspective, where it is important to understand how environmental differences can influence phenotypic traits and the physiological reaction to stressors. We tested the hypothesis that rearing fish in a more complex environment would reduce their stress response when presented with stressors. Specifically, we tested for the effect of structure in rearing tanks on the stress response of juvenile Chinook Salmon (Oncorhynchus tshawytscha) exposed to a handling and crowding stressor, something like hatchery fish might experience during transportation to new locations. For both rearing treatments (with and without structure), we compared fish that were subjected to the stressor to fish sampled from the respective rearing tank as the control. For the stressed treatment, we subjected fish to net capture followed by three hours in lowered water levels in a novel tank and then moved to a second novel holding tank. This process was designed to mimic typical stressors fish may experience at a hatchery. We analyzed plasma collected before the start of the stressor, during the stressor, and throughout 20 h post-stressor for cortisol in both stressed and unstressed fish. For both rearing treatments, fish that experienced the stressor had elevated plasma cortisol compared to control fish. However, the cortisol levels of fish in the stressed treatment reared with structure were significantly less than fish reared without structure. Additionally, plasma cortisol levels in structure-reared fish returned to baseline by 20 h post-stress while fish reared without structure had not fully recovered. Our findings suggest that increasing complexity of the rearing environment might be advantageous as a way of minimizing effects of handling-type stressors. Highlights • Critical test of the significance of rearing conditions on the stress response • Verification of physiological stress from routine handling and management practices • Lower cortisol in fish reared in a complex environment, highlighting potential mechanism affecting survival of stocked fish • Realistic structure for standard hatchery production to improve fish quality and survival [ABSTRACT FROM AUTHOR]

Abstract Microplastics are a significant issue in the world's oceans. These small plastic particles (<5 mm in size) are becoming globally ubiquitous in the marine environment and are ingested by various fish species. Here we investigate the incidence of microplastics in juvenile Chinook salmon and their nearshore marine environments on the east coast of Vancouver Island, British Columbia. We completed a series of beach seines, plankton tows and sediment cores in nearshore areas of importance to juvenile salmon. Microplastics were extracted from fish, water and sediment samples and concentrations were quantified. Microplastics analysis, consisting predominantly of fibrous plastics, showed juvenile Chinook salmon contained 1.2 ± 1.4 (SD) microplastics per individual while water and sediment samples had 659.9 ± 520.9 microplastics m−3 and 60.2 ± 63.4 microplastics kg−1 dry weight, respectively. We found no differences in microplastic concentrations in juvenile Chinook and water samples among sites but observed significantly higher concentrations in sediment at the Deep Bay site compared to Nanaimo and Cowichan Bay sites. Chinook microplastic concentrations were relatively low compared to literature values and, given the size and type of microplastics we observed, are unlikely to represent an immediate threat to fish in this area. However, microplastics less than 100 μm in size were not included in the study and may represent a greater threat due to their ability to translocate through tissues. Graphical abstract Image Highlights • Microplastics were found in juvenile Chinook salmon. • Greater than 90% of plastics identified were fibres. • There were no correlations between fish and environmental plastic concentrations. • More studies needed to fully determine risk to juvenile salmon. Microplastics were found in juvenile Chinook salmon and their nearshore environments during a critical time in their lifecycle. [ABSTRACT FROM AUTHOR]

When fish perceive stressful scenarios, their hypothalamus-pituitary-interrenal axis is activated resulting in the release of corticotropin releasing hormone, adrenocorticotropic hormone (ACTH), and finally cortisol. The physiologic stress response of fish has most often been linked to the reduced performance of the immune system, with a few exceptions where the immune system is activated. In this report, we tested the hypothesis that oxidative burst activity levels in juvenile Chinook salmon ( Oncorhynchus tshawytscha ) are altered when the fish is presented with a stressor. Fish were subjected to a stressor for 3 h and then allowed to recover for 20 h following the stressor. Plasma and spleens were collected from euthanized fish before the stressor, at the end of a 3 h stressor, and 23 h after the start of the experiment. Plasma was held at −80 °C until cortisol radioimmunoassay analysis was performed to confirm stress. Spleens were held in Dulbecco's Modified Eagle Medium overnight and analyzed the day following collection. Oxidative burst activity was measured in splenic leukocytes after being stimulated with phorbol 12-myristate 13-acetate. We found a significant increase in activated oxidative burst from fish subjected to the stressor as compared to unstressed fish. Speculation is given to ACTH being the leukocyte priming agent in this experiment rather than the cortisol itself. [ABSTRACT FROM AUTHOR]

Spinal abnormalities are common in farmed Chinook Salmon in New Zealand. We report spinal abnormalities in adult Chinook salmon which were predominantly hatchery reared and released as smolts and which we term free-living. We compare these to rates seen in farmed New Zealand salmon. 101 free-living adult salmon were radiographically assessed for spinal curvatures (lordosis, kyphosis, scoliosis; LKS) and other vertebral abnormalities. Severity of abnormality was assessed on a three-point scale. Abnormal vertebral bodies were detected in 88.1% of free-living salmon. Spinal curvatures were the most common abnormality type with 83.2% of fish showing this abnormality but only one free-living Chinook had LKS of severity greater than 1. Farmed Chinook salmon are reported to have LKS rates of 29% with 18% of LKS abnormalities of severity greater than 1. These results suggest that free-living Chinook salmon frequently develop spinal abnormalities, but these abnormalities are less severe than those observed in farmed salmon. [ABSTRACT FROM AUTHOR]

Association with physical structure or conspecifics can impact individual growth and survival. The necessity and strength of these associations changes with environmental conditions and ontogeny, acting in concert or opposition to influence an individual's behavior and ultimate success. We conducted a field experiment on the San Joaquin River, California, with juvenile Chinook salmon (Oncorhynchus tshawytscha) to test hypotheses related to the impacts of physical structure proximity and environmental and ontogenetic change on aggregating behavior of a migratory fish. We created orthogonal combinations of structural cover, turbidity, and juvenile Chinook salmon size and density by manipulating the location of artificial structure within net pens at three sites along the lower river and recorded observations of juvenile salmon swimming in aggregations with underwater video cameras. We selected the most parsimonious generalized linear mixed effects model via Akaike Information Criteria to analyze the effects of structure proximity, turbidity, and salmon size and density on aggregating behavior. The proportion of our observations composed of fish in aggregation increased significantly when fish were >3.5 m from structure; the strength of this effect declined significantly as turbidity, fish length, or fish density increased. We observed a significant decline in aggregation behavior when turbidity increased from 0.5 to 8.5 NTU and fish were more than 3.5 m from physical structure. Turbidity had minimal impact on behavior of fish within 1 m of structure. The proportion of our observations composed of fish in aggregation increased significantly when mean fish fork length increased from 45 mm to 80 mm, or fish density increased from ~0.2 n/m² to 3.5 n/m². Collectively, these results highlight how changes in the physical environment (i.e., structure and turbidity) and ontogeny interactively affect the frequency at which juvenile salmon swim in aggregation. [ABSTRACT FROM AUTHOR]

Spatial variation in fish densities across river networks suggests that the influence of food and habitat resources on assemblages varies greatly throughout watersheds. Conceptual models predict that in situ primary production should vary with river characteristics, but the influence of autochthonous resource availability on the capacity for river reaches to support fish is poorly understood. We estimated primary production throughout the South Fork and Middle Fork of the John Day River, Oregon, by measuring diel cycles in dissolved oxygen (DO) during July 2013. Using these data, we (1) evaluated the extent to which juvenile salmonid abundance and resource limitation correlated with areas of high gross primary production (GPP), (2) developed models to predict GPP from both site-level measurements and remotely sensed data, and (3) made predictions of GPP across the entirety of theMiddle Fork John Day River (MFJD) network and assessed the utility of these spatially continuous predictions for describing variation fish densities at broad scales. We produced reliable estimates of GPP at sites where DO loggers were deployed using measurements of solar exposure, water temperature, and conductivity measured at each site, as well as surrogates for these data estimated from remote sensing data sources. Estimates of GPP across fish sampling sites explained, on average, 58-63% of the variation in juvenile salmonid densities during the summer sampling period, and 51-83% during the fall sampling period, while continuous network predictions of GPP explained 44% of the variation in fish densities across 29 km of the MFJD. Further, GPP explained nearly half of the variation in juvenile steelhead dietary resource limitation, as inferred from bioenergetics modeling results. These results comprise a first effort at quantifying variation in autochthonous production across an entire river network and, importantly, provide a much-needed food-web context for guiding more effective fish and habitat management. [ABSTRACT FROM AUTHOR]