Interannual variability in the feeding and condition of subyearling Chinook salmon off Oregon and Washington in relation to fluctuating ocean conditions

Chinook salmon (Oncorhynchus tshawytscha) is one of several economically‐important species of salmon found in the Northeast Pacific Ocean. The first months at sea are believed to be the most critical for salmon survival, with the highest rate of mortality occurring during this period. In the present study, we examined interannual diet composition and body condition trends for late‐summer subyearling Chinook salmon caught off Oregon and Washington from 1998 to 2012. Interannual variability was observed in juvenile salmon diet composition by weight of prey consumed. Juvenile subyearling Chinook salmon were mainly piscivorous, with northern anchovy (Engraulis mordax) being especially important, making up half the diet by weight in some years. Annual diets clustered into two groups, primarily defined by their proportion of invertebrate prey (14% versus 39% on average). Diet composition was found to influence adult returns, with salmon from high‐invertebrate years returning in significantly larger numbers 2–3 yrs later. However, years that had high adult returns had overall lower stomach fullness and poorer body condition as juveniles, a counterintuitive result potentially driven by the enhanced survival of less fit individuals in better ocean conditions (top‐down effect). Ocean conditions in years with a higher percentage of invertebrates in salmon diets were significantly cooler from May to August, and bottom‐up processes may have led to a fall plankton community with a larger proportion of invertebrates. Our results suggest that the plankton community assemblage during this first fall may be critical in predicting adult returns of Chinook salmon in the Pacific Northwest.     

Food habits and marine survival of juvenile Chinook and coho salmon from marine waters of Southeast Alaska

Little is known about the food habits of juvenile Chinook (Oncorhynchus tshawytscha) and coho (Oncorhynchus kisutch) salmon in marine environments of Alaska, or whether their diets may have contributed to extremely high marine survival rates for coho salmon from Southeast Alaska and much more modest survival rates for Southeast Alaskan Chinook salmon. To address these issues, we documented the spatial and temporal variability of diets of both species collected from marine waters of Southeast Alaska during summers of 1997–2000. Food habits were similar: major prey items of both species included fishes, crab larvae, hyperiid amphipods, insects, and euphausiids. Multivariate analyses of diet composition indicated that the most distinct groups were formed at the smallest spatial and temporal scales (the haul), although groups also formed at larger scales, such as by month or habitat type. Our expectations for how food habits would influence survival were only partially supported. As predicted, Southeast Alaskan coho salmon had more prey in their stomachs overall [1.8% of body weight (BW)] and proportionally far fewer empty stomachs (0.7%) than either Alaskan Chinook (1.4% BW, 5.1% empty) or coho salmon from other regions. However, contrary to our expectations, coho salmon diets contained surprisingly few fish (49% by weight). Apparently, Alaskan coho salmon achieved extremely high marine survival rates despite a diet consisting largely of small, less energetically‐efficient crustacean prey. Our results suggest that diet quantity (how much is eaten) rather than diet quality (what is eaten) is important to marine survival.     

Early ocean distribution of juvenile Chinook salmon in an upwelling ecosystem

Extreme variability in abundance of California salmon populations is often ascribed to ocean conditions, yet relatively little is known about their marine life history. To investigate which ocean conditions influence their distribution and abundance, we surveyed juvenile Chinook salmon (Oncorhynchus tshawytscha) within the California Current (central California [37°30′N) to Newport, Oregon (44°00′N]) for a 2‐week period over three summers (2010–2012). At each station, we measured chlorophyll‐a as an indicator of primary productivity, acoustic‐based metrics of zooplankton density as an indicator of potential prey availability and physical characteristics such as bottom depth, temperature and salinity. We also measured fork lengths and collected genetic samples from each salmon that was caught. Genetic stock identification revealed that the majority of juvenile salmon were from the Central Valley and the Klamath Basin (91–98%). We constructed generalized logistic‐linear negative binomial hurdle models and chose the best model(s) using Akaike's Information Criterion (AIC) to determine which covariates influenced the salmon presence and, at locations where salmon were present, determined the variables that influenced their abundance. The probability of salmon presence was highest in shallower waters with a high chlorophyll‐a concentration and close to an individual's natal river. Catch abundance was primarily influenced by year, mean fork length and proximity to natal rivers. At the scale of sampling stations, presence and abundance were not related to acoustic indices of zooplankton density. In the weeks to months after ocean entry, California's juvenile Chinook salmon population appears to be primarily constrained to coastal waters near natal river outlets.     

Influence of ocean and freshwater conditions on Columbia River sockeye salmon Oncorhynchus nerka adult return rates

In recent years, returns of adult sockeye salmon Oncorhynchus nerka to the Columbia River Basin have reached numbers not observed since the 1950s. To understand factors related to these increased returns, we first looked for changes in freshwater production and survival of juvenile migrants. We then evaluated productivity changes by estimating smolt‐to‐adult return rates (SAR) for juvenile migration years 1985–2010. We found SAR varied between 0.2 and 23.5%, with the highest values coinciding with recent large adult returns. However, the largest adult return, in 2012, resulted not from increased survival, but from increased smolt production. We evaluated 19 different variables that could influence SARs, representing different facets of freshwater and ocean conditions. We used model selection criteria based on small‐sample corrected AIC to evaluate the relative performance of all two‐ and three‐variable models. The model with April upwelling, Pacific Northwest Index (PNI) in the migration year, and PNI in the year before migration had 10 times the AIC_c weight as the second‐best‐supported model, and R² = 0.82. The variables of April ocean upwelling and PNI in the migration year had high weights of 0.996 and 0.927, respectively, indicating they were by far the best of the candidate variables to explain variations in SAR. While our analyses were primarily correlative and limited by the type and amount of data currently available, changes in ocean conditions in the northern California Current system, as captured by April upwelling and PNI, appeared to play a large role in the variability of SAR.     

Temperature-mediated en route migration mortality and travel rates of endangered Snake River sockeye salmon

Abstract  Conservation efforts for endangered Snake River sockeye salmon ( Oncorhynchus nerka ) have been hindered by high en route adult mortality during their ∼1450 km freshwater spawning migration. Identifying causal factors for this mortality has been difficult given very small (often <10 fish) annual returns in recent decades. However, several hundred hatchery-bred fish returned in 2000 and we intercepted and radio-tagged 31 in mid-migration to monitor behaviours and survival. All fish initially migrated at similar rates, but later-timed fish eventually slowed migration and were far more likely to be unsuccessful. Late-season mortality was strongly associated with water temperatures near tolerance thresholds (21–24 °C). The data also suggest increased risk for fish in poor initial condition (i.e., with injuries or parasites) and probable recent selection against late-timed salmon. Results parallel temperature- and condition-related adult mortality in Columbia and Fraser River sockeye salmon populations and demonstrate the potential vulnerability of marginal southern populations to regional climate warming.     

Salish Sea Chinook salmon exhibit weaker coherence in early marine survival trends than coastal populations

Identifying factors that influence anadromous Pacific salmon (Oncorhynchus spp.) population dynamics is complicated by their diverse life histories and large geographic range. Over the last several decades, Chinook salmon (O. tshawytscha) populations from coastal areas and the Salish Sea have exhibited substantial variability in abundance. In some cases, populations within the Salish Sea have experienced persistent declines that have not rebounded. We analyzed a time series of early marine survival from 36 hatchery Chinook salmon populations spanning ocean entry years 1980–2008 to quantify spatial and temporal coherence in survival. Overall, we observed higher inter‐population variability in survival for Salish Sea populations than non‐Salish Sea populations. Annual survival patterns of Salish Sea populations covaried over smaller spatial scales and exhibited less synchrony among proximate populations relative to non‐Salish Sea populations. These results were supported by multivariate autoregressive state space (MARSS) models which predominantly identified region‐scale differences in survival trends between northern coastal, southern coastal, Strait of Georgia, and Puget Sound population groupings. Furthermore, Dynamic Factor Analysis (DFA) of regional survival trends showed that survival of southern coastal populations was associated with the North Pacific Gyre Oscillation, a large‐scale ocean circulation pattern, whereas survival of Salish Sea populations was not. In summary, this study demonstrates that survival patterns in Chinook salmon are likely determined by a complex hierarchy of processes operating across a broad range in spatial and temporal scales, presenting challenges to the management of mixed‐stock fisheries.     

Year-to-year variability in ocean recovery rate of Columbia River Upriver Bright fall Chinook salmon (Oncorhynchus tshawytscha)

Unusually large returns of several stocks of fall Chinook salmon (Oncorhynchus tshawytscha) from the U.S. Northwest commonly occurred during the late 1980s. These synchronous events seem to have been due to ocean rather than freshwater conditions because natal rivers of these stocks were geographically disconnected. We examined year‐to‐year variability in cohort strength of one of these stocks, Upriver Bright (URB) fall Chinook salmon from the Columbia River Hanford Reach for brood years 1976–99 (recovery years 1979–2002). We used the ocean recovery rate of coded‐wire‐tag (CWT) fish as an index of cohort strength. To analyse year‐to‐year variability in the ocean recovery rate, we applied a log‐linear model whose candidate explanatory variables were ocean condition variables, fishing effort, age of recovered fish, and fish rearing type (hatchery versus wild). Explanatory variables in the best model included fishing effort, and the quadratic term of winter sea surface temperature (SST) measured from coastal waters of British Columbia, Canada during the fish's first ocean year. The coefficient of the quadratic term of SST was significantly negative, so the model shape was convex. Our findings can be used to infer year‐to‐year variability in cohort strength of other fall Chinook salmon whose life history and ocean distributions are similar to the URB fish.     

Atlantic salmon living on the edge: Smolt behaviour and survival during seaward migration in River Minho

The Atlantic salmon (Salmo salar) population of the River Minho represents the southern natural distribution edge of the species. In line with the general trend for Atlantic salmon, this population has been declining over the years and is now at a critically low level. With river connectivity compromised by a large dam just 80 km upstream the River Minho's outlet, and an expected deterioration of climatic conditions, it is urgent to increase our knowledge of this population and identify survival bottlenecks that can be addressed. In this study, we used radio and acoustic telemetry to track Atlantic salmon smolts during their migration towards the sea and record both survival rates and possible causes of mortality. The recorded survival for the tagged migrating Atlantic salmon remained below 55% in the three studied years, indicating that the in‐river loss of smolts is likely a strong constraint to this population. From the smolts to which a likely cause of mortality could be attributed (34%), most appear to have been removed from the river (25%), with two confirmed events of bird predation and one of mammal predation. Interestingly, eight tags were recorded moving back upstream, likely indicating predation by larger fish. Increasing predator populations (e.g. cormorants, Phalacrocorax carbo) and invasive predators (e.g. American mink, Neovison vison) lead to elevated predation pressure on this already strained Atlantic salmon population, and further studies quantifying their impact in more detail could prove crucial for future management considerations.     

The use of a real-time PCR primer/probe set to observe infectivity of Yersinia ruckeri in Chinook salmon, Oncorhynchus tshawytscha (Walbaum), and steelhead trout, Oncorhynchus mykiss (Walbaum)

Yersinia ruckeri is the causative agent of enteric redmouth disease (ERM), a common pathogen affecting aquaculture facilities and implicated in large losses of cultured fish. Fisheries scientists continue to gain a greater understanding of the disease and the pathogen by investigating methods of identification and pre- and post-infection treatment. In this study, a real-time PCR probe set for Y. ruckeri was developed to detect daily changes in the bacterial load during pathogen challenges. Two species of fish, Chinook salmon, Oncorhynchus tshawytscha, and steelhead trout, Oncorhynchus mykiss, were exposed to two strains of Y. ruckeri (Hag and SC) during bath challenges. A subset of fish was killed daily for 14 days, and the kidney tissue was biopsied to enumerate copies of pathogen DNA per gram of tissue. While Chinook exposed to either the Hag or SC strains exhibited similar pathogen loads, those exposed to the Hag strain displayed higher mortality (～66%) than fish exposed to the SC strain (～24% mortality). Steelhead exposed to the Hag strain exhibited a greater pathogen load and higher mortality (～42%) than those exposed to the SC strain (<1% mortality). Steelhead challenged with either strain showed lower pathogen loads than Chinook. The study illustrates the efficacy of the probe set to enumerate Y. ruckeri bacterial growth in the kidneys of fish. Also, strains of Y. ruckeri display species-specific growth patterns that result in differential mortality and pathogen load.     

Juvenile river residence and performance of Snake River fall Chinook salmon

An animal's performance during its early life stage can greatly influence its survival to adulthood. Therefore, understanding aspects of early life history can be informative, particularly when designing management plans to rebuild a population. For a threatened population of fall Chinook salmon (Oncorhynchus tshawytscha) in the Snake River of Idaho, we reconstructed the early life history for 124 returning wild and hatchery adults using information recorded in their otoliths. Of our sampled wild adults (n = 61), 43% and 49% reared within the Snake River and Clearwater/Salmon rivers. We also found that only 21% of our sampled wild adults exhibited the historically common subyearling out‐migration strategy, in which juveniles exit freshwater shortly after hatching, while the remaining wild adults exhibited the yearling out‐migration strategy (i.e., individuals delay their freshwater exit). As expected, yearlings had, on average, a significantly larger body size than subyearlings at ocean entry. However, 35% of wild yearlings overlapped in size with wild subyearlings suggesting that spending more time in freshwater might not necessarily result in a larger body size. Lastly, we observed that variability in fork length at Snake River egress and ocean entry were best explained by migration strategy and where it reared, followed by hatch year and sex. Results from this study highlight the utility of adult otoliths in providing details about early life history, an understanding of which is critical to the conservation of Snake River fall Chinook salmon.     

Temporal and spatial responses of British Columbia steelhead (Oncorhynchus mykiss) populations to ocean climate shifts

The pattern of temporal change in recruitment of steelhead trout ( Oncorhynchus mykiss ) entering the ocean between 1963 and 1990 was geographically coherent in all regions of British Columbia. A major increase in recruitment was evident for smolts entering the ocean after 1977. Subsequently, an out-of-phase response occurred after 1990, indicating that the effect of a possible 1990 regime shift had both temporal and geographical structure. Steelhead entering northern regions had increasing recruitment, while steelhead entering southern BC coastal regions had sharply decreasing recruitment. The evidence clearly indicates that the overall recruitment response since 1977 was primarily shaped by changes in marine (not freshwater) survival. Similar sudden changes in adult recruitment also appear to be occurring for other species of Pacific salmon in BC and Oregon, such as coho ( O. kisutch ), which appear to occur suddenly and show considerable persistence. A possible explanation for the change is that ocean productivity declined in coastal regions of southern BC after 1990, reducing the marine growth of juvenile salmon. The Bakun upwelling index shows a pattern of geographical coherence along the west coast of North America that could in principle explain the observed pattern of changes in recruitment. However, no evidence for a temporal shift in this index occurring around 1977 and 1990 is apparent. The reason for the sudden and persistent decline in ocean survival is therefore uncertain.     

Forecasting climate-induced changes in the survival of Snake River spring/summer Chinook salmon (Oncorhynchus tshawytscha)

Effective conservation and management of natural resources requires accurate predictions of ecosystem responses to future climate change, but environmental science has largely failed to produce these reliable forecasts. The future response of Pacific salmon (Oncorhynchus spp.) to a changing environment and continued anthropogenic disturbance is of particular interest to the public because of their high economic, social, and cultural value. While numerous retrospective analyses show a strong correlation between past changes in the ocean environment and salmon production within the north Pacific, these correlations rarely make good predictions. Using a Bayesian time-series model to make successive 1-yr-ahead forecasts, we predicted changes in the ocean survival of Snake River spring/summer chinook salmon (O. tshawytscha) from indices of coastal ocean upwelling with a high degree of certainty (R² = 0.71). Furthermore, another form of the dynamic times-series model that used all of the available data indicated an even stronger coupling between smolt-to-adult survival and ocean upwelling in the spring and fall (R² = 0.96). This suggests that management policies directed at conserving this threatened stock of salmon need to explicitly address the important role of the ocean in driving future salmon survival.     

Marine and freshwater climatic factors affecting interannual variation in the timing of return migration to fresh water of sockeye salmon (Oncorhynchus nerka)

Interannual variation in the timing of the return migration to fresh water of adult sockeye salmon, Oncorhynchus nerka, from 46 populations throughout the species North American range was examined in a broad analysis of how timing patterns are affected by marine and freshwater conditions. Migration timing data (measured at various points along the migration, including just prior to freshwater entry, just after freshwater entry, and near the spawning grounds) were examined for correlations with sea‐surface temperatures (SST) prior to migration and to freshwater temperatures and flows during migration. Following a spring–summer period with warm SST, populations from southwestern Alaska tended to return early, Fraser River populations returned late, and populations from other regions showed no consistent patterns. Similarities between interannual timing of both nearby and distant populations indicated the presence of common or coincidental influences on timing. When riverine conditions related to timing, high flows and low temperatures were associated with late migrations, low flows and high temperatures were associated with early migrations. However, even counting stations at upriver locations showed correlations with SST. Notwithstanding some inconsistencies among the many populations examined and the indirect nature of the inferences, the results supported the hypotheses that (i) interannual variations in salmon distributions at sea reflect temperature conditions, and (ii) the date when salmon initiate homeward migration is a population‐specific trait, largely unaffected by the fish's location at sea.     

Variations in migration behaviour and mortality of Atlantic salmon smolts in four different hydroelectric facilities

Migration behaviour, route selection and mortality of Atlantic salmon, Salmo salar L., smolts were studied at four different hydroelectric facilities in the River Mustionjoki, Finland, in May 2017. Radio-tagged smolts were released upstream of the power stations and tracked by stationary antenna-receiver systems and hand-held receivers. Tracking revealed a general tendency of smolts to move downstream with the main flow, but also variable behaviour and mortality related to diverse conditions characteristic of each power station. Average migration delay at the power stations ranged between 13.8 and 101.1 h (median: 1.7–61.5 h). Estimated mortality ranges were 0%–50% in the forebays, 4%–64% in the power stations and 2–30%/km during river migration after passage of the dam. This study provided essential information on behaviour and mortality in relation to local conditions at each power station required for successful application of fish bypass systems in a salmon restoration project.     

Relationships between oceanic conditions and growth of Chinook salmon (Oncorhynchus tshawytscha) from California, Washington, and Alaska, USA

We model age‐specific growth rates of Chinook salmon (Oncorhynchus tshawytscha) with two life‐history behaviors from Alaska (i. Situk and ii.Taku Rivers), Puget Sound, Washington (iii., iv. Skagit River), and California (v. Smith River) relative to oceanic conditions in those regions. By analyzing over 20 yr of biological and physical data from the NE Pacific downwelling, upwelling, and transition zones, we are able to determine the factors affecting growth across much of the species’ range and between life‐history behaviors. With scale increment data from returning fish, we use path analysis and partial least squares regression to quantify the relationships between growth and regional‐ and large‐scale oceanic conditions (e.g., sea level height, sea surface temperature, upwelling). Alaskan fish with both ocean‐ and stream‐type behaviors were fit best by the environmental data from the winter in Alaska waters. Specifically, coastal and gyre factors such as sea surface temperature, river flow, and Ekman pumping positively correlated to growth, indicating a productive and strong Alaska Current promoted growth. Growth of fish from California was fit by local factors such as increased upwelling, lower coastal sea surface temperature, and wind stresses during summer and spring, indicating a productive and strong California Current promoted growth. For Puget Sound, Washington, growth of fish that migrate to sea in their first year was generally negatively correlated to a strong California Current. Puget Sound fish that spend a year in freshwater before migrating to sea were modeled well with environmental data from their source region for the first 2 yr at sea and by data from Alaska waters in their third year at sea. Results suggest that conditions in which the transition zone is dominated by neither the Alaska nor California Currents are best for increased growth of Puget Sound fish.     

Bayesian decision analysis for status of Snake River spring-summer Chinook salmon <Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis> populations at extinction risk

The viability of populations was assessed using population trend data and the Diffusion Approximation (DA) model. Various extinction risk metrics for a population are functions of the DA model parameters, and thus, estimates of the DA model parameters are key quantities. Using Bayesian methods, we showed uncertainty in those estimates, and further proceeded to a decision analysis to assess viability of populations. These methods were demonstrated using population trend data from return years since 1980 on naturally produced Snake River spring-summer Chinook salmon Oncorhynchus tshawytscha populations. Of 19 populations examined, the Catherine Creek population was assessed at serious risk, Tucannon River Spring and Grande Ronde Upper Main stem populations were assessed at minor risk, and the other populations were not at risk. This assessment helps managers to prioritize populations at risk for recovery management.     

Effects of temperature on Renibacterium salmoninarum infection and transmission potential in Chinook salmon,Oncorhynchus tshawytscha (Walbaum)

Renibacterium salmoninarum is a significant pathogen of salmonids and the causative agent of bacterial kidney disease (BKD). Water temperature affects the replication rate of pathogens and the function of the fish immune system to influence the progression of disease. In addition, rapid shifts in temperature may serve as stressors that reduce host resistance. This study evaluated the effect of shifts in water temperature on established R. salmoninarum infections. We challenged Chinook salmon with R. salmoninarum at 12 °C for 2 weeks and then divided the fish into three temperature groups (8, 12 and 15 °C). Fish in the 8 °C group had significantly higher R. salmoninarum‐specific mortality, kidney R. salmoninarum loads and bacterial shedding rates relative to the fish held at 12 or 15 °C. There was a trend towards suppressed bacterial load and shedding in the 15 °C group, but the results were not significant. Bacterial load was a significant predictor of shedding for the 8 and 12 °C groups but not for the 15 °C group. Overall, our results showed little effect of temperature stress on the progress of infection, but do support the conclusion that cooler water temperatures contribute to infection progression and increased transmission potential in Chinook salmon infected with R. salmoninarum.     

Relating spatial and temporal scales of climate and ocean variability to survival of Pacific Northwest Chinook salmon (Oncorhynchus tshawytscha)

Pacific Northwest Chinook, Oncorhynchus tshawytscha, have exhibited a high degree of variability in smolt‐to‐adult survival over the past three decades. This variability is summarized for 22 Pacific Northwest stocks and analyzed using generalized linear modeling techniques. Results indicate that survival can be grouped into eight distinct regional clusters: (1) Alaska, Northern BC and North Georgia Strait; (2) Georgia Strait; (3) Lower Fraser River and West Coast Vancouver Island; (4) Puget Sound and Hood Canal; (5) Lower Columbia Tules; (6) Columbia Upriver Brights, Willamette and Cowlitz; (7) Oregon and Washington Coastal; and (8) Klamath River and Columbia River Summers. Further analysis for stocks within each of the eight regions indicates that local ocean conditions following the outmigration of smolts from freshwater to marine areas had a significant effect on survival for the majority of the stock groups analyzed. Our analyses of the data indicate that Pacific Northwest Chinook survival covaries on a spatial scale of 350–450 km. Lagged time series models are presented that link large‐scale tropical Pacific conditions, intermediate‐basin scale northeastern Pacific conditions, and local sea surface temperatures to survival of Pacific Northwest stocks.     

A matter of timing: the role of ocean conditions in the initiation of spawning migration by late‐run Fraser River sockeye salmon (Oncorhynchus nerka)

Year 1995 marked the start of a major shift to earlier river entry of late‐run Fraser River sockeye salmon (Oncorhynchus nerka) en route to the spawning grounds. Earlier entry has typically been accompanied by considerably greater in‐river mortality. We examine this behavioral change using correlation analyses between the entry timing of the Adams River and Weaver Creek stocks and the surface marine conditions encountered by the stocks during their homing migration from the northeast Pacific several months earlier. For Adams stocks, maximum correlation is between entry timing and offshore winds, such that the weaker the wind stress in the direction of the prevailing surface currents in early July, the earlier the river entry in late summer. For Weaver stocks, maximum correlation is with salinity, such that the lower the surface salinity along the coast in August, the earlier the river entry. We hypothesize that oceanic changes lead to changes in late‐run sockeye physiology which then leads to changes in behavior. Physiological changes are postulated to arise from two types of preconditioning: Type‐1 occurs in the offshore region, whereby the weaker the prevailing currents that normally hinder eastward migration, the more endogenous energy available for maturation and the earlier the river entry. Type‐2 occurs in coastal regions, whereby the lower the salinity, the more rapid the osmoregulatory adaptation to freshwater (and possible susceptibility to water‐borne pathogens) and the earlier the entry. Results suggest that the earlier entry that began in the mid‐1990s is linked to weaker ocean currents and lower coastal salinities.