Snake River Spring Summer Chinook Research Articles

Improving Abundance Estimates of Spring–Summer Snake River Chinook Salmon for Fisheries Management

AbstractThe Columbia River basin is home to a run of spring–summer Chinook Salmon Oncorhynchus tshawytscha that returns to the Snake River drainage of Idaho, Oregon, and Washington in the Pacific Northwest. Historically, the run was one of the more productive throughout the Columbia River basin. However, Snake River spring–summer Chinook Salmon have experienced declines in abundance due to overfishing, habitat degradation, and dams. Several stocks are listed as threatened under the U.S. Endangered Species Act and are supported by mitigation hatcheries funded by Idaho Power Company, the Lower Snake River Compensation Plan, and the Bonneville Power Administration. To maximize tribal and state harvest of returning hatchery adults, minimize impacts on wild fish, and ensure that enough hatchery fish return to meet broodstock needs, careful fisheries management is required. Since 2008, managers have used hatchery adults, PIT‐tagged as juveniles and detected at Lower Granite Dam, to generate adult abundance estimates. In season, these estimates inform state and tribal harvest shares and ensure that broodstock needs are met. Postseason, they provide smolt‐to‐adult survival and return rates. Since 2012, parentage‐based tagging (PBT) has provided an alternative method to estimate stock‐ and age‐specific returns at Lower Granite Dam, since returning hatchery adults sampled at Lower Granite Dam can be assigned to their parents. We compared stock‐specific abundance estimates between PIT‐ and PBT‐derived methodologies for return years 2016–2019. Across all years, PIT tag estimates accounted for 65% of the PBT‐based estimates at Lower Granite Dam across all age‐groups and release sites combined. This underrepresentation across all groups equated to 49,833 fish that were not accounted for in PIT tag abundance estimates. It is clear that PBT‐based estimates should aide in‐season harvest management and postseason run reconstruction to avoid the known bias of estimates from PIT tags, especially during years of low returns when increased accuracy is critical.

Exploring Latent Mortality of Juvenile Salmonids Related to Migration through the Columbia River Hydropower System

AbstractThe ability to manage anthropogenic actions that affect the dynamics of animal populations requires the identification and understanding of life‐stage‐specific mortality. This understanding can be confounded when the expression of mortality is removed, in time or space, from its cause. For years, researchers studying endangered Snake River spring–summer Chinook salmon Oncorhynchus tshawytscha have debated the magnitude of mortality that is related to—but expressed after—passage through the Snake and Columbia River hydropower system (“latent” mortality). We conducted experiments with Chinook salmon to assess the magnitude of latent mortality from two sources: passage through juvenile bypass structures at dams, and transportation with larger juvenile steelhead O. mykiss present in the barge holds. Nearly 129,000 juvenile Chinook salmon (passive integrated transponder tagged) were exposed to different treatment conditions during downstream migration. Study fish were then held in seawater tanks for up to 223 d, and time to mortality was noted for each individual that died. We analyzed survival patterns by using statistical procedures for time‐to‐event data (i.e., survival analysis). Differential survival between treatment groups was taken to indicate latent mortality caused by the specific treatment. We used a nonparametric Kaplan–Meier analysis to visualize survival patterns and a parametric logistic regression analysis to model the effects of multiple factors. Chinook salmon that were transported with steelhead had significantly lower survival than those that were transported alone. However, there was little evidence for differential latent mortality between Chinook salmon that were not detected at the bypass systems of five dams along the migration route and those that were detected at two to five bypass systems. Our application of survival analyses to individuals subjected to various treatments and held for extended periods produced an effective combination that can be used to test for latent mortality; these results may serve as an initial assessment for further conservation investigations and as a guide to more‐targeted research.

Assessing Freshwater and Marine Environmental Influences on Life‐Stage‐Specific Survival Rates of Snake River Spring–Summer Chinook Salmon and Steelhead

AbstractPacific salmon Oncorhynchus spp. from the Snake River basin experience a wide range of environmental conditions during their freshwater, estuarine, and marine residence, which in turn influence their survival rates at each life stage. In addition, researchers have found that juvenile out‐migration conditions can influence subsequent survival during estuarine and marine residence, a concept known as the hydrosystem‐related, delayed‐mortality hypothesis. In this analysis, we calculated seasonal, life‐stage‐specific survival rate estimates for Snake River spring–summer Chinook salmon Oncorhynchus tshawytscha and steelhead O. mykiss and conducted multiple‐regression analyses to identify the freshwater and marine environmental factors associated with survival at each life stage. We also conducted correlation analyses to test the hydrosystem‐related, delayed‐mortality hypothesis. We found that the freshwater variables we examined (the percentage of river flow spilled over out‐migration dams and water transit time) were important for characterizing the variation in survival rates not only during freshwater out‐migration but also during estuarine and marine residence. Of the marine factors examined, we found that the Pacific Decadal Oscillation index was the most important variable for characterizing the variation in the marine and cumulative smolt‐to‐adult survival rates of both species. In support of the hydrosystem‐related, delayed‐mortality hypothesis, we found that freshwater and marine survival rates were correlated, indicating that a portion of the mortality expressed after leaving the hydrosystem is related to processes affected by downstream migration conditions. Our results indicate that improvements in life‐stage‐specific and smolt‐to‐adult survival may be achievable across a range of marine conditions through increasing spill percentages and reducing water transit times during juvenile salmon out‐migration.

The influence of the Columbia River plume on the survival of steelhead (Oncorhynchus mykiss) and Chinook salmon (Oncorhynchus tshawytscha): a numerical exploration

Are smolt-to-adult return rates (SARs) for wild steelhead (i.e., sea-run rainbow trout, Oncorhynchus mykiss ) and wild Snake River spring–summer Chinook salmon ( Oncorhynchus tshawytscha ) related to changes in the Columbia River plume at the time that juvenile migrants enter the ocean? We used three-dimensional (3D) numerical models of the baroclinic circulation in the Columbia River estuary–plume–shelf system to simulate within-season variation in plume size and location, comparing the results with SARs for each day that juvenile salmon entered the ocean for 1999–2003. We found that steelhead benefited from the plume environment at a narrow window of time around their ocean entry. However, when large-scale ocean conditions turned unfavorable, the contribution of local plume conditions to the overall variability in steelhead survival became not significant. A similar evaluation revealed that the plume did not affect survival of Chinook salmon, at least at the fine scale of variability considered. The differential response between the two species is consistent with observed and previously reported behavioral characteristics they exhibit. We speculate that steelhead mainly use the plume to move quickly away from coastal habitats and the predation pressures associated with this environment, for a more direct migration than Chinook salmon to ocean habitats in the Gulf of Alaska.

Bayesian decision analysis for status of Snake River spring?summer Chinook salmon Oncorhynchus tshawytscha 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.

Migration Timing, Growth, and Estimated Parr‐to‐Smolt Survival Rates of Wild Snake River Spring–Summer Chinook Salmon from the Salmon River Basin, Idaho, to the Lower Snake River

AbstractSurvival, growth, and juvenile migration timing are key life history traits for at‐risk salmon populations. To estimate these traits in threatened wild Snake River spring–summer Chinook salmon Oncorhynchus tshawytscha, we tagged fish as parr in 3–17 natal streams per year from 1991 to 2003. We injected passive integrated transponder tags into parr collected from streams within the Salmon River basin in Idaho. Each spring, after the previous summer's tagging, fish were detected as smolts in the juvenile fish bypass systems of lower Snake River dams. Estimated parr‐to‐smolt survival to Lower Granite Dam (excluding migration year 1992) ranged from 3% to 48% for individual populations and from 8% to 25% (yearly average = 16%) for all streams combined. From 1998 to 2004, estimated parr‐to‐smolt survival declined from 25% to 8%, in part because of parr density‐dependent effects. Overall annual average growth rates from tagging to detection at Little Goose Dam ranged from 39.7 to 43.3 mm during 2001–2004, and significant differences in growth were observed among sites and years. Growth of individuals was positively related to elapsed time between tagging and recapture and negatively related to fork length at tagging. Annual migration timing distributions for fish populations from the different streams varied highly within and between years. Timing of the 10th to 90th percentile passing Lower Granite Dam ranged from 20 to 45 d for the combined wild populations (average = 38 d). Median passage date was negatively related to autumn temperature, spring temperature, and March river flow, and was positively related to elevation of the tagging site. Baseline data generated by this project provide a foundation for understanding the biocomplexity of these populations, which is critical to effective recovery efforts for these threatened wild fish stocks.

Disease Susceptibility of Hatchery Snake River Spring-Summer Chinook Salmon with Different Juvenile Migration Histories in the Columbia River.

Various methods have been developed to mitigate the effects of dams on juvenile Pacific salmon Oncorhynchus spp. migrating to the Pacific Ocean through the Columbia River basin. In this study, we examined the health of hatchery Snake River spring and summer Chinook salmon relative to two mitigating strategies: dam bypass and transportation (e.g., barging). The health of out-migrants was assessed in terms of the difference in the incidence of mortality among fish, categorically grouped into no-bypass, bypass, and transportation life histories, in response to challenge with the marine pathogen Listonella anguillarum during seawater holding. These three life histories were defined as follows: (1) fish that were not detected at any of the juvenile bypass systems above Bonneville Dam were classified as having a no-bypass life history; (2) fish that were detected at one or more juvenile bypass systems above Bonneville Dam were classified as having a bypass life history; and (3) fish that were barged were classified as having the transportation life history. Barged fish were found to be less susceptible to L. anguillarum than in-river fish-whether bypassed or not-which suggests that transportation may help mitigate the adverse health effects of the hydropower system of the Columbia River basin on Snake River spring-summer Chinook salmon. The findings of this study are not necessarily transferable to other out-migrant stocks in the Columbia River basin, given that only one evolutionarily significant unit, that is, Snake River spring-summer Chinook salmon, was used in this study.

A Model‐Based Assessment of the Potential Response of Snake River Spring–Summer Chinook Salmon to Habitat Improvements

AbstractThe current recovery strategy for threatened Snake River Chinook salmon Oncorhynchus tshawytscha relies heavily on improvements to the quality of freshwater spawning and rearing habitat; however, the potential survival benefit from these actions is unknown. To address this issue, we created a model for predicting the early freshwater survival rates (egg to smolt) of this species as a function of five easily measured physical habitat variables and used this model to evaluate survival rates under five alternative future habitat states. Model validation showed that the predictions were reasonably accurate for individual stocks as well as for the trend in predictions across stocks. The results for the future habitat scenarios suggest that the potential for improving survival rates through habitat restoration is high for a few populations and low to nonexistent for most others while the potential for reduction in survival rates due to reduced habitat quality is great for all populations. The effects of modeled egg‐to‐smolt survival rate changes should be evaluated across the entire Chinook salmon life cycle to assess recovery potential.

Detecting juvenile survival effects of habitat actions: power analysis applied to endangered Snake River spring–summer chinook (Oncorhynchus tshawytscha)

Using 10 years of parr-to-smolt survival rate estimates for passive integrated transponder (PIT) tagged, endangered wild Snake River chinook (Oncorhynchus tshawytscha) (measured in eight spawning streams), we demonstrate that moderate increases in base-case survival may be detectable quickly, as required by recent U.S. National Marine Fisheries Service regulations. The regulations require that effects of tributary habitat actions on juvenile salmonid survival rates be detectable within 5 to 8 years. Simple log-linear regression models were employed where the natural log of survival is a function of parr size, parent stock abundance, tagging location, and year. The analysis uses before–after control–impact (BACI) statistical techniques. The results suggest that multiplicative survival rate changes of 30% should be detectable within 7 years, and increases of 50% within 3 years. Models with higher information-theoretic weights were more powerful than less plausible models. Models using juvenile survival were substantially more powerful than models using spawner–recruit data for the same stocks, but the analysis is no substitute for field studies, which are still very rare.

A LARGE-SCALE, MULTISPECIES STATUS ASSESSMENT: ANADROMOUS SALMONIDS IN THE COLUMBIA RIVER BASIN

Twelve salmonid evolutionarily significant units (ESUs) throughout the Columbia River Basin are currently listed as threatened or endangered under the Endangered Species Act; these ESUs are affected differentially by a variety of human activities. We present a standardized quantitative status and risk assessment for 152 listed salmonid stocks in these ESUs and 24 nonlisted stocks. Using data from 1980–2000, which represents a time of stable conditions in the Columbia River hydropower system and a period of ocean conditions generally regarded as poor for Columbia Basin salmonids, we estimated the status of these stocks under two different assumptions: that hatchery-reared spawners were not reproducing during the period of the censuses, or that hatchery-reared spawners were reproducing and thus that reproduction from hatchery inputs was masking population trends. We repeated the analyses using a longer time period containing both “good” and “bad” ocean conditions (1965–2000) as a first step toward determining whether recent apparent declines are a result of sampling a period of poor ocean conditions. All the listed ESUs except Columbia River chum showed declining trends with estimated long-term population growth rates (λ's) ranging from 0.85 to 1.0, under the assumption that hatchery fish were not reproducing and not masking the true λ. If hatchery fish were reproducing, the estimated λ's ranged from 0.62 to 0.89, indicating extremely low natural reproduction and survival. For most ESUs, there was no significant decline in population growth rates calculated for the 1980–2000 vs. 1965–2000 time periods, suggesting that the current population status for most ESUs is not solely a result of changes in ocean conditions, and that without other changes, risks will persist even during upturns in ocean conditions. However, estimated population growth rates for the Snake River spring–summer chinook salmon and steelhead ESUs were significantly lower during the longer time period. This difference may be due to a period of dam building on the Snake River during the 1960s and 1970s. For 33 stocks and seven ESUs, the probability of extinction could be estimated. The estimates were generally low for all ESUs with the exception of Upper Columbia River spring chinook and Upper Willamette River steelhead. The probability of 90% decline could be estimated for all stocks. The mean probability of 90% decline in 50 years was highest for Upper Columbia River spring chinook (95% mean probability across all stocks within the ESU) and Lower Columbia River steelhead (80% mean probability). We estimated the effects of two different management actions on long-term growth rates for the ESUs. Harvest reductions offer a means to mitigate risks for ESUs that bear substantial harvest pressure, but they are unlikely to increase population growth rates enough to produce stable or increasing trends for all ESUs. Similarly, anticipated improvements to passage survival through the Snake and mainstem Columbia hydropower systems may be important, but additional actions are likely to be necessary to recover affected ESUs.

Experimental management for Snake River spring–summer chinook (Oncorhynchus tshawytscha): trade-offs between conservation and learning for a threatened species

Using Snake River spring–summer chinook (Oncorhynchus tshawytscha) as an example, we explore trade-offs between conservation (restoring population abundance to self-sustaining levels) and learning (reliably estimating how management strategies affect productivity). The population has been studied extensively, especially since 1992, when the evolutionarily significant unit (ESU) was listed under the U.S. Endangered Species Act. Understanding both the conservation and learning dimensions is crucial in evaluating management actions. Using a Bayesian simulation model calibrated with 40+ years of spawner–recruit estimates, we performed population viability analyses to examine the biological risks of an array of management strategies. We also performed power analyses to estimate the precision of estimates of the actions' effects. The results suggest that if one can take actions that increase productivity and manage those actions as experiments, one can simultaneously increase fish numbers and reduce the uncertainty about the effects of those actions. However, because more powerful experiments will utilize controls where no action is taken, an experimental approach may increase risks to the ESU when compared to a strategy that tries to maximize productivity as soon as possible.

Statistical Relationship between Parr-to-Smolt Survival of Snake River Spring–Summer Chinook Salmon and Indices of Land Use

We used simple regression models to demonstrate an association between land use and parr survival of chinook salmon Oncorhynchus tshawytscha from overwintering areas in the Snake River drainage of Idaho and Oregon to the first main-stem dam encountered during emigration to the Pacific Ocean. We used data on tagged (passive integrated transponder tags) releases of naturally produced Snake River spring–summer chinook parr and subsequent tag detections, as well as indices of land use, vegetation, and road density. We spot-checked the land-use and vegetation indices in a field survey of spawning and rearing areas in the summer of 1999, and we believe that they are reliable indicators of land-use patterns. The models also employed month of release, length of parr at release, and a drought index as independent variables. The models were developed and tested using parr tagged from 1992 through 1998. Age-0 parr that reared in wilderness areas (a land-use category; not necessarily federally designated Wilderness Areas) had the highest survival during their last 6–9 months of freshwater residence. In contrast, parr that reared in young, dry forests (typically, intensively managed timber lands) had the lowest survival. Similarly, parr that reared in areas of low road density had substantially higher survival than those in areas of high road density. We concluded that in the area studied there is a close association between land-use indices and survival of chinook salmon parr during their last 6–9 months of freshwater residence. This analysis suggests that road-building and associated land-use activities in the region may have a detrimental effect on the survival of juvenile chinook salmon and that mitigative changes in these activities could be warranted because Snake River spring–summer chinook salmon are listed as threatened under the Endangered Species Act.

Prevalence of Marine-Mammal Tooth and Claw Abrasions on Adult Anadromous Salmonids Returning to the Snake River

Abstract During 1990, a relatively high percentage of adult anadromous salmonids returning to the Snake River had marine-mammal tooth and claw abrasions. From 1990 through 1993, annual incidence of these injuries ranged between 14.0 and 19.2% for spring–summer chinook salmon Oncorhynchus tshawytscha and between 5.4 and 14.2% for steelhead O. mykiss. Open wounds were observed on about one-third of the fish with abrasions. Although these results suggest that predation by pinnipeds may be an important mortality factor for Snake River spring–summer chinook salmon, further research is needed to accurately define the magnitude of the predation.