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Russell Perry

Publications and source records attributed to Russell Perry.

18 recordsLinked to original sources
USGS2026

Using a temporary emigration model to estimate abundance of stream fishes from hybrid removal surveys with and without block nets

Monitoring programs are often faced with a decision to allocate resources into either robust spatiotemporal coverage to estimate a population index (e.g., not true abundance) or confirming closed sampling conditions (e.g., with block nets) for an unbiased population estimate at the cost of spatiotemporal coverage. However, making accurate and precise abundance estimates at robust spatiotemporal scales is possible when combining open and closed sampling designs with integrated modeling techniques. We used simulations and a case study of backpack electrofishing surveys in the Santa Ana River, California to test the efficacy of an integrated abundance model (temporary emigration model, TE) to estimate abundance of fishes using removal sampling methods with a hybrid sampling design (sampling with and without block nets during removal sampling). We found that the TE model performed well under most modeling scenarios (sample size, amount of closure violation, number of samples collected during closure), although at least a few samples with block nets were necessary for all parameters to be estimable. When applied to fish surveys in the Santa Ana River, we found that catch of the fishes fit to the TE model (Santa Ana Sucker, Arroyo Chub, Channel Catfish, Largemouth Bass, Yellow Bullhead) showed little evidence that the closure assumption was violated when block nets were not used. Additionally, we found that the abundance of non-native fishes negatively affected the abundance of the native Santa Ana Sucker, which was also found to adversely affect the native fish’s access to critical habitat consisting of gravel and cobble substrate. Our results indicate that the TE model presents a viable solution to common sampling problems that impact many monitoring programs, where precise and accurate population estimates can be made at large spatiotemporal scales even when most samples violate the closure assumption.

California↗
USGS2025

Survival, travel time, and use of migration routes by juvenile steelhead in a modified river estuary

Greater understanding of the survival, travel time, and spatial distribution of juvenile salmonids among migration routes between their natal streams and the ocean is critical to the recovery of these threatened species. In the Sacramento–San Joaquin River Delta (Delta), a highly modified estuary in central California, USA, there is a critical need to evaluate how water management (e.g., water pumping) and environmental factors (e.g., water flow) impact these populations. While management actions can affect some environmental variables in the Delta, only recently have studies begun to uncover associations between these variables and key demographic parameters. In this study, we examine the effects of freshwater flows, water exports, tidal environment, and a temporary barrier on juvenile steelhead ( Oncorhynchus mykiss ) survival, travel times, and migration routing using a multiyear acoustic telemetry dataset and recent advancements in Bayesian multistate mark-recapture modeling. We found that no single covariate explained variation in juvenile steelhead population dynamics across the entire Delta, but that separate regions within the Delta showed association with specific environmental factors.

California↗
USGS2024

Back from the brink: Estimating daily and annual abundance of natural-origin salmon smolts from 30-years of mixed-origin capture-recapture data

Evaluating the status and trends of natural-origin anadromous fish populations over time requires robust estimates of out-migrating juvenile abundance. Information on abundance is typically acquired by capturing actively migrating fish as they pass stationary monitoring platforms. Challenges to estimation include protracted migration timing, temporally varying capture probabilities and the contemporaneous presence of unmarked hatchery-origin fish. The confounding effects of unmarked hatchery fish are especially pernicious in systems hosting multiple hatchery programs with variable mark-rates among releases. Here, we address this problem for a regionally and culturally important population of Chinook salmon ( Oncorhynchus tshawytscha ) supported by a hatchery-supplementation program implemented in response to the listing of this population under the U.S. Endangered Species Act. We developed a model to estimate daily and annual abundance of naturally produced age-0 fall Chinook salmon passing Lower Granite Dam (Snake River, USA) for each of the last 30 years. We accounted for variable hatchery marking rates by integrating two related data sources: 1) release-recapture data of fish with individually identifiable tags and 2) counts of marked and unmarked sample of fish captured each day. We fit joint parameters for daily fish arrival and capture probabilities to these data to estimate the daily abundance of hatchery- and natural-origin fish. Our results show that from 1992 to 2021, the annual abundance of juvenile natural-origin Snake River fall Chinook salmon increased by two orders of magnitude. These results are the first comprehensive evaluation of multi-decadal trends in abundance and run-timing for this population. Our approach can be adapted to other runs and locations within the Columbia River basin or similar systems where out-migrating fish are monitored at fixed locations.

Idaho, Oregon, Washington↗
USGS2024

Spatial and temporal surveys of salmon environmental DNA (eDNA) in a Seattle urban creek

Seattle Public Utilities (SPU) has a history of conducting traditional fish surveys in urban streams of Seattle, Washington. Limited staff resources have reduced SPU's capacity to monitor fish, and environmental DNA (eDNA) was recognized as an alternative survey method that could potentially improve the efficiency and capacity of SPU-sponsored fish surveys. We performed spatiotemporal surveys of eDNA to assess occupancy and distribution of Chinook Salmon ( Oncorhynchus tshawytscha ), Coho Salmon ( O . kisutch ), and Coastal Cutthroat Trout ( O . clarkii clarkii ) in Thornton Creek, Seattle, between October 2018 and December 2020. Peak Chinook and Coho eDNA detections occurred in October and October–November, respectively, coinciding with expected adult return time. Chinook and Coho eDNA was detected in May at the time when juveniles outmigrate through the Lake Washington basin. Coastal Cutthroat Trout eDNA was widespread and detected at high rates across seasons, reflecting their ubiquitous distribution. Results from multiscale occupancy modeling suggested that distance upstream affected site-level occupancy probabilities for adult Chinook, but not Coho. Model results also suggested that the probability of Coho and Chinook eDNA occurring in water samples was affected by survey year. Finally, model results suggested that the probability of detecting Chinook eDNA in PCR technical replicates was affected by survey year and collection day but detection of Coho eDNA was only affected by collection day. This study indicates eDNA surveys are effective for assessing distribution and occupancy of salmonids in Seattle's urban streams. Integrating eDNA surveys into urban stream monitoring programs can help alleviate the burden of limited assets facing many resource managers.

Washington↗
USGS2024

Hydrologic, water operations, reservoir temperature, river temperature, sediment transport, habitat, and fish population modeling for the Trinity River Water Management Plan

Humboldt County is developing a Water Management Plan that will describe a range of proposed annual releases from Trinity Reservoir consistent with the 1959 water delivery contract between Humboldt County and the U.S. Bureau of Reclamation (Reclamation). The 1959 contract states that Reclamation shall release not less than an annual quantity of 50,000 acre-feet into the Trinity River for the beneficial use of Humboldt County and other downstream users (Contract Water). The Water Management Plan will outline how Contract Water should be released for the benefit of fisheries in the Trinity River and lower Klamath River, with the primary goal of expanding a harvestable surplus of Tribal, recreational, and commercial fisheries. A set of annual Contract Water release scenarios were developed during five workshops conducted in 2022 and 2023 with interested parties including Humboldt County, state and federal resource agencies, tribal representatives, Reclamation, and the U.S. Department of the Interior Solicitor’s office. A suite of modeling and technical tools was used to analyze annual conditions with and without Contract Water releases. This Modeling Report describes the modeling tools used to assess Contract Water release scenarios, including CalSim II, HEC-5Q, RBM10, sediment transport models, Chinook Salmon habitat models, and the Stream Salmonid Simulator. Results from all models are summarized to provide a comparative overview of modeled release scenarios to modeled baseline conditions. Mean annual Contract Water release scenarios ranged from 50,000 acre-feet to 170,000 acre-feet, and varied in timing, magnitude, and duration, though all releases were made between October and April. As shown in Table ES-1, a key finding of this modeling report is Contract Water releases that had the greatest modeled increase in Chinook Salmon abundance relative to baseline conditions included those that released 50,000 acre-feet in the fall period from October through December as pulse flows or baseflows, and those that released 170,000 acre-feet from October through April as a combination of pulse flows and baseflows. Modeled beneficial effects on populations were primarily due to either (1) increases in habitat area during the spawning life stage in October through December, which decreased redd superimposition (e.g., the process of a later arriving spawner building a redd on top of an existing redd) and improved egg survival, or (2) increases in flow during the fry emergence and juvenile rearing life stage in March through April, which increased the fry and parr carrying capacity (e.g., the upper limit for the number of fry or parr that a habitat unit can support) of individual habitat units. Another key finding of this report is all Contract Water scenarios that released at least 50,000 acre-feet annually from Trinity Reservoir had similar effects on Trinity Reservoir storage, Central Valley Project (CVP) storage, CVP contract water deliveries, and Sacramento River water temperatures. Whether these scenarios were released annually as a fall baseflow, fall pulse flow, spring pulse flow, or spring baseflow, they all resulted in similar storage patterns in Trinity Reservoir – an annual reduction in storage relative to the baseline that was relatively small in wetter years and larger in drier years. As a result of lower Trinity Storage levels, Trinity River Division (TRD) exports to the CVP were reduced. Because the timing of exports is similar each year, reaching a peak in July through September, the reduction to exports occurred at the same time each year, independent of Contract Water release timing, resulting in similar storage, CVP delivery, and water temperature effects in the Sacramento River basin portion of the CVP. The water temperature effects on the Sacramento River were limited to the months of July and August, relatively minor, and were primarily attributed to changes in storage, release magnitude, and release temperature from Lake Shasta, and not due explicitly to inflows from the TRD.

California↗
USGS2023

Survival implications of diversion entrainment for outmigrating juvenile Chinook Salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss)

Efforts to ameliorate negative effects of diversion dams on aquatic species of concern are important in rivers where water withdrawal supports agricultural economies and are likely to become increasingly important with impending climate change. A multiyear study was conducted to evaluate the survival consequences of diversion dam passage for juvenile Chinook Salmon ( Oncorhynchus tshawytscha ) and steelhead ( O. mykiss ) in the highly managed Yakima River, Washington. Canal entrainment and passage were evaluated at four diversion dams encountered by seaward migrating juvenile salmon and steelhead. Fish pass dams via spillbays or enter canals with downstream fish-screening facilities designed to collect entrained fish and return them to the mainstem river. Percent entrainment into canals was substantial (6–59%) at three of the four diversion dams studied, and entrainment probability was positively associated with the proportion of streamflow diverted into canals. Survival probability estimates for groups of tagged fish that were entrained into canals were lower than survival probability estimates for tagged fish that passed through spillbays on the dams. Absolute differences in survival probabilities between routes ranged from 0.099 to 0.369, demonstrating that canal entrainment reduced survival of outmigrating juvenile Chinook Salmon and steelhead. We also found that entrainment resulted in migration delays, which could further affect survival because fish are increasingly exposed to predation and decreased water quality as water temperature increases throughout the migration season. These results highlight the need to limit entrainment of juvenile salmon and steelhead at diversion dams in rivers where salmon recovery is important.

Washington↗
USGS2023

Spatial and temporal overlap between hatchery- and natural-origin steelhead and Chinook salmon during spawning in the Klickitat River, Washington, USA

A goal of many segregated salmonid hatchery programs is to minimize potential interbreeding between hatchery- and natural-origin fish. To assess this on the Klickitat River, Washington, USA, we used radiotelemetry during 2009–2014 to evaluate spatiotemporal spawning overlap between hatchery-origin and natural-origin steelhead Oncorhynchus mykiss and spring Chinook Salmon O. tshawytscha. We estimated percentages of tagged fish that spawned naturally in the Klickitat River subbasin, emigrated from the Klickitat River, or died before spawning. For steelhead, 12% of hatchery-origin and 50% of natural-origin fish spawned naturally. For spring Chinook Salmon, 18% of hatchery-origin and 44% of natural-origin fish spawned naturally. Tag loss may result in underestimates in these percentages. Most hatchery-origin steelhead (90%) spawned downstream of rkm 32 and 75% spawned from November to mid-March, while the majority of natural-origin steelhead (64%) spawned upstream of rkm 32 and 75% spawned from mid-March to late May. Spawn timing of hatchery-origin Chinook Salmon (early August to mid-September) overlapped with that of natural-origin Chinook Salmon (late July to late September), and fish of both origins spawned in the same 30-km reach of the river. We estimated the percent of hatchery-origin spawners on the natural spawning grounds (pHOS) to be 12% for steelhead and 40% for spring Chinook Salmon across all study years. A kernel density analysis was used to estimate probability of spatiotemporal overlap between hatchery- and natural-origin spawners. For steelhead, we estimated this overlap to be 25% (95% CI 22.5–28%). For spring Chinook Salmon, tight spatial clustering of hatchery-origin fish resulted in a lower overlap estimate of 21% (13%-31%). We suggest adjusting pHOS estimates using these overlap estimates or similar spatiotemporal data on actual spawner proximity and possible interactions, and that these types of analyses be used in conjunction with gene flow analysis to accurately evaluate effects of individual hatchery programs.

Washington↗
USGS2022

Quantifying the effects of tides, river flow, and barriers on movements of Chinook Salmon smolts at junctions in the Sacramento–San Joaquin River Delta using multistate models

Successful migration of Chinook Salmon ( Oncorhynchus tshawytscha ) smolts seaward in the Sacramento – San Joaquin River Delta (hereafter, Delta) requires navigating a network of numerous branching channels. Within the Delta, several key junctions route smolts either towards more direct paths to the ocean or towards the interior Delta, an area associated with decreased survival. Movements within these junctions that determine route choice can be influenced by numerous behavioral and environmental factors, including the complex interplay between tidal and riverine hydraulics. Here, we apply continuous time multistate Markov models to examine the influence of tidal and riverine hydraulics, behavioral factors, and management actions on smolt movements. These models incorporate more information from acoustic telemetry data compared with previous approaches to modeling smolt movements in the Delta. By decomposing modeled flows into tidal and net flow signals we elucidate how each component influences movements into and out of distributary channels. Increasing net flows generally increased movement rates, while flood tides decreased seaward movement rates. Similarly, ebb tides increased downstream movements as fish go with the flow. We found less support for diel movement behaviors compared to flow metrics. Additionally, we quantify the effects of a large management action, the placement of a physical barrier, which was effective at decreasing entrainment into the interior Delta. Together, these results help inform management of Chinook Salmon and increase our understanding of the major factors driving smolt movements within these key junctions.

California↗
USGS2022

Using a mechanistic framework to model the density of an aquatic parasite Ceratonova shasta

Ceratonova shasta is a myxozoan parasite endemic to the Pacific Northwest of North America that is linked to low survival rates of juvenile salmonids in some watersheds such as the Klamath River basin. The density of C. shasta actinospores in the water column is typically highest in the spring (March–June), and directly influences infection rates for outmigrating juvenile salmonids. Current management approaches require quantities of C. shasta density to assess disease risk and estimate survival of juvenile salmonids. Therefore, we developed a model to simulate the density of waterborne C. shasta actinospores using a mechanistic framework based on abiotic drivers and informed by empirical data. The model quantified factors that describe the key features of parasite abundance during the period of juvenile salmon outmigration, including the week of initial detection (onset), seasonal pattern of spore density, and peak density of C. shasta . Spore onset was simulated by a bio-physical degree-day model using the timing of adult salmon spawning and accumulation of thermal units for parasite development. Normalized spore density was simulated by a quadratic regression model based on a parabolic thermal response with river water temperature. Peak spore density was simulated based on retained explanatory variables in a generalized linear model that included the prevalence of infection in hatchery-origin Chinook juveniles the previous year and the occurrence of flushing flows (≥171 m 3 /s). The final model performed well, closely matched the initial detections (onset) of spores, and explained inter-annual variations for most water years. Our C. shasta model has direct applications as a management tool to assess the impact of proposed flow regimes on the parasite, and it can be used for projecting the effects of alternative water management scenarios on disease-induced mortality of juvenile salmonids such as with an altered water temperature regime or with dam removal.

PeerJ↗
USGS2021

From site to system: Approaches for producing system-wide estimates of fish habitat in large rivers

Worldwide, many productive rivers are dam-regulated and rely on flow management strategies that must balance support of ecological processes with human water use. One component of evaluating this balance is to understand ecological consequences of alternative flow management strategies, which has often been accomplished by coupling population dynamics models with models that relate streamflow to habitat availability and quality. Numerous methods assign habitat availability to locations within a river basin: These include fine-scale field-measured values that are extrapolated to other locations within the basin having similar physical characteristics or equation-driven values created by functions of model-predicted values of physical characteristics. The array of options for creating habitat models is evolving rapidly as high-resolution remote-sensing data becomes more accessible and computational capacity improves. Our objective was to identify trade-offs among approaches that assign habitat relationships to large rivers and to create a decision support tool to supplement choices of extent and granularity. Using a selection of case studies that represent a breadth of scales and diverse trade-offs, we demonstrate the need for a transparent process of data evaluation and assessment to determine the appropriate fit for model scope or context that best supports management needs and recognize sources of uncertainty. The structured approach proposed here aims at improving future model development and refine population dynamics models that inform the management of rivers.

River Research and Applications↗
USGS2021

Identifying resting locations of a small elusive forest carnivore using a two-stage model accounting for GPS measurement error and hidden behavioral states

Studies of animal movement using location data are often faced with two challenges. First, time series of animal locations are likely to arise from multiple behavioral states (e.g., directed movement, resting) that cannot be observed directly. Second, location data can be affected by measurement error, including failed location fixes. Simultaneously addressing both problems in a single statistical model is analytically and computationally challenging. To both separate behavioral states and account for measurement error, we used a two-stage modeling approach to identify resting locations of fishers ( Pekania pennanti ) based on GPS and accelerometer data.

California, Oregon↗
USGS2021

Juvenile Chinook salmon survival, travel time, and floodplain use relative to riverine channels in the Sacramento–San Joaquin River Delta

Floodplains provide multiple benefits to both resident and migratory fish species, including juvenile Chinook Salmon Oncorhynchus tshawytscha , but direct comparisons of survival during migration through a floodplain versus riverine routes are scarce. The Yolo Bypass is a broad floodplain of the Sacramento River that floods in about 30% of years in response to large, uncontrolled runoff events. We analyzed data from an acoustic telemetry study conducted in winter 2016 to estimate the proportion of tagged juvenile Chinook Salmon entrained from the Sacramento River into the Yolo Bypass and their spatial distribution within the Yolo Bypass. In addition, we compared survival and travel time of Chinook Salmon that migrated through the Yolo Bypass to those migrating via alternative non‐floodplain migration routes at varying stages of a flood event that activated the Yolo Bypass. We found that entrainment into the Yolo Bypass ranged from 1% to 80% among different release groups, with the highest entrainment coinciding with the peak of the March 2016 flooding event. Survival for Chinook Salmon migrating through the Yolo Bypass was similar to survival of those migrating through main‐stem migration routes. At the relatively high flows necessary to enable flooding of the Yolo Bypass, survival estimates varied little among release groups and migration routes. Furthermore, mean daily survival rates for Chinook Salmon migrating through the flooded Yolo Bypass were comparable to those of fish migrating through the other non‐floodplain routes. Median travel times remained relatively constant during various stages of flooding in the Yolo Bypass. This research should help managers to better understand the potential costs and benefits to floodplain restoration and routing of migrating Chinook Salmon into off‐channel habitat.

California↗
USGS2020

Effects of tidally varying river flow on entrainment of juvenile salmon into Sutter and Steamboat Sloughs

Survival of juvenile salmonids in the Sacramento–San Joaquin Delta (Delta) varies by migration route, and thus the proportion of fish that use each route affects overall survival through the Delta. Understanding factors that drive routing at channel junctions along the Sacramento River is therefore critical to devising management strategies that maximize survival. Here, we examine entrainment of acoustically tagged juvenile Chinook Salmon into Sutter and Steamboat sloughs from the Sacramento River. Because these sloughs divert fish away from the downstream entrances of the Delta Cross Channel and Georgiana Slough (where fish access the low-survival region of the interior Delta), management actions to increase fish entrainment into Sutter and Steamboat sloughs are being investigated to increase through-Delta survival. Previous studies suggest that fish generally “go with the flow”—as net flow into a divergence increases, the proportion of fish that enter that divergence correspondingly increases. However, complex tidal hydrodynamics at sub-daily time-scales may be decoupled from net flow. Therefore, we modeled routing of acoustic tagged juvenile salmon as a function of tidally varying hydrodynamic data, which was collected using temporary gaging stations deployed between March and May of 2014. Our results indicate that discharge, the proportion of flow that entered the slough, and the rate of change of flow were good predictors of an individual’s probability of being entrained. In addition, interactions between discharge and the proportion of flow revealed a non-linear relationship between flow and entrainment probability. We found that the highest proportions of fish are likely to be entrained into Steamboat Slough and Sutter Slough on the ascending and descending limbs of the tidal cycle, when flow changes from positive to negative. Our findings characterize how patterns of entrainment vary with tidal flow fluctuations, providing information critical for understanding the potential effect of management actions (e.g., fish guidance structures) to modify routing probabilities at this location. Main Content View Larger 1 Sponsored by the Delta Science Program and the UC Davis Muir Institute ABSTRACT Survival of juvenile salmonids in the Sacramento–San Joaquin Delta (Delta) varies by migration route, and thus the proportion of fish that use each route affects overall survival through the Delta. Understanding factors that drive routing at channel junctions along the Sacramento River is therefore critical to devising management strategies that maximize survival. Here, we examine entrainment of acoustically tagged juvenile Chinook Salmon into Sutter and Steamboat sloughs from the Sacramento River. Because these sloughs divert fish away from the downstream entrances of the Delta Cross Channel and Georgiana Slough (where fish access SFEWS Volume 19 | Issue 2 | Article 4 https://doi.org/10.15447/sfews.2021v19iss2art4 * Corresponding author: rperry@usgs.gov 1 Western Fisheries Research Center US Geological Survey Cook, WA 98605 USA 2 California Water Science Center US Geological Survey Sacramento, CA 95819 USA 3 Current address: Mid-Columbia Fish and Wildlife Conservation Office Yakima Basin Program US Fish and Wildlife Service Yakima, WA 98903 USA the low-survival region of the interior Delta), management actions to increase fish entrainment into Sutter and Steamboat sloughs are being investigated to increase through-Delta survival. Previous studies suggest that fish generally “go with the flow”—as net flow into a divergence increases, the proportion of fish that enter that divergence correspondingly increases. However, complex tidal hydrodynamics at sub-daily time-scales may be decoupled from net flow. Therefore, we modeled routing of acoustic tagged juvenile salmon as a function of tidally varying hydrodynamic data, which was collected using temporary gaging stations deployed between March and May of 2014. Our results indicate that discharge, the proportion of flow that entered the slough, and the rate of change of flow were good predictors of an individual’s probability of being entrained. In addition, interactions between discharge and the proportion of flow revealed a non-linear relationship between flow and entrainment probability. We found that the highest proportions of fish are likely to be entrained into Steamboat Slough and Sutter Slough on the ascending and descending limbs of the tidal cycle, when flow changes from positive to negative. Our findings characterize how patterns of entrainment vary with tidal flow fluctuations, providing information critical for understanding the potential effect of management RESEARCH Effects of Tidally Varying River Flow on Entrainment of Juvenile Salmon into Sutter and Steamboat Sloughs Jason G. Romine 1,3 , Russell W. Perry* 1 , Paul R. Stumpner 2 , Aaron R. Blake 2 , Jon R. Burau 2 2 VOLUME 19, ISSUE 2, ARTICLE 4 actions (e.g., fish guidance structures) to modify routing probabilities at this location. KEY WORDS Telemetry, juvenile salmon, migration routing, survival INTRODUCTION The Sacramento–San Joaquin River Delta (hereafter referred to as “the Delta”) is a complex series of channels and embayments in west central California of the United States. The Delta has undergone drastic transformation through construction of dikes, levees, reclaimed land, dredged canals and cuts, and water export projects (Nichols et al. 1986). The loss of habitat coupled with introduction of non-native piscivorous fishes has led to the decline of several salmonid stocks that utilize the Delta (Lindley 2009; National Marine Fisheries Service 2014). The physical complexity of the Delta poses significant challenges for understanding how juvenile salmon negotiate the complex channel network and survive in different migration routes. Yet such information is critical for understanding how water-management actions, such as operation of water diversions, influence survival of juvenile salmon. Through-Delta survival of juvenile Chinook Salmon that emigrate from the Sacramento River ranges from 10% to 80%, depending on river flow and migration route (Perry et al. 2018). The Delta can be broken down into four primary routes: (1) Sacramento River, (2) Steamboat and Sutter sloughs, (3) Georgiana Slough, and (4) Delta Cross Channel (DCC). Fish that remain in the Sacramento River consistently have the highest survival (Perry et al. 2010, 2013, 2018). However, fish that enter the interior Delta—the region to the south of the Sacramento River (Figure 1)—have the lowest survival among all routes and survive at less than half the rate of fish in the Sacramento River, likely as a result of longer migration times and exposure to non-native predators (Newman and Brandes 2010; Perry et al. 2018). On average, fish that migrate through Steamboat and Sutter sloughs exhibit survival similar to fish that remain in the Sacramento River at high flows but have lower survival at low flows (Perry et al. 2018). Because of differences in survival among migration routes, the proportion of fish that use each route affects the total survival of the population. Therefore, understanding the drivers behind fish routing in the Delta is imperative to inform management actions that help in the recovery of imperiled salmonid populations in the Central Valley. For example, Perry et al. (2013) found that total survival through the Delta could be increased by up to 7 percentage points by eliminating entrainment into Georgiana Slough and the DCC. These findings led to investigation of management actions to reduce entrainment into the DCC (Plumb et al. 2016) and Georgiana Slough (Perry et al. 2014). Both physical and non-physical barriers have been tested at the entrance to Georgiana Slough divergence (Perry et al. 2014; Romine et al. 2016). A non-physical barrier was able to reduce entrainment to the interior Delta through Georgiana Slough (Perry et al. 2014), but a floating fish-guidance structure reduced entrainment to a lesser extent (Romine et al. 2016). Research and engineering solutions to minimize entrainment have focused on the Georgiana Slough divergence, the DCC divergence, and the Old River divergence in the San Joaquin River (Buchanan et al. 2013; SJRG 2013). However, there has been little focus on understanding fish routing dynamics at other primary river junctions in the Delta, such as Sutter and Steamboat sloughs. Sutter and Steamboat sloughs diverge from the Sacramento about 10 km upstream from the DCC and Georgiana slough, and represent the first major junction that juvenile salmon encounter as they enter the Delta from the Sacramento River ( Figure 1 ). Because Sutter and Steamboat sloughs are upstream of the entrance to the interior Delta via the DCC and Georgiana Slough (Figure 1), juvenile salmon that enter Sutter and Steamboat sloughs avoid entrainment into the interior Delta where survival is low. Thus, management actions to increase entrainment could increase overall.

Sacramento–San Joaquin Delta↗
USGS2019

A natural‐origin steelhead population's response to exclusion of hatchery fish

It is asserted that reduction or elimination of hatchery stocking will increase natural‐origin salmon Oncorhynchus spp. and steelhead O. mykiss production. We conducted an analysis of steelhead population census data (1958–2017) to determine whether elimination of summer steelhead stocking in the upper Clackamas River in 1998 increased the productivity of natural‐origin winter steelhead. A Bayesian state–space stock–recruitment model was fitted to the adult steelhead data set, and productivity was estimated as a function of hatchery‐origin spawner abundance as well as other environmental factors. When used as a predictive variable in our model, the abundance of hatchery summer steelhead spawners (1972–2001) did not have a negative effect on winter steelhead recruitment. However, spill at North Fork Dam (the gateway to the upper Clackamas River basin) and the Pacific Decadal Oscillation (an index of ocean conditions) were both negatively associated with winter steelhead recruitment. Moreover, winter steelhead abundance in the upper Clackamas River basin failed to rebound to abundances observed in years prior to the hatchery program, and fluctuations in winter steelhead abundance were correlated with those of other regional winter steelhead stocks. Our assessment underscores the need for studies that (1) directly quantify the effects of hatchery fish on the production of natural‐origin salmon and steelhead, (2) empirically test published theories about mechanisms of hatchery fish impacts on natural‐origin populations, and (3) document population responses to major changes in hatchery programs.

Oregon↗
USGS2019

Estimating annual Ceratonova shasta mortality rates in juvenile Scott and Shasta River coho salmon that enter the Klamath River mainstem

The impacts of Ceratonova shasta on Klamath River salmonids have been the focus of tremendous research and monitoring over the past decade. Knowledge gained from the various studies has resulted in a growing suite of decision support tools that can be used to predict the prevalence of infection and mortality that can be expected from varying exposure concentrations to C. shasta waterborne spores, exposure durations, and water temperatures. More recent efforts have shown that when coupled with estimates of abundance and temporal migration timing, these tools can be used to predict population-level rates of annual mortality due to ceratomyxosis. In this report, we apply those tools to estimate annual mortality rates of juvenile Coho Salmon Oncorhynchus kisutch originating from the Scott and Shasta rivers that result from exposure to C. shasta in the mainstem Klamath River. Additionally, we simulate how a water management flow regime targeted to reduce disease risk may translate into differing estimates of mortality rates. In general, we found large variation among annual mortality rate estimates, ranging from 0% to 68% across both rivers and across all years considered in this investigation. Further, we estimate that fish from the Shasta River experienced higher mortality rates owning to their prolonged exposure history. Finally, our simulations suggest that the flow regime targeting reduced disease risk could be effective at reducing annual Coho Salmon mortality rate estimates, with the extent of the estimated reductions related to the timing of the onset of measurable in-river waterborne spore concentrations and the overlap with the Klamath River residence for each source population.

California, Oregon↗
USGS2017

Building a state-space life cycle model for naturally produced Snake River fall Chinook salmon

In 1992, Snake River basin fall Chinook salmon (Oncorhynchus tshawytscha) were listed for protection under the U.S. Endangered Species Act (NMFS 1992) and the population remained below 1000 individuals until 2000. Since then, returns from natural production has rebounded to over 20,000 spawners owing to a host of factors including reduced harvest (Peters et al. 2001), stable minimum spawning flows (Groves and Chandler 1999), summer flow augmentation (Connor et al. 2003), predator control (Beamesderfer et al. 1996), hatchery supplementation (Rosenberger et al. 2017), improved juvenile passage structures (Adams et al. 2014), summer spill operations (Perry et al. 2006; Adams et al. 2008), and periods of favorable ocean conditions and food availability (Logerwell et al. 2003; Peterson et al. 2014). Given this change in abundance coincident with numerous management actions and fluctuation in environmental drivers, quantifying which factors contributed to the observed rebound in natural production can provide critical insights into future management actions for this at-risk population. Multistage life cycle models provide a powerful analytical framework for understating how each life stage of a population contributes to population growth rate (Moussalli and Hilborn 1986; Greene and Beechie 2004). Multistage models may also be used as an analytical framework to explicitly estimate demographic parameters of a population model. This approach has an advantage over single-stage stock-recruitment models by allowing population growth rates to be partitioned among life stages rather than aggregated over an entire life cycle. Such partitioning allows for estimating 1) stage-specific density dependence, and 2) stage-specific effects of environmental factors or management actions. For example, Zabel et al. (2006) estimated parameters of a multistage model used in the context of a population viability analysis for spring/summer Chinook salmon in the Snake River, but such an approach has yet to be applied to fall Chinook salmon in the Snake River basin. Typically, data informing estimates of abundance at particular “check points” in the life cycle determines the complexity of the multistage model that can be fit to the data. For fall Chinook salmon, we are developing a two-stage model that encompasses: 1) upstream passage of spawners at Lower Granite Dam (LGR) to the subsequent downstream passage of their progeny at the dam, and 2) downstream passage of juveniles at LGR to their subsequent return from the ocean and passage at the Dam 2‒6 years later. This approach partitions the life cycle of fall Chinook salmon both spatially and temporally, which allows us to fit and compare alternative models with covariates specific to each stage. Our previous report to the ISAB (Zabel et al. 2013) detailed methods for estimating abundance of naturally produced adults and juveniles passing Lower Granite Dam, which provides the requisite data for fitting a two-stage model. The intent of this report is to describe the structure of the two-stage life cycle model, present preliminary results from fitting the model to data, and outline future directions and developments. As is clear from the diversity of models presented in this report, “life cycle models” range from very simple theoretically based population models (e.g., the Beverton-Holt stock- recruitment model) to very complex spatially explicit simulation models linked to hydrosystem hydrodynamic models (e.g., the COMPASS model for a single transition in a life cycle model, Zabel et al. 2008). We chose to develop a model of intermediate complexity that casts the two- stage life cycle model in a state-space framework (Newman et al. 2014). We chose to use a state-space framework implemented in a Bayesian framework because: • It provides both a statistical estimation framework for retrospective statistical analysis and a stochastic simulation framework for prospective analysis to evaluate alternative management actions. • Abundance estimates are uncertain. A state-space framework accounts for observation uncertainty in the abundance estimates and other data (e.g., age structure) while simultaneously estimating process uncertainty. • It allows for missing data. By drawing missing data from an appropriate probability model, uncertainty owing to missing data can be propagated without having to omit data or assume fixed values for missing data. Thus, a two-stage state-space life cycle model for fall Chinook salmon strikes an appropriate balance between model complexity, tractability, and applicability given the goals of performing both retrospective and prospective analysis to guide future management of this population.

Idaho, Oregon, Washington, Wyoming↗
USGS2011

Analyses of potential factors affecting survival of juvenile salmonids volitionally passing through turbines at McNary and John Day Dams, Columbia River

This report describes analyses of data from radio- or acoustic-tagged juvenile salmonids passing through hydro-dam turbines to determine factors affecting fish survival. The data were collected during a series of studies designed to estimate passage and survival probabilities at McNary (2002-09) and John Day (2002-03) Dams on the Columbia River during controlled experiments of structures or operations at spillways. Relatively few tagged fish passed turbines in any single study, but sample sizes generally were adequate for our analyses when data were combined from studies using common methods over a series of years. We used information-theoretic methods to evaluate biological, operational, and group covariates by creating models fitting linear (all covariates) or curvilinear (operational covariates only) functions to the data. Biological covariates included tag burden, weight, and water temperature; operational covariates included spill percentage, total discharge, hydraulic head, and turbine unit discharge; and group covariates included year, treatment, and photoperiod. Several interactions between the variables also were considered. Support of covariates by the data was assessed by comparing the Akaike Information Criterion of competing models. The analyses were conducted because there was a lack of information about factors affecting survival of fish passing turbines volitionally and the data were available from past studies. The depth of acclimation, tag size relative to fish size (tag burden), turbine unit discharge, and area of entry into the turbine intake have been shown to affect turbine passage survival of juvenile salmonids in other studies. This study indicates that turbine passage survival of the study fish was primarily affected by biological covariates rather than operational covariates. A negative effect of tag burden was strongly supported in data from yearling Chinook salmon at John Day and McNary dams, but not for subyearling Chinook salmon or juvenile steelhead. The negative effect of tag burden in data we examined from yearling Chinook salmon supports the recent findings from laboratory studies of barotrauma effects. A curvilinear (quadratic) effect of turbine unit discharge was weakly supported in data from subyearling Chinook salmon at John Day Dam. The maximum survival from those data was estimated to occur at a discharge of 15.9 thousand cubic feet per second, but the estimate was imprecise (95 percent confidence interval of -1.7-33.7 thousand cubic feet per second). This estimate is within the range of 1 percent of peak turbine operating efficiency (12.0-21.6 thousand cubic feet per second), but is lower than the 17.2 thousand cubic feet per second discharge at peak operating efficiency (at a head of 102 feet near the median in the data we examined). Effects of water temperature were supported in four of the five examined data sets and were strongly supported in all but one. Spill percentage, head, and total discharge received weak or moderate support in some cases. The results are consistent with those of several controlled field experiments of turbine discharge. Studies based on the Hi-Z Turb'N tag (balloon tag) often show small, generally statistically insignificant, differences in survival at different turbine discharge levels. Some studies also show that a quadratic equation can be well fit to the relation of survival and turbine unit discharge. The lack of support for the operational covariates in most of the data sets we examined may be due to the small effect turbine discharge has even in controlled studies, the observational nature of the data we used, and the evaluation method. We assessed support of the data for models of linear and quadratic effects, whereas controlled experiments often statistically compare the point estimates of survival from each operational treatment studied. The results of our analyses suggest tag burden should be minimized or controlled for in analyses of future stu

Oregon;Washington↗