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Nicholas A. Som

Publications and source records attributed to Nicholas A. Som.

At least 19 recordsLinked to original sources
USGS2024

It's about time: A multistate semicontinuous time mark–recapture model to evaluate seasonal survival and movement rates of juvenile Coho Salmon in a small coastal watershed

Objective Many mark–recapture models assume that releases and recaptures are discrete events, and researchers often aggregate continuous recapture data (e.g., passive integrated transponder [PIT] detections) into coarse temporal scales to satisfy this assumption. This temporal discretization could result in parameter biases by ignoring the individual heterogeneity in the time susceptible to mortality after recapture and the conditions experienced (e.g., temperature and predation risk) before and after recapture. Our objectives were to (1) estimate the amount of bias in survival and emigration rates due to different temporal discretization durations when recapture events occur continuously and (2) apply this semicontinuous model to estimate rates of early emigration and overwinter survival for Coho Salmon Oncorhynchus kisutch in a coastal California watershed. Methods We developed a semicontinuous time multistate mark–recapture model to separately estimated emigration and survival rates throughout the year. We used weekly time-varying occasions paired with discrete spatial states and conducted extensive simulation trials to explore potential model bias. We then applied the model to an existing 4-year dataset of Coho Salmon PIT tag detections. Result Our simulations indicated that that the amount of bias in survival and movement rates decreased as the temporal discretization duration decreased. The confidence interval of the bias estimates included zero with a duration of 8 days, indicating that this duration was sufficiently short to model movement and survival. Results from our Coho Salmon analysis suggest that overwinter survival rate ranged from 0.72 to 0.83, which is higher than previous estimates for Coho Salmon in this region. We estimate that a substantial proportion of smaller juveniles (0.21–0.28 annually) move to downstream nonnatal rearing habitats before the spring smolt migration. Conclusion Our semicontinuous modeling approach can be implemented relatively easily and used to analyze continuous detection data to accurately estimate survival and movement rates. Our analysis of Coho Salmon PIT tag detections implies that previous low estimates of apparent overwinter survival of Coho Salmon were partially due to high movement rates to alternative rearing locations. This contrasts with conclusions from the previous research that suggested that overwinter survival was a major limiting factor for population recovery and implies that species recovery may be improved by considering multiple emigration patterns in the design of future research, monitoring, and restoration projects.

California↗
USGS2024

Effects of 2D hydrodynamic model resolution on habitat estimates for rearing Coho Salmon in contrasting channel forms

Estimating the impacts of water allocation decisions on fish populations and habitat availability is an important part of environmental flow assessments, especially in locations where water resources are limited. Two-dimensional hydrodynamic models (2DHMs) are commonly coupled with biological models to estimate fish habitat quality, area, and capacity across a range of proposed streamflows. Increasingly, resource managers are relying on landscape-scale model domains with coarse model resolutions to maintain feasible computational loads, but this may affect habitat estimates if the mesh element size of the model exceeds the spatial scale relevant to the organism. We investigated how coarsening the resolution of a 2DHM influences the area and spatial distribution of estimated Coho Salmon ( Oncorhynchus kisutch ) fry habitats. We used an interpolation scheme that upscaled mesh elements from a high-resolution (0.25 m 2 ) 2DHM to quantify and visualize the effects of 2DHM resolution on estimates of Coho Salmon fry habitat for two contrasting channel morphologies and across a broad range of streamflows. Estimates of Coho Salmon fry habitat at increasingly coarser resolutions led to 20%–50% reductions in weighted usable habitat area (WUA) across several streamflow scenarios for a complex channel type, but did not impact estimates in a confined, flume-like channel. Additionally, flow-to-habitat area relationships were not congruent at a given streamflow when resolution coarsened. Along with almost 500% more high-quality habitat area estimated in the complex channel type over the confined, discrepancies in habitat area increased with higher flows in areas defined as optimal for rearing Coho Salmon fry. Considering that complex channel types contain critical habitat for Coho Salmon fry, this study suggests coarse 2DHM resolutions may exclude important wetted edge and off-channel habitats from environmental flow assessments.

California↗
USGS2023

Calibration of the Trinity River Stream Salmonid Simulator (S3) with extension to the Klamath River, California, 2006–17

The Trinity River is managed in two sections: (1) the upper 64-kilometer (km) “restoration reach” downstream from Lewiston Dam and (2) the 120-km lower Trinity River downstream from the restoration reach. The Stream Salmonid Simulator (S3) has been previously constructed and calibrated for the restoration reach. In this report, we extended and parameterized S3 for the 120-km section of the lower Trinity River to the confluence with the Klamath River and then to the Pacific Ocean in northern California. S3 is a deterministic life-stage structured-population model that tracks daily growth, movement, and survival of juvenile salmon. A key theme of the model is that river discharge affects habitat availability and capacity, which in turn drives density-dependent population dynamics. To explicitly link population dynamics to habitat quality and quantity, the river environment is constructed as a one-dimensional series of linked habitat units, each of which has an associated daily timeseries of discharge, water temperature, and useable habitat area or carrying capacity. In turn, the physical characteristics of each habitat unit and the number of fish occupying each unit drive (1) survival and growth within each habitat unit and (2) movement of fish among habitat units. The physical template of the Trinity River was formed by classifying the river into 910 meso-habitat units that were designated into runs, riffles, or pools. For each habitat unit, we developed a timeseries of daily discharge, water temperature, amount of available spawning habitat, and fry and parr carrying capacity. Capacity timeseries were constructed using state-of-the-art models of spatially explicit hydrodynamics and quantitative fish habitat relationships developed for the Trinity River. These variables were then used to drive population dynamics such as egg maturation and survival, and in turn, juvenile movement, growth, and survival. We estimated key movement and survival parameters by calibrating the model to 12 years (2007–18) of weekly juvenile abundance estimates from two rotary screw traps: (1) the Pear Tree trap near the downstream end of the restoration reach and (2) the Willow Creek trap site is about 40.2 km upriver from the Trinity River’s confluence with the Klamath River. The calibration consisted of replicating historical conditions as closely as possible (for example: flow, temperature, spawner abundance, spawning location and timing, and hatchery releases), and then running the model to predict weekly abundance passing the trap location. We also evaluated four alternative model structures that included either no density-dependence, density-independent movement and survival, density-dependent survival, or density-dependent movement. Akaike information criterion model selection was used to evaluate the strength of evidence for alternative model structures to simulate the observed abundance estimates. Model selection supported the conclusion that the fully density-dependent model and density-dependent survival model was better supported by the data than the no density-dependence or density-dependent movement model. Because density-dependent movement was favored in past evaluations, we focus on the results from the fully density-dependent model. Parameter estimates from this model indicated that fry were less likely than parr to move downstream and that fry moved slower. Fry had a lower daily survival probability than parr. In contrast, hatchery fish had the highest probability of movement and the lowest daily survival probability. Fitting the model to both traps individually enabled us to independently compare the fit and performance of S3 at simulating fish abundance, timing, and growth of juvenile salmon in the upper restoration reach and lower Trinity River. We obtained a better fit to the data at the Willow Creek trap site than we obtained at the Pear Tree trap site, regardless of whether we fit the model to the abundances at the Pear Tree trap or Willow Creek trap. This better fit was surprising given that the S3 input data for the upper restoration reach required fewer assumptions than fitting to the Willow Creek trap site that is farther down river. Fitting S3 to weekly abundances at the Willow Creek trap site required making assumptions about (1) extrapolating capacity-flow relationships to unmeasured habitat units; (2) spatially allocating spawners within the lower Trinity River; and (3) approximating the abundance, timing, and size of juveniles entering from tributaries. The model provided better fit to the data at the Willow Creek trap site. In the weekly abundance estimates, in relation to the S3 simulated abundances, several migration years’ (2011, 2015–17) weekly abundance estimates appeared truncated and were near or at peak annual abundances in January, suggesting that a large fraction of juveniles was migrating as early as December at the Pear Tree trap site. Some early life dynamics may not be currently incorporated into S3. For example, the estimation of abundance at the Pear Tree trap may be biased because of size selectivity. Knowing about selectivity at the Pear Tree trap could greatly improve S3’s ability to predict weekly and peak abundances each year.

California↗
USGS2023

Simulating post-dam removal effects of hatchery operations and disease on juvenile Chinook salmon (Oncorhynchus tshawytscha) production in the Lower Klamath River, California

Executive Summary The Federal Energy Regulatory Commission has been considering the approval to breach four dams on lower Klamath River in southern Oregon and northern California. Approval of this application would allow for Strikeouts indicate text deletion hereafter. decommissioning and dam removal, beginning as early as 2023. This action would affect Klamath River salmon ( Oncorhynchus ssp.) populations, a critical food source for federally endangered Southern Resident Killer Whales ( Orcinus orca ). In the long run, reintroduction of salmon populations to the upper Klamath River Basin may increase salmon abundance available to Southern Resident Killer Whales, but in the near term, it is uncertain how changes in hatchery management and disease-caused mortality by the myxosporean parasite Ceratonova shasta will influence abundance of salmon populations entering the ocean. To assess this uncertainty, we used the Stream Salmonid Simulator (S3) to simulate population dynamics of juvenile Chinook salmon ( Oncorhynchus tshawytscha ) for nine different population sources that rear and migrate through the Klamath River. S3 is a spatially explicit population model that runs on a daily time-step and simulates daily growth, survival, and movement of juvenile Chinook salmon from the time of spawning through ocean entry. The key features of this model relevant to this report include (1) a C. shasta disease submodel; (2) a temperature-dependent bioenergetics model that calculates daily growth rates; (3) size-dependent movement; (4) density-dependent dynamics that are influenced by the effect of flow on suitable habitat area; and (5) habitat, river flow, and water temperature specific to each scenario. We constructed and ran four scenarios: two scenarios for dams in place (Dams In) and dams removed (Dams Out), and given these dam-removal conditions, a low- and high-spore scenario for C. shasta . Each scenario was run for nine water years representing a range of conditions from dry to wet. Previously published daily river flows and water temperatures for Dams In and Dams Out provided physical inputs for each scenario. Daily spore concentrations were simulated using a three-part mechanistic model that used river discharge, water temperature, and the prevalence of infection (POI) of hatchery-origin Chinook salmon juveniles with C. shasta in the previous year 3 . We constructed two spore scenarios for each Dams In and Dams Out scenario, a “Low Spore” scenario and a “High Spore” scenario resulting in four scenarios for comparison. Spore scenarios were established by setting the prior-year POI of hatchery fish to 0.15 and 0.75 in the estimation of spore concentrations. Hatchery releases under Dams Out differed from those under the current Dams In scenario. Hatchery releases under the Dams Out scenario were modified to emulate changes in hatchery production that would occur under Dams Out conditions. This included moving hatchery production and releases from Iron Gate Dam to a proposed hatchery at Fall Creek, which would be located about 11 kilometers (km) upstream of Iron Gate Dam. It is anticipated that the Fall Creek hatchery would produce fewer fish at smaller and larger sizes at different release timings. For salmon inputs, we used observed historical abundance of main-stem spawners from brood year 2009 and juvenile salmon entering from tributaries in water year 2010, which represented an average return year for the 2005–18 period. Main-stem spawning was allowed to shift upstream from Iron Gate Dam under the Dams Out scenario. We also included hatchery-origin fish as natural spawners that would have otherwise returned to Iron Gate Hatchery in the first 3 years following dam removal. The S3 model simulated considerably higher total abundance for Dams Out relative to the respective Dams In scenarios, and higher abundance for the Low Spore scenario relative to the High Spore scenario. The difference in abundance between the four combinations of the dam-removal and spore scenarios varied among population groups. For main-stem natural production, juvenile abundance at ocean entry was 2–3 times higher for Dams Out scenarios than for Dams In scenarios, and juvenile abundance for High Spore scenarios was lower than that for the Dams Out Low Spores scenario. For hatchery releases, abundance at ocean entry was similar between Dams In and Dams Out scenarios for most water years, despite lower release sizes from Fall Creek Hatchery under Dams Out. For tributary populations, abundance for the High Spore scenarios was consistently lower than for the Low Spore scenarios, but differences between dam-removal scenarios varied among water years, with Dams Out scenarios having similar or higher abundance than Dams In scenarios, and dry water years having the largest difference between Dams In and Dams Out scenarios. We determined that different factors affected the response of each population group. For main-stem natural production, survival from fry emergence to ocean entry was higher under Dams Out scenarios compared to Dams In scenarios because juveniles emerged later and tended to arrive at the ocean sooner and at larger sizes, causing the population to have less time-dependent in-river mortality. Owing to their late release timing, hatchery populations had high disease-caused mortality in Dams In and Dams Out High Spore scenarios. Furthermore, a high proportion of infected fish (those that would be expected to die at some future point) survived to the ocean. Iron Gate Hatchery fish had lower survival rates than releases from Fall Creek Hatchery because the last mid-June release group from the 2010 Iron Gate Hatchery release incurred nearly total mortality in most water years owing to water temperatures exceeding 24 degrees Celsius. Our analysis shows how the S3 model was able to track different populations and provide insights on how the differential response of each population combined to influence the simulated number of juvenile Chinook salmon arriving at the Pacific Ocean where they become available as a food source for Southern Resident Killer Whales.

California↗
USGS2023

A life cycle model for evaluating estuary residency and restoration potential in Chinook salmon

Understanding the spatial and temporal habitat use of a population is a necessary step for recovery planning. For Chinook salmon ( Oncorhynchus tshawytscha ), variation in their migration and habitat use complicate predicting how restoring habitats could impact total recruitment. To evaluate how juvenile life history variation affects a population’s response to potential restoration, we developed a stage-structured model for a Chinook salmon population in a northern California river with a seasonally closed estuary. We modeled the timing of juvenile migration and estuarine use as a function of freshwater conditions and fish abundance. We used the model to evaluate the sensitivity of the population to different estuary and freshwater restoration scenarios that could affect population parameters at different life stages. The population’s run size increased most in response to freshwater restoration that enhanced spawning productivity (egg and fry survival), followed by spawner capacity. In contrast, estuary restoration scenarios affected only a subset of Chinook salmon (average 15%), and as a result, did not have a large impact on the total recruitment of a cohort. Under current condition, estuary rearing fish were over six times less likely to survive than fish that migrate to the ocean in the spring or early summer before estuary closure. Because estuary residents experienced low survival in the estuary and in the ocean, improvements to both estuary survival and growth would be needed to increase their total survival. When life cycle monitoring data is available, life cycle models such as ours generate predictions at scales relevant to conservation and are an advantageous approach to managing and conserving anadromous salmon that use multiple habitats throughout their life cycle.

California↗
USGS2022

Extending the Stream Salmonid Simulator to accommodate the life history of coho salmon (Oncorhynchus kisutch) in the Klamath River Basin, Northern California

In this report, we apply the stream salmonid simulator (S3) to coho salmon ( Oncorhynchus kisutch ) in the Klamath River Basin by extending the original model to account for life history and disease dynamics specific to coho salmon. This version of S3 includes tracking of three separate life-history strategies representing the different time periods and ages at which fish leave natal tributaries such as the Scott and Shasta Rivers (age-0 spring, age-0 fall, or age-1 smolt). Once fish leave their natal tributaries and enter the Klamath River, the deterministic life-stage-structured population model simulates daily growth, movement, and survival. We extend the model to include non-natal tributary dynamics, where spring age-0 fish entry to non-natal tributaries is simulated based on environmental conditions in the main-stem Klamath River. Fish that use non-natal tributaries then reenter the Klamath River during the winter or spring as smolts and actively migrate downstream. We also consider the life history strategy where fish rear in natal tributaries and enter the Klamath River as age-1 smolts. In addition to simulating different life history pathways that coho salmon may take, we model disease dynamics, incorporating new information on Ceratonova shasta related infection and mortality. We incorporate competitive interactions between juvenile coho and Chinook salmon ( Oncorhynchus tshawytscha ) by simulating density-dependent movement dynamics in response to Chinook salmon abundance. Model simulations suggest that total abundance and survival to the ocean differed between life-history strategies. In general, spring age-0 fish that leave their natal tributaries in their first spring had lower survival compared with fish that remained in natal tributaries and out-migrated later. Spring age-0 fish also had higher disease related mortality, owing to their residence in the main-stem Klamath River overlapping with periods of elevated C. shasta spore concentrations. Age-0 fish leaving their natal tributaries in the fall had near-zero disease related mortality. Most non-natal tributary use occurred at upstream tributary locations and was variable between the brood years depending on passage timing and environmental conditions. The inclusion of Chinook salmon in simulations resulted in decreased abundance and survival of Coho salmon reaching the ocean. In addition, we developed an R package to facilitate use of and continued development of S3 as a tool to guide management of juvenile salmonid populations.

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↗
USGS2020

Disease in Central Valley salmon: Status and lessons from other systems

Chinook Salmon ( Oncorhynchus tshawytscha ) are increasingly vulnerable to anthropogenic activities and climate change, especially at their most southern species range in California’s Central Valley. There is considerable interest in understanding stressors that contribute to population decline and in identifying management actions that reduce the impacts of those stressors. Along the west coast of North America, disease has been linked to declining numbers of salmonids and identified as a key stressor resulting in mortality. In the Central Valley, targeted studies have revealed extremely high prevalence of infectious agents and disease. However, there has been insufficient monitoring to understand the effect that disease may have on salmon populations. In order to inform future research, monitoring, and management efforts, a two-day workshop on salmon disease was held at UC Davis on March 14-15, 2018. This paper summarizes the science presented at this workshop, including the current state of knowledge of salmonid disease in the Central Valley and current and emerging tools to better understand its impacts on salmon. We highlight case studies from other systems where successful monitoring programs have been implemented. First, in the Klamath River where the integration of several data collection and modeling approaches led to the development of successful management actions, and second in British Columbia where investment in researching novel technologies led to breakthroughs in the understanding of salmon disease dynamics. Finally, we identify key information and knowledge gaps necessary to guide research and management of disease in Central Valley salmon populations.

California↗
USGS2019

Using the stream salmonid simulator (S3) to assess juvenile Chinook salmon (Oncorhynchus tshawytscha) production under historical and proposed action flows in the Klamath River, California

Executive Summary The production of Klamath River fall Chinook salmon ( Oncorhynchus tshawytscha ) in northern California and southern Oregon is thought to be limited by poor survival during freshwater juvenile life stages, in part a result of Ceratonova shasta —a highly infectious disease that can lead to high fish mortality. Higher flushing river flows are thought to affect the concentration of C. shasta spores, and in turn, juvenile salmon infection and mortality. The Stream Salmonid Simulator (S3) model was built to simulate the spatiotemporal dynamics of the growth, movement, and survival of juvenile salmon from spawning through migration to the Pacific Ocean in response to river flow, habitat availability, water temperature, and C. shasta spore concentrations. The S3 model has been calibrated to juvenile fall Chinook salmon abundances at a trap site within the Klamath River, and was specifically designed to provide objective predictions of juvenile salmon abundance and survival in relation to proposed flow management alternatives and resulting fish infection and mortality by C. shasta . Infection by C. shasta in the Klamath River is location specific, occurring in a “disease zone” with high spore concentrations. The spatial extent of this disease zone (from river kilometer 289.6 to 212.9) has been incorporated in the S3 model for the Klamath River, enabling the assessment of disease effects on fish at specific spatial locations such as the trap sampling sites, and for fish that were or were not exposed to the disease zone as they emigrate the Klamath River to the Pacific Ocean. Given the information gained from field observations on spore concentrations in relation to river flow, deliberations by resource managers resulted in the incorporation of springtime flushing flows in a Proposed Action (PA) scenario developed in part to lower spore concentrations within the disease zone. A Historical (HI) scenario based on the observed flows, temperatures, and spore concentrations from 2004 to 2016 was used to compare and contrast the potential benefits to juvenile salmon from PA flows in relation to the HI conditions.

California↗
USGS2019

Application of the Stream Salmonid Simulator (S3) to Klamath River fall Chinook salmon (Oncorhynchus tshawytscha), California—Parameterization and calibration

Executive Summary In this report, we describe application of the Stream Salmonid Simulator (S3) to Chinook salmon ( Oncorhynchus tshawytscha ) in the Klamath River between Keno Dam in southern Oregon and the ocean in northern California. S3 is a deterministic life-stage-structured population model that tracks daily growth, movement, and survival of juvenile salmon. It can track different source populations or species, such as major tributary populations that enter a river like the Klamath River. A key theme of the model is that river flow affects habitat availability and capacity, which in turn drives density-dependent population dynamics. To explicitly link population dynamics to habitat quality and quantity, the river environment is constructed as a one-dimensional series of linked habitat units, each of which has an associated daily time series of discharge, water temperature, and useable habitat area or carrying capacity. In turn, the physical characteristics of each habitat unit and the number of fish occupying each unit affect survival and growth within each habitat unit and movement of fish among habitat units. The physical template of the Klamath River was formed by classifying the river into 2,635 mesohabitat units composed of runs, riffles, and pools. This template enabled modeling of the unimpounded Klamath River between the Keno Dam (the uppermost of four dams) and Iron Gate Dam (the lowermost dam) to address dam-removal scenarios. However, in this report, our focus was on parameterizing and calibrating the model under existing conditions, which included 1,706 discrete habitat units over the 312-kilometer (km) section of river between Iron Gate Dam and the ocean. For each habitat unit, we developed a time series of daily flow, water temperature, and amount of available habitat (weighted usable habitat area [WUA]) for spawners, fry, and parr. WUA time series were constructed using habitat suitability criteria for Chinook salmon applied to eight two-dimensional (2-D) hydrodynamic models that represented the geomorphic variability in habitat across the Klamath River. Results from the 2-D models were then extrapolated to unmodeled habitat units by scaling WUA curves for changes in habitat unit length and width. These variables were then used to drive population dynamics such as egg development and survival and juvenile movement, growth, and survival.

California, Oregon↗
USGS2019

Changes in adult Chinook salmon (Oncorhynchus tshawytscha) survival within the lower Columbia River amid increasing pinniped abundance

Significant effort towards conservation has contributed to the recovery of historically depleted pinniped populations world-wide. However, in several locations where pinnipeds have increased, they have been blamed for preventing the recovery of commercially valuable fish species through predation. Prompted by increasing pinniped abundance within the Columbia River (CR) USA, over a six year period, we used Passive Integrated Transponder tags to measure the survival of adult spring-run Chinook salmon (Oncorhynchus tshawytscha) through the estuary and lower CR to Bonneville Dam (Rkm 234). We estimated 51 751 - 224 705 salmon died annually from sources other than harvest. Mixed-effects logistic regression modelling identified pinniped predation as the most likely source. The odds of survival was estimated to decrease by 32% (95% CI: 6%-51% decrease) for every additional 467 sea lions, and to increase by 32% (95% CI: 8%-61% increase) for every increase of 1.5 in the log of American shad (Alosa sapidissima), a potential prey item for sea lions. A third covariate was the adipose clip status of the fish, indicating whether it was eligible for harvest.

Oregon, Washington↗
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↗
USGS2018

Application of the Stream Salmonid Simulator (S3) to the restoration reach of the Trinity River, California—Parameterization and calibration

Executive Summary In this report, we constructed and parameterized the Stream Salmonid Simulator (S3) for the 64-kilometer “Restoration Reach” of the Trinity River, just downstream of Lewiston Dam in northern California. S3 is a deterministic life-stage-structured population model that tracks daily growth, movement, and survival of juvenile salmon. A key theme of the model is that river flow affects habitat availability and capacity, which in turn drives density-dependent population dynamics. To explicitly link population dynamics to habitat quality and quantity, the river environment is constructed as a one-dimensional series of linked habitat units, each of which has an associated daily timeseries of discharge, water temperature, and useable habitat area or carrying capacity. In turn, the physical characteristics of each habitat unit and the number of fish occupying each unit drive survival and growth within each habitat unit and movement of fish among habitat units. The physical template of the Restoration Reach was formed by classifying the river into 356 meso-habitat units comprised of runs, riffles, and pools. For each habitat unit, we developed a timeseries of daily flow, water temperature, amount of available spawning habitat, and fry and parr carrying capacity. Capacity timeseries were constructed using state-of-the-art models of spatially explicit hydrodynamics and quantitative fish habitat relationships developed for the Trinity River. These variables were then used to drive population dynamics such as egg growth and survival and juvenile movement, growth, and survival.

California↗
USGS2018

Model structure of the stream salmonid simulator (S3)—A dynamic model for simulating growth, movement, and survival of juvenile salmonids

Fisheries and water managers often use population models to aid in understanding the effect of alternative water management or restoration actions on anadromous fish populations. We developed the Stream Salmonid Simulator (S3) to help resource managers evaluate the effect of management alternatives on juvenile salmonid populations. S3 is a deterministic stage-structured population model that tracks daily growth, movement, and survival of juvenile salmon. A key theme of the model is that river flow affects habitat availability and capacity, which in turn drives density dependent population dynamics. To explicitly link population dynamics to habitat quality and quantity, the river environment is constructed as a one-dimensional series of linked habitat units, each of which has an associated daily time series of discharge, water temperature, and usable habitat area or carrying capacity. The physical characteristics of each habitat unit and the number of fish occupying each unit, in turn, drive survival and growth within each habitat unit and movement of fish among habitat units. The purpose of this report is to outline the underlying general structure of the S3 model that is common among different applications of the model. We have developed applications of the S3 model for juvenile fall Chinook salmon ( Oncorhynchus tshawytscha ) in the lower Klamath River. Thus, this report is a companion to current application of the S3 model to the Trinity River (in review). The general S3 model structure provides a biological and physical framework for the salmonid freshwater life cycle. This framework captures important demographics of juvenile salmonids aimed at translating management alternatives into simulated population responses. Although the S3 model is built on this common framework, the model has been constructed to allow much flexibility in application of the model to specific river systems. The ability for practitioners to include system-specific information for the physical stream structure, survival, growth, and movement processes ensures that simulations provide results that are relevant to the questions asked about the population under study.

Open-File Report↗
USGS2018

A laboratory-calibrated model of coho salmon growth with utility for ecological analyses

We conducted a meta-analysis of laboratory- and hatchery-based growth data to estimate broadly applicable parameters of mass- and temperature-dependent growth of juvenile coho salmon ( Oncorhynchus kisutch ). Following studies of other salmonid species, we incorporated the Ratkowsky growth model into an allometric model and fit this model to growth observations from eight studies spanning ten different populations. To account for changes in growth patterns with food availability, we reparameterized the Ratkowsky model to scale several of its parameters relative to ration. The resulting model was robust across a wide range of ration allocations and experimental conditions, accounting for 99% of the variation in final body mass. We fit this model to growth data from coho salmon inhabiting tributaries and constructed ponds in the Klamath Basin by estimating habitat-specific indices of food availability. The model produced evidence that constructed ponds provided higher food availability than natural tributaries. Because of their simplicity (only mass and temperature are required as inputs) and robustness, ration-varying Ratkowsky models have utility as an ecological tool for capturing growth in freshwater fish populations.

Canadian Journal of Fisheries and Aquatic Sciences↗
USGS2018

N-mix for fish: estimating riverine salmonid habitat selection via N-mixture models

Models that formulate mathematical linkages between fish use and habitat characteristics are applied for many purposes. For riverine fish, these linkages are often cast as resource selection functions with variables including depth and velocity of water and distance to nearest cover. Ecologists are now recognizing the role that detection plays in observing organisms, and failure to account for imperfect detection can lead to spurious inference. Herein, we present a flexible N-mixture model to associate habitat characteristics with the abundance of riverine salmonids that simultaneously estimates detection probability. Our formulation has the added benefits of accounting for demographics variation and can generate probabilistic statements regarding intensity of habitat use. In addition to the conceptual benefits, model application to data from the Trinity River, California, yields interesting results. Detection was estimated to vary among surveyors, but there was little spatial or temporal variation. Additionally, a weaker effect of water depth on resource selection is estimated than that reported by previous studies not accounting for detection probability. N-mixture models show great promise for applications to riverine resource selection.

Canadian Journal of Fisheries and Aquatic Sciences↗
USGS2018

Estimating freshwater productivity, overwinter survival, and migration patterns of Klamath River Coho Salmon

An area of great importance to resource management and conservation biology in the Klamath Basin is balancing water usage against the life history requirements of threatened Coho Salmon. One tool for addressing this topic is a freshwater dynamics model to forecast Coho Salmon productivity based on environmental inputs. Constructing such a forecasting tool requires local data to quantify the unique life history processes of Coho Salmon inhabiting this region. Here, we describe analytical methods for estimating a series of sub-models, each capturing a different life history process, which will eventually be synchronized as part of a freshwater dynamics model for Klamath River Coho Salmon. Specifically, we draw upon extensive population monitoring data collected in the basin to estimate models of freshwater productivity, overwinter survival, and migration patterns. Our models of freshwater productivity indicated that high summer temperatures and high winter flows can both adversely affect smolt production and that such relationships are more likely in tributaries with naturally regulated flows due to substantial intraannual environmental variation. Our models of overwinter survival demonstrated extensive variability in survival among years, but not among rearing locations, and demonstrated that a substantial proportion (~ 20%) of age-0+ fish emigrate from some rearing sites in the winter. Our models of migration patterns indicated that many age-0+ fish redistribute in the basin during the summer and winter. Further, we observed that these redistributions can entail long migrations in the mainstem where environmental stressors likely play a role in cueing refuge entry. Finally, our models of migration patterns indicated that changes in discharge are important in cueing the seaward migration of smolts, but that the nature of this behavioral response can differ dramatically between tributaries with naturally and artificially regulated flows. Collectively, these analyses demonstrate that environmental variation interacts with most phases of the freshwater life history of Klamath River Coho Salmon and that anthropogenic environmental variation can have a particularly large bearing on productivity.

Arcata Fisheries Technical Report↗