Geology topics

Nicholas J. Hetrick

Publications and source records attributed to Nicholas J. Hetrick.

9 recordsLinked to original sources

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↗

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↗

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

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↗

USGS2016

Construction, calibration, and validation of the RBM10 water temperature model for the Trinity River, northern California

We constructed a one-dimensional daily averaged water-temperature model to simulate Trinity River temperatures for 1980–2013. The purpose of this model is to assess effects of water-management actions on water temperature and to provide water temperature inputs for a salmon population dynamics model. Simulated meteorological data, observed streamflow data, and observed water temperatures were used as model inputs to simulate a continuous 34-year time series of historical daily mean water temperature at eight locations along 112.2 river miles from Lewiston Dam near Weaverville, California, downstream to the Klamath River confluence. To demonstrate the utility of the model to inform management actions, we simulated three management alternatives to assess the effects of bypass flow augmentation in a drought year, 1994, and compared those results to the simulated historical baseline, referred to as the “No Action” alternative scenario. Augmentation flows from the Lewiston Dam bypass consist of temperature-controlled releases capable of cooling downstream water temperatures in hot times of the year, which can reduce the probability of disease outbreaks in fish populations. Outputs from the Trinity River water-temperature model were then used as inputs to an existing water-temperature model of the Klamath River to evaluate the effect of augmentation flow releases on water temperatures in the lower Klamath River. We structured the Trinity River water-temperature model in River Basin Model-10 (RBM10), which uses a simple equilibrium flow model, assuming discharge in each river segment on each day is transmitted downstream instantaneously. The model uses a heat-budget formulation to quantify heat flux at the air-water interface. Inputs for the heat budget are calculated from daily mean meteorological data, including net shortwave solar radiation, net longwave atmospheric radiation, air temperature, wind speed, vapor pressure, and a psychrometric constant needed to calculate the Bowen ratio. The modeling domain was divided into eight reaches ranging in length from 8.8 to 20.6 miles, which were calibrated and validated separately with observed water temperature data collected irregularly from 1980 to 2013. Root mean square errors of observed and simulated water temperatures for the eight reaches ranged from 0.25 to 1.12 degrees Celsius (°C). Mean absolute errors ranged from 0.18 to 0.89 °C. For model validation, a k -fold cross-validation technique was used. Validation root mean square error and mean absolute error for the eight reaches ranged from 0.24 to 1.11 °C and from 0.18 to 0.89 °C, respectively. Augmentation scenarios were based on historical hydrological and meteorological data, combined with prescribed flow and temperature releases from Lewiston Dam provided by the Bureau of Reclamation. Water releases were scheduled to achieve targeted flows of 2,500, 2,800, and 3,200 cubic feet per second in the lower Klamath River from mid-August through late September, coinciding with the upstream migration of adult fall-run Chinook salmon ( Oncorhynchus tshawytscha ). Water temperatures simulated at river mile 5.7 on the Klamath River showed a 5 °C decrease from the No Action historical baseline, which was near or greater than 23 °C when augmentation began in mid-August. Thereafter, an approximate 1 °C difference among augmentation scenarios emerged, with the decrease in water temperature commensurate to the level of augmentation. All augmentation scenarios simulated water temperatures equal to or less than 21 °C from mid-August through late September. Water temperatures equal to or greater than 23 °C are of particular interest because of a thermal threshold known to inhibit upstream migration of salmon. When temperatures exceed this approximate 23 °C threshold, Chinook salmon are known to congregate in high densities in thermal refugias and show extended residence times, which can potentially trigger epizootic outbreaks such as of Ichthyophthirius multifiliis (“Ich”) and Flavobacterium columnare (“Columnaris”) that were the causative factors of the Klamath River fish kill in 2002. A model with the ability to simulate water temperatures in response to management actions at the basin scale is a valuable asset for water managers who must make decisions about how best to use limited water resources, which directly affect the state of fisheries in the Klamath Basin.

California↗