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

January 6, 2023

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 year3. 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.

Citation Information

Publication Year 2023
Title Simulating post-dam removal effects of hatchery operations and disease on juvenile Chinook salmon (Oncorhynchus tshawytscha) production in the Lower Klamath River, California
DOI 10.3133/ofr20221106
Authors Russell W. Perry, John M. Plumb, Michael J. Dodrill, Nicholas A. Som, H. Eve Robinson, Nicholas J. Hetrick
Publication Type Report
Publication Subtype USGS Numbered Series
Series Title Open-File Report
Series Number 2022-1106
Index ID ofr20221106
Record Source USGS Publications Warehouse
USGS Organization Southwest Biological Science Center; Western Fisheries Research Center