The Federal Columbia River Power Supply (FCRPS) Biological Opinion (BiOp) calls for studies that estimate ecological and genetic impacts of hatchery fish on wild populations, and evaluate the effectiveness of hatchery supplementation measures to reduce potentially harmful effects of artificial production to aid recovery through hatchery reform. The FCRPS BiOp further explicitly calls for studies that examine the appropriate role of supplementation and the relationship between supplementation and habitat actions in salmon recovery. A basic premise of supplementation is that artificially produced fish will help develop self-sustaining spawning populations both by increasing current natural production and reestablishing populations in underutilized and recovered habitats. One hatchery reform measure that has been incorporated into many supplementation programs throughout the Columbia River Basin is the use of satellite acclimation facilities to repopulate underutilized habitat. However, the efficacy of these facilities in re-establishing naturally spawning populations and minimizing negative interactions between wild spawners and supplemented fish has not been established. Our studies have involved comprehensive carcass and redd mapping surveys and radio telemetry to examine the role of acclimation sites in homing and spawning of spring Chinook salmon released as part of the Yakima/Klickitat Fisheries Project (YKFP) supplementation program. In addition, we are examining the complex linkages between habitat quality and spawning site selection in supplemented Columbia River populations. These studies involve mapping and assessing habitat distribution and quality relative to supplementation rearing and release facilities, and coupling these findings to ongoing analysis of homing and spawning patterns. Our results have provided unique insights into the process of homing, straying, and spawning site selection, interactions and success of hatchery and wild spawners, and the efficacy of supplementation and acclimation sites in salmon recovery. These studies will help identify appropriate locations for recovery-related supplementation rearing and release facilities (acclimation sites), and ultimately allow us to develop scenario models predicting the spatial distribution of spawning relative to proposed supplementation facilities and available habitat (including future habitat restoration sites). The work is being conducted by Northwest Fisheries Science Center (NWFSC) scientists collaborating with the University of Washington, Yakima Nation, U.S. Geological Survey (USGS), and the Washington Department of Fish and Wildlife (WDFW). Products for this project include annual reports, peer-reviewed publications, presentation of results at local and national meetings, and consultation with the Northwest Regional Office (NWR) and supplementation managers. Comprehensive GIS data of Yakima River Spring Chinook spawners.

The Federal Columbia River Power Supply (FCRPS) Biological Opinion (BiOp) calls for studies that estimate ecological and genetic impacts of hatchery fish on wild populations, and evaluate the effectiveness of hatchery supplementation measures to reduce potentially harmful effects of artificial production to aid recovery through hatchery reform. The FCRPS BiOp further explicitly calls for studies that examine the appropriate role of supplementation and the relationship between supplementation and habitat actions in salmon recovery. A basic premise of supplementation is that artificially produced fish will help develop self-sustaining spawning populations both by increasing current natural production and reestablishing populations in underutilized and recovered habitats. One hatchery reform measure that has been incorporated into many supplementation programs throughout the Columbia River Basin is the use of satellite acclimation facilities to repopulate underutilized habitat. However, the efficacy of these facilities in re-establishing naturally spawning populations and minimizing negative interactions between wild spawners and supplemented fish has not been established. Our studies have involved comprehensive carcass and redd mapping surveys and radio telemetry to examine the role of acclimation sites in homing and spawning of spring Chinook salmon released as part of the Yakima/Klickitat Fisheries Project (YKFP) supplementation program. In addition, we are examining the complex linkages between habitat quality and spawning site selection in supplemented Columbia River populations. These studies involve mapping and assessing habitat distribution and quality relative to supplementation rearing and release facilities, and coupling these findings to ongoing analysis of homing and spawning patterns. Our results have provided unique insights into the process of homing, straying, and spawning site selection, interactions and success of hatchery and wild spawners, and the efficacy of supplementation and acclimation sites in salmon recovery. These studies will help identify appropriate locations for recovery-related supplementation rearing and release facilities (acclimation sites), and ultimately allow us to develop scenario models predicting the spatial distribution of spawning relative to proposed supplementation facilities and available habitat (including future habitat restoration sites). The work is being conducted by Northwest Fisheries Science Center (NWFSC) scientists collaborating with the University of Washington, Yakima Nation, U.S. Geological Survey (USGS), and the Washington Department of Fish and Wildlife (WDFW). Products for this project include annual reports, peer-reviewed publications, presentation of results at local and national meetings, and consultation with the Northwest Regional Office (NWR) and supplementation managers. GIS linked spatially continuous habitat assessments.

Field methods include the capture of fishes using backpack electrofishing using the same methodologies employed by Great Smoky Mountains National Park fish biologists. In particular, alternating current electricity generated by a backpack electrofisher will be used to capture fishes in three GSMNP basins: (1) Deep Creek, (2) Pigeon River, and (3) Little River. At each site where fishes are collected, the lower caudal fin lobe will be surgically removed from up to three targeted species: (1) Banded Sculpin (Cottus carolinae), (2) Mottled Sculpin (Cottus bairdi), and (3) Greenside Darter (Etheostoma blennoides). Tissue samples will be preserved in 1 ml microcenterfuge tubes containing DNA shield (a liquid designed to reduced DNA degradation during storage). Tissue samples will be transported to the research laboratory of Dr. Joshuah Perkin at Tennessee Technological University, digested, and DNA extracted before 96-well plates containing sampled are shipped for genotyping by sequencing at the Cornell University Institute of Biotechnology. Field methods will be employed to minimize mortality caused by electrofishing and tissue sample collection. Previous research has shown lower caudal fin lobe fin clips result in minimal mortality and fin ray regeneration will eventually proceed. All point data will be protected as sensitive data according to an existing data management plan between Dr. Joshuah Perkin and GSMNP staff (i.e., Matt Kulp and Kendra Straub).

1) The purpose of this project is to measure changes in juvenile salmon habitat occurrence and health following restoration activities at the Mirror Lake Complex and Horsetail Falls in the Lower Columbia River and estuary. Parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure. 2) Lyndal Johnson (NWFSC FTE) is the project lead, and other primary staff involved are Sean Sol and Paul Olson (NWFSC FTEs) and Kate Macneale (NWFSC term employee), but the project also involves other NWFSC FTEs, other term employees, contractors, and staff from other programs (Environmental Chemistry) and Divisions (FE, CB), as well as staff from collaborating agencies (e.g., the Lower Columbia River Estuary Partnership). 3) The project involves field surveys in which parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure. 4) Specific products to be produced include annual reports for the Lower Columbia Estuary Partnership, and manuscripts in peer-reviewed journals. 5) Specific audiences include (but are not limited to) the Bonneville Power Administration and other federal, state, and local agencies involved with salmon recovery and environmental management in the Columbia Basin (e.g., EPA, Washington Department of Ecology, Oregon Department of Environmental Quality, the City of Portland), the NMFS regional office, and other agency and academic scientists. 6) This is a stand-alone project, but it is also a component of a larger action effectiveness monitoring program overseen by the Estuary Partnership. 7) This is an ongoing project with a soft completion deadline; however, there are specific tasks to be completed on a yearly basis. Chinook salmon genetic stock identification.

1) The purpose of this project is to measure changes in juvenile salmon habitat occurrence and health following restoration activities at the Mirror Lake Complex and Horsetail Falls in the Lower Columbia River and estuary. Parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure. 2) Lyndal Johnson (NWFSC FTE) is the project lead, and other primary staff involved are Sean Sol and Paul Olson (NWFSC FTEs) and Kate Macneale (NWFSC term employee), but the project also involves other NWFSC FTEs, other term employees, contractors, and staff from other programs (Environmental Chemistry) and Divisions (FE, CB), as well as staff from collaborating agencies (e.g., the Lower Columbia River Estuary Partnership). 3) The project involves field surveys in which parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure. 4) Specific products to be produced include annual reports for the Lower Columbia Estuary Partnership, and manuscripts in peer-reviewed journals. 5) Specific audiences include (but are not limited to) the Bonneville Power Administration and other federal, state, and local agencies involved with salmon recovery and environmental management in the Columbia Basin (e.g., EPA, Washington Department of Ecology, Oregon Department of Environmental Quality, the City of Portland), the NMFS regional office, and other agency and academic scientists. 6) This is a stand-alone project, but it is also a component of a larger action effectiveness monitoring program overseen by the Estuary Partnership. 7) This is an ongoing project with a soft completion deadline; however, there are specific tasks to be completed on a yearly basis. Chinook salmon genetic stock identification.

Tabular dataset containing daily and cumulative counts of all fish species apart from Chum and Chinook salmon detected and recorded at the Andreafsky weir for the years 1994 through 2019, 2021, and 2023. Species included differed year by year depending on what was observed at the weir. Counts were done manually at the weir until the introduction of a video feed in 2007. NA refers to missing data whereas 0 refers to no observation made. Data was compiled by Randy Brown and Jeff Melagari for years 1994 through 2016. For 2017 on, data was taken from post season reports.

Tabular dataset containing daily and cumulative counts of all fish species apart from Chum and Chinook salmon detected and recorded at the Andreafsky weir for the years 1994 through 2019, 2021, and 2023. Species included differed year by year depending on what was observed at the weir. Counts were done manually at the weir until the introduction of a video feed in 2007. NA refers to missing data whereas 0 refers to no observation made. Data was compiled by Randy Brown and Jeff Melagari for years 1994 through 2016. For 2017 on, data was taken from post season reports.

1) The purpose of this project is to measure changes in juvenile salmon habitat occurrence and health following restoration activities at the Mirror Lake Complex and Horsetail Falls in the Lower Columbia River and estuary. Parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure. 2) Lyndal Johnson (NWFSC FTE) is the project lead, and other primary staff involved are Sean Sol and Paul Olson (NWFSC FTEs) and Kate Macneale (NWFSC term employee), but the project also involves other NWFSC FTEs, other term employees, contractors, and staff from other programs (Environmental Chemistry) and Divisions (FE, CB), as well as staff from collaborating agencies (e.g., the Lower Columbia River Estuary Partnership). 3) The project involves field surveys in which parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure. 4) Specific products to be produced include annual reports for the Lower Columbia Estuary Partnership, and manuscripts in peer-reviewed journals. 5) Specific audiences include (but are not limited to) the Bonneville Power Administration and other federal, state, and local agencies involved with salmon recovery and environmental management in the Columbia Basin (e.g., EPA, Washington Department of Ecology, Oregon Department of Environmental Quality, the City of Portland), the NMFS regional office, and other agency and academic scientists. 6) This is a stand-alone project, but it is also a component of a larger action effectiveness monitoring program overseen by the Estuary Partnership. 7) This is an ongoing project with a soft completion deadline; however, there are specific tasks to be completed on a yearly basis. Catch composition and salmon density.

Physical and chemical changes affect the biota within urban streams at varying scales ranging from individual organisms to populations and communities creating complex interactions that present challenges for characterizing and monitoring the impact on species utilizing these freshwater habitats. Salmonids, specifically cutthroat trout (Oncorhynchus clarkii) and coho salmon (Oncorhynchus kisutch), extensively utilize small stream habitats influenced by a changing urban landscape. This study used a comprehensive fish health assessment concurrent with the U.S. Geological Survey’s Pacific Northwest Stream Quality Assessment in 2015 to quantifiy impacts from disease in juvenile coho and cutthroat salmon, impacts to coho salmon growth within the context of environmental and ecological influences, and identify physiological responses in coho salmon from pollution. The data included in this release informed a study of the influence of near-term environmental condition on the growth of juvenile coho salmon (Oncorhynchus kisutch). It includes the inputs necessary for bioenergetic growth modeling and the output of those models.

Physical and chemical changes affect the biota within urban streams at varying scales ranging from individual organisms to populations and communities creating complex interactions that present challenges for characterizing and monitoring the impact on species utilizing these freshwater habitats. Salmonids, specifically cutthroat trout (Oncorhynchus clarkii) and coho salmon (Oncorhynchus kisutch), extensively utilize small stream habitats influenced by a changing urban landscape. This study used a comprehensive fish health assessment concurrent with the U.S. Geological Survey’s Pacific Northwest Stream Quality Assessment in 2015 to quantifiy impacts from disease in juvenile coho and cutthroat salmon, impacts to coho salmon growth within the context of environmental and ecological influences, and identify physiological responses in coho salmon from pollution. The data included in this release informed a study of the influence of near-term environmental condition on the growth of juvenile coho salmon (Oncorhynchus kisutch). It includes the inputs necessary for bioenergetic growth modeling and the output of those models.