This project evaluates data from coded wire tagging with that from parental based tagging to identify stock of origin for Chinook salmon landed in Washington state commercial troll fishery.

1. The purpose of this project is to measure and monitor impacts on ESA-listed populations and to estimate overall Chinook salmon stock composition in bycatch associated with the hake fisheries (including tribal and non-tribal, shoreside, and at-sea). The work is carried out by NOAA staff. 2. Fin clips collected by NOAA observers are characterized genetically allowing allocation of the mixture to source populations. 3. Written reports are produced regularly and forwarded to the NWR and interested parties. 4. The NWR is the primary management audience in facilitation of NOAA's MSA obligations to measure and monitor ESA impacts. 5. This is an ongoing project (see also Historical Salmon Genetic Stock Composition Estimates). 6. This is a stand-alone project in one sense, but is closely coordinated with stock composition studies in directed harvest as well as similar studies of historical bycatch using archival scale material. 7. There are no specific hard deadlines associated with this project. Chinook genetics bycatch in hake.

We are using genetic pedigree information to estimate the reproductive success of hatchery and wild fall-run Chinook salmon spawning in the Cedar River, Washington. Genotypes and associated phenotypes for Cedar River Chinook salmon.

A genetic analyses of samples from the Chinook salmon (Oncorhynchus tshawytscha) bycatch from the 2007-2013 Bering Sea-Aleutian Island and Gulf of Alaska trawl fisheries for walleye pollock (Gadus chalcogrammus) were undertaken to determine the overall stock composition of the bycatch. Samples were genotyped for 43 single nucleotide polymorphism (SNP) DNA markers and results were estimated using the Alaska Department of Fish and Game (ADF&G) SNP baseline.

This is a long-term (30-year) NWFSC Genetics and Evolution Program study to monitor the genetic characteristics and population dynamics of hatchery- and natural-origin Chinook salmon and steelhead in the Snake River Basin, which are both species listed as threatened under the US Endangered Species Act. Genetic tools are used to determine if naturally spawning hatchery fish are influencing the adaptive potential and viability of wild fish in the basin. This work involves long-term annual field work to collect DNA from threatened Chinook salmon and steelhead at numerous locations throughout the Snake and Salmon River Basin and analyze the genetic signatures from the collections in the context of a long-term historical baseline of hatchery production and natural variation in wild salmonid production there. Initiated in 1989, this study monitors genetic changes associated with hatchery propagation in multiple Snake River sub-basins for Chinook salmon and steelhead. We also derive estimates of reproductive success for individual families and groups of fish. The information obtained from this study directly addresses a critical knowledge gap identified by comanagers, which is: under what conditions does hatchery supplementation provide a sustained contribution to natural production? Co-managers are ODFW, CTUIR, NPT, WDFW, IDFG, and SBT. This type of monitoring work is now an essential part of hatchery reform and the goal of using widespread hatchery propagation in recovery of natural populations.

Genetic data of salmon bycatch samples collected by fisheries observers are used for mixed-stock analyses to determine geographic region of origin. This work is done at the Auk Bay Lab in Juneau Alaska. The data are loaded to the the North Pacific Halibut and Groundfish database maintained by FMA Division at the Alaska Fisheries Science Center in Seattle Washington

Radio telemetry was used to determine the distribution, locate spawning sites, and evaluate the tagging response of wild Chinook salmon Oncorhynchus tshawytscha returning to a large, free-flowing river basin. A total of 2,860 fish were radio tagged in the lower Yukon River and tracked upriver. Fish traveled to spawning areas throughout the basin, ranging from several hundred to over 3,000 km from the tagging site. We found similar distribution patterns across years, suggesting that the major components of the return were identified. Most spawning fish were clustered in a number of principal tributaries, although small numbers of fish were located in other spatially-isolated areas. The cumulative contribution of these minor stocks was appreciable, making up 28-31% of the tagged sample. There was suggestive evidence of mainstem spawning in upper reaches of the basin. Large-scale elevation and physiographic data were useful in categorizing spawning areas, with most fish returning to relatively entrenched upland rivers. Fish were largely absent in lowland reaches characterized by meandering, low gradient, alluvial channels often associated with main river floodplains. The fish generally responded well to the capture, handling, and tagging procedures with most (2,790, 97.6%) resuming upriver movements, although the fish initially displayed a negative tagging response, with slower migration rates observed immediately after release. The duration of this response was relatively short (several days) and less severe as the fish moved upriver. The swimming speeds of radio-tagged fish after the initial delay were comparable to estimates for untagged fish, further suggesting that the capture, handling, and tagging methods used were relatively benign. Identifying the primary components of the run (including both major and minor stocks) and determining site-specific utilization patterns can fundamentally enhance salmon management in large river basins, and facilitate research and conservation efforts.

The goal of the tidal-fluvial estuary study is to determine the estuary's contribution to the spatial structure and life history diversity of Columbia River salmon stocks and the implications for estuary restoration. The study targets salmon use of tidal-fresh habitats in the estuary from Rkm 75 to Bonneville Dam, and addresses four primary objectives: 1. Characterize the temporal and spatial distribution of Chinook salmon genetic stock groups throughout the estuary (March 2010 - March 2012). 2. Determine stock-specific habitat use, life histories, and performance of juvenile salmon in key habitat complexes to fill data gaps in the tidal fluvial reaches of the estuary (2012-2016). 3. Monitor juvenile salmon life histories and their contributions to adult returns in selected estuary tributaries, including tributary examples where tidal habitats have been restored (2012-2018). 4. Evaluate estuary restoration needs for recovery of all salmon ESUs and account for projected effects of climate change through application of a salmon life-cycle model (2011-1015). The study, funded by the U.S. Army Corps of Engineers, involves a large team of researchers organized by NOAA Fisheries, including researchers from the Oregon Health and Sciences University, University of Washington, and Washington Department of Fish and Wildlife. The study addresses critical uncertainties identified in the research, monitoring, and evaluation (RME) program for the Federal Columbia River Estuary Program (FCREP). The Estuary Program is intended to conserve and restore the estuary ecosystem to improve the performance of listed salmonid populations. Products from the tidal-fluvial study will include: 1. Descriptions of stock-specific temporal and spatial distributions of Chinook salmon throughout the estuary. 2. Estimates of variations in Chinook salmon stock composition and stock-specific growth, food habits, consumption rates, and bioenergetic efficiencies within selected tidal-fluvial habitats. 3. Estimated contributions of estuarine life histories among returning adult Chinook salmon from selected populations throughout the Columbia River Basin. 4. A hydrological model quantifying the dynamics of rearing habitat opportunities for juvenile salmon at estuary reach and habitat scales. 5. Improved life-cycle models to account for the estuarine life histories of juvenile salmon and estimating the potential effectiveness of estuary restoration actions on the recovery and viability of selected salmon stocks. These results will directly address information needs to support estuary actions specified in the Federal Columbia River Power System (FCRPS) Biological Opinion for the Columbia River. The tidal-fluvial estuary study is part of an ongoing estuary research program initiated in 2002. The current study expands upon earlier research conducted in the lower 100 km of the estuary from 2002 to 2008. Although all objectives will be addressed by 2018 to correspond with a review of progress implementing the FCRPS Biological Opinion, some sampling activities may extend beyond this date to allow brood-year reconstruction of estuary contributions to adult returns in selected streams (Objective 3). Bimonthly genetic stock group distribution for juvenile Chinook Salmon collected from 3 habitats each from 6 tidal-fluvial estuary reaches and monthly fish species composition, abundance, and length:weight; Chinook salmon life history and genetic stock ID.

This study is part of the Auke Bay Laboratoryb??s Ocean Carrying Capacity (OCC) which has extensively sampled salmon in the North Pacific since 1996 to obtain information on marine life history and migration patterns. Genetic stock identification techniques (protein electrophoresis) indicated that Bristol Bay stocks of immature sockeye salmon (Oncorhynchus nerka) made up the largest percentage in two samples taken near Unalaska Island in 1998. The substantial numbers of immature sockeye salmon captured at Cape Cheerful during May 1998 were unexpected, based on current migration models of western Alaska sockeye salmon. Immature sockeye constituted the largest percentage of our immature salmon catch captured at Cape Prominence during August 1998. This was also unexpected since immature chum salmon (O. keta) were the predominant catch during August 1996 and 1997 at the same location. These unexpected events may be due to changes in distribution resulting from the strong El NiC1o event during 1997-1998.

1) The purpose of this project is to document juvenile salmon habitat occurrence in the Lower Columbia River and estuary, and examine how habitat conditions influence their distribution, health, and abundance. We also want to monitor habitat conditions and indicators of salmon health in these environments. 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 (NFWSC 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 (i.e, the Lower Columbia River Estuary Partnership, USGS, PNNL, OHSU). 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 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 monitoring program overseen by the Estuary Partnership in which other tasks are conducted by collaborators in USGS, PNNL, and OHSU. 7) This is an ongoing project with a soft completion deadline; however, there are no final deadlines with specific tasks to be completed on a yearly basis. Genetic stock information for chinook salmon from Lower Columbia River sites.