Assist Oregon Department of Fish and Wildlife (ODFW) in determining the extent to which genetic introgression exists between Snake River hatchery steelhead straying into the John Day Basin and the local ESA-listed summer steelhead, and to verify the existing Technical Recovery Team (TRT) population designations within the John Day system. Results of this research will be used to inform the management and conservation of John Day River Basin steelhead. Genetics.

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.

Rainbow trout and steelhead consist of the same species and often inhabit the similar habitat types within the same watershed. Although their life histories differ from one another, there is thought to be genetic introgression between types. This study seeks to undertake genetic characterization of resident rainbow populations prior to reintroduction of steelhead in the Lewis River. Lewis River rainbow trout genetics.

The goals of this study are to develop methods to reduce wandering and straying of steelhead (Oncorhynchus mykiss) that are collected and barged from the Snake River to below Bonneville Dam. Salmon and steelhead that stray and spawn in non-natal streams are a significant conservation concern, because they may confound accurate assessment of the VSP parameters of recovering native populations and decrease the productivity of these populations through genetic introgression or ecological competition. These issues are a particular concern for listed mid-Columbia River stocks because salmon that are collected and barged downstream as juveniles have shown higher stray rates into these watersheds as returning adults relative to in-river migrants. However, while barging may contribute to elevated stray rates, there are substantial benefits from barging because transported Snake River steelhead consistently have higher smolt-to-adult returns than steelhead left to migrate in-river. Therefore, it is important to identify and develop strategies for reducing the stray rates of transported steelhead while maintaining the survival benefits consistently observed for barged steelhead. The specific aims of this proposal are as follows: 1) Conduct an analysis of existing coded wire (CWT) and PIT tag data to identify causative factors associated with straying by Columbia River salmonids, particularly as it relates to natural rates of straying and straying associated with transport. 2) Assess imprinting of barged and in-river migrants by monitoring imprinting associated changes in physiological function and gene expression as indicators of imprinting success. 3) Identify key environmental parameters (e.g. orienting current, water exchange rate, novel tributary water) that are important for imprinting barged fish and develop barging protocols to optimize imprinting success and thereby minimize straying using a controlled laboratory study. 4) Initiate tests of a modified barge protocol designed to maintain survival benefits while reducing wandering, delay, and straying behavior of returning adults. The work is being conducted by NWFSC scientists in collaboration with the University of Washington. Products for this project will include annual reports, peer-reviewed publications, presentation of results at local and national meetings, and consultation with the FCRPS managers. Physiological data on hatchery-reared steelhead.

The CalFish Abundance Database contains a comprehensive collection of anadromous fisheries abundance information. Beginning in 1998, the Pacific States Marine Fisheries Commission, the California Department of Fish and Game, and the National Marine Fisheries Service, began a cooperative project aimed at collecting, archiving, and entering into standardized electronic formats, the wealth of information generated by fisheries resource management agencies and tribes throughout California.Extensive data are currently available for chinook, coho, and steelhead. Major data categories include adult abundance population estimates, actual fish and/or carcass counts, counts of fish collected at dams, weirs, or traps, and redd counts. Harvest data has been compiled for many streams, and hatchery return data has been compiled for the states mitigation facilities. A draft format has been developed for juvenile abundance and awaits final approval. This CalFish Abundance Database shapefile was generated from fully routed 1:100,000 hydrography. In a few cases streams had to be added to the hydrography dataset in order to provide a means to create shapefiles to represent abundance data associated with them. Streams added were digitized at no more than 1:24,000 scale based on stream line images portrayed in 1:24,000 Digital Raster Graphics (DRG).These features generally represent abundance counts resulting from stream surveys. The linear features in this layer typically represent the location for which abundance data records apply. This would be the reach or length of stream surveyed, or the stream sections for which a given population estimate applies. In some cases the actual stream section surveyed was not specified and linear features represent the entire stream. In many cases there are multiple datasets associated with the same length of stream, and so, linear features overlap. Please view the associated datasets for detail regarding specific features. In CalFish these are accessed through the "link" that is visible when performing an identify or query operation. A URL string is provided with each feature in the downloadable data which can also be used to access the underlying datasets.The steelhead data that is available via the CalFish website is actually linked directly to the StreamNet website where the databases tabular data is currently stored. Additional information about StreamNet may be downloaded at http://www.streamnet.org. Complete documentation for the StreamNet database may be accessed at http://www.streamnet.org/def.html

The CalFish Abundance Database contains a comprehensive collection of anadromous fisheries abundance information. Beginning in 1998, the Pacific States Marine Fisheries Commission, the California Department of Fish and Game, and the National Marine Fisheries Service, began a cooperative project aimed at collecting, archiving, and entering into standardized electronic formats, the wealth of information generated by fisheries resource management agencies and tribes throughout California.Extensive data are currently available for chinook, coho, and steelhead. Major data categories include adult abundance population estimates, actual fish and/or carcass counts, counts of fish collected at dams, weirs, or traps, and redd counts. Harvest data has also been compiled for many streams.This CalFish Abundance Database shapefile was generated from fully routed 1:100,000 hydrography. In a few cases streams had to be added to the hydrography dataset in order to provide a means to create shapefiles to represent abundance data associated with them. Streams added were digitized at no more than 1:24,000 scale based on stream line images portrayed in 1:24,000 Digital Raster Graphics (DRG).These features represent abundance information resulting from counts at weirs, fish ladders, or other point-type monitoring protocols such as beach seining. The point features in this layer typically represent the location for which abundance data records apply. In many cases there are multiple datasets associated with the same point location, and so, point features overlap. Please view the associated datasets for detail regarding specific features. In CalFish these are accessed through the "link" field that is visible when performing an identify or query operation. A URL string is provided with each feature in the downloadable data which can also be used to access the underlying datasets.The steelhead data that is available via the CalFish website is actually linked directly to the StreamNet website where the databases tabular data is currently stored. Additional information about StreamNet may be downloaded at http://www.streamnet.org. Complete documentation for the StreamNet database may be accessed at http://www.streamnet.org/def.html

The CalFish Abundance Database contains a comprehensive collection of anadromous fisheries abundance information. Beginning in 1998, the Pacific States Marine Fisheries Commission, the California Department of Fish and Game, and the National Marine Fisheries Service, began a cooperative project aimed at collecting, archiving, and entering into standardized electronic formats, the wealth of information generated by fisheries resource management agencies and tribes throughout California.Extensive data are currently available for chinook, coho, and steelhead. Major data categories include adult abundance population estimates, actual fish and/or carcass counts, counts of fish collected at dams, weirs, or traps, and redd counts. Harvest data has been compiled for many streams, and hatchery return data has been compiled for the states mitigation facilities. A draft format has been developed for juvenile abundance and awaits final approval. This CalFish Abundance Database shapefile was generated from fully routed 1:100,000 hydrography. In a few cases streams had to be added to the hydrography dataset in order to provide a means to create shapefiles to represent abundance data associated with them. Streams added were digitized at no more than 1:24,000 scale based on stream line images portrayed in 1:24,000 Digital Raster Graphics (DRG).These features generally represent abundance counts resulting from stream surveys. The linear features in this layer typically represent the location for which abundance data records apply. This would be the reach or length of stream surveyed, or the stream sections for which a given population estimate applies. In some cases the actual stream section surveyed was not specified and linear features represent the entire stream. In many cases there are multiple datasets associated with the same length of stream, and so, linear features overlap. Please view the associated datasets for detail regarding specific features. In CalFish these are accessed through the "link" that is visible when performing an identify or query operation. A URL string is provided with each feature in the downloadable data which can also be used to access the underlying datasets.The steelhead data that is available via the CalFish website is actually linked directly to the StreamNet website where the databases tabular data is currently stored. Additional information about StreamNet may be downloaded at http://www.streamnet.org. Complete documentation for the StreamNet database may be accessed at http://www.streamnet.org/def.html

This project uses genetic parentage analysis to estimate the relative reproductive success of hatchery and wild steelhead spawning in the Wenatchee River, WA. The project collected data from 2008-2011; in FY16 the project is analyzing data and preparing reports and papers for publication. Genotypes and phenotypes of steelhead from the Wenatchee River.

The goals of this study are to develop methods to reduce wandering and straying of steelhead (Oncorhynchus mykiss) that are collected and barged from the Snake River to below Bonneville Dam. Salmon and steelhead that stray and spawn in non-natal streams are a significant conservation concern, because they may confound accurate assessment of the VSP parameters of recovering native populations and decrease the productivity of these populations through genetic introgression or ecological competition. These issues are a particular concern for listed mid-Columbia River stocks because salmon that are collected and barged downstream as juveniles have shown higher stray rates into these watersheds as returning adults relative to in-river migrants. However, while barging may contribute to elevated stray rates, there are substantial benefits from barging because transported Snake River steelhead consistently have higher smolt-to-adult returns than steelhead left to migrate in-river. Therefore, it is important to identify and develop strategies for reducing the stray rates of transported steelhead while maintaining the survival benefits consistently observed for barged steelhead. The specific aims of this proposal are as follows: 1) Conduct an analysis of existing coded wire (CWT) and PIT tag data to identify causative factors associated with straying by Columbia River salmonids, particularly as it relates to natural rates of straying and straying associated with transport. 2) Assess imprinting of barged and in-river migrants by monitoring imprinting associated changes in physiological function and gene expression as indicators of imprinting success. 3) Identify key environmental parameters (e.g. orienting current, water exchange rate, novel tributary water) that are important for imprinting barged fish and develop barging protocols to optimize imprinting success and thereby minimize straying using a controlled laboratory study. 4) Initiate tests of a modified barge protocol designed to maintain survival benefits while reducing wandering, delay, and straying behavior of returning adults. The work is being conducted by NWFSC scientists in collaboration with the University of Washington. Products for this project will include annual reports, peer-reviewed publications, presentation of results at local and national meetings, and consultation with the FCRPS managers. Physiological and field data on barged and in-river migrant steelhead.

Steelhead population abundance is depressed throughout much of its southern range, and several Distinct Population Segments (DPSs) are listed as threatened or endangered under the US Endangered Species Act (ESA). Some anadromous populations are associated with relatively large resident trout populations, and some of these resident populations can produce migrating smolts. We are trying to determine the genetic architecture, population history, and plasticity of anadromy and residency in this species, with the intent of determining whether the hybrid migratory strategy expressed in wild populations like this is key to maintaining long-term resilience and productivity of anadromous populations. This collection of NWFSC Genetics and Evolution Program studies represents a long-term collaboration between NWFSC and the Alaska Fisheries Science Center, the Southwest Fisheries Science Center, the National Park Service, the US Forest Service, the Lower Elwha Klallam Tribe, and the US Geological Survey to understand the intrinsic (biological, genetic) and extrinsic (environmental) factors that influence production, diversity, and variation in these characteristics in wild steelhead and the resident trout they interact with. It involves annual fieldwork to collect data on juvenile and adult fish and reconstruct their molecular pedigrees and conduct quantitative genetic analyses, as well as to assess temporal trends in abundance and productivity and the condition of their freshwater habitats. Genetic basis of migratory tendency and life history plasticity in Oncorhynchus mykiss.