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.

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.

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.

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 research was initiated by the Puget Sound Steelhead Technical Recovery Team to develop viability criteria for threatened Puget Sound steelhead and to support recovery planning of this species. It involves conventional population viability analysis (PVA) combined with decision support systems such as Bayesian Networks. These systems are parameterized with information on abundance, productivity, spatial structure, and diversity obtained from various sources, including PVAs of individual populations from time-series data of abundance, productivity, age structure, iteroparity, influence of resident fish on anadromous abundance, and influence of human activities such as hatchery production, harvest, and habitat alteration. The work will also focus on assessing status of these listed species every five years as part of NOAA Fisheries' coastwide status review updates for listed salmonids. These data will be outputs from life cycle models developed by the Puget Sound steehead recovery team to evaluate.

Critical habitat includes the stream channels within the designated stream reaches, and includes a lateral extent as defined by the ordinary high-water line (33 CFR 319.11). In areas where ordinary high-water line has not been defined, the lateral extent is defined by the bankfull elevation. Bankfull elevation is the level at which water begins to leave the channel and move into the floodplain and is reached at a discharge which generally has a recurrence interval of 1 to 2 years on the annual flood series. Critical habitat in lake areas is defined by the perimeter of the water body as displayed on standard 1:24,000 scale topographic maps or the elevation of ordinary high water, whichever is greater.See the final rule (81 FR 9252) for descriptions of areas excluded from this critical habitat designation. Military areas ineligible for designation (qualifying Integrated Natural Resource Management Plan) were not clipped out of the data. Excluded Habitat Conservation Plan (HCP) lands and Indian lands were not clipped out of the data.

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.

This study evaluates system-level effects of several estuary restoration projects on juvenile Chinook salmon production in the Skagit River estuary. The monitoring encompasses juvenile out-migration from rivers, estuary rearing, and shoreline and subtidal neritic residency. NWFSC is responsible for sampling neritic systems. Excel spreadsheets and Filemaker Pro databases.

The incised and degraded habitat of Bridge Creek is thought to be limiting a population of ESA-listed steelhead (Oncorhynchus mykiss). A logical restoration approach is to improve their habitat through reconnecting the channel with portions of its former floodplain (now terraces) to increase both stream and riparian habitat complexity. Using conventional restoration techniques to achieve such objectives can be quite costly, because it involves moving and grading large volumes of fill with heavy equipment that exposes bare ground, and is usually followed by extensive revegetation efforts. Here, we seek a cost-effective, process-based approach to restore geomorphic, hydrologic and ecological functions of this degraded system helping a small, extant beaver population build longer-lived dams. Currently, the beaver population is limited because their dams are short-lived. Most beaver dams are constructed within the incision trench and during high discharge events; the full force of flood waters are concentrated on these dams rather than dissipating across floodplains. Consequently most dams breach and fail within their first season. The primary hypothesis we are testing is that by assisting beaver to create stable colonies and aggrade incised reaches of Bridge Creek, there will be measurable improvements in riparian and stream habitat conditions and abundance of native steelhead. The main restoration design challenge is to help beaver build dams that will last long enough to lead to the establishment of stable colonies. If this can be accomplished, the beaver dams should promote enough aggradation to reverse channel incision and reap a number of well documented positive ecosystem benefits associated with dynamic beaver dam complexes that will benefit steelhead and other species. We are assisting the beaver using an extremely simple and cost-effective restoration treatment. The treatment involves installing round wooden fence posts across potential floodplain surfaces (now terraces) and the channel, approximately 0.5 to 1 m apart and at a height intended to act as the crest elevation of an active beaver dam. This report provides details of the design rationale and design hypotheses employed and summarizes the placement of the 84 BDS structures installed in four reaches in 2009. Additionally, the ongoing monitoring campaign devised to test these design hypotheses is discussed and some preliminary observations from the first year of the campaign are presented. Five variants of the restoration treatment were used; post lines only, post lines with wicker weaves, construction of starter dams, reinforcement of existing active beaver dams, and reinforcement of abandon beaver dams. The biodegradable posts are intended to buy enough time for (1) beaver to occupy the structures and build on or maintain the structures as their own dams, and (2) for aggradation in the slackwaters of the pond from the dam to take place and promote reconnection with a floodplain (terrace). Just as with natural beaver dams, individual dams are expected to be transient features on the landscape, expanding and contracting, coming and going as they lose functionality for beaver (e.g. when a pond fills with sediment). The treatment design is geared to saturate four distinct reaches of Bridge Creek with beaver dam support (BDS) structures so that enough potential dams are available to the current beaver population that they can pick and choose the best sites to establish stable multi-dam complexes to support healthy and persistent colonies. Physical and biological data.

NOAA Fisheries is a cooperator with the Washington Department of Fish and Wildlife and the Lummi, Nooksack, and Stillaguamish Tribes in a 10-year program to rebuild the South Fork Nooksack River spring Chinook and Stillaguamish River fall Chinook stocks through a captive broodstock program. Raw data on rearing density, loading density, water temperature, ration, and feed size may be available. Raw data on administration of therapeutic drugs may be available.