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.

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.

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.

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.

Relatively little scientific research or monitoring has occurred in the Pacific Northwest or elsewhere on the biological effectiveness of restoration efforts in heavily urbanized watersheds. With the overarching goal of improving ecological health of its urban creeks, the City of Seattle is testing innovative approaches to stormwater management. We report here on four years of pre-project monitoring data collected over 2006-2009 for one such technique: Natural Drainage Systems (NDS). This low-impact development approach is designed to modify the quantity, quality, and timing of stormwater delivery to creeks and other water bodies. Seattle Public Utilities has proposed a large-scale NDS within the Pipers Creek basin of North Seattle that will treat approximately 60% of the Venema Creek sub-basin. The focus of NOAAs research effort has been to develop appropriate monitoring parameters and collect baseline data to evaluate the effectiveness of this major restoration action. Our selection of study parameters was guided by specific project goals and includes measures of physical habitat, contaminant loading, and in-stream biota. We found that the biological health of Pipers Creek is poor compared to forested streams in the Puget Sound region, but comparable to other urban streams in the City of Seattle. The fish community is dominated by cutthroat trout Oncorhynchus clarki; scores for the benthic index of biological integrity (B-IBI) range from very poor to poor; and diatom assemblages are composed of a relatively high proportion of species tolerant of high nutrient levels, organic enrichment, and sedimentation. Despite poor stream health, densities of cutthroat trout in three of our five study reaches were higher than many urban streams and approaching densities of cutthroat found in natural streams. This may be due to the migratory nature of cutthroat trout, as about half these fish were detected migrating from our study area to lower Piper Creek or Puget Sound. Results from heavy metal sampling were inconsistent. Zinc concentrations in soil, black fly larvae, and mayfly nymphs collected from Pipers Creek study reaches were significantly higher than for forested streams. We did not detect any differences in copper concentrations between urban and non-urban streams. We hypothesize that in-stream biological health will improve relative to current baseline conditions following Venema NDS implementation, with treated reaches beginning to more closely resemble forested conditions. Based on statistical power analyses, we recommend that post-project monitoring focus on rate and taxonomic composition metrics rather than simple density measurements. Given the City of Seattles considerable investment of restoration funds towards NDSs, it is critical that post-project data be collected so as to explicitly test these hypotheses. Metal concentrations in soil, periphyton, and benthic invertebrate taxa.

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 Multnomah Channel Wetland Restoration Monitoring Project characterizes wetlands use by juvenile salmonids and other fishes in the Multnomah Channel Marsh Natural Area (MCMNA) and nearby habitats of the Columbia River estuary. The project is a collaborative program by federal, state, and municipal organizations evaluating the ecological effectiveness of floodplain restoration actions at the MCMNA on behalf of at-risk juvenile salmonids. The project uses a wide range of sampling methods to document fish, invertebrate prey, vegetation, and physical habitat conditions and to experimentally assess salmon performance. Sampling methods include: PIT arrays and remote detection systems to monitor salmon access, residency, and movements to and from the wetland; experimental net pens to compare salmon food and relative growth potential within different vegetation types; beach seines, traps, PIT detectors, electro-shockers, and other gear to monitor fish abundance and salmon stock composition; and benthic cores, insect fallout traps, emergent traps, and neuston nets to determine invertebrate prey composition, abundance, and transport from the wetland site. Fish samples are also collected along the main-stem estuary, Multnomah Channel, and other wetlands to investigate the effects of river flow and water elevation on fish access to the MCMNA. Invertebrate and fish stomach samples are analyzed at the main campus of Oregon State University (Corvallis, OR) and at the Oregon Department of Fish and Wildlife Corvallis Research Laboratory. Other activities, vessels, and sampling equipment are staged from the Pt. Adams Research Station in Hammond, OR. Species abundance, length, weight, residence time data for juvenile salmon in main stem Columbia R, Multnomah Channel. Mark and recapture data.

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.

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.

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). PIT detection data (residence time, travel time) in estuary wetland channels from juvenile salmon tagged by this project and other projects.