The primary objectives of this study are to estimate a predation rate by harbor seals on steelhead smolt in Puget Sound, and determine whether predation by harbor seals differs by region. Nisqually River steelhead will be acoustic tagged, and 12 - 18 seals will be fitted with GPS/acoustic receiver instrument packs. Tag detection capabilities will be expanded by i) monitoring harbor seals in South and Central Puget Sound and Admiralty Inlet, ii) placing stationary receivers at seal haulouts and at random locations not frequented by harbor seals, iii) conducting mobile tracking to locate tags remaining in Puget Sound after the smolt outmigration period. Seal time at depth and locations will be quantified in such a manner that estimates the amount of time seals spend at haulout locations to estimate the probability that a tag consumed by a harbor seal would be defecated near a haulout site. Data on harbor seal abundance, behavior, steelhead tag locations, and smolt abundance will be combined to estimate the predation rate and total number of smolts consumed by harbor seals. In addition, recent fish health assays indicate high infection prevalence (87-100%) and intensity (800-2500 cysts/fish) of Nanophyetus salmonica in steelhead outmigrating from Central (Green) and South (Nisqually) Puget Sound Rivers. South and Central Puget Sound steelhead populations generally experience lower early marine survival rates than those from North Puget Sound rivers, where Nanophyetus infections in assayed steelhead were absent. High infection intensity among freshwater outmigrants could contribute to rapid mortality shortly after seawater entry. This study will use acoustic telemetry to evaluate differences in the early marine survival (near river mouth to Pacific Ocean) of specific pathogen-free (SPF) and Nanophyetus-infected Puget Sound steelhead smolts. This approach will help us understand effects of Nanophyetus infection at different stages of the steelhead smolt migration through Puget Sound. Steelhead smolt locations.

This database archives genetic tissue samples from marine mammals collected primarily from the U.S. east coast. The collection includes samples from field programs, fisheries bycatch, and stranding data. A range of researchers have contributed samples to this archive, so some of the data records are confidential. Data includes field identification numbers, location and date information, collection information, and disposition of samples. These samples are primarily intended to support analyses of the genetic relationships and phylogeny of cetaceans in U.S. and Caribbean waters.

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 database archives genetic tissue samples from marine mammals collected in the North-Central Gulf of Mexico from 2010-2015. The collection includes samples from field sampling programs and stranding data. Data includes field identification numbers, location and date information, collection information, and disposition of samples. These data support stock delineation studies and a variety of other analyses related to cetacean genetics in the Gulf of Mexico related to the Deepwater Horizon oil spill.

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

Raw DNA chromatogram data produced by the ABI 373, 377, 3130 and 3730 automated sequencing machines in ABI format. These are from fish (primarily Sebastes spp., Seriola lalandi, and several shark species) and invertebrates (primarily Haliotis spp.). These data are in either of 2 formats, ".fsa" files containing chromatograms used for genotyping, and ".ab1" files containing chromatograms of DNA sequences. These data are used for studies on taxonomy, population connectivity, species identification, and studies of mating systems

The standardized NEFSC Sea Scallop Survey began in 1980 and has covered an area from Cape Hatteras to Georges Bank. The survey aims to determine the distribution and abundance of scallops and associated fauna utilizing two sampling devices: the 8-foot wide New Bedford style dredge, standardized sea scallop dredge and the stereo-optic towed camera array (HabCam). Fifteen minute dredge hauls are made at stations that are randomly selected using the NEFSC shellfish strata to provide unbiased abundance measurements. The HabCam is conducted using transects across bathymetry lines in the same area as the dredge tows. Various vessels have served as a platform for the survey, including NOAA vessels: FRV Albatross IV, FRV Oregon II, FRV Chapman, FV Tradition and currently, the UNOLS vessel RV Hugh R. Sharp.

Samples of skin and other tissues are collected from marine mammals along the North-Central Gulf of Mexico from live animals through remote biopsy or live-capture or stranded animals during 2010-2014. DNA is extracted from these samples, sequenced, and analyzed using a variety of methods to support phylogenetic studies, stock delineation studies, and a variety of other analyses related to cetacean genetics associated with the Natural Resources Damage Assessment associated with the Deepwater Horizon oil spill. These data sets include the sequence and other genetic data collected from these samples along with analytical results. These data support stock delineation studies and a variety of other analyses related to cetacean genetics and are incorporated into the Deepwater Horizon Damage Assessment and Restoration Plan.

Fisheries and Oceans Canada (DFO) has been conducting surface water trawl surveys since 1992 in the coastal waters of British Columbia, Washington, Oregon and Alaska and in the high seas of the Gulf of Alaska. These surveys initially focused on determining the migratory patterns (1992-2002) and on the growth and physiology (2003-2016) of juvenile Pacific Salmon. Since 2016, these surveys have been broadened to monitor the whole pelagic ecosystem, retaining a focus on juvenile Pacific Salmon. Data were collected from sites in the inland sea waters of British Columbia and Washington State, USA, that comprise the Strait of Georgia, Strait of Juan de Fuca and Puget Sound since 2001 and are ongoing.

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.