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California Current Ecosystem Assessment (trawl sample)
This layer is intended to represent information collected during NOAA Fisheries’ California Current Ecosystem Survey. The California Current Ecosystem Survey started in 2006 and is led by NMFS Southwest Fisheries Science Center. This survey monitors West Coast coastal pelagic fish species (CPS) including the northern and central sub-populations of Northern Anchovy, the northern subpopulation of Pacific Sardine, Jack Mackerel, Pacific Mackerel, Pacific Herring, their prey items, and the biotic and abiotic environments of the California Current Ecosystem. These data are used to estimate the distribution, biomass, and demographics of species of interest to inform stock assessments. The CCES survey typically occurs annually between July and September on the West Coast of the U.S. and Canada, with a recent expansion into Mexico thanks to a collaboration with the Instituto Mexicano Investigación en Pesca y Acuacultura Sustentables (IMIPAS, formerly INAPESCA). During the day multifrequency, scientific echosounders, a continuous underway fish egg sampler (CUFES), and an underway conductivity-temperature-depth (UCTD) probe are all used to collect data. At night, surface trawls are conducted in locations where coastal pelagic species were observed acoustically during the day. The trawls serve to estimate the species composition and demographics of the fishes sampled acoustically during the day. In recent years, sampling from NOAA ships has been augmented with acoustic sampling by unmanned surface vehicles (Saildrone USVs), and with acoustic and purse-seine sampling from industry fishing vessels off WA, OR, and CA. The sampling from fishing vessels expands the survey into areas that are inhabited by CPS but are too shallow for the NOAA ships to safely navigate.
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Northern California Current Ecosystem Survey (transect)
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This layer is intended to represent the geographic extent of NOAA Fisheries’ Northern California Current Ecosystem Survey transects. The Northern California Current Ecosystem Surveys started in 1996 and is led by NMFS Northwest Fisheries Science Center. These surveys expand the biophysical sampling conducted along the Newport Line out to the edge of the U.S. Exclusive Economic Zone. These surveys help us understand lower trophic level responses to environmental variability across the Pacific Northwest and California Current ecosystem. We also incorporate information on the abundance and distribution of mid-trophic level nekton, marine mammals, and birds. These samples inform broad-scale analyses of hydrography, phytoplankton, zooplankton, larval and juvenile fish, and ocean acidification and hypoxia. This survey is also part of a larger collaboration with Oregon State University researchers studying the marine biodiversity and size structure across broad spatial scales in the northern California Current. The Northern California Current Ecosystem Survey samples seasonally from northern Washington to the Oregon/California border, and offshore to 200 nautical miles off Newport, Oregon and 150 nautical miles off Crescent City, California on the NOAA Ship Bell M. Shimada. Seasonal sampling efforts include CTD, acoustic transects, zooplankton, ichthyoplankton, and macro-plankton sampling via bongo and Methot nets, as well as midwater and beam trawls.
California Current Cetacean and Ecosystem Assessment Survey (extent)
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This layer is intended to represent the geographic extent of NOAA Fisheries’ California Current Cetacean and Ecosystem Assessment Survey. The California Current Cetacean and Ecosystem Assessment Survey started in 1991 and is led by NMFS Southwest Fisheries Science Center. This survey includes ship-, aerial-, and land-based surveys of marine mammals throughout the California Current Large Marine Ecosystem. Survey data have been used to estimate cetacean population size and trends, delineate cetacean population stock structure, describe cetacean and seabird distributions and hotspots, develop species distribution models, and inform marine mammal stock assessment reports pursuant to statutory requirements under the Marine Mammal Protection Act (MMPA). Research vessels conduct line-transect surveys, typically every three years, in summer and fall and span waters out 300 nautical miles offshore, from the US-Canada to US-Mexico border. NOAA research vessels (David Starr Jordan, McArthur, McArthur II, Reuben Lasker, Bell M. Shimada) collect visual sightings data for cetaceans and seabirds, passive acoustic (e.g., towed or drifting array) data for cetaceans, tissue biopsy sampling used for genetics analysis, and oceanographic sampling.
Fisheries Online Information System - Survey of pelagic and demersal habitats within the northern California Current
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The Northwest Fisheries Science Center (NWFSC) conducts a comprehensive groundfish bottom trawl survey encompassing the U.S. West Coast between the borders with Canada and Mexico (Keller et al. 2008) and water depths of 50 to 1280 meters. This survey was not designed to quantitatively sample the young-of-the-year (YOY) life history stage. Since 1996, the Zooplankton Program at the NWFSC has conducted biweekly hydrography and plankton cruises along the Newport Hydrographic line (NH-Line) across the central Oregon shelf (44.67N) (e.g., Peterson and Keister 2003, Peterson 2009). On each cruise, hydrographic measurements and zooplankton samples are collected at stations ranging from 1 to 25 miles from shore. These zooplankton cruises build on and complement a broad range of historic and ongoing oceanographic sampling focused on the NH-Line. For FY11, the NWFSC received Cooperative Research funding to conduct a seasonal fishing vessel-based survey of young-of-the-year (YOY) groundfishes along the NH-Line synoptically with the Zooplankton Labs plankton/physical oceanography sampling program. The YOY groundfish, ichthyoplnakton and zoopplankton work are, in part, operating as a cooperative survey of pelagic and demersal habitats within the northern California Current,. The database stores data from ongoing field collections made by the OSU Fisheries Oceanography Research Team in collaboration with NOAA Fisheries. Field activities include plankton tows, benthic beam trawls, water column hydrographic profiles, and in-situ video observations of fish behavior.
Coastal Assessment Framework - National Assessment of Estuary and Coastal Habitats
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Under the National Fish Habitat Partnership, scientists at the NEFSC, NWFSC, and Silver Spring Headquarters are compiling information on the nation's estuarine and coastal habitats and the species they support in order to assess their current potential for restoration and protection. National project headed up by F/ST. Jihong Dai documents InPort metadata. Geographic data on the nation's coasts and estuaries.
Oceanographic Trawl Data - Juvenile Salmon & Ocean Ecosystem Survey
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FY20 will mark the 23nd year of sampling, making the Juvenile Salmon and Ocean Ecosystem Survey (JSOES) the longest running salmon survey on the west coast. JSOES has clearly demonstrated correlations between ocean conditions and the distribution, abundance, and survival of juvenile Columbia River (CR) salmon in the Northern California Current (NCC) nearshore ecosystem. For example, our ocean indicators provide managers from the federal and state governments, tribes, and other agencies/groups the ability to forecast adult returns one to two years in advance for coho and spring/summer Chinook salmon. We continue to show the importance of evaluating ocean conditions to support management decisions and to provide context for efforts by the Northwest Power and Conservation Council (NWPCC) and BPA to restore and enhance salmon production. The primary goal of our work is to develop a mechanistic understanding of how trophic dynamics and conditions in the ocean and CR plume affect survival of juvenile salmonids. This knowledge will allow us to improve forecasts in a quantitative rather than qualitative manner, and decouple the effects of mitigation efforts in the freshwater environment from the effects of a changing ocean environment. These improved forecasts will lead to well-informed recommendations for an ecosystem approach to management strategies based on the full suite of river, plume, and ocean environments. Nekton and juvenile salmon collections from surface trawl.
eDNA Survey
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Scientists at NOAA's Northeast Fisheries Science Center (NEFSC) are using environmental DNA (eDNA) to identify fish communities and monitor ecosystems by collecting a water sample and analyzing the DNA found in it, identifying the species that left it behind without capturing a single animal. As animals swim, they shed scales, tissue, and waste, leaving traces of DNA in the water. A water sample is first collected from the ocean and filtered to concentrate DNA in it. NOAA scientists then make millions of copies of a target DNA region through polymerase chain reaction (PCR) to make enough genetic material for high throughput sequencing. The metabarcoding process described above for eDNA analysis allows scientists to look for many species in the same sample. The final step is like a matching game, in which the DNA sequences are compared with a reference library of known species to find a match. The eDNA method is particularly useful for detecting species that are not easily captured, including rare or migratory species. It can also help in areas that are difficult to sample because of challenging ocean conditions, sensitive habitats, or a rugged seafloor. An eDNA analysis provides a snapshot of the community of species at the time of sampling and over time. This can help us detect shifts in marine ecosystems. eDNA samples have been collected on NOAA Ecosystem Monitoring (EcoMon) surveys since 2019. These samples will help develop best eDNA practices using metabarcoding, an innovative way to determine what fish species live in what parts of the ocean without actually seeing any fish.
Physical oceanography - Developing end-to-end models of the California Current Large Marine Ecosystem
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The purpose of this project is to develop spatially discrete end-to-end models of the California Current LME, linking oceanography, biogeochemistry, food web interactions, habitat, fisheries, economics, monitoring, and management into a common model framework. This framework allows for thought experiments, including evaluation of alternate management strategies, identifying robust indicators, and assessing relative importance of different ecosystem drivers in regulating important processes. NMFS personnel are conducting this work in broad collaboration with other NOAA scientists, academics, and NGOs. The specific work entails model development, scoping issues with stakeholders and policy makers, running scenarios, and analyzing and writing up the results. Products will include peer-reviewed papers, presentations, and workshops with modelers and/or stakeholders. Management audiences include NMFS west coast regions and the PFMC. The project is an on-going, stand-alone project with no firm deadline for completion. Outputs of the ROMS model. Metadata and .nc datafile at https://www.nodc.noaa.gov/oceanacidification/data/0131198.xml Generated from Atlantis ecosystem model, version AtlantisTrunk5425. Model code from CSIRO Australia, available via SVN after contacting CSIRO staff at http://atlantis.cmar.csiro.au/.
eDNA survey
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Scientists at NOAA Northeast Fisheries Science Center (NEFSC) are using environmental DNA (eDNA) to identify fish communities and monitor ecosystems by collecting a water sample and analyzing the DNA found in it, identifying the species that left it behind without capturing a single animal. As animals swim, they shed scales, tissue, and waste, leaving traces of DNA in the water. A water sample is first collected from the ocean and filtered to concentrate DNA in it. NOAA scientists then make millions of copies of a target DNA region through polymerase chain reaction (PCR) to make enough genetic material for high throughput sequencing. The metabarcoding process described above for eDNA analysis allows scientists to look for many species in the same sample. The final step is like a matching game, in which the DNA sequences are compared with a reference library of known species to find a match. The eDNA method is particularly useful for detecting species that are not easily captured, including rare or migratory species. It can also help in areas that are difficult to sample because of challenging ocean conditions, sensitive habitats, or a rugged seafloor. An eDNA analysis provides a snapshot of the community of species at the time of sampling and over time. This can help us detect shifts in marine ecosystems. eDNA samples have been collected on NOAA Ecosystem Monitoring (EcoMon) surveys since 2019. These samples will help develop best eDNA practices using metabarcoding, an innovative way to determine what fish species live in what parts of the ocean without actually seeing any fish.
CROOS - Collaborative Research on Oregon Ocean Salmon
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Goal 1: Improve understanding of salmon ocean ecology by integrating stock-specific distribution patterns over space and time with biological and environmental data. Goal 2: Integrate multiple disciplines to develop and apply new scientific technology to improve fisheries management strategies across geo-political boundaries. Goal 3: Improve economic opportunities for fishermen and coastal communities. The Oregon Salmon Commission, California Salmon Council, and Washington Trollers Association lead the Collaboration. Partners include Oregon Sea Grant, Community Seafood Initiative, Columbia River Inter-Tribal Fish Commission, University of California Santa Cruz, Oregon State University, Oregon and Washington Departments of Fish and Wildlife, California and Idaho Departments of Fish and Game, National Marine Fisheries Service Northwest, and Southwest Fisheries Science Centers. Fishermen sample Chinook salmon at sea. Genetic Stock Identification (GSI) analysis is used to determine stock of origin. Scales are examined to determine age, and other biological and physical data are taken. The purpose is to develop Fishery information system with multiple goals. The target audience is the Pacific Fishery Management Council (PFMC) and Pacific Salmon Commission (PSC) Management, as well as fishermen, scientists, marketers, educators, and the general public. This is a stand-alone project, with one principal point of contact in NMFS. This project is ongoing. Chinook genetics for stock identification.
AFSC/NMML/CCEP: California Current Ecosystem Program and Cascadia Research Collective: Aerial and small boat line transect data in waters of OR/WA/BC from 1989, 1990, 1991, 1996, 1997, 2002, and 2003
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The National Marine Mammal Laboratory (NMML) a division of NOAA's Alaska Fisheries Science Center (Seattle, WA) and Cascadia Research Collective (Olympia, WA) conducted aerial and small boat line transects to estimate the abundance of harbor porpoises in waters of Oregon, Washington, and British Columbia, Canada. This dataset contains line transect survey data with effort (line length) and sighting data (species, group size, distance/angle) and associated covariate data.
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