AndreaBozzo/ceres-open-data-index huggingface dataset:
Trinidad Head Line (station)

This layer is intended to represent the geographic extent of NOAA Fisheriesâ Trinidad Head Line Survey. The  Trinidad Head Line ocean observing program  started in 2007 and is led by NMFS Southwest Fisheries Science Center. This survey collects oceanographic and biological samples that inform quantitative studies of the California Current Large Marine Ecosystem. The Southwest Fisheries Science Center and Cal Poly Humboldt (CPH) have conducted frequent ocean observing cruises to characterize seasonal and interannual variability in the plankton ecosystem in coastal waters off northern California. In combination, these data give insight into how coastal ecosystems respond to seasonal cycles and larger scale climate dynamics, and contribute to a much broader coastwide collaborative effort to understand the dynamics of the California Current Large Marine Ecosystem.  At five stations that span the continental shelf and upper continental slope, physical, biological, and chemical parameters are measured. Historically there have been six stations, but the sixth station is no longer an active sampling location as of 2014. Cruises occur approximately monthly throughout the year. Oceanographic parameters are measured throughout the water column (to a maximum depth of 500 m), and water samples are collected for assays of nutrients, chlorophyll, eDNA, and domoic acid. Zooplankton samples are collected from the upper 100 meters of the water column and analyzed to quantify changes in size of dominant krill species and variability in the community structure of krill, copepods, and larval fish in response to climate forcing.

Tags: california, california current ecosystem, doc/noaa/nmfs/nwfsc, hydrography, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, ocean observing, pacoos, story map: noaa fisheries west coast offshore scientific surveys, trinidad head, united states, zooplankton
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Elwha Master Datafile - Elwha dam removal neashore monitoring

Removal of two dams on the Elwha River, Washington will help restore natural sediment processes to the coastal environment near the river mouth.  We are interested in the responses of fish associated with shallow subtidal and intertidal habitats because they function as spawning and rearing habitat for many fish species including the ecologically important forage fish and federally protected species of Pacific salmon.  Since 2006, we have been collecting species composition and size distribution of the intertidal/subtidal fish community in the Eastern and Central Strait of Juan de Fuca.  Potential reference site and treatment sites (where sediment changes are expected to occur) were sampled on a monthly basis from April to September using a beach seine.  We found over 45 species of fish, mostly juvenile stages, using this portion of the Strait of Juan de Fuca representing two groups- fish occurring in the water column and those living on or near the bottom.  The water column species tended to be very abundant and included both migrants (e.g., juvenile salmon) and residents (surf smelt).  Although the same species tended to be present each year, they often exhibited dramatic between year variability in abundance.  This suggests the importance of using multiple years of data to evaluate changes resulting from dam removal.  Treatment and reference areas exhibited some significant differences and we found seasonality in the fish assemblage structure.  Our results suggest that some promising bio-indicators of short and long term change in sediment processes are:  1) numbers of species, 2) species diversity, 3) composition and sizes of benthic species, 4) abundance by life history stage of surf smelt, and 5) presence of migratory species like juvenile salmon.  We will continue this work following dam removal to track the changes due to dam removal.
For this project, the data was stored in .xls and access files.

Tags: doc/noaa/nmfs/nwfsc, fe (fish ecology) division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Aquatic Invertebrates - Thornton Creek Restoration Project Effectiveness Monitoring

NOAA has designed and is currently implementing a hyporheic monitoring plan for the Thornton Creek watershed in North Seattle. This work is being conducted for Seattle Public Utilities, who in 2015 completed two large-scale floodplain reconnection projects in the Thornton Creek Watershed.  This study will evaluate restoration effectiveness by comparing control and treatment study reaches to each other and to forested references streams before and after restoration. NOAAs data collection focuses on hyporheic invertebrates, water temperature, and nutrient concentrations.

Taxonomic and density data for aquatic invertebrates collected at project sites.

Tags: doc/noaa/nmfs/nwfsc, fe (fish ecology) division, national marine fisheries service, noaa. u.s. department of commerce, non-noaa funded, northwest fisheries science center
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Production Data - Captive Broodstock Gene Rescue Program for Odd Year Class Elwha River Pink Salmon

Conduct captive brood stock gene rescue program for Elwha River odd-year class pink salmon.
Information on the number of smolts received into the program is maintained and summarized by year.  The production of adults transferred to the Elwha Hatchery for restoration activities is also annually summarized.

Tags: artificial propagation, doc/noaa/nmfs/nwfsc, instrument not applicable, manchester research station, migrated from resource enhancement and utilization technologies division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, salmon
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Barged/In-river steelhead migrant data - Evaluation of methods to reduce straying rates of barged juvenile 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 and field data on barged and in-river migrant steelhead.

Tags: barging, big beef creek hatchery, biological, columbia river, doc/noaa/nmfs/nwfsc, homing, migrated from resource enhancement and utilization technologies division, migration, national marine fisheries service, noaa. u.s. department of commerce, non-noaa funded, northwest fisheries science center, straying
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Video Direct Count Data - Bycatch Reduction Engineering Research

Through key regional collaborations with the Pacific States Marine Fisheries Commission, Oregon Department of Fish and Wildlife, Alaska Fisheries Science Center, and the fishing industry, the Marine Habitat Ecology Team at the  NWFSC has been able to pursue a wide-ranging array of conservation engineering projects relevant to reducing bycatch in the west coast groundfish and ocean shrimp trawl fisheries. Examples of types of research projects pursued during any given year include: 1) Reducing Chinook salmon, eulachon, rockfish, and Pacific halibut bycatch in midwater and bottom trawl fisheries using Bycatch Reduction Devices (BRDs), 2) Examining selectivity characteristics of codends that differ in mesh size and configuration in bottom trawl fisheries, and 3) Testing other novel bycatch engineering modifications to mobile and fixed gears. Much of our current work has been in response to the fishing industries concerns over catches of overfished and rebuilding rockfishes and Pacific halibut allocated in the Pacific coast Groundfish Trawl Rationalization Catch Share Program. The trawl rationalization program, starting in January 2011, established formal Annual Catch Limits (ACLs) and individual catch share quotas. In addition to ACLs, fishing opportunities may also be limited by hard caps or IBQs for non-groundfish species (e.g., Chinook salmon, and Pacific halibut). Bycatch of overfished and prohibited species in the west coast groundfish trawl fishery has the potential to constrain the fishery such that a substantial portion of available harvest may be left in the ocean.
Direct species counting and behavioral observations from video data.

Tags: doc/noaa/nmfs/nwfsc, fram (fishery resource analysis and monitoring) division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
CROOS - Collaborative Research on Oregon Ocean Salmon

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.

Tags: aquatic ecosystems, bycatch reduction device, cb legacy data sets, climate change, doc/noaa/nmfs/nwfsc, fisheries ecology, instrument not applicable, national marine fisheries service, nearshore ocean, newport research facility, noaa. u.s. department of commerce, northern california current system, northwest fisheries science center, unknown physical collection device
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Predator Gut Isotopes - Characterizing ecosystem role of sharks

This work uses white muscle tissues collected from sixgill and sevengill sharks to characterize the diet of each species. Tissues from prey species have also been prepared in order to initialize the models. We used mixing models to determine the probabilities of each prey species being in the diet of these top predators. These data will be used to predict which prey groups are impacted by these species, and then used in conjunction with patterns of daily, seasonal, and annual movement patterns to examine the variation in predatory impact across space and time among the various prey groups.
Shark tissue stable isotope signatures from Northeast Pacific coastal habitats.

Tags: 10, 2-1, animal and plant collection device, balance, cb (conservation biology) division, doc/noaa/nmfs/nwfsc, drying oven, instrument not applicable - instrument not applicable, lipid extractor, macn, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, predators, puget sound, stable isotopes, wa, wamarine, willapa bay
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Sex control experiments - Development of methods to sterilize sablefish

Methods for reproductive sterilization are broadly needed in marine aquaculture due to biosafety concerns associated with escapement of farmed fish and potential genetic contamination of wild stocks. Current methods for sterilization have been primarily tested in freshwater fishes and are often ineffective, particularly in males. The proposed activity builds upon our recent success in producing the first-ever monosex female stocks of sablefish for aquaculture and seeks to develop eco-friendly, non-GMO methods for reproductive sterilization. We will use sablefish as our model marine species for sterilization and continue to collaborate with University of Maryland faculty with expertise in cutting-edge techniques for sterilization. Development of sustainable marine aquaculture is a high priority at the local (NWFSC), regional (WCR), and national levels (NOAA, DOC, Congress). Our sablefish sex control/sterilization project was also highlighted as a critical priority and outstanding area of research in the NOAA Aquaculture Science Review published 28 Feb 2019. We ultimately aim to transfer a sterilization technology to the US sablefish aquaculture industry and expand our methodology to other important species, with the goal of improving sustainability of marine aquaculture and mitigating impacts on the environment.
In these experiments sablefish sex ratio data are collected using gonadal histology and a genetic sex marker.

Tags: doc/noaa/nmfs/nwfsc, gonadal sex differentiation, manchester research station, migrated from resource enhancement and utilization technologies division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, reproductive biology, sablefish, sex control, sustainable aquaculture, video camera
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Joint U.S.-Canada Integrated Ecosystem and Pacific Hake Acoustic Trawl Survey (CTD Cast)

This layer is intended to represent CTD Cast locations from NOAA Fisheriesâ Joint U.S.-Canada Integrated Ecosystem and Pacific Hake Acoustic Trawl Survey. The Joint U.S.-Canada Integrated Ecosystem and Pacific Hake Acoustic Trawl Survey started in 1977 and is a collaborative effort between the Northwest Fisheries Science Center and Fisheries and Oceans Canada Pacific Region. This survey produces the Pacific hake biomass estimate that is essential to the management of the west coast fishery. Data collected are used to generate biological information and inform stock assessments made by the Hake Treaty Joint Technical Committee, a body formed by the U.S.-Canada International Hake/Whiting Treaty. The survey is typically conducted on a biennial basis. Because this is an international survey, two research vessels cover the entire U.S. and Canadian West Coasts. The survey design includes 10-nm spaced transects that run approximately perpendicular to the coast for the area that extends from Point Conception, California in the south to the West Coast of Vancouver Island in the north, and 20-nm transects north of WCVI to Dixon Entrance, Alaska. Transects are conducted using a NOAA Fishery Survey Vessel equipped with scientific echosounders and fishing nets to validate fish aggregations identified in the acoustic data. Midwater trawls are also equipped with a stereo camera to assist in determining the species composition of collected organisms.

Tags: acoustic survey, acoustics, alaska, bell m. shimada, california, canada, doc/noaa/nmfs/nwfsc, echo integration-trawl survey, hake, iats, meruccius productus, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, oregon, pacific hake, pacific whiting, story map: noaa fisheries west coast offshore scientific surveys, united states, washington
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
EPA Townetting CTD casts - Evaluating the ecological health of Puget Sound's pelagic foodweb

To evaluate effects of human influence on the health of Puget Sound's pelagic ecosystems, we propose a sampling program across multiple oceanographic basins measuring key attributes of the pelagic foodweb. We will quantify seasonal abundance and composition of pelagic biota from lower trophic levels (e.g., bacteria and phytoplankton) to middle trophic levels (e.g., zooplankton, small pelagic fishes, and jellyfish), as well as assess the individual condition of forage fish and juvenile salmon. 

The goals of this program:

1) Determine how foodweb endpoints vary across natural and anthropogenic gradients.

2) Determine how these characteristics vary across Puget Sound.

3) Evaluate a number of biological metrics for monitoring ecosystem health.

These outputs will improve our basic understanding of pelagic ecology in Puget Sound, better define what comprises a healthy pelagic ecosystem in Puget Sound, determine foodweb-relevant indicators that are sensitive to human influence, and help prioritize regional protection and restoration efforts. Work is conducted by NOAA personnel and contractors in collaboration with tribal partners (Squaxin, Port Gamble/S'Klallam), undergraduate research interns, and citizen volunteers.
Access database containing all conductivity/temperature/depth (CTD) casts.

Tags: admiralty inlet, bacterial communities, chlorophyll a, ctd, doc/noaa/nmfs/nwfsc, ecosystem, fe (fish ecology) division, food web, heterotrophic production, hood canal, low dissolved oxygen, marine microbes, microbial abundance, national marine fisheries service, nearshore pelagic, noaa. u.s. department of commerce, north central ps basin, northwest fisheries science center, nutrients, puget sound, rosario basin, salmon, south central ps basin, south ps basin, whidbey basin north, whidbey basin south
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Food web model output - Trophic impacts of bald eagles in the Puget Sound food web

This project is developing models to examine the ecological roles of bald eagles in the Puget Sound region. It is primarily being done by NMFS FTEs, in collaboration with scientists from the State of Washington and University of Washington. Trophic ecology of bald eagles will be described using ecosystem-scale food web models and bioenergetics models. Working models and scientific manuscripts will be the main products. The target audience is the Puget Sound Partnership, resource management agencies, and stakeholders in the Puget Sound area. This is an on-going, stand-alone project without a firm deadline.
Spreadsheet.

Tags: bald eagle, bioenergetics modeling, cb (conservation biology) division, climate change, doc/noaa/nmfs/nwfsc, ecosystem modeling, food web, instrument not applicable, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, puget sound
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Reference stand condition - Effects of Thinning on Forest Structure important to the recovery of ESA-listed species

This study evaluates the effects of thinning regimes designed to accelerate the development of late-successional forest structure for the benefit of salmon and other ESA-listed species. The focus is to ensure that proposed thinning activities (primarily by federal agencies such as BLM and USFS) do not delay the recovery of habitat important to these ESA-listed species. Currently thinning actions undertaken by BLM and USFS have resulted in the substantial delay in the recovery of instream habitat. The results from this study are intended to be provided to these agencies so that they can make management decisions consistent with the restoration and recovery of habitat important to ESA-listed species, in particular, instream habitat.
Data of DF forest reference stands.

Tags: doc/noaa/nmfs/nwfsc, esa, fe (fish ecology) division, forest thinning, instrument not applicable, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, salmon, western oregon
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Killer whale morphology - Variation in morphology of killer whale ecotypes

We are using elliptic Fourier analysis to determine the patterns of variation in morphology of dorsal fin shape, saddle patch shape, and eye patch shape of resident, transient, and offshore killer whales in the northeastern Pacific ocean. We will also be looking for evidence of genetic variation underlying these patterns in southern resident killer whales.
Morphology and heritability of morphology by ecotype, sex (if available), age (if available), and parentage (if available).

Tags: cb (conservation biology) division, doc/noaa/nmfs/nwfsc, instrument not applicable, morphometrics, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc montlake, quantitative genetics
Organization: National Oceanic and Atmospheric Administration, Department of Commerce