AndreaBozzo/ceres-open-data-index huggingface dataset:
Biological - Elwha River Dam Removal Study

This project monitors ecosystem response to dam removals on the Elwha River, Washington State. The Elwha Dam removal project is the largest project of its kind in the world and is the largest restorative action that has taken place in any Western U.S. Evolutionarily Significant Unit (ESU). Ecosystem response includes changes to aquatic habitat, the food web, and all aspects of the viable salmon parameters of listed and non-listed salmonid species. The project is based on the development and implementation of the Elwha Monitoring and Adaptive Management Guidelines (EMAM), which was developed as a collaborative effort between the Watershed Program at the NWFSC, the Lower Elwha Klallam Tribe (LEKT), the United States Department of Fish and Wildlife Service (USFWS), the United States Geologic Survey (USGS), the Washington Department of Fish and Wildlife (WDFW), and the National Park Service (NPS). We employ a variety of metrics to efficiently monitor ecosystem condition over space and time. This project will provide data to assess changes for the listed Elwha River populations (Chinook salmon and steelhead), and help determine whether those populations are improving, static, or declining. Such analyses are crucial to help inform future large-scale dam removals for multiple ESUs across the Western U.S.
All relevant biological data.

Tags: dam removal, doc/noaa/nmfs/nwfsc, effectiveness monitoring, elwha river, fe (fish ecology) division, floodplain, gps, instrument not applicable - instrument not applicable, juvenile salmonid, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc montlake, restoration, salmon
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Wenatchee Chinook Parentage - Evaluate the reproductive success of hatchery and wild Chinook salmon in the Wenatchee River

This project addresses a key uncertainty for evaluating whether hatchery supplementation programs have a net positive contribution to recovery of listed populations.  Specifically, what is the relative reproductive success of naturally spawning hatchery fish and what are causes of poor reproductive success of hatchery fish?  We are addressing these questions by focusing on the spring Chinook salmon in the Wenatchee River, part of the endangered Upper Columbia River spring Chinook salmon ESU.  Our study design uses genetic parentage analysis to assign progeny (sampled at both the smolt and adult life stages) to naturally spawning hatchery and wild origin fish.  The progeny counts for each spawner are a measure of reproductive success, and by comparing the mean reproductive success of hatchery and wild spawners, we obtain an estimate of the relative reproductive success (RRS) of the hatchery origin fish.  A key part of the study is to include co-variables, such as age, size, run timing, spawning location, and spawning behavior, in the analysis so that the proximate causes of differences in RRS between hatchery and wild fish can be evaluated.   The study was initiated in 2004, and we have sampled 10 years of adults and 8 years of smolts.  In several papers and reports generated by this project, we have reported on the RRS of spawners sampled in 2004-2007, and 2010, and have found that spawning age, size, and location, in addition to hatchery/wild origin, are important co-factors explaining variation in reproductive success.  This has been a highly influential study that addresses a critical uncertainty identified in both recovery plans and biological opinions and has had strong support from the West Coast Regional Office.
Microsatellite data from spring run Wenatchee River Chinook salmon.

Tags: aquaculture, artificial propagation, cb (conservation biology) division, dna sequencer, doc/noaa/nmfs/nwfsc, esa, genotype, hatchery, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, salmon, wenatchee river
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Fish culture data - 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.
Raw data on rearing densities, tanks, water temperature, mortalities, ration and feed size may be available.

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, obsolete, reproductive biology, sablefish, sex control, sustainable aquaculture, temperature sensor
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Wenatchee River steelhead reproductive success - Estimate the relative reproductive success of hatchery and wild steelhead in the Wenatchee River, WA

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.

Tags: cb (conservation biology) division, dna sequencer, doc/noaa/nmfs/nwfsc, genetics, montlake nwfsc, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, reproductive success, wenatchee river
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Seasonal transport - A study to determine the seasonal effects of transporting fish from the Snake River to optimize a transportation strategy

The goal of this U.S. Army Corps of Engineers (USACE) - funded study that began in 2004 is to determine if the smolt-to-adult return rates (SARs), transport/in-river ratio, and differential post-hydropower system mortality of transported and in-river Chinook salmon and steelhead are related to their size and time of ocean entry. Juvenile spring/summer Chinook and steelhead are PIT-tagged each week of the migration at Lower Granite Dam, and either barged or returned to the river to migrate. A portion of the in-river migrants are collected at Bonneville Dam and re-measured to calculate growth during migration. When adult returns are complete, SARs and Transport Benefit ratios will be calculated and correlated with biological and physical conditions in the river, plume, and ocean environment. This information can then be used to make management decisions on when to release fish from hatcheries, and whether to transport smolts or leave them in the river to optimize SARs. Annual reports of project progress and a final report will be provided to the USACE upon project completion.

Seasonal transport data.

Tags: barging, biological, chinook salmon, doc/noaa/nmfs/nwfsc, fe legacy data sets, lower granite dam, national marine fisheries service, noaa. u.s. department of commerce, non-noaa funded, northwest fisheries science center, pit tag
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Estuarine chinook capacity - Estimating changes in juvenile Chinook rearing area and carrying capacity in estuarine and freshwater habitats of the Puget Sound region

This project has two objectives: 

1. Estimate the amount of rearing habitat available to juvenile Chinook salmon currently and historically (i.e., ~1850s) throughout the Puget Sound region

2. Estimate the carrying capacity of the habitat in the region to support juvenile Chinook under current and historical conditions.

Krista Bartz is the principal investigator for the project, and most of the analytical work is complete (as of May 2012). The remaining work involves completing a manuscript describing the work. Specific product for this project is a manuscript (likely the North American Journal of Fisheries Management).

Audience for the project was initially intended to be NWFSC staff involved in parameterizing a Puget Sound-wide life-cycle model for Chinook salmon. Since ~2008, when that effort stalled, there has been a resurgence in interest in developing such a model.

This is a one-time, stand-alone with soft deadlines in October 2012 to send the manuscript for internal review and December 2012 to send the manuscript to the journal.
Estimates of changes in Chinook salmon juvenile rearing capacity in rivers and estuaries throughout Puget Sound, using pre-settlement conditions as the baseline.

Tags: cb legacy data sets, chinook salmon, doc/noaa/nmfs/nwfsc, habitat capacity, instrument not applicable, montlake, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, obsolete, puget sound
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Light Experiment data - Snake River sockeye salmon captive propagation

In the early 1990s, Redfish Lake sockeye salmon from the Sawtooth Basin in Idaho were on the brink of extinction, and they were listed as endangered under the US Endangered Species Act in 1991. To prevent extinction, a gene rescue captive broodstock program was established for the stock that consisted of taking most of the remaining gene pool into captive culture at specialized conservation hatcheries at the Manchester Research Station and the Idaho Department of Fish and Game Eagle Hatchery. 

Efforts through the decade of the 1990s consisted of developing techniques for successful culture of sockeye salmon to adulthood, establishing rearing and spawning protocols to ensure preservation of stock diversity, and habitat enhancement at the rearing lakes. In the early 2000s, the program began to include a demographic focus to boost the population through rearing and release of enough juveniles to produce some adult returns. For the last few years, NWFSC eyed egg production has resulted in over 150,000 smolts being released into the Stanley basin annually for recovery, with plans to increase NWFSC eyed egg production to support release of half a million smolts in the Stanley Basin by 2017.  In 2011, and for the fourth year in a row, record numbers of sockeye adults have returned to their native home in Idaho.
This work collected data on the length, weight, and reproductive characteristics of sockeye salmon reared in outside and inside tanks.

Tags: artificial propagation, doc/noaa/nmfs/nwfsc, instrument not applicable, migrated from resource enhancement and utilization technologies division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc manchester, salmon, snake river
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Fish Culture data - Snake River sockeye salmon captive propagation

Gene rescue captive broodstock program was established for ESA-listed endangered Snake River sockeye salmon from Redfish Lake, Idaho.  The program has consisted of taking most of the remaining gene pool into captive culture at specialized conservation hatcheries at the Manchester Research Station and the Idaho Department of Fish and Game Eagle Hatchery.  Fish are being released to native habitats as part of recovery efforts.
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.

Tags: artificial propagation, doc/noaa/nmfs/nwfsc, instrument not applicable, migrated from resource enhancement and utilization technologies division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc manchester, salmon, snake river
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Fish Sampling in the Multnomah Channel Marsh Natural Area near Portland Oregon from 2014-03-24 to 2015-07-15

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.

Tags: columbia river estuary, doc/noaa/nmfs/nwfsc, fe (fish ecology) division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, restoration (habitat restoration)
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Coral reef ecosystem marine protected area monitoring in Fagamalo, American Samoa: comprehensive assessment of coral demography (adult and juvenile corals) from belt transect surveys in 2015

In 2010 the village of Fagamalo, Tutuila, American Samoa, designated a no-take Marine Protected Area that sees the protection of 2.25 square kilometers of ocean. Because little is known regarding the status of living marine communities in the area, and at the request of the American Samoa Department of Marine and Wildlife Resources, NOAA scientists conducted surveys to assess the status of the benthic communities and establish a baseline against which to compare temporal change.

The data described here were collected via belt transect surveys of coral demography (adult and juvenile corals) by the NOAA Coral Reef Ecosystem Program (CREP) according to protocols established by the NOAA National Coral Reef Monitoring Program (NCRMP).  In  2015 data were collected at 18 stratified randomly selected sites. These data include:

1) an assessment of coral colony density and size-class distribution for the selected monitoring sites; 
2) an assessment of coral recruitment at the monitoring sites; and 
3) an evaluation of coral colony condition, including mortality, disease, and bleaching.

These data can be accessed online via the NOAA National Centers for Environmental Information (NCEI) Ocean Archive. Additionally, photoquadrat benthic images were also collected (documented and archived separately).

Tags: 1083, american samoa, baseline studies, belt transect, benthic biology, benthic missions, benthos analysis, biology, biosphere, coastal processes, coral, coral - census, coral - colony size, coral - species identification, coral colony size and condition, coral communities, coral diseases, coral mortality, coral reef conservation program, coral reef ecology, coral reef ecosystem division, coral reef ecosystem monitoring training and capacity building to support improved resource manageme, coral reef ecosystem program, coral reefs, corals, country/territory, cred, crep, doc/noaa/nmfs/pifsc, earth science, ecosystem sciences division, fagamalo (14s170w0047), in situ biological, marine biology, national marine fisheries service, nmfs, noaa, numeric data sets, ocean basin, oceans, pacific islands fisheries science center, pacific ocean, pifsc, reef monitoring and assessment, south pacific ocean, survey - biological, survey - coral reef, survey - swimmer/diver, transect monitoring, tutuila island, u.s. department of commerce, united states of america, us doc, zoology
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
DIDSON ultrasonic video data - Untrawlable Habitat Strategic Initiative

The NWFSC FRAM Marine Habitat Ecology Team is involved in many aspects of the UHSI program but has focused on the application of DIDSON imaging sonars to aid in quantifying avoidance/attraction biases in fishes relative to two types of mobile sampling vehicles used for direct visual surveys. During 2016, the team is currently building databases from information collected during the 2014 and 2015 field season and conducting ongoing data analysis. In 2016, the MHE will be working with the UHSI Team on planning for and conducting field research in the Southern California Bight.
Ultrasonic 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
Tagging, Mux, smolt, habitat and flow data - Movement and Survival of Juvenile Salmonids in Small Streams

The Strait of Juan de Fuca Intensively Monitored Watershed (IMW) began in 2004 to test the watershed-scale response of steelhead and coho salmon to watershed restoration. The Strait IMW includes two treatment watersheds (East Twin River and Deep Creek) and one control watershed (West Twin River). Restoration treatments included LWD placement, road and culvert removal, off-channel habitat creation, and riparian planting. Monitoring of physical habitat as well as coho and steelhead parr densities began in 2004 using the EPAâs EMAP site selection and sampling protocols. Smolt and adult monitoring predates the IMW program and began as early as 1998 in some watersheds. Preliminary results suggest an increase in pool habitat and small increases in steelhead adults and smolts in East Twin River, as well as adult coho in Deep Creek. PIT tagging has revealed a large outmigration of age-0 coho in the fall that contributes to the adult return, stream swapping by juveniles, and varying return times for coho adults. Current research has answered a portion of our original questions and has raised new ones. Restoration treatments were completed fairly recently or are still in progress. As habitat typically does not respond immediately to treatment, additional years of monitoring are needed to determine watershed-scale fish response. Moving forward, analysis of otoliths to validate PIT tag data and new restoration methods such as carcass or nutrient enhancement may be merited.
PIT tagging and habitat data. Includes fish weight, length, location, and PIT tag number. Habitat data includes wood measurements and stream surveys.

Tags: animal mounted instrument, deep creek, doc/noaa/nmfs/nwfsc, east twin river, fe legacy data sets, imw, movement, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, olympic peninsula, oncorhynchus kisutch, oncorhynchus mykiss, pit tag, salmon, survival, unknown physical collection device, washington state, west twin river
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Gene expression data - 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.
Data on the expression of various genes in the gonads of sablefish during sex differentiation are collected.

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, obsolete, quantitative pcr machine, reproductive biology, sablefish, sex control, sustainable aquaculture
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Enzyme activity - Evaluating the impacts of pesticides on ESA-listed salmon and their habitats

Long-running science support for the agency (Office of Protected Resources, others) related to the use of modern pesticides throughout the United States as a limiting factor for endangered species conservation and recovery. This work is currently supporting several national ESA Biological Opinions, and is under review by the National Academy of Sciences. The NAS panel recommendations are expected in the summer of 2013, and these will guide additional research in FY14 and beyond.
Measurements from salmonids of enzyme activity following exposure to pesticides.

Tags: doc/noaa/nmfs/nwfsc, ecotoxicology, endangered species act, instrument not applicable, migrated from environmental conservation division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc montlake, nwfsc mukilteo, salmon, stormwater
Organization: National Oceanic and Atmospheric Administration, Department of Commerce