AndreaBozzo/ceres-open-data-index huggingface dataset:
Killer Whale Genetic Data - Incidence of inbreeding and inbreeding depression in Southern Resident Killer Whales

The southern residents face several well-documented external threats. However, the population might also be subject to internal factors that limit population growth, including a reduction in fitness due to inbreeding. Understanding how inbreeding affects individual fitness and thus the health status of the population is critical for evaluating the relative influence of other factors on southern resident recovery. Assessing the risk of inbreeding depression â specifically called for in the NMFS recovery plan â is important for conducting accurate Population Viability Analyses and correctly understanding the urgency of recovery efforts. Here, we propose using genomic methods to evaluate inbreeding and inbreeding depression in the southern resident population and a comparable but healthier Alaskan resident population. Measures of inbreeding will serve as an important health marker, supporting the integration of individual metrics aimed at understanding population performance.

Measures of inbreeding can be obtained directly by estimating variation at millions of DNA markers in an individualâs genome. Complete genomic sequences for 100 southern and 50 Alaska residents will be collected in collaboration with the genomics company BGI. Inbreeding values for each individual will be obtained using genome wide measures of homozygosity and relatedness.  We will then combine measured of inbreeding with data on individual fitness, to evaluate whether inbreeding leads to inbreeding depression. Generalized additive models will be used to determine whether survivorship, fecundity and size-at-age is influenced by different levels of inbreeding. Using this data, we will measure the degree of current and predicted future of inbreeding in the southern residents and compare this risk with the Alaska residents that have experienced consistent population growth. We will then evaluate whether inbreeding depression explains individual variance in fitness, and estimate its influence on the status of southern residents, using Population Viability Analyses.
Microsatellite, SNP, and mtDNA sequence data from southern resident killer whales.

Tags: cb (conservation biology) division, dna sequencer, doc/noaa/nmfs/nwfsc, genetics, killer whale, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc montlake, puget sound
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Migration of steelhead - Genetic Basis of Migratory Tendency and Life History Plasticity in Oncorhynchus mykiss

Steelhead population abundance is depressed throughout much of its southern range, and several Distinct Population Segments (DPSs) are listed as threatened or endangered under the US Endangered Species Act (ESA). Some anadromous populations are associated with relatively large resident trout populations, and some of these resident populations can produce migrating smolts. We are trying to determine the genetic architecture, population history, and plasticity of anadromy and residency in this species, with the intent of determining whether the hybrid migratory strategy expressed in wild populations like this is key to maintaining long-term resilience and productivity of anadromous populations. This collection of NWFSC Genetics and Evolution Program studies represents a long-term collaboration between NWFSC and the Alaska Fisheries Science Center, the Southwest Fisheries Science Center, the National Park Service, the US Forest Service, the Lower Elwha Klallam Tribe, and the US Geological Survey to understand the intrinsic (biological, genetic) and extrinsic (environmental) factors that influence production, diversity, and variation in these characteristics in wild steelhead and the resident trout they interact with. It involves annual fieldwork to collect data on juvenile and adult fish and reconstruct their molecular pedigrees and conduct quantitative genetic analyses, as well as to assess temporal trends in abundance and productivity and the condition of their freshwater habitats.
Genetic basis of migratory tendency and life history plasticity in Oncorhynchus mykiss.

Tags: cb (conservation biology) division, dna sequencer, doc/noaa/nmfs/nwfsc, national marine fisheries service, nmfs little port walter, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc manchester, nwfsc montlake, pedigree reconstruction, population viability analysis, quantitative genetics, steelhead
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
ISEMP - Integrated Status and Effectiveness Project

ISEMP has the overarching objective of developing management decision support tools from quantitative relationships of stream habitat quality and quantity's impact on anadromous salmonid population abundance and productivity in the Columbia River basin. ISEMP's data collection, management and analysis task and the resulting products can be organized into seven focal areas - three that are primarily data collection (ISEMP data streams) and four that are primarily data processing (ISEMP data management, monitoring guidance, and decision support tools).
Fish.

Tags: cb (conservation biology) division, doc/noaa/nmfs/nwfsc, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Chiller Design Model - Impact of chiller failure on the short-term temperature variation in the incubation of salmonids

In salmon recovery programs it is commonly necessary to chill incubation and early rearing temperatures to match wild development times. The most common failure mode for a chiller system is failure of the chiller or circulating pumps. Following chiller failure, the water temperature can rise from 5-7 C to 10-13 C depending on the well temperatures and ambient air temperatures.

The speed and magnitude of the temperature increases depends on how the chillers are designed. The simplest design is a direct-coupled chiller with chilled gas/process water heat exchanger. Other chiller designs include both chilled glycol and water reservoirs. The addition of these reservoirs serves to reduce the maximum rate of temperature change following chiller failure. Increased deformities have been observed in direct-coupled chiller systems for sockeye salmon following chiller failures.
This model can be used to size glycol and water reservoirs to control the rise in temperature following chiller failure.

Tags: doc/noaa/nmfs/nwfsc, efs (environmental and fisheries sciences) division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Growth Data  - Developing diets and feeding strategies for improved growth and performance of juvenile and adult sablefish

Feed costs and time to harvest are key factors affecting the economic viability of domestic sablefish (Anoplopoma fimbria) aquaculture. Use of fast growing all-female monosex stocks dramatically reduces time to harvest, but our research to date indicates that the commercial salmon feeds typically used by industry are not optimally formulated for sablefish and there is still a high degree of potential for improved growth and feed conversion. The effects of dietary balance of protein, fat, and carbohydrate on productive performance, growth and feed conversion at any post-juvenile stage of development are unknown, and there are no commercial diets specifically formulated for sablefish aquaculture in the marketplace. Dietary nutrient imbalances combined with inappropriate feeding schedules and strategies contribute to poor nutrient utilization and are unlikely to fully support the growth potential of this species, impeding continued efforts to improve performance during grow-out to harvest. Thus, research activity focuses on establishing performance optimized diets and feeding strategies that support maximum growth, efficient feed conversion and other economically important traits such as fillet yield.
Fish in experiments are often PIT tagged and regularly checked for growth in fork length and body weight.

Tags: 11-ketotestosterone, aquaculture, aquafeeds, balance, doc/noaa/nmfs/nwfsc, efs (environmental and fisheries sciences) division, genetics, growth, igf1, length board, marine fishes, metabolism, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, obsolete, sablefish
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Field and laboratory notes on development of a PIT-tag system for spillways - Research and Development of New Marking and Monitoring Technologies

This project addresses how to expand the current fish-tracking technologies to enable the fisheries community to successfully carry out the actions, research, and monitoring activities outlined in the 2000, 2004, and 2008 BiOps, 2004 UPA, Fish and Wildlife Program, and 2003 systemwide passage summary. The goal of the project is to satisfy these needs by developing interrogation systems that will collect data on migrating juvenile and adult salmonids through mainstem Columbia River Basin (CRB) dams, including juvenile salmon transiting surface-bypass systems and all life-stages transiting small streams. These fish-tracking technologies are then used to assess the effectiveness of management actions and strategies for recovery of ESA-listed fish populations.

For example, development of PIT-tag systems that will work in large streams or even rivers are essential for determining the effectiveness of all types of restoration programs on stock recovery supported by BPA. In addition, these systems would help delineate the different types of interactions between hatchery and wild stocks in the field. Within this project, we propose to develop technologies that help monitor the stocks at critical (and if possible, all) life stages and critical locations. For example, many juvenile salmonids now use unmodified spillbays, spillbays outfitted with temporary spillway weirs (TSWs) or removable spillway weirs (RSWs), and turbines during their migration, but we are unable to monitor them in these locations because they lack PIT-tag interrogation systems. Consequently, we are collecting fewer data points for the different survival models. Therefore, we are proposing to start or continue development programs for interrogation systems (tags, antennas, receivers, etc) that will enable us to monitor these migrating fish through these pathways. Besides project administration, the proposed work for the performance period (October 2010-January 2012) covers four main research areas or work elements:

1. Finished development of the ogee-based PIT-tag system for Ice Harbor Dam.

2. Install and evaluate the ogee-based system for Ice Harbor Dam.

3. Continue the development of in-stream interrogation systems -- antennas and multiplexing transceiver.

4. Evaluate alternative interrogation technologies - HDX systems and ISO transceivers.

PIT-tag system development data and notes.

Tags: administrative, biological, columbia river, dams, dams throughout the columbia river basin, decision-making, doc/noaa/nmfs/nwfsc, effectiveness monitoring, fe (fish ecology) division, laboratory at sand point, management strategy evaluation, national marine fisheries service, noaa. u.s. department of commerce, non-noaa funded, northwest fisheries science center, pit tag, salmon, stream sites throughout the northwest
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Tidal energy site - Tidal energy site mammal/bird survey

A vessel-based line visual transect survey was conducted for birds and marine mammals near the proposed Snohomish County PUD Admiralty Inlet tidal energy site coincident with acoustic surveys for fish. An observer collected sightings by species (as well as angle and distance) to allow for distribution and density-based estimates to be developed.
Mammal & bird habitat.

Tags: admiralty inlet, cb legacy data sets, doc/noaa/nmfs/nwfsc, habitat characteristics, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, population surveys
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
California Current Ecosystem Assessment (transect)

This layer is intended to represent the geographic extent of NOAA Fisheriesâ 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 InvestigaciÃ³n 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.

Tags: alaska, california, doc/noaa/nmfs/nwfsc, mexico, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, oregon, story map: noaa fisheries west coast offshore scientific surveys, united states, washington
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Spawning 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.
The fork length to the nearest mm, weight to the nearest gram, fecundity, and green egg weight to the nearest mg of every female spawned is recorded. The fork length to the nearest mm, weight to the nearest gram, milt weight to the nearest 0.01 gram, milt volume, spermatocrit, and milt motility of every male spawned is recorded. The eyed egg weight and % survival to the eyed stage for every batch of fertilized eggs is recorded. A record is maintained describing which male is crossed with which female.

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
Steelhead migration - Tracking steelhead migration from the Columbia River through the Pacific Ocean

Tag juvenile Columbia River steelhead in the Columbia estuary with acoustic tags to determine their marine distributions. This was a small pilot project to test our ability to 1) use fish collected by the Columbia Estuary Purse Seine project as a source for tagging, 2) use a mobile tagging station to tag 100 fish, and 3) perhaps get some detections at various fixed and mobile receivers in estuarine and marine waters. While many fish were detected leaving the estuary, only one was detected in marine waters off Willapa Bay. Since this is a pilot project, no reports were produced.

Field data fisheries independent survey. This project was foronly 1 year and no longer exists.

Tags: acoustic tags, cb (conservation biology) division, columbia river, cr estuary, doc/noaa/nmfs/nwfsc, elephant seals, fishery-independent surveys, genotype, habitat, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, np ocean, ocean/climate, program dissolved, protected species and marine mammals, sightings/strandings
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Coastal Assessment Framework - National Assessment of Estuary and Coastal Habitats

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.

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
SPS Abundance - Salmon spawner abundance data compilation and database management

The Northwest Fisheries Science Center's (NWFSC) Salmon Population Summary (SPS) database provides public access to demographic data compiled for ESA-listed salmonid populations as part of the NWFSC's technical recovery planning efforts. The database contains data collected by co-managers (WDFW, ODFW, IDFG, and Tribes) and compiled in cooperation with NWFSC staff for: spawning abundance, age structure of wild spawners, fraction of natural spawners that are of wild origin, and the reduction in spawning abundance due to harvest. For some populations, additional data fields are also available. The data correspond to the populations identified by the NMFS Technical Recovery Teams, and are used in part to assess population and ESU-level recovery criteria for many listed ESUs. Most importantly, this data is critical for informing 5 year ESA salmon reviews, and makes 5 year status review data available to the public.
Abundance of ESA-listed salmonids.

Tags: abundance, cb (conservation biology) division, doc/noaa/nmfs/nwfsc, esa, instrument not applicable, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, salmon, sps database
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Juvenile Fish Data - Coastwide Cooperative Pre-recruit Survey

The Pre-recruit survey project is collaborative involving researchers from the FE Division based in 3 laboratories (Newport, Seattle and Hammond), scientists from the Southwest Fisheries Science Center (Santa Cruz), along with researchers from several universities (Oregon State University, University of Oregon, University of Washington, University of California, Santa Cruz).  In concert with a similar SWFSC survey effort through California, the purpose of this project is to conduct annual surveys within the coastal ecosystem off Oregon and Washington to quantify the environmental conditions and biota found along the California Current and to elucidate ecosystem-level processes affecting managed and protected marine resources.  

This project currently supports three main efforts:

1. An annual sampling regime of the hydrology, plankton, small fish, and predators along transects over the Continental Shelf from Oregon and Washington. This consistent survey has generated significant information on within- and between-year variability in the California Current Marine Ecosystem and has yielded valuable insights into the food web off our coast. 

2. Collection of specimens for diet analysis, growth, containment load, and other studies related to the ecology and production of commercially important taxa and their relationships within the food web.

3. Parameters and ecological processes quantified during this effort are used in forecasts involving species, assemblages, and ecosystems and also to parameterize ecosystem models used to evaluate cumulative risks and managerial strategies.
We towed a Cobb Trawl at 30 m at all stations.

Tags: acoustic automated analysis, bell m. shimada, climate indicators, doc/noaa/nmfs/nwfsc, ecosystem indicator, fe legacy data sets, fish eggs and larvae, food web, instrument not applicable, juvenile fishes, krill, national marine fisheries service, newport, noaa. u.s. department of commerce, northwest fisheries science center, northwest fisheries science center (nwfsc) in newport, oceanography, oregon, oregon coast located within marine layer area number 1, zooplankton
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
IGP2010 microbial - Bacterial community profiling at sewage treatment plant outfalls

Penn Cove (in the Whidbey Basin) is designated as a category 5, 303d impaired water body due to low dissolved oxygen. In addition to runoff from adjacent developed and agricultural lands, treated effluent from two sewage treatment plants (STPs) and freshwater from the nearby Skagit River flow into Penn Cove. This project investigates the structure and function of microbial communities in the context of inorganic nutrients and physical parameters to assess any detectable influence of STPs.

Work is conducted by NOAA personnel with assistance from undergraduate research interns. Data collected across four different seasons include bacterial/archeal abundance (biomass), heterotrophic production (productivity), bacterial diversity, chlorophyll A, inorganic nutrient concentrations, dissolved oxygen concentration, and seawater temperature.

Anticipated products are presentations at scientific meetings related to marine dissolved oxygen and to local management authorities (e.g., county government) as well as publication in the referred literature. The project is a seed project to develop further capacity to assess additional low dissolved oxygen sites.
FileMaker Pro of field & lab analyses.

Tags: bacterial communities, chlorophyll a, dna sequencer, doc/noaa/nmfs/nwfsc, gps, heterotrophic production, low dissolved oxygen, marine microbes, microbial abundance, migrated from resource enhancement and utilization technologies division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nutrients, penn cove & saratoga passage, puget sound, quantitative pcr machine, sonde and probe, unknown instrument, water sampler bottle - niskin bottle
Organization: National Oceanic and Atmospheric Administration, Department of Commerce