AndreaBozzo/ceres-open-data-index huggingface dataset:
AFSC/ABL: Rockfish allozyme species identification (Sebastes aleutianus and borealis)

Rougheye rockfish (Sebastes aleutianus) and shortraker rockfish (Sebastes borealis) were collected from the Washington coast, the Gulf of Alaska, the southern Bering Sea, and the eastern Kamchatka coast of Russia (areas encompassing most of their geographic distribution) for population genetic analyses. Using starch gel electrophoresis, we analyzed 1027 rougheye rockfish and 615 shortraker rockfish for variation at 29 protein coding loci. No genetic heterogeneity was found among shortraker rockfish throughout the sampled regions, although shortraker in the Aleutian Islands region, captured at deeper depths, were found to be significantly smaller in size than the shortraker caught in shallower waters from Southeast Alaska. Genetic analysis of the rougheye rockfish revealed two evolutionary lineages that exist in sympatry with little or no gene flow between them. When analyzed as two distinct species, neither lineage exhibited heterogeneity among regions. Sebastes aleutianus seems to inhabit waters throughout the Gulf of Alaska and more southern waters, whereas S. sp. cf. aleutianus inhabits waters throughout the Gulf of Alaska, Aleutian Islands, and Asia. The distribution of the two rougheye rockfish lineages may be related to depth where they are sympatric. The paler color morph, S. aleutianus, is found more abundantly in shallower waters and the darker color morph, Sebastes sp. cf. aleutianus, inhabits deeper waters. Sebastes sp. cf. aleutianus, also exhibited a significantly higher prevalence of two parasites, N. robusta and T. trituba, than did Sebastes aleutianus, in the 2001 samples, indicating a possible difference in habitat and (or) resource use between the two lineages.

Tags: alaska, alaska fisheries science center, auke bay laboratories, doc/noaa/nmfs/afsc, national marine fisheries service, noaa, u.s. department of commerce
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
AFSC FIT Pacific cod tagging data from the Bering Sea, 2002-2006

Data from opportunistic tagging studies in the southest Bering Sea 2002-2003.  Individually numbered loop spaghetti tags released during research cruises; all recoveries from fishing industry.  Main release groups in February 2003 at two locations: 1) N of Cape Sarichef, Unimak Island, and 2) off Amak Island, north of the Alaska peninsula.   Other smaller releases at several locations in southeat Bering Sea from April 2002  to November 2003.   Pacific cod (Gadus macrocephalus) caught with commercial and research pot gear from depths of 50-150 meters; length of tagged fish primarily 50-80 cm.  Data in MS Access format (digital tabular).  Data include lat/long of capture and release locations, release date/time, fish length and condition at release.  Recovery data includes location and date  of recovery, recovering vessel and gear, fishery observer, recipient for tag reward.  Most recovery locations in lat/lon to nearest minute, some to state or federal stat area only; variables code quality of recovery location and date info.  Most records include length, weight, sex, and condition of recovered fish, some otoliths collected.  Recoveries primarily documented by fishery observers on vessel or at delivery plant.  Database includes tags recovered through Dec 2007.  Total of 6871 tags released, 2634 tags recovered.  Important caveats: 1) tags released opportunistically, not in design or associated with quantitative model, 2) most tage releases were in main commercial fishing ground during fishing season, assumptions of mixing with overall population are invalid, 3) all recoveries through industry, spatial and temporal distribution of recovery effort very non-uniform, some areas little or no effort.  Raw data including coordinates of tag recoveries and vessel information are considered observer data and are confidential under the Magnuson-Stevens Act.

Tags: alaska continental shelf, alaska fisheries science center, amak island, bering sea, doc/noaa/nmfs/afsc, fish movement surveys, national marine fisheries service, noaa, pribilof islands, southeast bering sea, tagging, u.s. department of commerce, unimak island, unimak pass, western gulf of alaska
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
AFSC/RACE/SAP/Shavey: DNA extraction from archived Giemsa-stained blood smears using polymerase chain reaction to detect host and parasitic DNA

These are the data from a laboratory experiment in which DNA content was removed from blood smears and extracted.  The blood smears were either stained with Giemsa-stain or remained un-stained. Some of the un-stained smears were coverslipped. Host and parasitic DNA was amplified using conventional PCR.

Tags: alaska, alaska fisheries science center, bering sea, blood smear, canada, disease, dna extraction, doc/noaa/nmfs/afsc, gulf of alaska, national marine fisheries service, newfoundland, noaa, se alaska, shellfish assessment program, u.s. department of commerce, washington state coast
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
AFSC/RACE/GAP/Nichol: Archival tag depth and temperature data from Pacific cod

Data from 250 recaptured (624 released) depth and temperature recording archival (data storage) tags attached to Pacific cod off Kodiak Island and in the eastern Bering Sea from 2001 to 2003, were used to describe the vertical movement patterns of Pacific cod.  Three publications resulted from the research with subject matter including: 1) P. cod behavior as related to barotrauma; 2) P. cod vertical distribution as related to survey trawl catchability; 3) P. cod diel vertical migration.  Please see publications for more detail.

Tags: alaska fisheries science center, doc/noaa/nmfs/afsc, groundfish assessment program, national marine fisheries service, noaa, ora-30625: method dispatch on null self argument is disallowed, u.s. department of commerce
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
AFSC/RACE/GAP/McConnaughey: Fishpac Projects-2006-Seaboss-Infauna

The broad scope of the Essential Fish Habitat (EFH) mandate requires an efficient process for describing and mapping the habitat needs of federally managed species.  For example, research indicates surficial sediments affect the distribution and abundance of many groundfish species, yet traditional sampling with grabs and cores is impractical over areas as large as the Bering Sea shelf.  Acoustic tools are suitable for large-scale surveying and show great promise as a substitute for direct-sampling methods, but they have not been proven useful for EFH purposes.

Tags: acoustic sediment classification, afsc/race/gap/mcconnaughey: fishpac projects-2006-seaboss, alaska fisheries science center, bering sea, doc/noaa/nmfs/afsc, grain size analysis, habitat mapping, multibeam echosounder, national marine fisheries service, noaa, side scan sonar, u.s. department of commerce
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
AFSC/RACE/GAP/McConnaughey:Trawlex chronic effects-1996- Mean Size

The eastern Bering Sea has experienced rapid and intensive development of commercial trawl fisheries. Because of good record keeping and the relatively brief history of fishing it is possible to reconstruct the spatial and temporal patterns of exploitation. Previously unfished (UF) areas can be identified and directly compared with heavily fished (HF) areas to investigate long-term consequences for the benthos. Using this approach, macrofauna populations in a shallow (48 m average) soft-bottom area were studied during 1996. Catch data were extracted from the AFSC NORPAC database for years 1973-2001 to provide a summary of trawl catch effort, specific focus was placed on the area within Fisheries Management Area 512. The total number of hauls and tonnage for each data point are provided. Foreign, domestic, and Joint Venture fishing vessels are also described.

Tags: afsc/race/gap/mcconnaughey:trawlex chronic effects-1996, alaska fisheries science center, doc/noaa/nmfs/afsc, national marine fisheries service, noaa, u.s. department of commerce
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Obsolete - AFSC/RACE/EcoFOCI: 2010 Chukchi Acoustics, Oceanography, and Zooplankton (CHAOZ) Study - 1AE10

Data collected on this cruise included the following:  acoustic recordings of marine species detected by sonobuoys; oceanographic measurements including water temperature, salinity, dissolved nutrient concentrations, chlorophyll concentrations, zooplankton net and acoustic samples; date, time and location of all sightings of marine mammals and seabirds as well as group characteristics; photographic data for individual identification.

We deployed 24 moorings in the working area (17 passive acoustic, 1 activie acoustic, 6 oceanographic).  In addition to the mooring and oceanographic work, the vessel will transited to Barrow Canyon and attempted to recover (without success) 3 moorings lost the previous year.

Tags: alaska fisheries science center, arctic ocean, biological data, chlorophyll, chukchi sea, doc/noaa/nmfs/afsc, fish, fish eggs, fish juveniles, fish larvae, hydrographic data, ichthyoplankton, national marine fisheries service, noaa, northern bering sea, nutrients, obsolete data set, plankton, recruitment processes program, stimulated fluorescence, u.s. department of commerce, zooplankton
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
AFSC/NMML: Shore-based counts of the Eastern North Pacific gray whale stock from central California, 1967 - 2007

The National Marine Fisheries Service (NMFS) has conducted shore-based counts of the Eastern North Pacific stock of gray whales (Eschrichtius robustus) 26 years from 1967 to 2008 at Granite Canyon (or nearby at Yankee Point), 13 km south of Carmel, in central California.  Convenient access to the Granite Canyon research station (owned by NOAA but operated by the State of California Department of Fish and Game) and the narrowness of the whales' migratory corridor in this area permitted an efficient counting process at this site.  All counts were conducted during the 2-month southbound migration (mid-December to late February) rather than the protracted 3-month northbound migration.  The routine nature of these counts and the consistency in research protocol lend themselves to inter-annual trend analyses.  Research protocol has been based on single observers independently searching for whales and recording data on environmental conditions and the time, location, count, and direction of travel for each sighting.  The counting system and observer performance has been tested through paired, independent observational effort; aerial surveys; thermal imagery; radio-tagging of whales; systematic observations through high-powered (25x) binoculars; and teams of observers tracking specific whale pods through the viewing area.

Tags: abundance, alaska fisheries science center, cetacean assessment and ecology program, doc/noaa/nmfs/afsc, national marine fisheries service, noaa, u.s. department of commerce, winter
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
AFSC/RACE/GAP/McConnaughey: Fishpac Projects-2012-Sonar Output

The broad scope of the Essential Fish Habitat (EFH) mandate requires an efficient process for describing and mapping the habitat needs of federally managed species.  For example, research indicates surficial sediments affect the distribution and abundance of many groundfish species, yet traditional sampling with grabs and cores is impractical over areas as large as the Bering Sea shelf.  Acoustic tools are suitable for large-scale surveying and show great promise as a substitute for direct-sampling methods, but they have not been proven useful for EFH purposes.

Tags: acoustic sediment classification, afsc/race/gap/mcconnaughey: fishpac projects-2012, alaska fisheries science center, bering sea, doc/noaa/nmfs/afsc, grain size analysis, habitat mapping, multibeam echosounder, national marine fisheries service, noaa, side scan sonar, u.s. department of commerce
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Bering-Okhotsk Seal Survey (BOSS) Identified Hot Spots (2012-13)

US surveys were conducted of the Bering Sea pack ice for bearded, spotted, ribbon, and ringed seals using digital cameras and thermal imagers mounted in the belly ports of two fixed-wing aircraft from 6 April to 23 May 2012 and 4 April to 9 May 2013. U.S. flights were flown at a target altitude of 1,000 ft (300 m) to maximize the area surveyed while maintaining the required imaging resolution and minimizing the chance of disturbance to seals and other wildlife. A NOAA Twin Otter (N56RF) aircraft housed three FLIR SC645 thermal imagers, which recorded continuous data in the 7.5-13.0 Âµm wavelength. Each thermal imager was paired with a Canon Mark III 1Ds digital single-lens reflex camera fitted with a 100-mm Zeiss lens. All six instruments were mounted in an open-air belly port. The combined thermal swath width was approximately 1,500 ft (470 m) at an altitude of 1,000 ft. A contracted Aero Commander aircraft carried two sets of paired thermal imagers (SC645) and digital SLR cameras (Nikon D3X) and surveyed a maximum swath width of approximately 900 ft (280 m). Color cameras collected images at a 1-1.2 second interval. In 2013 the two aircraft flew a total of 36 surveys covering more than 17,000 nmi (32,090 km) of trackline and collected about 913,000 images. Combined with the 2012 survey effort, the U.S. BOSS team covered 31,000 nmi of trackline and collected 1.8 million images.

Tags: 2012-2013 bering-okhotsk seal survey (boss), alaska, alaska fisheries science center, bearded seal, bering sea, doc/noaa/nmfs/afsc, national marine fisheries service, noaa, ribbon seal, ringed seal, spotted seal, u.s. department of commerce
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
AFSC/REFM: FEAST (Forage Euphausiid in Space and Time NPRB B.70 Model output for 1970-2009 Hindcast (Run V146), Kerim Aydin and Andre Punt

Weekly biophysical and fish model output of FEAST. Part of The Bering Sea Project, FEAST is a high resolution (~10km2) spatial model that uses a Regional Ocean Modeling System for the Bering Sea (ROMS Bering-10K), with two way feedback to a Nutrient-Phytoplankton-Zooplankton Model and two way feedback to a multispecies bioenergetics fish model.

Tags: alaska, alaska fisheries science center, bering sea, bsierp, doc/noaa/nmfs/afsc, ene to end models, feast, hindcast, lower trophic levels, model output, modeled data, national marine fisheries service, noaa, non-federal funding, npz, physical oceanography, roms, u.s. department of commerce
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
AFSC/REFM: Steller sea lion economic survey data, U.S., 2007, Lew

The project will produce a valuation function that depends on factors related to Steller sea lion (SSL) protection measures, and may include some combination of the expected aggregate size of the population and improvements to the ESA listing status resulting from protection measures, cost of the protection measures, and effects of protection measures on local economies, fishery participants, and consumer fish prices.  This function can be used to identify non-consumptive use values for SSLs and how these values are affected by protection measures, thereby providing valuable information to policy makers.

Tags: alaska, alaska fisheries science center, commercial fisheries, doc/noaa/nmfs/afsc, economic values, eumetopias jubatus, national marine fisheries service, noaa, non-market valuation, stated preference, steller sea lion, u.s. department of commerce
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
AFSC/RACE/GAP/McConnaughey: Fishpac Projects-2009-Grabs

The broad scope of the Essential Fish Habitat (EFH) mandate requires an efficient process for describing and mapping the habitat needs of federally managed species.  For example, research indicates surficial sediments affect the distribution and abundance of many groundfish species, yet traditional sampling with grabs and cores is impractical over areas as large as the Bering Sea shelf.  Acoustic tools are suitable for large-scale surveying and show great promise as a substitute for direct-sampling methods, but they have not been proven useful for EFH purposes.

Tags: acoustic sediment classification, afsc/race/gap/mcconnaughey: fishpac projects-2009, alaska fisheries science center, bering sea, doc/noaa/nmfs/afsc, grain size analysis, habitat mapping, multibeam echosounder, national marine fisheries service, noaa, side scan sonar, u.s. department of commerce
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
AFSC/RACE/GAP/McConnaughey: Fishpac Projects-2012-Reson 7111

The broad scope of the Essential Fish Habitat (EFH) mandate requires an efficient process for describing and mapping the habitat needs of federally managed species.  For example, research indicates surficial sediments affect the distribution and abundance of many groundfish species, yet traditional sampling with grabs and cores is impractical over areas as large as the Bering Sea shelf.  Acoustic tools are suitable for large-scale surveying and show great promise as a substitute for direct-sampling methods, but they have not been proven useful for EFH purposes.

Tags: acoustic sediment classification, afsc/race/gap/mcconnaughey: fishpac projects-2012, alaska fisheries science center, bering sea, doc/noaa/nmfs/afsc, grain size analysis, habitat mapping, multibeam echosounder, national marine fisheries service, noaa, side scan sonar, u.s. department of commerce
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
AFSC/NMML: Video Analysis for Group Count and Calf Proximity of Beluga Whales in Cook Inlet, Alaska, 2005 - 2022

As a part of NMFS management of the endangered beluga whale population in Cook Inlet, Alaska, aerial surveys have been conducted during summer since 1993 to monitor their distribution and abundance.  When beluga whale groups are found, observers make counts from the bubble windows while one observer records the group with a video camera.  The video has been used to count the number of animals in the group to correct for missed animals in the observer counts.  In 1996, a second video camera was added; the first video camera had a lens set at a wide angle to view the entire beluga group while the second video camera was zoomed to approximately 10x to magnify a subsample of individual whales in the group.  The zoomed video has been used to examine color ratios of white adults relative to smaller and darker juveniles and calves and correct for those individuals missed due to their size or coloration.  In 2005, a computer program was designed to digitize the process for analyzing the video, which had been conducted manually prior to that year.  The program allows an analyst to digitally mark and number each individual whale image, track it across the screen, and measure relative whale size.  The dataset described here includes the data from the years that video was analyzed using the computer program, 2005-2012, 2014, 2016, 2018, 2021, and 2022.

Tags: abundance, aerial, alaska, alaska fisheries science center, cetacean assessment and ecology program, cook inlet, doc/noaa/nmfs/afsc, national marine fisheries service, noaa, summer, u.s. department of commerce, video analysis
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
AFSC/RACE/GAP/McConnaughey: Pribilof Hydro-2009-From Archiver-Catchability Experiment, Bering Sea 38 KHz Acoustic Sediment Classification

In stock assessment models, catchability is the link between an index of relative abundance from a fishery-independent survey and the modeled population size. For bottom trawl surveys that estimate the population size using swept-area methods, catchability can be estimated because it is largely determined by sampling efficiency (i.e., the proportion of animals within the sampled area that is caught) which can be experimentally measured. However, estimating survey catchability is complicated because trawl efficiency has been shown to vary over a survey area in response to variation in bottom sediment type. Catchability experiments have been conducted on the bottom trawl used for the annual Eastern Bering Sea (EBS) survey, resulting in a survey-wide estimate of catchability for snow crab (Chionoecetes opilio) which, when included in the stock assessment model, produced significant changes in the Allowable Catch Limit. This catchability model accounted for spatial variation in trawl efficiency as a function of crab size, sex, depth, and sediment type. Unfortunately, sediment data over the geographic distribution of snow crab are quite fragmentary due to the remoteness of the area, and direct estimates of sediment properties such as grain size are generally unavailable at the trawl-sampling locations. In some cases, estimates were based on sediments collected over 60 miles away. The option to collect sediment data at all 270 trawl-sampling stations included in the snow crab distribution is prohibitively expensive considering the additional ship time required and the sample processing costs. 

This project examined whether indices of bottom type, derived from calibrated ES-60 acoustic data collected at each snow crab sampling station and processed with IMPACT software produced by the Quester Tangent Corporation, are more informative in the snow crab bottom trawl catchability model than measured values of sediment type that were broadly extrapolated. This determination was based solely on the amount of spatial variation in the snow crab efficiency model that is explained by the two kinds of sediment information. While the currently used data are based on a directly measurable attribute of the sediment (mean grain diameter), the acoustically derived index is related to this attribute but also to a variety of previously unmeasured variables affecting the time-dependent shape of the bottom echo.

Tags: acoustic sediment classification, afsc/race/gap/mcconnaughey: pribilof hydro-2009-from archiver, alaska, alaska fisheries science center, bering sea, catchability, doc/noaa/nmfs/afsc, national marine fisheries service, noaa, qtc, u.s. department of commerce
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
AFSC/RACE/GAP/McConnaughey: Fishpac Projects-2006-Klein 7180-38 kHz

The broad scope of the Essential Fish Habitat (EFH) mandate requires an efficient process for describing and mapping the habitat needs of federally managed species.  For example, research indicates surficial sediments affect the distribution and abundance of many groundfish species, yet traditional sampling with grabs and cores is impractical over areas as large as the Bering Sea shelf.  Acoustic tools are suitable for large-scale surveying and show great promise as a substitute for direct-sampling methods, but they have not been proven useful for EFH purposes.

Tags: acoustic sediment classification, afsc/race/gap/mcconnaughey: fishpac projects-2006-klein 7180, alaska fisheries science center, bering sea, doc/noaa/nmfs/afsc, grain size analysis, habitat mapping, multibeam echosounder, national marine fisheries service, noaa, side scan sonar, u.s. department of commerce
Organization: National Oceanic and Atmospheric Administration, Department of Commerce