AndreaBozzo/ceres-open-data-index huggingface dataset:
AFSC/RACE/EcoFOCI: NPRB_1220:Mitochondrial DNA-based identification of eggs, larvae and dietary components of commercially and ecologically important fish species and selected invertebrates in the northeast Pacif

Accurate identification of various life history stages and prey items of marine fishes and invertebrates is central for understanding distribution,abundance, trophic ecology, and biodiversity of these species. Taxonomic approaches have been successfully applied to ichthyoplankton identification and diet analysis efforts for many years. Identification to the species level requires varying degrees of taxonomic expertise. and diagnostic characters for eggs or larvae in some species have not been elucidated.              
                In the current dataset we assembled a mitochondrial DNA (mtDNA) database for which 
                used standard laboratory protocols (restriction fragment length polymorphism 
                and Sanger DNA sequencing) to accurately identify any life history stages of selected fish and 
                shrimp species, with special emphasis on those species that have been difficult or impossible 
                to identify by conventional taxonomic means. Fish and shrimp specimens were collected between 2010 - 2013.  
                We developed a restriction fragment length polymorphism (RFLP)protocol, based upon mitochondrial DNA sequences 
                to distinguish between Pacific halibut and Greenland halibut, but were unable to develop one to discriminate 
                between Bering flounder and flathead sole.  We used direct Sanger sequencing of mitochondrial DNA for species 
                identification of 32 species of sculpin and four species of caridean shrimp. PCR products from fish and shrimp 
                samples were sequenced using an ABI 3730 automated sequencer (Applied Biosystems, Inc). DNA sequences from museum 
                voucher specimens were compared with entries in the public databases for those species. Sequences from voucher 
                specimens have greater taxonomic authority for use in species identification than those without vouchers, 
                adding greater confidence to species identifications based upon our data.

Tags: alaska, alaska fisheries science center, bering sea, chuckchi sea, control region, cytochrome b, cytochrome oxidase, dna barcoding, doc/noaa/nmfs/afsc, gut contents, mitochondrial dna, national marine fisheries service, nd1, noaa, non-federal funding, oregon state, puget sound, recruitment processes program, species identification, u.s. department of commerce, washington state
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
AFSC/RACE/GAP/Zimmermann: Aleutians Sediments

We assembled 2.1 million National Ocean Service (NOS) bathymetric soundings extending 1,900 km along the Aleutian Islands from Unimak Island in the east to the Russian border in the west, and ranging approximately 500 km north of the central Aleutians to Petrel and Bowers Banks, and also the surrounding deep waters of the southeastern Bering Sea. These bathymetry data are available from the National Geophysical Data Center (NGDC: http://www.ngdc.noaa.gov), which archives and distributes data that were originally collected by the NOS and others. While various bathymetry data have been downloaded previously from NGDC, compiled, and used for a variety of projects, our effort differed in that we compared and corrected the digital bathymetry by studying the original analog source documents - digital versions of the original survey maps, called smooth sheets. Our editing included deleting erroneous and superseded values, digitizing missing values, and properly aligning all data sets to a common, modern datum. We also digitized 25,000 verbal surficial sediment descriptions from the smooth sheets, providing the largest single source of sediment information for the Aleutians.

Tags: alaska, alaska fisheries science center, aleutian islands, doc/noaa/nmfs/afsc, groundfish assessment program, national marine fisheries service, noaa, north pacific ocean, point, sediment, u.s. department of commerce
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Alaska Phocid Food Habits

Relatively little is known of the diet and foraging behaviors of the four species of ice-associated seals (ribbon seal, bearded seal, spotted seal, and ringed seal) and harbor seals in Alaska. What is known comes largely from stomach contents of animals harvested during subsistence hunting near coastal communities. Diet and foraging ecology are likely highly sensitive to the availability of suitable habitats and sea ice conditions. They may be particularly vulnerable to climatic change and other disruptions from more direct anthropogenic effects such as offshore oil and gas development. Our ability to predict and manage for such impacts, however, is limited by our inadequate knowledge of seal ecology. This database contains diet data obtained by scat samples from seals across a variety of research projects. Scat samples were collected from ribbon and spotted seals in the pack ice in the Bering Sea during April, May, and June of 2007-2010, and 2014. The diet data in this database were obtained by analyzing otoliths from these scats. Scat samples have also been collected from harbor seals from Lake Iliamna in July-August 2015, and from the Aleutian Islands in September 2015. Diet data based on otoliths from these scats will also be recorded in this dataset.

Tags: alaska, alaska fisheries science center, alaska phocid captures and specimens collected, bearded seal, bering sea, doc/noaa/nmfs/afsc, food habits, national marine fisheries service, noaa, ribbon seal, spotted seal, u.s. department of commerce
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
AFSC/RACE/GAP/Nichol: Archival tag depth and temperature data from Atka mackerel

Atka mackerel Pleurogrammus monopterygius were captured and tagged with depth and temperature recording devices (archival tags) on 23 July 2000 in Seguam Pass, Aleutian Islands, Alaska. Nine of the 117 tagged fish were recovered in Seguam Pass during September 2000, and an additional 5 fish recovered thereafter (14 total). In addition, 413 tags were released in Tanaga Pass in 2002,  with 10 recoveries. Fish were tagged externally just below the dorsal fin. Atka mackerel displayed strong diel behavior, with vertical movements away from the bottom occurring almost exclusively during daylight hours and little to no movement at night. Vertical movements occurred when light levels at 150 m were greater than 7.31 Ã 10â5 Âµmol photons mâ2 sâ1, or approximately between 08:00 and 23:00 h Alaska Daylight Time (ADT; GMT â 8) during August. Daytime vertical movements were correlated with light intensity, time of day and current velocity. The occurrence of vertical movements tended to increase with increasing light during the morning and early afternoon, but then decrease with increasing hour of the day after 13:00 h ADT. The magnitude of surface-directed vertical excursions was reduced during spring tide periods, when current velocities are highest. By comparison, the magnitude of slope-directed excursions was greater during spring tide periods and reduced during neap tide periods. Eight fish were at liberty for 42 to 44 d and 1 for 65 d. Two of the tagged males displayed nest guarding behavior for the majority of their time at liberty. Depths for these 2 males (115 to 117 m) were much deeper than previously observed for Atka mackerel spawning grounds. Given that Atka mackerel are more likely to be on the bottom during the night and less likely during the day, the variance of abundance estimates from bottom trawl surveys may be reduced by accounting for these diel differences.

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-2012-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-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
Alaska Northern Fur Seal Tag Data, 1992-2017

This dataset contains information regarding the capture and tagging  of northern fur seals on the Pribilof Islands and Bogoslof Island, Alaska, from 1992 to 2017.

Tags: alaska ecosystems program, alaska fisheries science center, capture, capture recapture, doc/noaa/nmfs/afsc, national marine fisheries service, noaa, northern fur seal, pribilof islands, st. george island, st. paul island, tag, tag resight, u.s. department of commerce
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Alaska Steller Sea Lion Food Habits Data 1990-2009

This data set contains Steller sea lion diet data based on analysis of scats collected during summer (May-September) and winter (November-April) rookeries and haulouts in Alaska during 1990 to 2009. Prey items from 87 prey taxa were identified using hard parts including bones, otoliths, and cephalopod beaks. Frequency of occurrence  was calculated for 375 site-year-season combinations, and used in the analysis published by Sinclair et al. (2013). This dataset includes the  thirteen primary prey taxa (frequency of occurrence >= 5%) identified in the Sinclair et al. (2013) study.

Tags: alaska, alaska ecosystems program, alaska fisheries science center, aleutian islands, bering sea, bone, diet, doc/noaa/nmfs/afsc, food habits, gulf of alaska, national marine fisheries service, noaa, north pacific ocean, otolith, prey, prey item, scat, spew, u.s. department of commerce
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
AFSC/RACE/GAP/McConnaughey: Fishpac Projects-2012-SVP.Raw

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/REFM: Pacific cod genetics in the Aleutian Islands 2004-2007

Landscape genetics of Pacific cod Gadus macrocephalus within the Bering Sea and Aleutian Islands (BSAI) management area of Alaska was examined in samples from nine spawning locations, including one temporal replicate sample, using 17 microsatellite DNA markers. This study examined fine-scale population structure of Pacific cod in the BSAI with the goal of identifying breaks in genetic continuity associated with physical barriers to migration and larval transport. Samples were taken from spawning fish collected from the western Aleutian Islands east to Unimak Pass and as far north as the Pribilof Islands. Overall, this work confirms previous studies, which found that genetic differentiation between samples is proportional to the distance between them, and also resolves population structure on a scale not previously possible. Results indicate that dispersal is not continuous at a fine scale and several distinct genetic groups were identified that correspond to differences in the physical environment of the BSAI. The data provide evidence for limited connectivity among spawning groups; in particular, there is evidence that a barrier exists between the Aleutian Islands and the eastern Bering Sea. In addition, analysis of molecular variance and Monmonier algorithm results suggest that, within the Bering Sea, the Unimak Pass and Pribilof Islands spawning groups may be distinct from each other, and the Wombling analysis indicates that samples west of Amchitka Pass in the western Aleutians may be distinct from those in the eastern Aleutians.

Tags: alaska fisheries science center, aleutian islands, bering sea, doc/noaa/nmfs/afsc, genetics, microsatellites, national marine fisheries service, noaa, non-federal funding, population structure, u.s. department of commerce
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Data from "Crossing to safety: Dispersal, colonization and mate choice in evolutionarily distinct populations of Steller sea lions, Eumetopias jubatus."

Data sets used to support analysis published by O'Corry-Crowe et al (2014) Crossing to safety: Dispersal, colonization and mate choice in evolutionarily distinct populations of Steller sea lions, Eumetopias jubatus. Molecular Ecology 23(22): 5415-5434. Data include Steller sea lion genetic data obtained from samples collected from pups on natal rookeries. The genetic data are genotypes at 16 microsatellite loci and haplotypes at mtDNA, spatial data, and allelic and haplotypic frequencies.

Tags: alaska, alaska ecosystems program, alaska fisheries science center, aleutian islands, bering sea, colonization, density dependence, doc/noaa/nmfs/afsc, eumetopias jubatus, gulf of alaska, microsatellites, mixed-stock, national marine fisheries service, noaa, southeast alaska, steller sea lion, u.s. department of commerce
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
AFSC/ABL: Fish, Energy, Diet, and Zooplankton (FEDZ) Laboratory Database

The FEDZ lab processes fish from large boat surveys conducted by the Auke Bay Laboratories for diet information.

Tags: alaska fisheries science center, auke bay laboratories, bering sea, doc/noaa/nmfs/afsc, feeding habitat, fish, gulf of alaska, icy strait, marine invertebrates, national marine fisheries service, noaa, u.s. department of commerce, zooplankton
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Bering-Okhotsk Seal Survey (BOSS) On-Effort Flight Tracks (2012-13)

Aerial surveys were flown during the spring of 2012 and 2013 as part of the Bering Okhotsk Seal Surveys (BOSS) project to gather data on distribution and abundance of ice-associated seals in the eastern Bering Sea. The distributions of these seals are broad and patchy, resulting in surveys that cover large areas and encounter rapidly changing environmental conditions. Surveys were flown using a fixed-wing aircraft with a paired system of digital cameras and thermal imagers operated by observers and mounted in the belly port.  Flight tracks were recorded with an attitude and heading reference system (AHRS) that also recorded location information at one second intervals.  A secondary flight track was recorded with a GPS which was used to supplement location information when there was a glitch with the AHRS. BOSS on-effort flight tracks were used to calculate total distance and area flown for estimating seal abundance, in addition to georeferencing digital and thermal imagery collected in flight. On-effort flight tracks (survey effort) were initially determined by the observer based on environmental conditions and later refined based on aircraft attitude and imagery review. The spatial data are provided in the geographic (epsg:4326) coordinate reference system.

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/RACE/GAP/McConnaughey: Pribilof Hydro-2009-From Archiver-Shell Hash Multibeam Bathymetry Survey - 8m resolution

The "add on" project area surveyed depths between the 27 and 175 meter depths around St. George Island and St Paul Island in the Central Bering Sea. Full bottom coverage, consisting of 100% multibeam data was achieved within the limits of hydrography for this survey. One hundred percent backscatter data was acquired and stored by TerraSond, Ltd to be processed by the client. The data were collected from the R/V Mount Mitchell by Terrasond, Inc using a Simrad EM710 multibeam echosounder.

Tags: afsc/race/gap/mcconnaughey: pribilof hydro-2009-from archiver, alaska, alaska fisheries science center, bering sea, doc/noaa/nmfs/afsc, multibeam backscatter, national marine fisheries service, noaa, pribilof islands, seafloor habitat, u.s. department of commerce
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
AFSC/RACE/GAP/McConnaughey: Fishpac Projects-2006-SCS

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, 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/CCEP: Harbor seal demography in Washington; capture, tagging, branding data from 1981 to 2007

The National Marine Mammal Laboratories' California Current Ecosystem Program (AFSC/NOAA) in collaboration with Washington Department of Fish and Wildlife captured and sampled Pacific harbor seals (Phoca vitulina) to study the demography of this species in Washington. This database provides capture, recapture, branding and resighting information for harbor seals in Washington from 1981 to 2007. Datasets include: Captures, Recapture, and Resight.  Captures and Recapture information includes speno, date, age-class, age qualifier, sex, weight, length, health, tag number, brand number, location for all age classes and axial girth for pups and subadults.  It also notes if samples were taken for disease screening (blood and swabs), contaminants (blubber), genetics (skin) and if animals were instrumented and with what type(s) of instrument. Resights information includes speno, date, tag, brand, reproductive information, location.

Tags: age-specific natality, alaska fisheries science center, california current ecosystems program, demography, doc/noaa/nmfs/afsc, hot-iron branding, length, life history, longitudinal studies, national marine fisheries service, noaa, pacific harbor seal, puget sound, repoductive success, reproduction, survival, tagging, u.s. department of commerce, washington state coast, weight
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
AFSC/NMML: North Pacific Right Whale Vessel Surveys in the Southeastern Bering Sea, 2007 - 2011

The North Pacific right whale (NPRW) was heavily hunted between the 17th and the 20th centuries.  Protection was supposedly afforded by international treaties in the 1930s and 1940s, but the illegal capture of hundreds of individuals by the Soviet Union, primarily in the 1960s drastically impacted the recovery of the species.  Currently, only a small remnant of this population (estimated at approximately 30 individuals) inhabits the southeastern Bering Sea (SEBS). There is an increasing body of evidence suggesting that the middle shelf domain constitutes the primary habitat of NPRWs in the SEBS during the summer. Despite substantial observation effort from various sources in some other areas, the only region in the Bering Sea where NPRWs have been consistently seen is the middle shelf. Vessel surveys were conducted in the summers of 2007 - 2011 in the EBS mostly within the NPRW critical habitat boundary (located on the middle shelf of the SEBS). A total of eight NPRW individuals were identified from photographs taken during the survey.

Tags: abundance, alaska fisheries science center, bering sea, biopsy sampling, cetacean assessment and ecology program, chukchi sea, distribution, doc/noaa/nmfs/afsc, line-transect survey, national marine fisheries service, noaa, photo-identification, summer, u.s. department of commerce
Organization: National Oceanic and Atmospheric Administration, Department of Commerce