AndreaBozzo/ceres-open-data-index huggingface dataset:
Microsatellite genotype scores for a contemporary, range-wide sample of Santa Ana sucker in southern California

These data consist of microsatellite genotype scores for all samples of Santa Ana sucker (Catostomus santaanae) used in the study. Scores represent the allele calls for each microsatellite locus (i.e. DNA fragment length containing the microsatellite repeats), with each locus containing two scores representing the two allele copies detected. Included are five tables: Full dataset (includes genotypes from all samples), Santa Clara River samples only (includes genotypes only from samples collected in the Santa Clara River), Convert File format key (explains the data file format), Population identifiers (translates the numerical population identifiers to actual collecting sites), CASA sampling points (one coordinate given for each general collection site). Whole specimens are accessioned at the Los Angeles County Museum of Natural History (catalog numbers 58475-58481). GenBank accession numbers for the DNA sequences are: MF918422 - MF918481. These data support the following publication: Richmond, J.Q., Backlin, A.R., Galst‐Cavalcante, C., O'Brien, J.W. and Fisher, R.N., Loss of dendritic connectivity in southern California's urban riverscape facilitates decline of an endemic freshwater fish. Molecular Ecology.

Tags: Los Angeles, San Gabriel, Santa Ana, Santa Clara River watersheds, USDOI, USGS, admixture, data.gov, dendritic network, endangered species, fish, genetics, hybridization, metapopulation, southern California
Organization: United States Geological Survey
Summary of stranded southern sea otters, 1985-2017

The southern sea otter (Enhydra lutris nereis), also known as California sea otter, was listed as threatened in 1977 under the Endangered Species Act. Since 1985, stranded otters from throughout their California coastal range have been collected and analyzed to inform resource management on recovery and conservation of the species. This data set is a complete 31 year compilation. Future annual stranding recovery information will be published when available. Stranded sea otters were collected by members of the sea otter stranding network (USGS, California Department of Fish and Wildlife (CDFW), Monterey Bay Aquarium (MBA), and the Marine Mammal Center (TMMC)) during routine beach walks and (more often) following reports by the general public and representatives of management agencies (e.g., California State Parks, Municipal Harbor Patrols, County Parks). The intent is to document and recover all stranded southern sea otters, however, certain areas such as the Big Sur coastline are under-represented due to access and logistical constraints. All beach-cast sea otters (most of which are dead, but also live moribund animals that would have died without intervention) are examined and the date and geographic location of each recovered animal is recorded, as well as the sex, age class, general condition, and circumstantial cause(s) of death if evidence is apparent, e.g., boat-strike trauma, net entanglement, shark bite wounds.

Tags: California, Marine Nearshore, Stranded southern sea otters, USDOI, USGS, data.gov, ecology, health and disease, marine biology, marine ecosystems, sea otters
Organization: United States Geological Survey
SAR 2017 Reach Fish Data

Data included in this dataset includes: 1) 2017 reach fish data for the Santa Ana Sucker (Catostomus santaanae) and the Arroyo Chub (Gila orcutti) in the upper Santa Ana River.

Tags: USDOI, USGS, arroyo-chub-gila-orcutti, data.gov, habitat use, population estimate, santa-ana-river-california, santa-ana-sucker-catostomus-santaanae
Organization: United States Geological Survey
National Fish Habitat Action Plan (NFHAP) 2010 HCI Scores and Human Disturbance Data (linked to NHDPLUSV1) for California

This shapefile contains landscape factors representing human disturbances summarized to local and network catchments of river reaches for the state of California. This dataset is the result of clipping the feature class 'NFHAP 2010 HCI Scores and Human Disturbance Data for the Conterminous United States linked to NHDPLUSV1.gdb' to the state boundary of California. Landscape factors include land uses, population density, roads, dams, mines, and point-source pollution sites. The source datasets that were compiled and attributed to catchments were identified as being: (1) meaningful for assessing fish habitat; (2) consistent across the entire study area in the way that they were assembled; (3) representative of conditions in the past 10 years, and (4) of sufficient spatial resolution that they could be used to make valid comparisons among local catchment units. In this data set, these variables are linked to the catchments of the National Hydrography Dataset Plus Version 1 (NHDPlusV1) using the COMID identifier. They can also be linked to the reaches of the NHDPlusV1 using the COMID identifier. Catchment attributes are available for both local catchments (defined as the land area draining directly to a reach; attributes begin with "L_" prefix) and network catchments (defined by all upstream contributing catchments to the reach's outlet, including the reach's own local catchment; attributes begin with "N_" prefix). This shapefile also includes habitat condition scores created based on responsiveness of biological metrics to anthropogenic landscape disturbances throughout ecoregions. Separate scores were created by considering disturbances within local catchments, network catchments, and a cumulative score that accounted for the most limiting disturbance operating on a given biological metric in either local or network catchments. This assessment only scored reaches representing streams and rivers (see the process section for more details). Please use the following citation: Esselman, P., D.M. Infante, L. Wang, W. Taylor, W. Daniel, R. Tingley, J. Fenner, A. Cooper, D. Wieferich, D. Thornbrugh and J. Ross. (April 2011) National Fish Habitat Action Plan (NFHAP) 2010 HCI Scores and Human Disturbance Data (linked to NHDPLUSV1) for California. National Fish Habitat Partnership Data System. http://dx.doi.org/doi:10.5066/F7JD4TSG

Tags: Anthropogenic factors, Aquatic habitats, Atlantic Coast FHP, Catchment areas, Connecticut, DC, Delaware, Environmental conditions, Florida, Georgia, Habitat suitability, Inland water environments, Landscape ecology, Maine, Maryland, Massachusetts, New Hampshire, New Jersey, New York, North Carolina, Pennsylvania, Rhode Island, River basins, Rivers, South Carolina, Streams, USDOI, USGS, Vermont, Virginia, Water quality measurement, West Virginia, data.gov
Organization: United States Geological Survey
Fish assemblages in southern California kelp forests.

This is a point file of fish assemblages calculated from diver surveys in kelp forests in Southern California.   Visual census data was combined for two separate southern California datasets.  The Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO) provided information collected at 15 sites, and Vantuna Research Group (VRG) at 29 sites.  Visual transect surveys were completed by SCUBA divers along the bottom of the kelp forest.  The VRG dataset provided fish counts along 2m x 60m transects which were subsequently averaged for comparison with the PISCO dataset. The PISCO dataset provided mean counts along a 2m x 30m transect which were doubled before combining with the VRG data.   Fish that were not present in at least 5% of the trawls were removed from this analysis, resulting in a site by species matrix of 44 sites and 45 species.  Site groups were calculated using the Bray-Curtis dissimilarity coefficient with average means clustering

Tags: Channel Islands National Marine Sanctuary, Environmental Monitoring, NOAA, National Ocean Service, Southern California, U.S. Department of Commerce, continent--north-america--united-states-of-america--california, data.gov, docnoaanosnccos--national-centers-for-coastal-ocean-science, earth-science--biological-classification--animalsvertebrates--fish, earth-science--biosphere--ecological-dynamics--community-dynamics--community-structure, earth-science--biosphere--ecological-dynamics--ecosystem-functions, earth-science--biosphere--ecological-dynamics--speciespopulation-interactions--usefeeding-habitats, earth-science--biosphere--ecosystems--marine-ecosystems--benthic, earth-science--biosphere--ecosystems--marine-ecosystems--pelagic, earth-science--human-dimensions--environmental-governancemanagement--environmental-assessments, earth-science--oceans--marine-biology--fish, earth-science-services--models--dynamic-vegetationecosystem-models, geographic-information--polygons
Organization: National Oceanic and Atmospheric Administration
Environmental Sensitivity Index (ESI) Atlas: Central California (Including Monterey Bay Sanctuary), maps and geographic information systems data (NODC Accession 0013176)

Environmental Sensitivity Index (ESI) maps have been developed for the coastal areas of Central California from Point Conception to Point Reyes National Seashore. The ESI maps are a compilation of information from three main categories: shoreline types, sensitive biological resources, and human-use resources. The individual map pages in this atlas are divided according to the U.S. Geological Survey (USGS) 7.5-minute, 1-24,000-scale topographic quadrangle index. Black and white scanned images of these maps are used as a backdrop for each map page in the atlas. Biological data dates vary from the mid 1990s to 2006, and were compiled in 2006. Data include files for use in desktop GIS systems (shape files and database), .PDF maps, detailed documentation, user guide, and extensive metadata.

Tags: NOAA, data.gov, earth-science--biological-classification, earth-science--biological-classification--animalsinvertebrates, earth-science--biological-classification--animalsinvertebrates--arthropods--crustaceans, earth-science--biological-classification--animalsinvertebrates--arthropods--crustaceans--amphipods, earth-science--biological-classification--animalsinvertebrates--mollusks, earth-science--biological-classification--animalsinvertebrates--mollusks--bivalves, earth-science--biological-classification--animalsvertebrates, earth-science--biological-classification--animalsvertebrates--amphibians, earth-science--biological-classification--animalsvertebrates--birds, earth-science--biological-classification--animalsvertebrates--fish, earth-science--biological-classification--animalsvertebrates--mammals, earth-science--biosphere--ecosystems--marine-ecosystems--benthic, earth-science--oceans--coastal-processes--shorelines, ocean--pacific-ocean--north-pacific-ocean, oceanography
Organization: National Oceanic and Atmospheric Administration
Sensitivity of Coastal Environments and Wildlife to Spilled Oil: Central California: FISHL (Fish Lines)

This data set contains sensitive biological resource data for anadromous fish and rare fish species occurrences in Central California.  Vector lines in this data set represent the beginning points for coastal anadromous runs, juvenile rearing and adult congregation areas for anadromous species, and sensitive habitat for rare species (tidewater goby). Species-specific abundance, seasonality, status, life history, and source information are stored in relational data tables (described below) designed to be used in conjunction with this spatial data layer.This data set comprises a portion of the Environmental Sensitivity Index (ESI) data for Central California.  ESI data characterize the marine and coastal environments and wildlife by their sensitivity to spilled oil.  The ESI data include information for three main components: shoreline habitats, sensitive biological resources, and human-use resources. See also the FISH (Fish Polygons) data layer, part of the larger Central California ESI database, for additional fish information.

Tags: Central California, Coastal Zone Management, Coastal resources, ESI, Environmental Monitoring, Fish, NOAA, Oil spill planning, Sensitivity maps, Wildlife, data.gov
Organization: National Oceanic and Atmospheric Administration
Channel Islands, Kelp Forest Monitoring, Survey, Random Point Contact, 1982-2007

This dataset from the Channel Islands National Park's Kelp Forest Monitoring Program has estimates of substrate composition and percent cover of selected algal and invertebrate taxa. The data summary data presented here represents the mean percent cover of the indicator species at the site. Sampling is conducted annually between the months of May-October, so the Time data in this file is July 1 of each year (a nominal value). The actual measurements were taken at various depths, so the Depth data in this file is the depth of the station's temperature logger, which is a typical depth.

Tags: NOAA, algae, all, animals, aquatic, arborea, articulated, astrangia, atmosphere, balanophyllia, balanus, bare, biological, biology, biosphere, brown, bryozoans, californica, channel, cinp, classification, coastal, cobble, combined, contact, coralline, corynactis, cystoseira, data.gov, depth, desmarestia, diaperoecia, diopatra, earth-science--biological-classification--animalsvertebrates--fish, earth-science--biological-classification--plants--macroalgae-seaweeds, earth-science--biosphere--aquatic-ecosystems--coastal-habitat, earth-science--biosphere--aquatic-ecosystems--marine-habitat, ecosystems, eisenia, elegans, encrusting, excluding, farlowii, fish, forest, gelidium, gigartina, green, habitat, hydroids, identifier, including, invertebrates, islands, kelp, lajollaensis, laminaria, latitude, leucetta, longitude, losangelensis, macroalgae, macrocystis, marine, mean, miscellaneous, monitoring, ophiothrix, ornata, pachymastia, pachythyone, phragmatopoma, plants, point, polymastia, pterygophora, pyrifera, random, red, rock, rubra, sand, sargassum, seaweeds, serpulorbis, spiculata, spinosus, spirobrancus, sponges, spp, squamigerus, station, statistics, stddev, stderr, substrate, survey, time, tunicates, vertebrates
Organization: National Oceanic and Atmospheric Administration
Artificial Reefs

An artificial reef is a human-made underwater structure, typically built to promote marine life in areas with a generally featureless bottom. These reefs help control erosion, block ship passage, or improve surfing. Many reefs are built using objects intended for other purposes, including the sinking oil rigs, scuttling ships, or deploying rubble or construction debris. Other artificial reefs are purpose-built using materials such as PVC or concrete. Regardless of construction method or source material, artificial reefs generally provide hard surfaces where algae and invertebrates such as barnacles, corals, and oysters can attach. The accumulation of attached marine life in turn provides an intricate structure of food for fish assemblages. This data set is NOT a complete collection of artificial reefs on the seafloor, nor are the locations to be considered exact. The presence and location of the artificial reefs have been derived from multiple state websites. These data are intended for coastal and ocean planning.

Tags: Atlantic, Gulf of Mexico, NOAA, National, Pacific, United States, United States Territories, artificial, coastal, continent--north-america--united-states-of-america, data.gov, earth-science--human-dimensions--environmental-governancemanagement, fish, fisheries, habitat, haven, marine, oysters, reef, reefs, refugia
Organization: National Oceanic and Atmospheric Administration
Estuarine Living Marine Resources: West Coast Regional Distribution and Abundance (NCEI Accession 0161540)

This is the West Coast regional component of NOAAâs Estuarine Living Marine Resources (ELMR) Project, a national database of ecologically and economically important fishes and invertebrates in the Nation's estuaries.  The distribution and relative abundance are depicted in a consistent format for 47 species of fishes and invertebrates, in 32 estuaries in coastal California, Oregon, and Washington State. Species were selected according to a set of criteria, which consider their commercial, recreational, and ecological value, as well as their utility as an indicator of environmental stress. For each species, five life stages are considered - adults, juveniles, larvae, spawning, and eggs - with some exceptions based on individual species life history. Each estuary is subdivided into one to three salinity zones (Tidal Fresh, Mixing, and Seawater). Relative abundance was ranked on a five-tier scale by month for each life stage of each species, in each salinity zone of each estuary. Details of the methods and resulting life history summaries for the West Coast ELMR component can be found in Monaco et al. (1990) and Emmett et al. (1991).

Tags: Elkhorn Slough National Estuarine Research Reserve, NOAA, Point Reyes National Seashore, San Francisco Bay National Estuarine Research Reserve, South Slough National Estuarine Research Reserve, Tijuana River National Estuarine Research Reserve, data.gov, earth-science--biological-classification, earth-science--biological-classification--animalsinvertebrates, earth-science--biological-classification--animalsvertebrates--fish, earth-science--oceans--salinitydensity--salinity, modelsanalysis--data-analysis--environmental-modeling, nccos-research-data-type--derived-data-product, nccos-research-location--geographic-area--estuaries, nccos-research-location--marine-protected-area--national-estuarine-research, nccos-research-location--marine-protected-area--national-parks, nccos-research-location--region--west-coast, nccos-research-location--us-states-and-territories--california, nccos-research-location--us-states-and-territories--oregon, nccos-research-location--us-states-and-territories--washington, nccos-research-priority--marine-spatial-ecology-mse, nccos-research-topic--ecologicalbiological-characterization, ocean--pacific-ocean--north-pacific-ocean, oceanography, west-coast---uscanada
Organization: National Oceanic and Atmospheric Administration
Sensitivity of Coastal Environments and Wildlife to Spilled Oil: Northern California: FISHL (Fish Lines)

This data set contains sensitive biological resource data for anadromous and threatened/endangered stream species in Northern California.  Vector lines in this data set represent trout and salmon spawning runs and sensitive stream species. Species-specific abundance, seasonality, status, life history, and source information are stored in relational data tables (described below) designed to be used in conjunction with this spatial data layer.  This data set comprises a portion of the Environmental Sensitivity Index (ESI) data for Northern California.  ESI data characterize the marine and coastal environments and wildlife by their sensitivity to spilled oil.  The ESI data include information for three main components: shoreline habitats, sensitive biological resources, and human-use resources. See also the FISH (Fish Polygons) data layer, part of the larger Northern California ESI database, for additional fish information.

Tags: Coastal Zone Management, Coastal resources, ESI, Environmental Monitoring, Fish, NOAA, Northern California, Oil spill planning, Sensitivity maps, Wildlife, data.gov
Organization: National Oceanic and Atmospheric Administration
Pelagic fish eggs counts, sea surface temperature, salinity, wind speed and direction measured using a Continuous Underway Fish Sampler (CUFES) in the North Pacific from various platfoms from 1996-03-15 to 2017-07-26 (NCEI Accession 0174136)

This data set contains pelagic fish eggs counts, sea surface temperature, salinity, wind speed and direction were collected on various platforms using a Continuous Underway Fish Sampler (CUFES)  from 1996-03-15 to 2017-07-26 as part of the The California Cooperative Oceanic Fisheries Investigation work during cruises conducted by the  National Marine Fisheries Service Southwest Fisheries Science Center (SWFSC) Fisheries Resources Division. Data are typically collected every 30 min while the ship is underway. Eggs are identified as Pacific sardine, northern anchovy, jack mackerel, hake, squid, or other fish eggs.

Tags: CalCOFI, DEPM - daily egg production method, NOAA, anchovy, daily egg production, data.gov, earth-science--atmosphere--atmospheric-winds--surface-winds--wind-direction, earth-science--atmosphere--atmospheric-winds--surface-winds--wind-speed, earth-science--biological-classification--animalsvertebrates--fish, earth-science--oceans--ocean-temperature--sea-surface-temperature, earth-science--oceans--salinitydensity--salinity, hake, jack mackerel, ocean--pacific-ocean--north-pacific-ocean, oceanography, sardine, squid
Organization: National Oceanic and Atmospheric Administration
Giant seabass habitat suitability model for Channel Islands National Marine Sanctuary Biogeographic Assessment

The National Marine Sanctuary Program (NMSP) updates and revises the management plans for each of its 13 sanctuaries. This process, which is open to the public, enables each site to revisit the reasons for sanctuary designation and assess whether they are meeting their goals, as well as to set new goals consistent with the mandates of the National Marine Sanctuaries Act. Issues raised by the public during this process are evaluated and a determination is made as to whether they will be incorporated into the updated plan. Many of these issues focus on topics such as the implementation of marine zoning or sanctuary boundary adjustments, both of which require information on the distribution of resources within and around the sanctuary. Recognizing this, NMSP and NOAA?s National Centers for Coastal Ocean Science (NCCOS) formalized an agreement to collaborate in the revision process by developing such information through a series of biogeographic assessments conducted in selected sanctuaries. The resulting products are then supplied to sanctuary managers and staff for use in the policy and decision making process. This collaborative effort began along the west coast of the U.S. with the Cordell Bank, Gulf of Farallones, and Monterey Bay national marine sanctuaries, and is herein centered on the Channel Islands National Marine Sanctuary (CINMS).

Tags: CA, Channel Islands, Channel Islands National Marine Sanctuary, Environmental Monitoring, NOAA, National Ocean Service, Southern California, U.S. Department of Commerce, continent--north-america--united-states-of-america--california, data.gov, docnoaanosnccos--national-centers-for-coastal-ocean-science, earth-science--biological-classification--animalsvertebrates--fish--ray-finned-fishes--perch-like-fi, earth-science--biosphere--ecological-dynamics--community-dynamics--community-structure, earth-science--biosphere--ecological-dynamics--ecosystem-functions, earth-science--biosphere--ecological-dynamics--speciespopulation-interactions--usefeeding-habitats, earth-science--biosphere--ecosystems--marine-ecosystems--benthic, earth-science--biosphere--ecosystems--marine-ecosystems--pelagic, earth-science--human-dimensions--environmental-governancemanagement--environmental-assessments, earth-science--oceans--marine-biology--fish, earth-science-services--models--dynamic-vegetationecosystem-models, geographic-information--polygons
Organization: National Oceanic and Atmospheric Administration