AndreaBozzo/ceres-open-data-index huggingface dataset:
Historical methyl mercury in San Francisco Bay

San Francisco Bay, California is considered a mercury-impaired watershed. Elevated concentrations of mercury are found in water and sediment as well as fish and estuarine birds. Sources of mercury to the watershed since 1845 include sediment-associated mercury from mercury mining, mercury losses from gold amalgamation activities in mines of the Sierra Nevada, aerial deposition of mercury from global and regional emissions to air, and the direct discharge of mercury to Bay waters associated with the urbanization and industrialization of the estuary. We assessed historical trends in mercury bioaccumulation by measuring mercury concentrations in feathers of the endangered California Ridgway’s rail (formerly California Clapper Rail) using museum specimens. We developed a structural equation model to attribute variation in historical mercury bioaccumulation in rails to sources of mercury, and estimated the toxicological consequences of extreme mercury exposure to rails from known correlations between feather and blood mercury concentrations.

Tags: Feathers, Ice Cores, Lake Tahoe, Mercury, San Francisco Bay, Sediment, Structural Equation Model, USDOI, USGS, Wyoming, california-ridgways-rail, data.gov
Organization: United States Geological Survey
Fish Abundance and Distribution in Restored Tidal Wetlands in the Northern Sacramento-San Joaquin Delta, California, 2017-2018

Field data for fishes sampled using bottom gill nets and otter trawls during daylight hours in the northern part of the Sacramento-San Joaquin Delta, California, USA. Two adjacent tidal wetlands were targeted for sampling: Little Holland Tract and Liberty Island Conservation Bank

Tags: Aquatic Biology, Cache Slough Complex, California, Fish Biology, Sacramento-San Joaquin Delta, Tidal Wetland, USDOI, USGS, United States, data.gov
Organization: United States Geological Survey
Recent historical and projected (years 2006–99) areas (km2) of managed, flooded habitats used by waterbirds overwintering in Central Valley, California basins for 17 climate, urbanization, and water management scenarios.

The dataset summarizes areas of Central Valley waterbird habitats (i.e., wetland and cropland types) that are available for each of 17 projected scenarios by planning basin, scenario, habitat, and month (August – April of the following year). The dataset also includes relatively recent (year 2005) area of habitat (i.e., “existing_km2”) for comparison with habitat areas based on scenarios. In contrast with the dataset referenced as "Table A1", which solely includes the three managed, flooded cropland habitats, cropland habitats in this dataset are defined as winter-flooded rice, unplowed dry rice, winter-flooded corn, unplowed dry corn, and other winter-flooded cropland (in Tulare basin). Wetlands are defined as summer-irrigated seasonal wetland, seasonal wetland that is not summer irrigated, and semipermanent wetland (combines semipermanent and permanent wetland types). Also in contrast with the "Table A1" dataset, these data include habitat areas for each month of August– April, and for Suisun Basin in addition to the other eight basins defined in the Central Valley Joint Venture Implementation Plan (2006). Data on availability of waterbird habitats is summarized by planning basin, scenario, habitat, and month in 5 metrics (in addition to existing area): the least available area; areas available in ≥ 25%, ≥ 50%, and ≥ 75% of years; and maximum available area. These data support the following publication: Matchett EL, Fleskes JP. 2018. Waterbird habitat in California’s Central Valley basins under climate, urbanization, and water management scenarios. Journal of Fish and Wildlife Management. Online early. doi:10.3996/122016-JFWM-095

Tags: Central Valley of California, USDOI, USGS, basin, birds, climate change, cropland, data.gov, habitat alteration, habitats, urbanization, water availability, water resource management, water resources, water use, waterbirds, wetland restoration, wetlands
Organization: United States Geological Survey
Conventional PCR results for detecting Tetracapsuloides bryosalmonae in fish tissue and water samples

We developed and validated conventional and quantitative real-time PCR assays for the detection of DNA from the myxozoan parasite Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease in fish. Assays were tested on fish tissue and on field-collected water samples to assess diagnostic and environmental DNA capabilities. The specificity, sensitivity, and broad applicability of the present assays surpass previous methods for detecting T. bryosalmonae DNA from fish tissue and water samples.

Tags: California, East Gallatin River, Idaho, Montana, PCR, Proliferative Kidney Disease, Sypes Canyon, Tetracapsuloides bryosalmonae, USDOI, USGS, Wyoming, data.gov, environmental DNA, fish, molecular biology, parasites
Organization: United States Geological Survey
Attributes for MRB_E2RF1 Catchments by Major River Basins in the Conterminous United States: NLCD 2001 Tree Canopy

This tabular data set represents the mean percent tree canopy from the Canopy Layer of the National Land Cover Dataset 2001 (LaMotte and Wieczorek, 2010), compiled for every MRB_E2RF1 catchment of Major River Basins (MRBs, Crawford and others, 2006). The source data set represents tree canopy percentage for the conterminous United States for 2001. The Canopy Layer of the National Land Cover Data Set for 2001 was produced through a cooperative project conducted by the Multi-Resolution Land Characteristics (MRLC) Consortium. The MRLC Consortium is a partnership of Federal agencies (http://www.mrlc.gov), consisting of the U.S. Geological Survey (USGS), the National Oceanic and Atmospheric Administration (NOAA), the U.S. Environmental Protection Agency (USEPA), the U.S. Department of Agriculture (USDA), the U.S. Forest Service (USFS), the National Park Service (NPS), the U.S. Fish and Wildlife Service (USFWS), the Bureau of Land Management (BLM), and the USDA Natural Resources Conservation Service (NRCS). The MRB_E2RF1 catchments are based on a modified version of the U.S. Environmental Protection Agency's (USEPA) ERF1_2 and include enhancements to support national and regional-scale surface-water quality modeling (Nolan and others, 2002; Brakebill and others, 2011). Data were compiled for every MRB_E2RF1 catchment for the conterminous United States covering New England and Mid-Atlantic (MRB1), South Atlantic-Gulf and Tennessee (MRB2), the Great Lakes, Ohio, Upper Mississippi, and Souris-Red-Rainy (MRB3), the Missouri (MRB4), the Lower Mississippi, Arkansas-White-Red, and Texas-Gulf (MRB5), the Rio Grande, Colorado, and the Great basin (MRB6), the Pacific Northwest (MRB7) river basins, and California (MRB8).

Tags: CALI, COGB, California, Catchment, Conterminous United States, GLMR, Inlandwaters, LMTG, MORI, MRB, MRB1, MRB2, MRB3, MRB4, MRB5, MRB6, MRB7, MRB8, MRB_E2RF1, MRB_E2RF1WS, Major River Basins, Missouri, NAWQA, NEMA, New England and Mid-Atlantic, PANW, Pacific Northwest, SAGT, SPARROW, South Atlantic-Gulf and Tennessee, Tree canopy, USDOI, USGS, data.gov, great-lakes-ohio-upper-mississippi-and-souris-red-rainy, lower-mississippi-arkansas-white-red-and-texas-gulf, rio-grande-colorado-and-great-basin
Organization: United States Geological Survey
Native Fish Population and Habitat Study, Santa Ana River, California, 2015

Data included in this dataset include: 1) population estimate data; 2) microhabitat use data; and 3) microhabitat availability data for the Santa Ana Sucker (Catostomus santaanae) and the Arroyo Chub (Gila orcutti) in the Santa Ana River.

Tags: California, Santa Ana River, USDOI, USGS, arroyo-chub-gila-orcutti, data.gov, habitat use, population estimate, santa-ana-sucker-catostomus-santaanae
Organization: United States Geological Survey
Fishes of Ryer Island, Suisun Bay, California, 2016-2017 (ver. 1.1, June 2019)

This data set includes field data for fishes sampled using gill nets and otter trawls during daylight hours in and around Ryer Island, Suisun Bay, California. This data release includes all measured environmental parameters and fish taxa included in the analysis. For prior versions of the data contact Dennis Steinke at dsteinke@usgs.gov. First released 17 April 2019 Revised 12 June 2019, ver. 1.1

Tags: Aquatic Biology, Fish Ecology, Low Salinity Zone, Ryer Island, Sacramento-San Joaquin Delta, San Francisco Bay Delta, San Francisco Estuary, State of California, Suisun Bay, Tidal Wetland, USDOI, USGS, United States of America, data.gov
Organization: United States Geological Survey
DNA fingerprinting of Southern Mule Deer (Odocoileus hemionus fuliginatus) to determine movement across California State Route 67

The goal of this project was to primarily assess east-west connectivity across Route 67 and secondarily, north-south connectivity across Scripps Poway Parkway and Poway Road, two highly trafficked roads to the west of Route 67. We collected deer scat piles from both sides of these crossings in spring between March and June of 2015, and again in fall throughout October 2015. Collected pellets were extracted and amplified using protocols and loci developed by Bohonak and Mitelberg (2014). DNA fingerprinting results were used to investigate mule deer movement in the region directly by identifying individuals which had been captured multiple times throughout the study period. We also assessed movement indirectly through pedigree reconstruction and population structure analyses. The shapefile below contains 126 deer scat piles and the genotypes obtained at 15 microsatellite markers and one sex specific genetic marker. These represented 71 unique individual genotypes (45 females, 26 males) with 9 recapture events and 46 resampling events (defined as scat piles collected at the same location within one week of each other and matching the same unique genotype). These data support the following publicaton; Mitelberg, A. & Vandergast, A.G. (2016) Non-invasive genetic sampling of Southern Mule Deer ( Odocoileus hemionus fuliginatus) reveals limited movement across California State Route 67 in San Diego County. Western Wildlife, 3, 8-18. References: Bohonak, A., Mitelberg, A. 2014. Social Structure and Genetic Connectivity in the Southern Mule Deer: Implications for Management. San Diego State University. San Diego: Report Prepared for California Department of Fish and Game.

Tags: Mule deer, San Diego, USDOI, USGS, data.gov, microsatellite genotyping, scat, southern-mule-deer-odocoileus-hemionus-fuliginatus
Organization: United States Geological Survey
National Fish Habitat Action Plan (NFHAP) 2010 HCI Scores for the Conterminous United States - by EDU

This shapefile contains summaries of habitat condition indices (HCI scores) from the National Fish Habitat Action Plan (NFHAP) 2010 assessment for Ecological Drainage Units (EDUs) in the Conterminous United States. Initial HCI scores were developed using landscape factors representing human disturbances summarized to local and network catchments of river reaches throughout the Conterminous United States. Habitat condition scores were 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. More information on the NFHAP 2010 assessment of the Conterminous United States can be found at the following links: http://dx.doi.org/doi:10.5066/F7B56GN1 . To summarize data into EDUs a length-weighted average was used (i.e. the cumulative HCI value for each river reach within an EDU was weighted by the reach length with the formula (H1*L1+H2*L2...+HX*LX)/(H1+H2...+HX) where H = reach HCI score, L = reach length).

Tags: Alabama, Anthropogenic factors, Aquatic habitats, Arizona, Arkansas, California, Catchment areas, Colorado, Connecticut, Conterminous United States, Delaware, District of Columbia, Environmental conditions, Florida, Georgia, Habitat suitability, Idaho, Illinois, Indiana, Inland water environments, Iowa, Kansas, Kentucky, Landscape ecology, Louisiana, Lower 48 states, Maine, Maryland, Massachusetts, Michigan, Minnesota, Mississippi, Missouri, Montana, Nebraska, Nevada, New Hampshire, New Jersey, New Mexico, New York, North Carolina, North Dakota, Ohio, Oklahoma, Oregon, Pennsylvania, Rhode Island, River basins, Rivers, South Carolina, South Dakota, Streams, Tennessee, Texas, USA, USDOI, USGS, Utah, Virginia, Washington, Water quality measurement, West Virginia, Wisconsin, Wyoming, data.gov
Organization: United States Geological Survey
Abundance and Distribution of Clear Lake Hitch in Clear Lake, Lake County, California, 2017-2019 (ver. 2.0, November 2019)

Field data for fishes sampled using bottom and surface gill nets during daylight hours in Clear Lake, Lake County, California. This data release includes all measured environmental parameters and fish taxa included in the analysis. First posted: December 20, 2018 Revised: November 2019

Tags: California, Hitch, Lake, Lavinia exilicauda, USDOI, USGS, United States, aquatic biology, aquatic ecosystems, data.gov, limnology, native species
Organization: United States Geological Survey
National Fish Habitat Action Plan (NFHAP) 2010 HCI Scores - by HUC8

This shapefile contains summaries of habitat condition indices (HCI scores) from the National Fish Habitat Action Plan (NFHAP) 2010 National Assessments for 8 digit Hydrological Unit Codes (HUC8s) of the United States. Initial HCI scores were developed in three separate assessments (Conterminous U.S., Hawaii, and Alaska) due to differences in data availability across these regions. In the initial NFHAP 2010 Alaska assessment HCI values were attributed to HUC12s. For this reason, to summarize data into HUC8s for Alaska an area-weighted average was used (i.e. the cumulative HCI score assigned to each HUC12 within a HUC8 was weighted by reach area using the formula (H1*A1+H2*A2...+HX*AX)/(A1+A2...+AX) where H = HCI score of the HUC12 and A = Area of the HUC12). To summarize data into HUC8s for the Conterminous United States and Hawaii a length-weighted average was used (i.e. the cumulative HCI score assigned to each river reach within a HUC was weighted by reach length using the formula (H1*L1+H2*L2...+HX*LX)/(L1+L2...+LX) where H = reach HCI score and L = reach length). Although data from all three assessments are summarized to HUC8s in this shapefile, it is important that values are not compared across assessment regions. More information on the three assessments can be found at the following links: Conterminous United States (http://dx.doi.org/doi:10.5066/F7B56GN1) ; Alaska (http://dx.doi.org/doi:10.5066/F7KD1VWD); Hawaii (http://dx.doi.org/doi:10.5066/F7V9863B).

Tags: Alabama, Alaska, Anthropogenic factors, Aquatic habitats, Arizona, Arkansas, California, Catchment areas, Colorado, Connecticut, Conterminous United States, Delaware, District of Columbia, Environmental conditions, Florida, Georgia, Habitat suitability, Hawaii, Idaho, Illinois, Indiana, Inland water environments, Iowa, Kansas, Kentucky, Landscape ecology, Louisiana, Lower 48 states, Maine, Maryland, Massachusetts, Michigan, Minnesota, Mississippi, Missouri, Montana, Nebraska, Nevada, New Hampshire, New Jersey, New Mexico, New York, North Carolina, North Dakota, Ohio, Oklahoma, Oregon, Pennsylvania, Rhode Island, River basins, Rivers, South Carolina, South Dakota, Streams, Tennessee, Texas, USA, USDOI, USGS, Utah, Virginia, Washington, Water quality measurement, West Virginia, Wisconsin, Wyoming, data.gov
Organization: United States Geological Survey
Occurrence locations and trait data for freshwater fishes, amphibians, and reptiles native to the state of Oregon

These datasets include occurrence points and trait data for freshwater fishes, amphibians, and reptiles native to Oregon State. Occurrence data were extracted from the VertNet database and include points within Oregon, Washington, and Idaho, as well as points found within ecoregions that overlap with Oregon state (U.S. EPA Level III EcoRegions). Occurrence points include records from years 1930-2002, and only records with associated museum voucher specimens were included. Database was updated to include one record per species, per year, at a given location. Records were evaluated by taxonomic experts for each species, and suspicious records were either verified or excluded. Trait data were gathered from published and openly available sources. Each column (trait value) for each taxon is described in detail in the datasets, including procedures for replacements of missing values.

Tags: California, Idaho, Nevada, Oregon, Pacific Northwest, USDOI, USGS, Utah, Washington, amphibians, area of occupancy, data.gov, ectothermic vertebrate species, fish, life history traits, multispecies study, population and community ecology, rarity, reptiles, traits-based ecology, vertebrates, vulnerability
Organization: United States Geological Survey
Attributes for MRB_E2RF1 Catchments by Major River Basins in the Conterminous United States: NLCD 2001 Imperviousness

This tabular data set represents the mean percent impervious surface from the Imperviousness Layer of the National Land Cover Dataset 2001, (LaMotte and Wieczorek, 2010), compiled for every MRB_E2RF1 catchment of selected Major River Basins (MRBs, Crawford and others, 2006). The source data set represents imperviousness for the conterminous United States for 2001. The Imperviousness Layer of the National Land Cover Data Set for 2001 was produced through a cooperative project conducted by the Multi-Resolution Land Characteristics (MRLC) Consortium. The MRLC Consortium is a partnership of Federal agencies (http://www.mrlc.gov), consisting of the U.S. Geological Survey (USGS), the National Oceanic and Atmospheric Administration (NOAA), the U.S. Environmental Protection Agency (USEPA), the U.S. Department of Agriculture (USDA), the U.S. Forest Service (USFS), the National Park Service (NPS), the U.S. Fish and Wildlife Service (USFWS), the Bureau of Land Management (BLM), and the USDA Natural Resources Conservation Service (NRCS). The MRB_E2RF1 catchments are based on a modified version of the U.S. Environmental Protection Agency's (USEPA) ERF1_2 and include enhancements to support national and regional-scale surface-water quality modeling (Nolan and others, 2002;Brakebill and others, 2011). Data were compiled for every MRB_E2RF1 catchment for the conterminous United States covering New England and Mid-Atlantic (MRB1), South Atlantic-Gulf and Tennessee (MRB2), the Great Lakes, Ohio, Upper Mississippi, and Souris-Red-Rainy (MRB3), the Missouri (MRB4), the Lower Mississippi, Arkansas-White-Red, and Texas-Gulf (MRB5), the Rio Grande, Colorado, and the Great basin (MRB6), the Pacific Northwest (MRB7) river basins, and California (MRB8).

Tags: CALI, COGB, California, Catchment, Conterminous United States, GLMR, Imperviousness, Inlandwaters, LMTG, MORI, MRB, MRB1, MRB2, MRB3, MRB4, MRB5, MRB6, MRB7, MRB8, MRB_E2RF1, MRB_E2RF1WS, Major River Basins, Missouri, NAWQA, NEMA, New England and Mid-Atlantic, PANW, Pacific Northwest, SAGT, SPARROW, South Atlantic-Gulf and Tennessee, USDOI, USGS, data.gov, great-lakes-ohio-upper-mississippi-and-souris-red-rainy, lower-mississippi-arkansas-white-red-and-texas-gulf, rio-grande-colorado-and-great-basin
Organization: United States Geological Survey
Attributes for MRB_E2RF1 Catchments by Major River Basins in the Conterminous United States: NLCD 2001 Land Use and Land Cover

This tabular data set represents the estimated area of land use and land cover from the National Land Cover Dataset 2001 (LaMotte, 2008), compiled for every MRB_E2RF1 catchment of the Major River Basins (MRBs, Crawford and others, 2006). The source data set represents land use and land cover for the conterminous United States for 2001. The National Land Cover Data Set for 2001 was produced through a cooperative project conducted by the Multi-Resolution Land Characteristics (MRLC) Consortium. The MRLC Consortium is a partnership of Federal agencies (http://www.mrlc.gov), consisting of the U.S. Geological Survey (USGS), the National Oceanic and Atmospheric Administration (NOAA), the U.S. Environmental Protection Agency (USEPA), the U.S. Department of Agriculture (USDA), the U.S. Forest Service (USFS), the National Park Service (NPS), the U.S. Fish and Wildlife Service (USFWS), the Bureau of Land Management (BLM), and the USDA Natural Resources Conservation Service (NRCS). The MRB_E2RF1 catchments are based on a modified version of the U.S. Environmental Protection Agency's (USEPA) ERF1_2 and include enhancements to support national and regional-scale surface-water quality modeling (Nolan and others, 2002; Brakebill and others, 2011). Data were compiled for every MRB_E2RF1 catchment for the conterminous United States covering the South Atlantic-Gulf and Tennessee (MRB2), the Great Lakes, Ohio, Upper Mississippi, and Souris-Red-Rainy (MRB3), the Missouri (MRB4), the Lower Mississippi, Arkansas-White-Red, and Texas-Gulf (MRB5) and the Pacific Northwest (MRB7) river basins.

Tags: CALI, COGB, California, Catchment, Conterminous United States, GLMR, Inlandwaters, LMTG, MORI, MRB, MRB1, MRB2, MRB3, MRB4, MRB5, MRB6, MRB7, MRB8, MRB_E2RF1, MRB_E2RF1WS, Major River Basins, Missouri, NAWQA, NEMA, NLCD01 land use and land cover, New England and Mid-Atlantic, PANW, Pacific Northwest, SAGT, SPARROW, South Atlantic-Gulf and Tennessee, USDOI, USGS, data.gov, great-lakes-ohio-upper-mississippi-and-souris-red-rainy, lower-mississippi-arkansas-white-red-and-texas-gulf, rio-grande-colorado-and-great-basin
Organization: United States Geological Survey
SANA1M.TIF - South Anacapa Island sidescan sonar backscatter image in nearshore Benthic Habitat mapping Project S. California map Series. (UTM 10N, NAD83)

The sidescan sonar image of the nearshore seafloor (0 to 100 m water depths) of the South Anacapa area was mosaicked from data collected in 1999 and 2000. A Klein 2000 sidescan system was used for geophysical surveying. A Triton Elics Isis brand side-scan data recording system was used on the cruise. The survey was navigated with a Leica Differential Global Positioning System (DGPS) which provided a ship position with accuracy of 1-5 m in DGPS mode. At times during the cruise differential signal was interrupted. In non-differential mode, the receiver provided a position with 30-50 m accuracy. A KVH Industries Inc. azimuth digital gyro-compass provided ship headings with 0.5 degree accuracy. Navigation data were recorded using Yo-Nav (Gann, 1992). The sidescan fish was towed approximately 30 m above the seafloor. The distance of the fish behind the ship was not known during this survey and must be estimated when the data are processed in order to produce the sidescan image mosaics. The resolution of the processed data mosaics is 0.2 m. The data are presented here at a resolution of 1 m. This is one of a collection of digital files of a geographic information system of spatially referenced data related to the USGS Coastal and Marine Geology Program Nearshore Benthic Habitat Mapping Project. The sidescan data were processed using USGS MIPS sonar processing software (Chavez, 1984). See <http://walrus.wr.usgs.gov/nearshorehab> for more information about this data set.

Tags: Anacapa Island, CA, CMGP, California, Channel Islands, Channel Islands National Marine Sanctuary, Coastal Geology, Coastal and Marine Geology Program, Isis, Klein, MIPS, Marine Geology, North Pacific Ocean, Northern Pacific Ocean, Santa Barbara, Southern California, U.S. Geological Survey, USA, USDOI, USGS, United States, Ventura, Western Region Coastal and Marine, cruise identifier B-1-99-SC, data.gov, remote-sensing image, rv-ballena, sidescan sonar, west coast
Organization: United States Geological Survey