AndreaBozzo/ceres-open-data-index huggingface dataset:
Stream water chemistry and benthic macroinvertebrate data from the North Fork Clear Creek and Clear Creek, Colorado, USA, from 2011-2019, before and after acid mine drainage treatment

Stream water chemistry and benthic macroinvertebrate data collected in the North Fork of Clear Creek and Clear Creek, CO, USA before and after the diversion and treatment of acid mine drainage by a high-density sludge lime process water treatment plant. Stream water chemistry and benthic macroinvertebrate samples were collected from November 2011 through October 2019 at 6 sites located above and below the North Clear Creek Water Treatment Plant (NCCWTP). The NCCWTP became fully operational in September 2017. Measured water chemistry included pH, conductivity, alkalinity, ferrous iron, total and dissolved concentrations of metals and major geochemical cations, and dissolved organic carbon. Replicate (n=5) benthic macroinvertebrate samples were collected using a 0.1 square meter Hess sampler at targeted riffle habitats among sites. Benthic samples were processed from detrital material in the laboratory using a subsampling technique to reach 300+ invertebrates, and identified to the lowest taxonomic resolution possible, typically to genus (except for chironomids that were identified to subfamily).

Tags: aquatic-ecosystems, aquatic-insects, biota, clear-creek, community-ecology, ecological-restoration, macroinvertebrates, north-fork-clear-creek, remediation, usgs-635ffedad34ebe442505e74d, water-quality
Organization: Department of the Interior
Population Structure and Genetic Diversity of Eastern North American Moose

Hair samples were collected in discrete areas during radio-collar studies in Vermont under the auspices of University of Vermont IACUC protocol #17-035 (n=106), New Hampshire (n=34), and Maine (n=57).  Hair and tissue samples were opportunistically collected from animals that were harvested, died in vehicle collisions, or translocated throughout Vermont (n = 105), Quebec (n = 198), Massachusetts (n = 5), and New York (n = 24). Of the 317 previously identified autosomal moose SNPs, 136 loci were utilized to develop a MALDI-TOF MS genotyping assay.  After filtering problematic loci and individuals, genotypes from 112 of 136 SNPs (82%) were obtained for 507 individuals and all loci met Hardy-Weinberg expectations in the nine geographic regions samples.

Tags: biota, genetic-diversity, genetics, moose, usgs-63615205d34ebe4425065436
Organization: Department of the Interior
Digital elevation model of South Fork Toutle River, Mount St. Helens, based on June–July 1980 airborne photogrammetry

The lateral blast, debris avalanche, and lahars of the May 18th, 1980, eruption of Mount St. Helens, Washington, dramatically altered the surrounding landscape. The eruption produced mudflows in the South Fork Toutle River basin, which drains the western slopes of the volcano. Orthophotography was acquired shortly after the eruption (June 19 and July 1). Survey extent includes South Fork Toutle River, from its headwaters at Talas and Toutle Glaciers to its mouth at the confluence with North Fork Toutle River near Toutle, Washington. In 2004, Photo Sciences, Inc., under contract to the U.S. Geological Survey (USGS), used softcopy photogrammetry techniques to produce a contour map, breaklines, and masspoints. A USGS aerial solution (year 2000) provided control for the 1980 triangulation. The USGS used these data to produce a digital elevation model (DEM) of the survey area. This USGS data release contains digital elevation and shaded relief data as 4-meter resolution raster datasets (sft_1980dem.tif and sft_1980dem_hs.tif, respectively). The DEM can be used to develop sediment budgets and models of sediment erosion, transport, and deposition.

Tags: biota, cascade-range, cowlitz-county, dem, digital-elevation-model, elevation-data, geomorphology, hydrology, loowit, mount-st-helens, photogrammetry, sediment, south-fork-toutle-river, topography, toutle-river, usa, usgs-635ff369d34ebe442505e71f, volcanic-landforms, volcano, wa
Organization: Department of the Interior
Coastal wetland elevation survey of Weeks Bay National Estuarine Research Reserve, Alabama, 2016–2018

This data release includes elevation data collected from 2016–2018 within coastal wetland habitats at Weeks Bay National Estuarine Research Reserve, Alabama, and at Ogburn Marsh within the reserve. A total of 771 points were surveyed for elevation via Real-Time Kinematic (RTK) GPS.

Tags: alabama, elevation, environment, gulf-of-mexico, land-surveying, marsh-ecosystems, united-states-of-america, usgs-635fd990d34ebe442505e6e7, weeks-bay-national-estuarine-research-reserve, wetland-ecosystems
Organization: Department of the Interior
A neutral landscape approach to evaluating the umbrella species concept for greater sage-grouse in northeast Wyoming, USA

Greater sage-grouse (Centrocercus urophasianus) has been identified as a potential umbrella species with the assumption that conservation of their habitats in sagebrush ecosystems may benefit multiple other wildlife species, but co-occurrence with an umbrella species does not necessarily guarantee species will respond positively to management for sage-grouse. This may be particularly true for ecotones, such as at the eastern edge of the sage-grouse range where sagebrush steppe and Great Plains grasslands intersect. We used a novel application of neutral landscape models (Etherington et al., 2015) to evaluate observed and expected overlap between greater sage-grouse habitat (1994-2010; Fedy et al., 2014) and distribution of eight grassland songbird species (2008-2018; Monroe et al., 2021) in northeast Wyoming. Data formatting necessary for this analysis produced 17 rasters including sage-grouse habitat (nestGRSG300.tif and summerGRSG300.tif), songbird species distribution (grspFP300.tif, holaFP300.tif, larbFP300.tif, laspFP300.tif, loshFP300.tif, vespFP300.tif, wekiFP300.tif, wemeFP300.tif), songbird community metrics (total density and richness) thresholded at the 0.5 (abund_50_300.tif and rich_50_300.tif), 0.75 (abund_75_300.tif and rich_75_300.tif), and 0.9 quantiles (abund_90_300.tif and rich_90_300.tif), and a general mask to constrain simulations to pixels with songbird predictions (mask300.tif). We also include rasters for grasshopper sparrow (Ammodramus savannarum), sage-grouse nesting habitat, and associated masks but with pixels aggregated to 90 meters, 150 m, 450 m, and 600 m to evaluate sensitivity of results to raster resolution. Finally, in code.zip we provide example Python code to simulate neutral landscape models (nlm_umbrella_larb_habitat.py) and R code to determine the spatial autocorrelation parameter (h) for sage-grouse nesting and summer (brood-rearing) habitat using semivariograms (h_parameter_code.R).

Tags: biogeography, biota, birds, community-ecology, ecosystem-monitoring, grassland-ecosystems, grassland-songbirds, habitat-suitability-indices, habitats, keystone-species, mathematical-simulation, migratory-species, monte-carlo-simulation, natural-resource-management, neutral-landscape-models, northeast-wyoming, sagebrush, shrubland-ecosystems, species-co-occurrence, umbrella-species, united-states-of-america, usgs-635c09bdd34ebe442504b1d6, wyoming
Organization: Department of the Interior
CRB  global species occurrences

This dataset represents global occurrences for CRB and consists of a table of coordinates, associated mean annual temperatures and precipitation values, and occurrence type used to create bioclim habitat suitability models for CRB. These global occurrences are classified into 4 types: 1) all available global data (excluding Hawaii); 2) only occurrences within CRB's native range; 3) only occurrences in the species non-native range (excluding Hawaii); 4) only occurrences in the species insular non-native range (excluding Hawaii).

Tags: biota, coconut-rhinoceros-beetle, crb, hawaii, hawaiian-islands, oahu, oryctes-rhinoceros, usgs-635b2275d34ebe442504740b
Organization: Department of the Interior
Geomorphons for Kalamazoo River Reference Reach upstream of Plainwell, Michigan, 2021

This dataset contains the 10 most common geomorphon forms for an approximately 500 meter (m) reach of the Kalamazoo River upstream of Plainwell, Michigan (MI), in raster and polygon format. Geomorphons are a terrain analysis approach that identify 3-dimensional forms in a landscape based on comparison of the relative elevations of a central pixel to the pixels in its surrounding viewshed. The approach breaks down a landscape into it's component forms (flat, summit, ridge, shoulder, spur, slope, hollow, footslope, valley, and depression), which can serve as a basis for interpreting distinct hydrogeomorphic units and processes associated with them (Jasiewicz and Stepinski, 2013). Polygon features were developed from the original raster output, and are slightly simplified to remove small (&lt;5 square meters) landforms. 
The geomorphons were developed from a digital elevation model (DEM) comprising topographic and bathymetric data for the Plainwell reach, developed from elevation data collected by several different methods. Bathymetric data in the river channel were collected in October, 2021 with a single beam sonar and Acoustic Current Doppler Profiler operated along two longitudinal transects and 48 cross-sectional transects, respectively. River bank topographic data were collected with a backpack-mounted terrestrial lidar unit concurrently with the bathymetric data. Floodplain elevations were obtained from aerial lidar data collected in 2015. All ground points from the respective datasets were projected to the same coordinate system and used to generate a DEM with 1m resolution covering the channel bed, banks, and floodplain, and valley walls through the reference reach.
Jasiewicz, J., &amp; Stepinski, T.F.. 2013. Geomorphons — a Pattern Recognition Approach to Classification and Mapping of Landforms. Geomorphology 182: 147–56. https://doi.org/10.1016/j.geomorph.2012.11.005.

Tags: bathymetry, biota, digital-elevation-models, geomorphology, geospatial-datasets, great-lakes, inlandwaters, kalamazoo-county-mi, kalamazoo-river-huc-04050003, lidar, sonar-methods, topography, usgs-635b06ffd34ebe44250473a2
Organization: Department of the Interior
Kaloko-Honokohau National Historical Park Orangeblack Hawaiian damselfly oviposition sites, 2016-2017

This data release includes metadata and tabular data that documents substrates on which female Orangeblack Hawaiian damselfies (Megalagrion xanthomelas) displayed oviposition (egg-laying) behaviors at Kaloko-Honokohau National Historical Park during 2016-2017.

Tags: anchialine-pool, biota, damselfly, endangered-species, hawaii, hawaii-island, koloko-honokohau-national-historical-park, oviposition-sites, usgs-635b024fd34ebe4425047317
Organization: Department of the Interior
Comparison of 2010 to 2021 Channel Cross Sections of Kalamazoo River Reference Reach upstream of Plainwell, Michigan

This dataset contains a comparison of topographic cross-sections spanning the river channel in a reach of the Kalamazoo River upstream of Plainwell, Michigan (MI), measured at two different time periods, 2010 and 2021. The 2021 cross-section data were extracted from a digital elevation model (DEM) comprising topographic and bathymetric data collected by several different methods. Bathymetric data in the river channel were collected in October, 2021 with a single beam sonar and Acoustic Current Doppler Profiler operated along two longitudinal transects and 48 cross-sectional transects, respectively. River bank topographic data were collected with a backpack-mounted terrestrial lidar unit concurrently with the bathymetric data. Floodplain elevations were obtained from aerial lidar data collected in 2015. All ground points from the respective datasets were projected to the same coordinate system and used to generate a DEM with 1m resolution covering the channel bed, banks, and floodplain, and valley walls through the reference reach. The 2010 cross-section data were collected by survey level and were located with a GPS coordinate. We used that coordinate to generate a cross-section in the same location, perpendicular to and spanning the river channel. This cross-section is coincident with cross-section 42 in the channel cross-sections spreadsheet associated with this data release, although the section's ends were extended by 10m to fully encompass the 2010 survey data. We extracted elevations at approximately 1m spacing along the cross-section from the topobathy DEM developed from our new data. To compare the historic data with the new transect, we shifted the local station and elevation coordinates of the historic data to align the left top of bank with the new data. Data are provided in both CSV format (tabular only) and Excel spreadsheet format (tabular and graphical).

Tags: bathymetry, digital-elevation-models, elevation, geomorphology, geospatial-datasets, great-lakes, inlandwaters, kalamazoo-county-mi, kalamazoo-river-huc-04050003, lidar, sonar-methods, topography, usgs-635b0204d34ebe4425047313
Organization: Department of the Interior
Valley Cross Sections of Kalamazoo River Reference Reach upstream of Plainwell, Michigan, 2021

This dataset contains topographic cross sections spanning the river channel, floodplain and valley walls for an approximately 500 meter (m) reach of the Kalamazoo River upstream of Plainwell, Michigan (MI). The five cross sections are oriented perpendicular to the valley axis and spaced evenly along the 500m reach to represent variability in channel and floodplain geometry. Bankfull hydraulic geometry attributes and complexity  metrics were calculated for each cross section, as were floodplain inundation dimensions for flow stages at multiples ranging from 0.9 to 2.0 of the bankfull depth. The cross section data were extracted from a digital elevation model (DEM) comprising topographic and bathymetric data collected by several different methods. Bathymetric data in the river channel were collected in October, 2021 with a single beam sonar and Acoustic Current Doppler Profiler operated along two longitudinal transects and 48 cross-sectional transects, respectively. River bank topographic data were collected with a backpack-mounted terrestrial lidar unit concurrently with the bathymetric data. Floodplain elevations were obtained from aerial lidar data collected in 2015. All ground points from the respective datasets were projected to the same coordinate system and used to generate a DEM with 1m resolution covering the channel bed, banks, and floodplain, and valley walls through the reference reach.
Cross-section data are provided in tabular and graphical form in an Excel spreadsheet. The data are also provided as individual CSV files for each cross-section (in a zipped archive), which contain X and Y coordinates in addition to elevations and cross-sectional distance values.The CSV files contain the same data  as the Mecklenburg Excel files, but are provided additionally in that format to be readable by non-proprietary, open-source software and to provide the X,Y coordinate data for each transect point. The spatial location of the cross-sections is provided by an associated polyline shapefile contained in this data release. Cross-sections are named by their distance, in meters, downstream from the start of the reference reach.

Tags: bathymetry, digital-elevation-models, elevation, geomorphology, geospatial-datasets, great-lakes, inlandwaters, kalamazoo-county-mi, kalamazoo-river-huc-04050003, lidar, sonar-methods, topography, usgs-635b0153d34ebe4425047311
Organization: Department of the Interior
Channel Cross Sections of Kalamazoo River Reference Reach upstream of Plainwell, Michigan, 2021

This dataset contains topographic cross sections spanning the river channel for an approximately 500 meter (m) reach of the Kalamazoo River upstream of Plainwell, Michigan (MI). The 30 cross sections are oriented perpendicular to the channel and spaced evenly along the 500m reach to represent variability in channel geometry. Bankfull hydraulic geometry attributes and complexity  metrics were calculated for each cross section. The cross section data were extracted from a digital elevation model (DEM) comprising topographic and bathymetric data collected by several different methods. Bathymetric data in the river channel were collected in October, 2021 with a single beam sonar and Acoustic Current Doppler Profiler operated along two longitudinal transects and 48 cross-sectional transects, respectively. River bank topographic data were collected with a backpack-mounted terrestrial lidar unit concurrently with the bathymetric data. Floodplain elevations were obtained from aerial lidar data collected in 2015. All ground points from the respective datasets were projected to the same coordinate system and used to generate a DEM with 1m resolution covering the channel bed, banks, and floodplain, and valley walls through the reference reach.
Cross-section data are provided in tabular and graphical form in an Excel spreadsheet. The data are also provided as individual CSV files for each cross-section (in a zipped archive), which contain X and Y coordinates in addition to elevations and cross-sectional distance values. Cross-sections are named by their distance, in meters, downstream from the start of the reference reach. The spatial location of the cross-sections is provided by an associated polyline shapefile included in this data release.

Tags: bathymetry, digital-elevation-models, elevation, geomorphology, geospatial-datasets, great-lakes, inlandwaters, kalamazoo-county-mi, kalamazoo-river-huc-04050003, lidar, sonar-methods, topography, usgs-635b004ad34ebe4425047309
Organization: Department of the Interior
TRAD: Thermal traits of anurans database for the Southeastern United States.

We present TRAD: Thermal traits of anurans database for the Southeastern United States, a database of thermal trait values related to physiological (critical thermal minima and maxima, preferred temperature, mass) and behavioral thermoregulation (activity period, retreat emergence temperature, basking temperature, foraging temperature minimum and maximum) for 40 anuran species found within the southeastern United States. Using a species-centric approach, we collated this database by first identifying trait values from large reservoirs of amphibian ecology and natural history and then searching the literature using primarily Web of Science to thoroughly identify available thermal trait data. The TRAD database provides a data reservoir for thermal trait data that extends the ecological trait data stored in ATraiU (Moore et al., 2020). In total, the TRAD database contains 858 reported trait values from 267 peer reviewed papers, dissertations, thesises, or rarely guides. TRAD has a 43.9% matrix completion, 47.5% median trait coverage (species with at least one value for each trait) and 44% median trait completeness (traits with at least one value for each species).

Tags: amphibians, anatomy-and-physiology, animal-behavior, biota, usgs-635affc2d34ebe44250472fd
Organization: Department of the Interior
Kaloko-Honokohau National Historical Park Temporal changes in water conditions in four anchialine pools supporting Orangeblack Hawaiian damselfly, 2016

This data release includes metadata and tabular data that documents water temperature and salinity measured at four core pools supporting the Orangeblack Hawaiian damselfly (Megalagrion xanthomelas) at Kaloko-Honokohau National Historical Park during 10 September-31 October 2016.

Tags: anchialine-pool, biota, damselfly, endangered-species, hawaii, hawaii-island, koloko-honokohau-national-historical-park, usgs-635b0464d34ebe4425047356, water-salinity, water-temperature
Organization: Department of the Interior
Footprint of bathymetry data collected for a Kalamazoo River Reference Reach upstream of Plainwell, Michigan, in 2021

This dataset is a polygon shapefile delineating the footprint of bathymetric data collected in October, 2021 for an approximately 500 meter (m) reach of the Kalamazoo River upstream of Plainwell, Michigan (MI). Bathymetric data in the river channel were collected with a single beam sonar and Acoustic Current Doppler Profiler operated along 2 longitudinal transects and 48 cross-sectional transects, respectively.

Tags: bathymetry, digital-elevation-models, elevation, geomorphology, geospatial-datasets, great-lakes, inlandwaters, kalamazoo-county-mi, kalamazoo-river-huc-04050003, lidar, sonar-methods, topography, usgs-635afe99d34ebe44250472df
Organization: Department of the Interior
Strain induced molecular heterogeneity in ancient sedimentary organic matter mapped at nanoscales using optical photothermal infrared spectroscopy

Here we report ultra-high resolution infrared mapping of organic matter functional group distribution in Tasmanites (algal microfossils) from the Upper Devonian Ohio Shale using optical photothermal infrared spectroscopy (O-PTIR). O-PTIR is capable of rapidly measuring the vibrational response of samples in situ with ~500-nm spatial resolution, well below the infrared diffraction limit. Our results indicate that organic matter within the fold apices regions (zones of greatest deformation) of relatively large Tasmanites is more aliphatic and less oxygen-rich than organic matter in the surrounding Tasmanites body. This contrasts with data from relatively thinner Tasmanites which show statistically invariant chemical differences between the fold apices and body regions. These findings indicate that deformation strain due to mechanical stress during burial can alter the molecular structure of sedimentary organic matter to different degrees across nanometer to micron length scales leading to chemical heterogeneity. However, chemical differences induced to organic matter by this mechanism appear be minor compared to those from thermal alteration. Finally, the data presented here represent the first application of O-PTIR to study sedimentary organic matter highlighting the great promise this analytical approach has for future studies evaluating the molecular composition of geologic materials.

Tags: alginite, biota, deformation, huron-member, ohio, ohio-shale, optical-photothermal-infrared-spectroscopy, organic-matter, shale, tasmanites, usgs-635aa238d34ebe44250471a8
Organization: Department of the Interior
Round goby detection by environmental DNA, trawl, and angling in Lakes Huron and Michigan

This data set is associated with an examination of environmental DNA (eDNA) from the invasive round goby (Neogobius melanostomus) in parallel with traditional fish surveys in the Great Lakes. Data resulting from bottom trawling surveys and angler hook and line methods include round goby fish count and biomass at different depths and seasons at multiple sites of Lake Huron and Lake Michigan (trawls), and breakwall locations of Lake Michigan at Portage Lakefront, Portage, Indiana and Washington Park, Michigan City, Indiana (angling). Data from eDNA water samples targeting round goby were analyzed by two molecular methods: droplet digital PCR (ddPCR) and quantitative PCR (qPCR); eDNA copy numbers are presented for both these methods separately.

Tags: animal-tracking, biota, environment, environmental-dna, field-methods, field-sampling, fish, freshwater-ecosystems, inland-fishery-resources, inlandwaters, invasive-species, lake-huron, lake-michigan, polymerase-chain-reaction, usgs-635aa1c1d34ebe442504719f
Organization: Department of the Interior