AndreaBozzo/ceres-open-data-index huggingface dataset:
Microsatellite data, boundaries of subpopulation centers, and estimated effective migration for greater sage-grouse collected in western North America between 1992 and 2015

Characterizing genetic structure across a species’ range is relevant for management and conservation as it can be used to define population boundaries and quantify connectivity.  Here, we characterized population structure and estimated effective migration in Greater Sage-grouse (Centrocercus urophasianus). Our objectives were to (1) describe large-scale patterns of population genetic structure and gene flow and (2) to characterize genetic subpopulation centers across the range of Greater Sage-grouse. Samples from 2,134 individuals were genotyped at 15 microsatellite loci. Using standard STRUCTURE and spatial principal components analyses, we found evidence for four or six areas of large-scale genetic differentiation and, following our novel method, 12 subpopulation centers of differentiation. The subpopulation centers defined here could be monitored to maintain genetic diversity and connectivity with other subpopulation centers. Many areas outside subpopulation centers are contact zones where different genetic groups converge and could be priorities for maintaining overall connectivity. Our novel method and process of leveraging multiple different analyses to find common genetic patterns provides a path forward to characterizing genetic structure in wide-ranging, continuously distributed species. The files associated with this data release include the raw genetic data (both a full data set and one thinned to create even sampling distribution), the estimated effective migration surface, and boundaries of subpopulation centers at K=6 from a Structure analysis using 25, 50, and 75% kernel density estimates to determine genetically distinct groups.

Tags: biota, genetics, subpopulation-center, usgs-61c2427bd34e2ca389d9e7cd
Organization: Department of the Interior
Central Valley Hydrologic Model version 2 (CVHM2): Surface Water Network for Water Years 1922 - 2019 (ver. 2.0, December 2023)

This digital dataset contains the monthly inflows and diversions to the surface-water network in the updated Central Valley Hydrologic Model (CVHM2) for water years 1922-2019. The surface-water network simulates the Central Valley’s complex conveyance network through the Streamflow Routing Package (SFR2) and the Farm-Process (FMP4) at 65 inflow locations with 271 stream segments and 13 bifurcations, and 571 diversion locations providing 564 of semi-routed diversions and 7 non-routed diversions. The semi-routed deliveries are routed through the simulated surface-water network, while the non-routed delivery is simulated through linkages between the SFR2 and FMP4 packages in MODFLOW-OWHM. Surface water data for CVHM2 is presented in two child items: inflow and bifurcation names, locations, and magnitude; diversion names, locations, and magnitude for semi-routed and non-routed diversions. Each child item contains metadata, a shapefile, and a csv file containing the data.

Tags: alameda-county, amador-county, butte-county, calaveras-county, california, central-valley, central-valley-aquifer, central-valley-california, central-valley-hydrologic-model, colusa-county, contra-costa-county, el-dorado-county, flow-model-cvhm2, fresno-county, geoscientificinformation, glenn-county, groundwater, groundwater-availability-of-the-central-valley-aquifer, humboldt-county, hydrogeology, hydrology, inland-waters, inlandwaters, kern-county, kings-county, lake-county, madera-county, mariposa-county, mendocino-county, merced-county, model, monterey-county, napa-county, nevada-county, placer-county, sacramento-county, sacramento-valley, san-benito-county, san-joaquin-county, san-joaquin-valley, san-luis-obispo-county, santa-barbara-county, santa-clara-county, shasta-county, solano-county, sonoma-county, stanislaus-county, surface-water, sutter-county, tehama-county, texture-model, trinity-county, tulare-county, tuolumne-county, usgs-61e7442ed34e3618e01cf68f, ventura-county, yolo-county, yuba-county
Organization: Department of the Interior
SPARROW model input datasets and predictions of total dissolved solids loads in streams of the Upper Colorado River Basin watershed

This data release contains bootstrap values of mean-annual total dissolved solids (TDS) loads predicted by a SPARROW model for individual stream reaches in the Upper Colorado River Basin watershed in the predict.txt file.  Also included are the input variables required to execute the model, including dissolved solids sources, landscape characteristics,  and calibration data from water quality monitoring stations in the input.txt file. Further details on model construction and results are described in Miller et al. (2017, https://doi.org/10.3133/sir20175009).

Tags: arizona, biota, colorado, hydrology, mathematical-modeling, new-mexico, streamflow, usgs-61c2096dd34e2ca389d9e704, utah, water-quality, water-resources, wyoming
Organization: Department of the Interior
Barrier island geomorphology and seabeach amaranth metrics at 50-m alongshore transects, and 5-m cross-shore points for 2008 — Assateague Island, MD and VA.

Understanding how sea-level rise will affect coastal landforms and the species and habitats they support is critical for developing approaches that balance the needs of humans and native species. Given this increasing need to forecast sea-level rise effects on barrier islands in the near and long terms, we are developing Bayesian networks to evaluate and to forecast the effects of sea-level rise on shoreline change, barrier island geomorphology, and habitat availability for species such as piping plover (Charadrius melodus) and seabeach amaranth (Amaranthus pumilus). We use publicly available data products, such as lidar, orthophotography, and vegetation/substrate maps to extract metrics of barrier island characteristics for Assateague Island National Seashore. The metrics are used to conduct statistical analyses and used to training and test probabilistic models developed for barrier island systems.  This data release contains the extracted metrics of barrier island geomorphology, and field collected species information (amaranth)  that are input to Bayesian networks to evaluate the occurrence probabilities for a suite of barrier island characteristics and ultimately habitat suitability. While the data presented here samples conditions at Assateague Island National Seashore in 2008, this work is one component of a larger research and management program that seeks to understand the future states of barrier island systems and resulting impacts to coastal habitat driven by sea-level rise.

Tags: assateague-island, assateague-island-national-seashore, atlantic-ocean, barrier-island, bayesian-network, chincoteague-national-wildlife-refuge, cmhrp, coastal-and-marine-hazards-and-resources-program, coastal-erosion, coastal-habitat, coastal-hazards, coastal-processes, delmarva-peninsula, environment, erosion, geographic-information-systems, geomorphology, geoscientificinformation, geospatial-analysis, geospatial-datasets, gis, hazards, land-use-and-land-cover, maryland, md, mean-high-water, mean-lower-low-water, mhw, mllw, navd88, north-america, north-american-vertical-datum-1988, probability, sea-level-change, sea-level-rise, shoreline-change, transect-sampling, u-s-geological-survey, united-states, usa, usgs, usgs-61c1f949d34eafc738ca042f, va, virginia, woods-hole-coastal-and-marine-science-center
Organization: Department of the Interior
Assateague Island Seabeach Amaranth Survey Data — 2001 to 2018

Seabeach amaranth (Amaranthus pumilus) is a federally threatened plant species that was once prevalent on beaches of the U.S. mid-Atlantic coast.  For much of the 20th century, seabeach amaranth was absent and thought to be extinct along this coast presumably due to development and recreational pressure.  Few plants were observed over much of the 20th century and the species was federally listed as endangered in 1993.  To re-establish a population, the Natural Resources staff at Assateague Island National Seashore (ASIS) planted seabeach amaranth cultivars for three growing seasons from 2000 to 2002.  To monitor the impact of this effort, the Natural Resources staff conducted yearly surveys on Assateague Island to locate seabeach amaranth from 2001 to the present.  These surveys were undertaken, typically during early August, to monitor the presence and dispersal of the plant following the effort to re-establish a population.  The surveys were conducted in coordination with Maryland Department of Natural Resources.  Surveys measured the location of each plant found using GPS and noted several parameters including: 1) plant size, 2) evidence of grazing by insects or ungulates (2005 and later) and noted if the plant was protected by cages put in place by ASIS Natural Resources staff.

Tags: assateague-island, assateague-island-national-seashore, atlantic, barrier-island, beaches, biota, coastal-habitat, coastal-plants, delmarva-peninsula, environment, field-activity-logs, field-inventory-and-monitoring, geographic-information-systems, geoscientificinformation, geospatial-analysis, geospatial-datasets, gis, grazing, maryland, md, national-park-service, north-atlantic, organisms, seabeach-amaranth, usgs-61c1f5fbd34eafc738ca0410, va, vascular-plants, vegetation, virginia
Organization: Department of the Interior
Seed germination requirements and seed responses to salinity for three rare wetland plants of spring-fed arid systems at Bitter Lake National Wildlife Refuge near Roswell, New Mexico 2018-2020

This file includes seed germination experiments observations from seeds collected during the fall of 2018 and 2020 at Bitter Lake National Wildlife Refuge, near Roswell, New Mexico. Seeds of Cirsium wrightii, Agalinis calycina, and Helianthus paradoxus were collected by manually clipping seed heads from plants across the wetland management units. Seeds were placed in brown paper bags and transported to the lab. In the lab, seeds from 2018 were immediately used for experiments by placing them in an incubator using petri dishes. Seeds collected in 2020 received cold stratification and salinity treatments. Following cold stratification, seeds were placed in the incubator and received salinity treatments. Seeds were monitored for germination .

Tags: biota, bitter-lake-national-wildlife-refuge, cinega, germination, new-mexico, salinity, soil-moisture, usgs-61c1eb85d34eafc738ca03c7, wetland-management
Organization: Department of the Interior
North American Grid-Based Offshore Sampling Frame: Continental United States

This shapefile represents the offshore grid-based sampling frame intended for use with the North American Bat Monitoring Program (NABat). The grid consists of 10 km x 10 km cells spanning the oceanic waters surrounding the continental United States.

Tags: bats, biota, grid, nabat, north-america, sample-frame, united-states, usgs-61bd0075d34ee9cd54ed274e
Organization: Department of the Interior
North American Grid-Based Offshore Sampling Frame: Alaska and Canada

This shapefile represents the offshore grid-based sampling frame intended for use with the North American Bat Monitoring Program (NABat). The grid consists of 10 km x 10 km cells spanning the oceanic waters surrounding Alaska and Canada.

Tags: alaska, bats, biota, canada, grid, nabat, north-america, sample-frame, usgs-61bcfea0d34ee9cd54ed25ed
Organization: Department of the Interior
Population genetic analysis of the snake-infecting fungus, Ophidiomyces ophidiicola, in the eastern United States

Snake fungal disease (SFD; ophidiomycosis), caused by the pathogen Ophidiomyces ophidiicola (Oo), has been documented in wild snakes in North America and Eurasia, and is a potentially emerging disease in the eastern USA. However, a lack of historical disease data has made it challenging to determine whether Oo is a recent arrival to the USA or whether SFD emergence is due to other factors. Here, we examined the genomes of 82 Oo strains to determine the pathogen’s history in the eastern USA. This dataset contains metadata on the strains used in that study.

Tags: biota, fungal-whole-genome-sequencing, ophidiomyces, ophidiomycosis, snake-fungal-disease, usgs-61bcf884d34ee9cd54ed2512
Organization: Department of the Interior
Model Archive Summary for acoustic derived suspended-sediment concentration at 14211720 Willamette River at Portland, OR

Model archive summary describing the development of an acoustic derived suspended sediment time series computation model.  The model archive summary describes the methods and techniques used to develop the model for the Willamette River at Portland site – USGS site ID# 14211720. The time series suspended sediment data will help determine the suspended sediment concentration at the site in real-time enabling science entities, managers, and others, track the movement of sediment in the Lower Columbia River System.

Tags: geomorphology, hydrology, multnomah-county, portland-or, sedimentology, usgs-61bcf0ead34ee9cd54ed24f5, water-quality, willamette-river
Organization: Department of the Interior
Monthly Diversions from the Surface Water Network of the Central Valley Hydrologic Model Version 2 (CVHM2)

This digital dataset contains the monthly diversions from the surface water network in the updated Central Valley Hydrologic Model (CVHM2) for water years 1922-2019. The volume of water transported by surface-water diversions were updated in the CVHM2 from several sources, including:
•	The C2VSIM developed by DWR,
•	The WestSIM model,
•	Delta Mendota Canal turnout delivery data obtained from SLDMWA,
•	Delta delivery data obtained from Montgomery Watson.
The surface water diversions are simulated through the Streamflow Routing Package (SFR2) using 571 diversion locations providing 564 semi-routed and 7 non-routed diversions. Linkages between SFR2 and the Farm-Process (FMP4) simulate the semi-routed and non-routed deliveries through the stream network from a specified diversion location. The semi-routed deliveries (SRD) are regulated by a diversion limit at each location so that FMP4 can only divert from the stream network up a certain amount, specified in the file, SRD_Diversion_Limit.csv. The non-routed deliveries (NRD) are “piped” from a diversion location to a given subregion to meet farm demand. A list of the diversion locations and associated subregions for the NRDs is provided in NRD_ID.csv.  Simulating diversions in this way simplified how diversions were simulated and made it easier to account for the volumes from the diversions in the input and output datasets. When compared to the CVHM1, the number of diversions in the CVHM2 were greatly increased in the Delta as well as the Western San Joaquin Valley. This dataset also includes the diversion names, locations, monthly magnitudes, and the non-routed delivery model input file for FMP4.

Tags: alameda-county, amador-county, butte-county, calaveras-county, california, central-valley, central-valley-aquifer, central-valley-california, central-valley-hydrologic-model, colusa-county, contra-costa-county, el-dorado-county, flow-model-cvhm2, fresno-county, geoscientificinformation, glenn-county, groundwater, groundwater-availability-of-the-central-valley-aquifer, humboldt-county, hydrogeology, hydrology, inland-waters, inlandwaters, kern-county, kings-county, lake-county, madera-county, mariposa-county, mendocino-county, merced-county, model, monterey-county, napa-county, nevada-county, placer-county, sacramento-county, sacramento-valley, san-benito-county, san-joaquin-county, san-joaquin-valley, san-luis-obispo-county, santa-barbara-county, santa-clara-county, shasta-county, solano-county, sonoma-county, stanislaus-county, surface-water, sutter-county, tehama-county, texture-model, trinity-county, tulare-county, tuolumne-county, usgs-61e74461d34e3618e01cf691, ventura-county, yolo-county, yuba-county
Organization: Department of the Interior
Bathymetric data for the Maumee River between Defiance and Toledo, Ohio, 2019

As part of the Great Lakes Restoration Initiative (GLRI) project template 774-18 entitled “Development of monitoring and response methodologies, and implementation of an Adaptive Management Framework to work towards Eradication of Grass Carp in Lake Erie” an integrated bathymetric/hydrodynamic/water-quality survey of the Maumee River (Ohio) was completed by the U.S. Geological Survey (USGS) in the summer of 2019. These data were collected to inform the development of a one-dimensional hydraulic model and associated Fluvial Egg Drift Simulator (FluEgg) model of the Maumee River downstream from Defiance, Ohio. The data contained in this data release were collected by the USGS Ohio-Kentucky-Indiana Water Science Center to inform the development of these models by the USGS Central Midwest Water Science Center. 
The survey was completed over two periods of time: June 24–28, 2019, and July 29 to August 1, 2019. The first survey period concentrated on the reach between Waterville, Ohio, and Lake Erie, while the second period concentrated on the reach between Defiance, Ohio, and Grand Rapids, Ohio. Survey data include bathymetry (riverbed elevations), three-dimensional water velocity, discharge, and basic water-quality parameters. However, this data release is limited to only the bathymetry data (riverbed elevations) from the survey. A total of 251 cross sections were surveyed (141 upstream from and 110 downstream from Grand Rapids Dam, respectively) and data were also collected along streamwise transits between sections. Due to rapids, high-water, access, and safety concerns, no data were collected in the 23.9-kilometer reach downstream from the dam at Grand Rapids, Ohio. The upstream-most cross section is 280 meters downstream from the low-head dam approximately 6.6 kilometers downstream from Defiance, Ohio. The downstream-most cross section is located 290 meters downstream from the U.S. Coast Guard Station at Toledo, Ohio (3900 N Summit St, Toledo, OH 43611). All data were collected by a manned survey vessel with a two-person survey crew of trained hydrographers. All data were georeferenced using a Trimble R10 Global Navigation Satellite System (GNSS) receiver mounted on the survey vessel and connected to the Ohio Department of Transportation (ODOT) real-time virtual reference station (VRS) network. Depths were measured using the 600 kHz vertical beam from a 1200 kHz Teledyne RD Instruments RiverPro acoustic Doppler current profiler (ADCP) deployed on a fixed mount from the survey vessel. The GNSS receiver was mounted directly above the ADCP and the offset between the GNSS antenna and the face of the vertical beam transducer was measured in the field and accounted for in post-processing. The sampling frequency varied slightly with the dynamic configuration of the ADCP but was generally between 1 to 2 Hertz.

Tags: bathymetry, defiance-county, henry-county, lucas-county, maumee-river, ohio, river-reaches, surface-water-non-marine, united-states, usgs-61bcbe9cd34ee9cd54ed2330, wood-county
Organization: Department of the Interior
Mississippi Barrier Islands imagery (Cat, East and West Ship, Horn and Petit Bois) acquired February 2020

To document current Mississippi barrier  island conditions, imagery was acquired February 28, 2020 using Airborne GPs and field control ground markers.  For ground control, markers were established and surveyed in using Real Time Kinematic (RTK) survey equipment.  The imagery collected will be processed to produce a mosaic of all 4 islands (Cat, East and West Ship, Horn and Petit Bois) and interpreted to classify wetland marshes.   The classified data will not only quantify how much marsh is being affected, but the data will also provide a spatial aspect as to where these degrading marsh fragmentations are occurring.  The data will be correlated with other data such as salinity, prescribed burns, flooding frequency and flooding duration data to better understand what events may be causing marsh deterioration.

Tags: cat-island, east-and-west-ship-island, environment, horn-island, mississippi-barrier-island, mscip, petit-bois-island, usgs-61bcb53bd34ee9cd54ed2324
Organization: Department of the Interior
Hawaiʻi Island Survival of Ceratocystis in Frass 2019-2020

This data release includes data and metadata used in the estimation of Ceratocystis lukuohia survival in ambrosia beetle frass under various temperature and humidity conditions on Hawaiʻi Island. Data were used in the analysis of the manuscript, "Ceratocystis lukuohia-infested ambrosia beetle frass as inoculum for Ceratocystis wilt of Metrosideros polymorpha." Frass was exposed at two locations including Volcano and Hilo, as well as a control incubator and frass was tested for viable C. lukuohia propagules through a carrot baiting technique over time.

Tags: ceratocystis, frass, rapid-ohia-death, usgs-61bbc0f7d34e9e224ac19596
Organization: Department of the Interior
Aerial images, digital elevation models, channel width maps, and river metrics along the Colorado River in Canyonlands National Park, Utah (1940 - 2018)

These data consist of rectified aerial photographs, measurements of active channel width, measurements of river and floodplain bathymetry and topography, and ancillary data. These data are specific to the corridor of the Colorado River in Canyonlands National Park between Potash, Utah and the confluence of the Green and Colorado Rivers near Spanish Bottom, Utah. The time period for these data are 1940 to 2018. The shapefile data are measurements of features of the active river channel and floodplains of the Colorado River. The raster data are aerial images and digital elevation models (DEMs) for segments of the Colorado River in Canyonlands National Park, Utah. The aerial images depict the river channel and adjacent floodplains for most of the corridor of the Colorado River in Canyonlands National Park upstream from the confluence with the Green River. The images were acquired from public sources and orthorectified and mosaiced for this study. The DEMs cover the river channel and adjacent floodplain for the Lockhart Creek segment of the Colorado River within Canyonlands National Park and include both bathymetric and topographic data. The bathymetric data were collected by the U.S. Geological Survey Grand Canyon Monitoring and Research Center with funding provided by the National Park Service. The topographic data are airborne lidar data that were collected for the state of Utah by a contractor. The lidar data are available at https://doi.org/10.5069/G9RV0KSQ.

Tags: active-channel-width, active-river-channel, aerial-photography, bathymetric-data, bathymetry, bathymetry-measurement, canyonlands-national-park, colorado-river, data-release, digital-elevation-models, floodplains, green-river, image-collections, image-mosaics, inlandwaters, land-surveying, lockhart-canyon, lockhart-creek, meander-canyon, measurements, orthorectified, potash, raster-data, rectified-aerial-photographs, river-channel, river-corridor, river-reaches, river-systems, shapefile, spanish-bottom, topographic-data, topographic-maps, topography, usgs-61bbbaa2d34e9e224ac19571, utah, vector-data
Organization: Department of the Interior