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Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

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USGS2020

Paleo-metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA

Fossil rodent middens are powerful tools in paleoecology. In arid parts of western North America, packrat ( Neotoma spp.) middens preserve plant and animal remains for tens of thousands of years. Midden contents are so well preserved that fragments of endogenous ancient DNA (aDNA) can be extracted and analyzed across millennia. Here, we explore the use of shotgun metagenomics to study the aDNA obtained from packrat middens up to 32,000 C 14 years old. Eleven Illumina HiSeq 2500 libraries were successfully sequenced, and between 0.11% and 6.7% of reads were classified using Centrifuge against the NCBI “nt” database. Eukaryotic taxa identified belonged primarily to vascular plants with smaller proportions mapping to ascomycete fungi, arthropods, chordates, and nematodes. Plant taxonomic diversity in the middens is shown to change through time and tracks changes in assemblages determined by morphological examination of the plant remains. Amplicon sequencing of ITS2 and rbcL provided minimal data for some middens, but failed at amplifying the highly fragmented DNA present in others. With repeated sampling and deep sequencing, analysis of packrat midden aDNA from well-preserved midden material can provide highly detailed characterizations of past communities of plants, animals, bacteria, and fungi present as trace DNA fossils. The prospects for gaining more paleoecological insights from aDNA for rodent middens will continue to improve with optimization of laboratory methods, decreasing sequencing costs, and increasing computational power.

Ecology and Evolution↗

USGS2025

Flood-inundation maps for 14.8 miles of Little and Big Papillion Creeks in Omaha, Nebraska, 2023

Digital flood-inundation map libraries for two reaches that constitute 14.8 miles of Little and Big Papillion Creeks in Omaha, Nebraska, were created by the U.S. Geological Survey (USGS) in cooperation with the Papio-Missouri River Natural Resource District. The flood-inundation maps, which can be accessed through the USGS Flood Inundation Mapping Program website at https://www.usgs.gov/mission-areas/water-resources/science/flood-inundation-mapping-fim-program , depict estimates of the areal extent and depth of flooding corresponding to selected water levels (stages) at Little Papillion Creek at Irvington, Nebr. (USGS station 06610750), Little Papillion Creek at Ak-Sar-Ben at Omaha, Nebr. (USGS station 06610765), and Big Papillion Creek at Q Street at Omaha, Nebr. (USGS station 06610770) streamgages. Near-real-time stages at these streamgages may be obtained from the USGS National Water Information System database at https://doi.org/10.5066/F7P55KJN or from the National Weather Service Advanced Hydrologic Prediction Service at https://water.weather.gov/ahps/ . Flood profiles were computed for two different reaches that constitute 14.8 miles of stream length in the study area by using hydraulic models. The models were calibrated by adjusting roughness coefficients to best represent the current (2022) stage-streamflow relation at the streamgages within the study reach. The hydraulic models were then used to compute water-surface profiles at 1-foot stage intervals for selected stage ranges to represent various flooding scenarios at the streamgages in each reach. The simulated water-surface profiles then were combined with a digital elevation model using a geographic information system, which had a 10-foot grid spacing to delineate the flooding extents and water depths for each stage. The availability of these flood-inundation maps, along with information regarding current stage from the USGS streamgages, can provide emergency management personnel and residents with information that is critical for flood response activities and post flood recovery efforts.

Nebraska↗

USGS2016

Flood-inundation map library for the Licking River and South Fork Licking River near Falmouth, Kentucky

Digital flood inundation maps for a 17-mile reach of Licking River and 4-mile reach of South Fork Licking River near Falmouth, Kentucky, were created by the U.S. Geological Survey (USGS) in cooperation with Pendleton County and the U.S. Army Corps of Engineers–Louisville District. The inundation maps, which can be accessed through the USGS Flood Inundation Mapping Science Web site at http://wim.usgs.gov/FIMI/FloodInundationMapper.html , depict estimates of the areal extent and depth of flooding corresponding to selected water levels (stages) at the USGS streamgage on the Licking River at Catawba, Ky., (station 03253500) and the USGS streamgage on the South Fork Licking River at Hayes, Ky., (station 03253000). Current conditions (2015) for the USGS streamgages may be obtained online at the USGS National Water Information System site ( http://waterdata.usgs.gov/nwis ). In addition, the streamgage information has been provided to the National Weather Service (NWS) for incorporation into their Advanced Hydrologic Prediction Service (AHPS) flood warning system ( http:/water.weather.gov/ahps/ ). The flood hydrograph forecasts provided by the NWS are usually collocated with USGS streamgages. The forecasted peak-stage information, also available on the NWS Web site, may be used in conjunction with the maps developed in this study to show predicted areas of flood inundation. In this study, flood profiles were computed for the Licking River reach and South Fork Licking River reach by using a one-dimensional step-backwater model. The hydraulic model was calibrated by using the most current (2015) stage-discharge relations for the Licking River at Catawba, Ky., and the South Fork Licking River at Hayes, Ky., USGS streamgages. The calibrated model was then used to calculate 60 water-surface profiles for a sequence of flood stages, at 2-foot intervals, referenced to the streamgage datum and ranging from an elevation near bankfull to the elevation associated with a major flood that occurred in the region in 1997. To delineate the flooded area at each interval flood stage, the simulated water-surface profiles were combined with a digital elevation model of the study area by using geographic information system software. The availability of these flood inundation maps for Falmouth, Ky., along with online information regarding current stages from the USGS streamgages and forecasted stages from the NWS, provides emergency management personnel and local residents with information that is critical for flood response activities such as evacuations, road closures, and post-flood recovery efforts.

Kentucky↗

USGS2016

PhasePApy: A robust pure Python package for automatic identification of seismic phases

We developed a Python phase identification package: the PhasePApy for earthquake data processing and near‐real‐time monitoring. The package takes advantage of the growing number of Python libraries including Obspy. All the data formats supported by Obspy can be supported within the PhasePApy. The PhasePApy has two subpackages: the PhasePicker and the Associator, aiming to identify phase arrival onsets and associate them to phase types, respectively. The PhasePicker and the Associator can work jointly or separately. Three autopickers are implemented in the PhasePicker subpackage: the frequency‐band picker, the Akaike information criteria function derivative picker, and the kurtosis picker. All three autopickers identify picks with the same processing methods but different characteristic functions. The PhasePicker triggers the pick with a dynamic threshold and can declare a pick with false‐pick filtering. Also, the PhasePicker identifies a pick polarity and uncertainty for further seismological analysis, such as focal mechanism determination. Two associators are included in the Associator subpackage: the 1D Associator and 3D Associator, which assign phase types to picks that can best fit potential earthquakes by minimizing root mean square (rms) residuals of the misfits in distance and time, respectively. The Associator processes multiple picks from all channels at a seismic station and aggregates them to increase computational efficiencies. Both associators use travel‐time look up tables to determine the best estimation of the earthquake location and evaluate the phase type for picks. The PhasePApy package has been used extensively for local and regional earthquakes and can work for active source experiments as well.

Seismological Research Letters↗

USGS2017

Flood-inundation maps for the Meramec River at Valley Park and at Fenton, Missouri, 2017

Two sets of digital flood-inundation map libraries that spanned a combined 16.7-mile reach of the Meramec River that extends upstream from Valley Park, Missouri, to downstream from Fenton, Mo., were created by the U.S. Geological Survey (USGS) in cooperation with the U.S. Army Corps of Engineers, St. Louis Metropolitan Sewer District, Missouri Department of Transportation, Missouri American Water, and Federal Emergency Management Agency Region 7. The flood-inundation maps, which can be accessed through the USGS Flood Inundation Mapping Science website at https://water.usgs.gov/osw/flood_inundation/ , depict estimates of the areal extent and depth of flooding corresponding to selected water levels (stages) at the cooperative USGS streamgages on the Meramec River at Valley Park, Mo., (USGS station number 07019130) and the Meramec River at Fenton, Mo. (USGS station number 07019210). Near-real-time stage data at these streamgages may be obtained from the USGS National Water Information System at https://waterdata.usgs.gov/nwis or the National Weather Service (NWS) Advanced Hydrologic Prediction Service at http:/water.weather.gov/ahps/ , which also forecasts flood hydrographs at these sites (listed as NWS sites vllm7 and fnnm7, respectively). Flood profiles were computed for the stream reaches by means of a calibrated one-dimensional step-backwater hydraulic model. The model was calibrated using a stage-discharge relation at the Meramec River near Eureka streamgage (USGS station number 07019000) and documented high-water marks from the flood of December 2015 through January 2016. The calibrated hydraulic model was used to compute two sets of water-surface profiles: one set for the streamgage at Valley Park, Mo. (USGS station number 07019130), and one set for the USGS streamgage on the Meramec River at Fenton, Mo. (USGS station number 07019210). The water-surface profiles were produced for stages at 1-foot (ft) intervals referenced to the datum from each streamgage and ranging from the NWS action stage, or near bankfull discharge, to the stage corresponding to the estimated 0.2-percent annual exceedance probability (500-year recurrence interval) flood, as determined at the Eureka streamgage (USGS station number 07019000). The simulated water-surface profiles were then combined with a geographic information system digital elevation model (derived from light detection and ranging data having a 0.28-ft vertical accuracy and 3.28-ft horizontal resolution) to delineate the area flooded at each flood stage (water level). The availability of these maps, along with internet information regarding current stage from the USGS streamgages and forecasted high-flow stages from the NWS, will provide emergency management personnel and residents with information that is critical for flood response activities such as evacuations and road closures and for postflood recovery efforts.

Missouri↗

USGS2015

EverVIEW: a visualization platform for hydrologic and Earth science gridded data

The EverVIEW Data Viewer is a cross-platform desktop application that combines and builds upon multiple open source libraries to help users to explore spatially-explicit gridded data stored in Network Common Data Form (NetCDF). Datasets are displayed across multiple side-by-side geographic or tabular displays, showing colorized overlays on an Earth globe or grid cell values, respectively. Time-series datasets can be animated to see how water surface elevation changes through time or how habitat suitability for a particular species might change over time under a given scenario. Initially targeted toward Florida's Everglades restoration planning, EverVIEW has been flexible enough to address the varied needs of large-scale planning beyond Florida, and is currently being used in biological planning efforts nationally and internationally.

Computers & Geosciences↗

USGS2005

Examining patterns of bat activity in Bandelier National Monument, New Mexico, using walking point transects

We conducted a preliminary study using small field crews, a single Anabat II detector coupled with a laptop computer, and point transects to examine patterns of bat activity at a scale of interest to local resource managers. The study was conducted during summers of 1996–1998 in Bandelier National Monument in the Jemez Mountains of northern New Mexico, a landscape with distinct vegetation zones and high species richness of bats. We developed simple models that described general patterns of acoustic activity within 4 vegetation zones based primarily on nightly variation and a qualitative index of habitat complexity. Bat acoustic activity (number of bat passes&sol point) did not vary dramatically among a limited sample of transects within a vegetation zone during 1996. In 1997 and 1998, single transects within each vegetation zone were established, and bat activity did not vary annually within these zones. Acoustic activity differed among the 4 vegetation zones of interest, with the greatest activity occurring in riparian canyon bottomland, intermediate activity in coniferous forest and a 1977 burned zone, and lowest activity in piñon-juniper woodlands. We identified 68.5% of 2,529 bat passes recorded during point-transect surveys to species using an echolocation call reference library we established for the area and qualitative characteristics of bat calls. Bat species richness and composition differed among vegetation zones. Results of these efforts were consistent with general knowledge of where different bat species typically forage and with the natural history of bats of New Mexico, suggesting such a method might have value for drawing inferences about bat activity in different vegetation zones.

Southwestern Naturalist↗

USGS1992

Map showing bottom topography of the Pacific Continental Margin, Cape Mendocino to Point Conception

All contours, geographic outlines, and political boundaries shown on this map of the bottom topography, or bathymetry, of the Pacific continental margin between 34? and 41? N. latitudes were plotted from digital data bases in the library of the U.S. Geological Survey (USGS)-National Oceanic and Atmospheric Administration (NOAA) Joint Office for Mapping and Research (JOMAR). These digital data were obtained and compiled from many sources; consequently, data quality varies within particular data bases as well as from one data base to another. Bathymetric contours were digitized from a map compiled by Chase and others (1981) and from the unpublished large scale versions of that map (T.E. Chase, unpub. maps, 1981). Data for the area seaward of the continental slope (~2000 m depth) were obtained primarily from the U.S. Coast and Geodetic Survey (C&GS) 1955 Pacific Exploratory Survey, a systematic and detailed (~8 -nmi trackline spacing) survey between Mexico and Canada. The USGS provided data from cruises S3-78-NC, S15-79-NC, L2-77-NC, Ll0-76-NC, and Bartlett 72. Data were also obtained from Scripps Institution of Oceanography cruises Merazine, Blue Flash, Kayak B, Scan I, and Seven Tow (Chase and Menard, 1971; Chase and others, 1975; Wilde and others, 1976; Wilde and others, 1978). The 200-m contour was derived from the National Ocean Survey charts 1306N-20 (1975), 1307N-l1B (1974a), 1307N-18B (1974b), and C&GS chart 1308N-12 (1969). Sea-floor depths were corrected for sound velocity in sea water using Matthew's (1939) tables. Onshore topographic contours were generated by computer from a modified version of 3-arc-second elevation data provided by the Defense Mapping Agency. The United States digital shoreline was obtained from the NOAA, NOS, Nautical Charting Division, National Atlas files. The coastline of Canada was digitized from Canadian Hydrographic Service bathymetric maps. The primary source of names of the sea floor features was the "Gazetteer of Undersea Features" (Defense Mapping Agency, 1990). Acknowledgments Christopher Hines assisted in the construction and verification of the digital data bases. Reviews and suggestions by Edward C. Escowitz and Florence Wong and advice provided by Will Stettner regarding the cartographic design substantially improved the quality of this map. References Cited Chase, T.E., and Menard, H.W., 1971, Bathymetric atlas of the northeastern Pacific Ocean: U.S. Naval Oceanographic Office Publication 1303, scale 1:2,000,000 at 33° latitude, 48 p. Chase, T.E., Wilde, Pat, and Normark, W.R., 1975, Oceanographic data of the Monterey Deep Sea Fan: San Diego, University of California, Institute of Marine Resources Publication TR 58, scale 1:898,524 at 35° latitude. Chase, T.E., Wilde, Pat, Normark, W.R., Miller, C.P., Seekins, B.A., and Young, J.D., 1981, Offshore topography of the Western United States between 32° and 49° North latitudes: U.S. Geological Survey Open-File Report 81-443, scale 1:864,518 at 38° latitude, 2 sheets. Coast and Geodetic Survey, 1969, Point St. George to Point Delgada: Coast and Geodetic Survey Bathymetric Map 1308N-12, scale 1:250,000. Defense Mapping Agency, 1990, Gazetteer of undersea features (4th ed.): Washington, D.C., Defense Mapping Agency. Matthews, D.J., 1939, Tables of the velocity of sound in pure water and sea water (2d ed.): London, Admiralty, Hydrographic Department, H.D. 282, 52 p. National Ocean Survey, 1974a, Vicinity Pt. Sur to Pt. Reyes: National Ocean Survey Bathymetric Map 1307N-11B, scale 1:250,000. National Ocean Survey, 1974b, Pt. Reyes to Tolo Bank: National Ocean Survey Bathymetric Map 1307N-18B, scale 1:250,000. National Ocean Survey, 1975, Cape San Martin to Point Conception: National Ocean Survey Bathymetric Map 1306N-20, scale 1:250,000. Wilde, Pat, Normark, W.R., and Chase, T.E., 1976, Oceanographic data off central California 37° to 40° North including the Delgada Deep Sea Fan: Berkeley, University of California, Lawrence Berkeley Laboratory Publication 92, scale 1 :864,581 at 38° latitude. Wilde, Pat, Chase, T.E., Holmes, M.L., Normark, W.R., Thomas, J.A., McCulloch, D.S., and Kulm, L.D., 1978, Oceanographic data off northern California-southern Oregon 40° to 43° North including the Gorda Deep Sea Fan: Berkeley, University of California, Lawrence Berkeley Laboratory Publication 251, scale 1:815,482 at 42° latitude.

IMAP↗

USGS2011

Modules based on the geochemical model PHREEQC for use in scripting and programming languages

The geochemical model PHREEQC is capable of simulating a wide range of equilibrium reactions between water and minerals, ion exchangers, surface complexes, solid solutions, and gases. It also has a general kinetic formulation that allows modeling of nonequilibrium mineral dissolution and precipitation, microbial reactions, decomposition of organic compounds, and other kinetic reactions. To facilitate use of these reaction capabilities in scripting languages and other models, PHREEQC has been implemented in modules that easily interface with other software. A Microsoft COM (component object model) has been implemented, which allows PHREEQC to be used by any software that can interface with a COM server—for example, Excel®, Visual Basic®, Python, or MATLAB". PHREEQC has been converted to a C++ class, which can be included in programs written in C++. The class also has been compiled in libraries for Linux and Windows that allow PHREEQC to be called from C++, C, and Fortran. A limited set of methods implements the full reaction capabilities of PHREEQC for each module. Input methods use strings or files to define reaction calculations in exactly the same formats used by PHREEQC. Output methods provide a table of user-selected model results, such as concentrations, activities, saturation indices, and densities. The PHREEQC module can add geochemical reaction capabilities to surface-water, groundwater, and watershed transport models. It is possible to store and manipulate solution compositions and reaction information for many cells within the module. In addition, the object-oriented nature of the PHREEQC modules simplifies implementation of parallel processing for reactive-transport models. The PHREEQC COM module may be used in scripting languages to fit parameters; to plot PHREEQC results for field, laboratory, or theoretical investigations; or to develop new models that include simple or complex geochemical calculations.

Computers & Geosciences↗