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USGS2012

Concurrent speciation in the eastern woodland salamanders (Genus Plethodon):DNA sequences of the complete albumin nuclear and partialmitochondrial 12s genes

Salamanders of the North American plethodontid genus Plethodon are important model organisms in a variety of studies that depend on a phylogenetic framework (e.g., chemical communication, ecological competition, life histories, hybridization, and speciation), and consequently their systematics has been intensively investigated over several decades. Nevertheless, we lack a synthesis of relationships among the species. In the analyses reported here we use new DNA sequence data from the complete nuclear albumin gene (1818 bp) and the 12s mitochondrial gene (355 bp), as well as published data for four other genes (Wiens et al., 2006), up to a total of 6989 bp, to infer relationships. We relate these results to past systematic work based on morphology, allozymes, and DNA sequences. Although basal relationships show a strong consensus across studies, many terminal relationships remain in flux despite substantial sequencing and other molecular and morphological studies. This systematic instability appears to be a consequence of contemporaneous bursts of speciation in the late Miocene and Pliocene, yielding many closely related extant species in each of the four eastern species groups. Therefore we conclude that many relationships are likely to remain poorly resolved in the face of additional sequencing efforts. On the other hand, the current classification of the 45 eastern species into four species groups is supported. The Plethodon cinereus group (10 species) is the sister group to the clade comprising the other three groups, but these latter groups (Plethodon glutinosus [28 species], Plethodon welleri [5 species], and Plethodon wehrlei [2 species]) probably diverged from each other at approximately the same time.

Molecular Phylogenetics and Evolution↗

USGS1979

Geologic interpretation of aeromagnetic map of the Seward and Blying Sound quadrangles, Alaska

An aeromagnetic survey of the Seward and northern part of the Blying Sound quadrangles was flown by Geometrics, Inc., during 1975-77 to provide magnetic data to aid in an appraisal of the mineral resources. Background details of the regional geology and major structures are described in a companion report by Tysdal and Case (1979), and interpretation of the gravity data are described in a report by Case and others (1979). Preliminary reports of a paleomagnetic investigation have been reported by Hillhouse and Gromme (1977), and a more complete analysis of the results is in preparation. The aeromagnetic survey was flown at a nominal height of 300 m above the surface and flight lines were spaced about 1.7 km apart. Total magnetic field was measured by a proton-precession magnetometer. The International Geomagnetic Reference Field (IGRF), updated to 1976, was removed, and the residual values were computer-contoured to produce the aeromagnetic map (sheet 1). Detailed aeromagnetic maps at scale 1:63,360 and a map at scale 1:250,000 have been released as Open File Reports 78-1080 through 1083 (U.S. Geological Survey, 1978). Magnetic anomalies in the Seward-Blying Sound region are somewhat less complex than in other parts of south-central Alaska, primarily because of the huge volume of relatively nonmagnetic flysch that constitutes the Valdez and Orca Groups. Several rather isolated groups of mafic-ultramafic rocks are significantly more magnetic than the flysch assemblages, and cause distinctive patterns of magnetic anomalies. A few of the granitic plutons are magnetic, but most appear to have little or no magnetic expression.

Alaska↗

USGS2012

Gap Analysis of Benthic Mapping at Three National Parks: Assateague Island National Seashore, Channel Islands National Park, and Sleeping Bear Dunes National Lakeshore

The National Park Service (NPS) Inventory and Monitoring (I&M) Program initiated a benthic habitat mapping program in ocean and coastal parks in 2008-2009 in alignment with the NPS Ocean Park Stewardship 2007-2008 Action Plan. With more than 80 ocean and Great Lakes parks encompassing approximately 2.5 million acres of submerged territory and approximately 12,000 miles of coastline (Curdts, 2011), this Servicewide Benthic Mapping Program (SBMP) is essential. This report presents an initial gap analysis of three pilot parks under the SBMP: Assateague Island National Seashore (ASIS), Channel Islands National Park (CHIS), and Sleeping Bear Dunes National Lakeshore (SLBE) (fig. 1). The recommended SBMP protocols include servicewide standards (for example, gap analysis, minimum accuracy, final products) as well as standards that can be adapted to fit network and park unit needs (for example, minimum mapping unit, mapping priorities). The SBMP requires the inventory and mapping of critical components of coastal and marine ecosystems: bathymetry, geoforms, surface geology, and biotic cover. In order for a park unit benthic inventory to be considered complete, maps of bathymetry and other key components must be combined into a final report (Moses and others, 2010). By this standard, none of the three pilot parks are mapped (inventoried) to completion with respect to submerged resources. After compiling the existing benthic datasets for these parks, this report has concluded that CHIS, with 49 percent of its submerged area mapped, has the most complete benthic inventory of the three. The ASIS submerged inventory is 41 percent complete, and SLBE is 17.5 percent complete.

Assateague Island National Seashore;Channel Island↗

USGS2024

Population and spatial dynamics of desert bighorn sheep in Grand Canyon during an outbreak of respiratory pneumonia

Introduction: Terrestrial species in riverine ecosystems face unique constraints leading to diverging patterns of population structure, connectivity, and disease dynamics. Desert bighorn sheep ( Ovis canadensis nelsoni ) in Grand Canyon National Park, a large native population in the southwestern USA, offer a unique opportunity to evaluate population patterns and processes in a remote riverine system with ongoing anthropogenic impacts. We integrated non-invasive, invasive, and citizen-science methods to address questions on abundance, distribution, disease status, genetic structure, and habitat fragmentation. Methods: We compiled bighorn sightings collected during river trips by park staff, commercial guides, and private citizens from 2000–2018 and captured bighorn in 2010–2016 to deploy GPS collars and test for disease. From 2011–2015, we non-invasively collected fecal samples and genotyped them at 9–16 microsatellite loci for individual identification and genetic structure. We used assignment tests to evaluate genetic structure and identify subpopulations, then estimated gene flow and recent migration to evaluate fragmentation. We used spatial capture-recapture to estimate annual population size, distribution, and trends after accounting for spatial variation in detection with a resource selection function model. Results and discussion: From 2010–2018, 3,176 sightings of bighorn were reported, with sightings of 56–145 bighorn annually on formal surveys. From 2012–2016, bighorn exhibiting signs of respiratory disease were observed along the river throughout the park. Of 25 captured individuals, 56% were infected by Mycoplasma ovipneumoniae , a key respiratory pathogen, and 81% were recently exposed. Pellet sampling for population estimation from 2011–2015 yielded 1,250 genotypes and 453 individuals. We detected 6 genetic clusters that exhibited mild to moderate genetic structure ( F ST 0.022–0.126). The river, distance, and likely topography restricted recent gene flow, but we detected cross-river movements in one section via genetic recaptures, no subpopulation appeared completely isolated, and genetic diversity was among the highest reported. Recolonization of one large stretch of currently empty habitat appears limited by the constrained topology of this system. Annual population estimates ranged 536–552 (95% CrI range 451–647), lamb:ewe ratios varied, and no significant population decline was detected. We provide a multi-method sampling framework useful for sampling other wildlife in remote riverine systems.

Arizona↗

USGS1987

Streamflow characteristics of the Colorado River Basin in Utah through September 1981

This report summarizes discharge data and other streamflow characteristics developed from gag ing-station records collected through September 1981 at 337 stations in the Colorado River Basin in Utah. Data also are included for 14 stations in adjacent areas of the bordering states of Arizona, Colorado, and Wyoming (fig. 1). The study leading to this report was done in cooperation with the U.S. Bureau of Land Management, which needs the streamflow data in order to evaluate impacts of mining on the hydrologic system. The report also will be beneficial to other Federal, State, and county agencies and to individuals concerned with water supply and water problems in the Colorado River Basin. The streamflow characteristics in the report could be useful in many water-related studies that involve the following: Definition of baseline-hydrologic conditions; studies of the effects of man's activities on streamflow; frequency analyses of low and high flows; regional analyses of streamflow characteristics; design of water-supply systems; water-power studies; forecasting of stream discharge; time-series analyses of streamflow; design of flood-control structures; stream-pollution studies; and water-chemistry transport studies. The basic data used to develop the summaries in this report are records of daily and peak discharge collected by the U.S. Geological Survey and other Federal agencies. Much of the work of the Geological Survey was done in cooperation with Federal, State, and county agencies. Discharge records included in the report generally were for stations with at least 1 complete water year of record and nearby stations that were on the same stream and had different streamflow characteristics. A water year is a 12-month period ending September 30, and it is designated by the calendar year in which it ends. For streams that have had significant changes in regulation by reservoirs or diversions, the records before and after those changes were used separately to provide streamflow characteristics for each period of homogeneous streamflow and to show the change in the characteristics. Summaries for annual peak discharge are included only for stations with 5 or more years of data. The summaries of annual lowest and highest mean-discharge frequency are reported for stations with 10 or more years of daily-discharge record and for which computer-generated frequency curves provided a reasonable fit of the plotted data.

Utah↗

USGS1995

Seismic Sources and Recurrence Rates as Adopted by USGS Staff for the Production of the 1982 and 1990 Probabilistic Ground Motion Maps for Alaska and the Conterminous United States

The construction of a probabilistic ground-motion hazard map for a region follows a sequence of analyses beginning with the selection of an earthquake catalog and ending with the mapping of calculated probabilistic ground-motion values (Hanson and others, 1992). An integral part of this process is the creation of sources used for the calculation of earthquake recurrence rates and ground motions. These sources consist of areas and lines that are representative of geologic or tectonic features and faults. After the design of the sources, it is necessary to arrange the coordinate points in a particular order compatible with the input format for the SEISRISK-III program (Bender and Perkins, 1987). Source zones are usually modeled as a point-rupture source. Where applicable, linear rupture sources are modeled with articulated lines, representing known faults, or a field of parallel lines, representing a generalized distribution of hypothetical faults. Based on the distribution of earthquakes throughout the individual source zones (or a collection of several sources), earthquake recurrence rates are computed for each of the sources, and a minimum and maximum magnitude is assigned. Over a period of time from 1978 to 1980 several conferences were held by the USGS to solicit information on regions of the United States for the purpose of creating source zones for computation of probabilistic ground motions (Thenhaus, 1983). As a result of these regional meetings and previous work in the Pacific Northwest, (Perkins and others, 1980), California continental shelf, (Thenhaus and others, 1980), and the Eastern outer continental shelf, (Perkins and others, 1979) a consensus set of source zones was agreed upon and subsequently used to produce a national ground motion hazard map for the United States (Algermissen and others, 1982). In this report and on the accompanying disk we provide a complete list of source areas and line sources as used for the 1982 and later 1990 seismic hazard maps for the conterminous U.S. and Alaska. These source zones are represented in the input form required for the hazard program SEISRISK-III, and they include the attenuation table and several other input parameter lines normally found at the beginning of an input data set for SEISRISK-III.

Open-File Report↗

USGS1971

A procedure for evaluating environmental impact

In a recent article in "Science" discussing the Environmental Policy Act of 1969, Gillette (1971) states "The law's instructions for preparing an impact report apparently are not specific enough to insure that an agency will fully, or even usefully, examine the environmental effects of the projects it plans." This report contains a procedure that may assist in developing uniform environmental impact statements. The Department of the Interior and the Council on Environmental Quality will appreciate comments on the procedure here proposed. The heart of the system is a matrix which is general enough to be used as a reference checklist or a reminder of the full range of actions and impacts on the environment that may relate to proposed actions. The marked matrix also serves as an abstract of the text of the environmental assessment to enable the many reviewers of impact reports to determine quickly what are considered to be the significant impacts and their relative importance as evaluated by the originator of the impact report. Many exhaustive studies of the use of matrices for environmental studies are now being undertaken. (See Sorensen, 1971.) This comparatively simple system is intended as a guide for the many people who are faced with the evaluation and preparation of environmental impact reports before the results of these studies have been completed. It should be borne in mind that there is presently no uniformity in approach or agreement upon objectives in an impact analysis and this generalized matrix is a step in that direction. The procedure does not limit the development of detail in any specific aspect of the environment; a separate expanded matrix for any environmental aspect can easily be developed within the framework provided.

Circular↗

USGS1997

A manual for a laboratory information management system (LIMS) for light stable isotopes

The reliability and accuracy of isotopic data can be improved by utilizing database software to (i) store information about samples, (ii) store the results of mass spectrometric isotope-ratio analyses of samples, (iii) calculate analytical results using standardized algorithms stored in a database, (iv) normalize stable isotopic data to international scales using isotopic reference materials, and (v) generate multi-sheet paper templates for convenient sample loading of automated mass-spectrometer sample preparation manifolds. Such a database program is presented herein. Major benefits of this system include (i) an increase in laboratory efficiency, (ii) reduction in the use of paper, (iii) reduction in workload due to the elimination or reduction of retyping of data by laboratory personnel, and (iv) decreased errors in data reported to sample submitters. Such a database provides a complete record of when and how often laboratory reference materials have been analyzed and provides a record of what correction factors have been used through time. It provides an audit trail for stable isotope laboratories. Since the original publication of the manual for LIMS for Light Stable Isotopes, the isotopes 3 H, 3 He, and 14 C, and the chlorofluorocarbons (CFCs), CFC-11, CFC-12, and CFC-113, have been added to this program.

Open-File Report↗

USGS1998

A manual for a Laboratory Information Management System (LIMS) for light stable isotopes

Open-File Report↗

USGS1981

Selected hydrogeologic data from the Northern Great Plains area of Montana

Selected hydrologic data have been used in a 4-year study of aquifers of Cenozoic and Mesozoic age in the northern Great Plains to define the hydrologic system and to generate hydrologic maps. Records of 6,754 wells and 188 springs are tabulated in the report. The well data include site location, county, date completed, depth of well, casing diameter, type of lift, use of water, principal aquifer, altitude of land surface, water level, discharge, specific capacity, specific conductance, and water temperature. The spring data include site location, county, use of water, principal aquifer, altitude of land surface, type of spring, discharge, date discharge measured, specific conductance, and water temperature. Locations of the wells and springs are shown on a map at a scale of 1:1,000,000. (USGS)

Open-File Report↗

USGS1992

Availability and quality of water from the alluvial, glacial-drift, and Dakota aquifers and water use in southwest Iowa

A ground-water resources investigation was conducted in southwest Iowa to describe the availability, quality, and use of water from the alluvial, glacial-drift, and Dakota aquifers in a nine-county area. Historical water quality was examined for each aquifer, and water samples were collected for major ions, trace metals, radionuclides, and selected pesticides. Selected aspects of surface-water resources in the study area also were examined to more fully evaluate alluvial aquifers. The flood plain of the Missouri River valley was not included except for the accounting of the water use in the area. Four principal alluvial aquifers consisting of sand and gravel deposits in the valleys of the Nishnabotna, Tarkio, Nodaway, and One Hundred and Two Rivers are present. Yields to wells have been reported as large as 2,000 gallons per minute; however, most yields are less than 100 gallons per minute. Nitrate concentrations greater than the drinking-water regulation and agricultural herbicides have been detected in 6 of 27 samples from municipal water supplies. Four types of glacial-drift aquifers are present-loess, inter-till sand and gravel, basal sand and gravel, and buried-channel aquifers. The glacial-drift aquifers are most commonly used by rural water users or users that do not have access to alluvial aquifers. These aquifers are discontinuous and unpredictable in location. Hydraulic and water-quality data generally are unavailable for these aquifers. Wells completed in loess commonly yield less than 10 gallons per minute, although there are reports of yields as large as 20 gallons per minute. Yields of 10 to 120 gallons per minute appear to be possible for inter-till and basal sand and gravel aquifers. Yields of more than 150 gallons per minute are possible from some buried-channel aquifers. The Dakota aquifer is comprised of bedrock of Cretaceous age and is present as erosional remnants and outliers in several counties, mainly Cass and Montgomery. Yields of more than 150 gallons per minute to wells completed in the Dakota aquifer have been reported, although yields of 20 gallons per minute or less are more typical. The drinking-water regulation for nitrate has been exceeded in some samples from the Dakota aquifer. The quantity of water withdrawn for municipal, rural-domestic, livestock, and other permitted water users was determined for each of the three principal aquifer types. The total water use within the study area was about 91.8 million gallons per day; 35.3 percent was from alluvial ground-water sources. Alluvial aquifers supplied most of the water from ground-water sources. The largest use of water is for permitted irrigation purposes, mostly from the Missouri River alluvial aquifer.

Iowa↗

USGS2010

Method for Estimating Annual Atrazine Use for Counties in the Conterminous United States, 1992-2007

A method was developed to estimate annual atrazine use during 1992 to 2007 on sixteen crops and four agricultural land uses. For each year, atrazine use was estimated for all counties in the conterminous United States (except California) by combining (1) proprietary data from the Doane Marketing Research-Kynetec (DMRK) AgroTrak database on the mass of atrazine applied to agricultural crops, (2) county harvested crop acreage, by county, from the 1992, 1997, 2002, and 2007 Censuses of Agriculture, and (3) annual harvested crop acreage from National Agriculture Statistics Service (NASS) for non-Census years. DMRK estimates of pesticide use on individual crops were derived from surveys of major field crops and selected specialty crops in multicounty areas referred to as Crop Reporting Districts (CRD). The CRD-level atrazine-use estimates were disaggregated to obtain county-level application rates by dividing the mass (pounds) of pesticides applied to a crop by the acreage of that crop in the CRD to yield a rate per harvested acre. When atrazine-use estimates were not available for a CRD, crop, or year, an estimated rate was developed following a hierarchy of decision rules that checked first for the availability of a crop application rate from surveyed atrazine application rate(s) for adjacent CRDs for a specific year, and second, the rates from surveyed CRDs within for U.S. Department of Agriculture Farm Production Regions for a specific year or multiple years. The estimation method applied linear interpolation to estimate crop acreage for years when harvested acres for a crop and county were not reported in either the Census of Agriculture or the NASS database, but were reported by these data sources for other years for that crop and county. Data for atrazine use for the counties in California was obtained from farmers' reports of pesticide use collected and published by the California Department of Pesticide Regulation-Pesticide Use Reporting (DPR-PUR) because these data are more complete than DMRK survey data. National and state annual atrazine-use totals derived by this method were compared with other published pesticide-use estimates and were highly correlated. The method developed is designed to be applicable to other pesticides for which there are similar data; however, for some pesticides that are applied to specialty crops, fewer surveys are usually available to estimate application rates and there are a greater number of years with unreported crop acreage, potentially resulting in greater uncertainty in use

Scientific Investigations Report↗

USGS1976

Design of a ground-water level observation network

In January 1971, a cooperative study was initiated by the Hydrological Service of Israel and the U.S. Geological Survey to develop concepts and systems analytic techniques for the design of ground water data collection systems with the objective of providing hydrologic information for planning and managing water resource systems. This report summarizes the results of the study which was completed in January 1972. While some of the results pertain specifically to the data program of the Hydrological Service of Israel, the analytic techniques of design developed in the course of this study are quite general and by no means restricted to problems in Israel. Because of the statistical orientation of the study and the fact that the analytic design techniques are not dependent upon the dynamic characteristics of ground water, the techniques are, with appropriate modification, applicable to the design of other types of hydrologic data collection systems.

Open-File Report↗

USGS2005

Water resources data, Kansas, water year 2004

Water-resources data for the 2004 water year for Kansas consist of records of stage, discharge, and water quality of streams; elevation and contents of lakes and reservoirs; and water levels of ground-water wells. This report contains records for water discharge at 155 complete-record gaging stations; elevation and contents at 17 lakes and reservoirs; water-quality records at 2 precipitation stations, water-level data at 14 observation wells; and records of specific conductance, pH, water temperature, dissolved oxygen, and turbidity at 16 gaging stations and 2 lakes with water-quality monitors. Also included are discharge data for 29 high-flow partial-record stations. These data represent that part of the National Water Information System collected by the U.S. Geological Survey in cooperation with local, State, and Federal agencies in Kansas.

Water Data Report↗

USGS1993

Approximate altitude of water levels in wells completed in the Chicot and Evangeline aquifers in Fort Bend County and adjacent areas, Texas, January-February 1991

This report was prepared in cooperation with the Fort Bend Subsidence District, and presents maps of the approximate altitude of water levels in wells completed in the Chicot and Evangeline aquifers (figs. -2) during January-February 1991 in Fort Bend County and adjacent areas, Texas. These approximate altitudes of water levels give an approximate depth to potable ground water within Fort Bend County and can be used to estimate depth for installing well pumps.

Texas↗

USGS1989

Chemical composition of ferromanganese crusts in the world ocean: A review and comprehensive database

A comprehensive database of chemical and mineralogical properties for ferromanganese crusts collected throughout the Atlantic, Pacific, and Indian Oceans, and has been assembled from published and unpublished sources which provide collection and analytical information for these samples. These crusts, their chemical compositions and natural distribution, have been a topic of interest to scientific research, as well as to industrial and military applications. Unlike abyssal ferromanganese nodules, which form in areas of low disturbance and high sediment accumulation, crusts have been found to contain three to five times more cobalt than these nodules, and can be found on harder, steeper substrates which can be too steep for permanent sediment accumulation. They have also been documented on seamounts and plateaus within the U.S. exclusive economic zone in both Pacific and Atlantic Oceans, and these are therefore of strategic importance to the United States Government, as well as to civilian mining and metallurgical industries. The data tables provided in this report have been digitized and previously uploaded to the National Oceanic and Atmospheric Administration National Geophysical Data Center in 1991 for online distribution, and were provided in plain text format. The 2014 update to the original U.S. Geological Survey open-file report published in 1989 provides these data tables in a slightly reformatted version to make them easier to ingest into geographic information system software, converted to shapefiles, and have completed metadata written and associated with them.

Open-File Report↗

USGS2003

Water Resources Data, Kansas, Water Year 2002

Water-resources data for the 2002 water year for Kansas consist of records of stage, discharge, and water quality of streams; elevation and contents of lakes and reservoirs; and water levels of ground-water wells. This report contains records for water discharge at 149 complete-record gaging stations; elevation and contents at 20 lakes and reservoirs; waterquality records at 2 precipitation stations, water-level data at 18 observation wells; and records of specific conductance, pH, water temperature, dissolved oxygen, and turbidity at 11 gaging stations. Also included are discharge data for 26 high-flow partial-record stations, miscellaneous onsite water-quality data collected at 142 stations, and suspended-sediment concentration for 12 stations. These data represent that part of the National Water Information System collected by the U.S. Geological Survey in cooperation with local, State, and Federal agencies in Kansas.

Water Data Report↗

USGS2002

Water Resources Data, Kansas, Water Year 2001

Water-resources data for the 2001 water year for Kansas consist of records of stage, discharge, and water quality of streams; elevation and contents of lakes and reservoirs; and water levels of ground-water wells. This report contains records for water discharge at 145 complete-record gaging stations; elevation and contents at 20 lakes and reservoirs; waterquality records at 2 precipitation stations, water-level data at 19 observation wells; and records of specific conductance, pH, water temperature, dissolved oxygen, and turbidity at 11 gaging stations. Also included are discharge data for 26 high-flow partial-record stations, miscellaneous onsite water-quality data collected at 140 stations, and suspended-sediment concentration for 12 stations. These data represent that part of the National Water Information System collected by the U.S. Geological Survey in cooperation with local, State, and Federal agencies in Kansas.

Water Data Report↗