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USGS2016

Population viability analysis for endangered Roanoke logperch

A common strategy for recovering endangered species is ensuring that populations exceed the minimum viable population size (MVP), a demographic benchmark that theoretically ensures low long-term extinction risk. One method of establishing MVP is population viability analysis, a modeling technique that simulates population trajectories and forecasts extinction risk based on a series of biological, environmental, and management assumptions. Such models also help identify key uncertainties that have a large influence on extinction risk. We used stochastic count-based simulation models to explore extinction risk, MVP, and the possible benefits of alternative management strategies in populations of Roanoke logperch Percina rex , an endangered stream fish. Estimates of extinction risk were sensitive to the assumed population growth rate and model type, carrying capacity, and catastrophe regime (frequency and severity of anthropogenic fish kills), whereas demographic augmentation did little to reduce extinction risk. Under density-dependent growth, the estimated MVP for Roanoke logperch ranged from 200 to 4200 individuals, depending on the assumed severity of catastrophes. Thus, depending on the MVP threshold, anywhere from two to all five of the logperch populations we assessed were projected to be viable. Despite this uncertainty, these results help identify populations with the greatest relative extinction risk, as well as management strategies that might reduce this risk the most, such as increasing carrying capacity and reducing fish kills. Better estimates of population growth parameters and catastrophe regimes would facilitate the refinement of MVP and extinction-risk estimates, and they should be a high priority for future research on Roanoke logperch and other imperiled stream-fish species.

Journal of Fish and Wildlife Management↗

USGS2001

Serological responses and immunity to superinfection with avian malaria in experimentally-infected Hawaii Amakihi

Six of seven Hawaii Amakihi ( Hemignathus virens ) with chronic malarial infections had no increases in peripheral parasitemia, declines in food consumption, or loss of body weight when rechallenged with the homologous isolate of Plasmodium relictum 61 to 62 days after initial infection. Five uninfected control amakihi exposed at the same time to infective mosquito bites developed acute infections with high parasitemias. Reductions in food consumption and loss of body weight occurred in all control birds and three of these individuals eventually died. When surviving birds were rechallenged >2 yr later with either the same parasite isolate or an isolate of P. relictum collected on the island of Kauai, all individuals were immune to superinfection. Chronically infected birds developed antibodies to a common suite of malarial antigens ranging in size from 22 to 170 kDa that were detectable as early as 8 days post infection on immunoblots of SDS-polyacrylamide gels. Antibodies to this suite of malarial antigens persisted as long as 1,248 days after initial infection and were consistently detectable at times when parasites were not easily found by microscopy on Giemsa-stained blood smears. The immunoblotting method that is described here appears to be an effective technique for identifying birds with chronic, low-intensity malarial infections when circulating parasites are not easily detectable by microscopy. Hawaiian honeycreepers that are capable of recovering from acute infections develop concomitant immunity to superinfection, making them functionally immune in areas where malaria transmission has become endemic.

Journal of Wildlife Diseases↗

USGS2018

Standard Operating Procedure 1.2.14 Wadeable Stream Reach Selection and Location of Sampling Points—Version 1.0

The following standard operating procedure (SOP) outlines the procedure for selecting stream reaches to be used in Monitoring Wadeable Stream Habitat Conditions in Southeast Coast Network Parks: Protocol Narrative (McDonald et al. 2018a). The techniques and procedures outlined in this SOP are based on methods used by the U.S. Environmental Protection Agency (EPA 2013), the U.S. Department of Agriculture (USDA) (Harrelson et al. 1994), and the U.S. Geological Survey (USGS; (Fitzpatrick et al. 1998). Procedures have been customized for use in streams draining the Piedmont and Coastal Plain parks in the Southeast Coast Network.

Southeast Coast Network Standard Operating Procedu↗

USGS1998

Nonlethal evaluation of the physiological health of unionid mussels: Method for biopsy and glycogen analysis

In long-lived unionid mussels, many short-term measures of growth are of limited value. Changes in physiological condition may be an early indication of stress, because the increased energy demand associated with stress often results in a depletion of glycogen reserves, the principal storage form of carbohydrates in unionid mussels. Our goal was to nonlethally extract tissue from freshwater mussels and then to develop a rapid and dependable method for the analysis of glycogen in the tissue extracts. A biopsy technique was developed to remove between 5 and 10 mg of foot tissue in Amblema plicata plicata. The survival rate did not differ between biopsied and non-biopsied mussels during a 581-d observation period, demonstrating that the biopsy technique will allow nonlethal evaluation of the physiological condition of individual mussels through measurement of changes in contaminant, genetic, and biochemical indicators in tissue. We also modified the standard alkaline digestion and phenol-sulfuric acid analysis of glycogen for use on the small samples of biopsied tissue and to reduce analysis time and cost. We present quality control data, including method detection limits and estimates of precision and bias. The modified analytical method is rapid and accurate and has a method detection limit of 0.014 mg glycogen. Glycogen content in the biopsied samples was well above the method detection limit; it ranged from 0.09 to 0.36 mg, indicating that the method should be applicable to native mussels.

Journal of the North American Benthological Societ↗

USGS2007

Development and evaluation of a gas chromatographic method for the determination of triazine herbicides in natural water samples

A multi-residue method is described for the determination o triazine herbicides in natural water samples. The technique uses solvent extraction followed by gas chromatographic separation and detection employing nitrogen-selective devices. Seven compounds can be determined simultaneously at a nominal detection limit of 0.1 μg/L in a 1-litre sample. Three different natural water samples were used for error analysis via evaluation of recovery efficiencies and estimation of overall method precision. As an alternative to liquid-liquid partition (solvent extraction) for removal of compounds of interest from water, solid-phase extraction (SPE) techniques employing chromatographic grade silicas with chemically modified surfaces have been examined. SPE is found to provide rapid and efficient concentration with quantitative recovery of some triazine herbicides from natural water samples. Concentration factors of 500 to 1000 times are obtained readily by the SPE technique.

International Journal of Environmental Analytical ↗

USGS2019

Characterization of Big Chino subbasin hydrogeology near Paulden, Arizona, using controlled source audio-frequency magnetotelluric surveys

The Big Chino subbasin is located in central-northwest Arizona in the transition zone between the Colorado Plateau and the Basin and Range Province. The controlled source audio-frequency magnetotelluric (CSAMT) geophysical method, a low-impact, non-intrusive, electrical resistance sounding technique, was used to evaluate the subsurface hydrogeology of the southern third of the Big Chino subbasin. The Big Chino subbasin is a northwest-trending, late Tertiary graben bordered by the Big Chino Fault along its northeast flank where there is as much as 1,100 meters of displacement. The main water-bearing stratigraphic unit of the basin is Tertiary alluvial-fill sediment. The Devonian Martin Formation provides water to wells near Drake and the Mississippian Redwall Limestone provides water to wells east of the basin and in the Paulden area. The purpose of the CSAMT surveys was to improve the conceptual model of the aquifer by constraining the basin geometry and identifying stratigraphic units and their subsurface extents. CSAMT methods were used to map the subsurface along 100 kilometers (62 miles) of survey lines across the southern third of the subbasin. Of 21 survey lines, 14 were west of the town of Paulden and another 7 were east of Paulden. Data were cleaned and prepared for entry into Zonge SCS2D software and then inverted to provide a two-dimensional resistivity profile for each survey line. Final inversion models representing the best fit to measured data were compared to driller’s logs or borehole data where present. Data from the CSAMT lines west and north of Paulden are consistent with thicker alluvial basin deposits that range from 100 meters thick to a few hundred meters thick. Data from the CSAMT lines east of Paulden are consistent with thinner alluvial and basalt deposits overlying Paleozoic Martin Formation and Redwall Limestone, Tapeats Sandstone, and Precambrian granite and schist.

Arizona↗

USGS2014

Fluvial sediment fingerprinting: literature review and annotated bibliography

The U.S. Geological Survey has evaluated and adopted various field methods for collecting real-time sediment and nutrient data. These methods have proven to be valuable representations of sediment and nutrient concentrations and loads but are not able to accurately identify specific source areas. Recently, more advanced data collection and analysis techniques have been evaluated that show promise in identifying specific source areas. Application of field methods could include studies of sources of fluvial sediment, otherwise referred to as sediment “fingerprinting.” The identification of sediment is important, in part, because knowing the primary sediment source areas in watersheds ensures that best management practices are incorporated in areas that maximize reductions in sediment loadings. This report provides a literature review and annotated bibliography of existing methodologies applied in the field of fluvial sediment fingerprinting. This literature review provides a bibliography of publications where sediment fingerprinting methods have been used; however, this report is not assumed to provide an exhaustive listing. Selected publications were categorized by methodology with some additional summary information. The information contained in the summary may help researchers select methods better suited to their particular study or study area, and identify methods in need of more testing and application.

Open-File Report↗

USGS2016

Detecting sea-level hazards: Simple regression-based methods for calculating the acceleration of sea level

This report documents the development of statistical tools used to quantify the hazard presented by the response of sea-level elevation to natural or anthropogenic changes in climate and ocean circulation. A hazard is a physical process (or processes) that, when combined with vulnerability (or susceptibility to the hazard), results in risk. This study presents the development and comparison of new and existing sea-level analysis methods, exploration of the strengths and weaknesses of the methods using synthetic time series, and when appropriate, synthesis of the application of the method to observed sea-level time series. These reports are intended to enhance material presented in peer-reviewed journal articles where it is not always possible to provide the level of detail that might be necessary to fully support or recreate published results. The purpose of this report is to document and compare three simple methodologies that have previously been used to provide estimates with associated errors of the acceleration of sea-level elevation. These techniques have been used by coastal scientists and planners in assessing coastal risk over a wide range of spatial and temporal scales. Because relative sea-level (SL) elevation time series contain energetic fluctuations at many time scales, extracting what can be relatively small rate and acceleration signals (along with estimates of the error) from much larger “noise” has proven to be both difficult and controversial. Acceleration is a preferred measure of SL response to recent changes in the Earth’s climate because over time scales of 100 years or less slow vertical land motions (such as glacial isostatic adjustment) contribute only to the linear signal and not to acceleration, thus reducing the complexity of the analysis. Hence acceleration is useful if the goal of a study is to characterize and quantify the hazard associated with the changing relative elevation of water with respect to land on decadal time scales. Although in some cases it may be necessary to determine the cause of relative sea level rise, as a first step, it is important to accurately estimate the magnitude of the threat. Most researchers agree that global sea level (GSL) rose persistently through much of the 20th century at about 1.5–2.0 millimeters per year (mm/yr). There is far less agreement about whether the rate of sea-level rise (SLR) is increasing (that is, an acceleration in SL). Recent studies, and most of their predecessors, use tide gage data to quantify SL acceleration, A SL (t). In the current study, three techniques were used to calculate acceleration from tide gage data, and of those examined, it was determined that the two techniques based on sliding a regression window through the time series are more robust compared to the technique that fits a single quadratic form to the entire time series, particularly if there is temporal variation in the magnitude of the acceleration. The single-fit quadratic regression method has been the most commonly used technique in determining acceleration in tide gage data. The inability of the single-fit method to account for time-varying acceleration may explain some of the inconsistent findings between investigators. Properly quantifying A SL (t) from field measurements is of particular importance in evaluating numerical models of past, present, and future SLR resulting from anticipated climate change.

Open-File Report↗

USGS1978

Range charts and no-space graphs

No-space graphs present one solution to the familiar problem: given data on the occurrence of fossil taxa in separate, well-sampled sections, determine a range chart; that is, a reasonable working hypothesis of the total range in the area in question of each taxon studied. The solution presented here treats only the relative sequence of biostratigraphic events (first and last occurrences of taxa) and does not attempt to determine an amount of spacing between events. Relative to a hypothesized sequence, observed events in any section may be in-place or out-of-place. Out-of-place events may indicate (1) the event in question reflects a taxon that did not fill its entire range (unfilled-range event), or (2) the event in question indicates a need for the revision of the hypothesized sequence. A graph of relative position only (no-space graph) can be used to facilitate the recognition of in-place and out-of-place events by presenting a visual comparison of the observations from each section with the hypothesized sequence. The geometry of the graph as constructed here is such that in-place events will lie along a line series and out-of-place events will lie above or below it. First-occurrence events below the line series and last-occurrence events above the line series indicate unfilled ranges. First-occurrence events above the line series and last-occurrence events below the line series indicate a need for the revision of the hypothesis. Knowing this, the stratigrapher considers alternative positionings of the line series as alternative range hypotheses and seeks the line series that best fits his geologic and paleontologic judgment. No-space graphs are used to revise an initial hypothesis until a final hypothesis is reached. In this final hypothesis every event is found in-place in at least one section, and all events in all sections may be interpreted to represent in-place events or unfilled-range events. No event may indicate a need for further range revision. The application of the no-space graph method requires the assumption of lack of reworking and the assumption that taxa that are present in a single horizon indicate taxa whose ranges overlap. When applied to hypothetical and actual data, the no-space graph technique produces geologically reasonable range charts that compare favorably with results produced by other methods.

Computers & Geosciences↗

USGS1975

Uranium determination in natural water by the fissiontrack technique

The fission track technique, utilizing the neutron-induced fission of uranium-235, provides a versatile analytical method for the routine analysis of uranium in liquid samples of natural water. A detector is immersed in the sample and both are irradiated. The fission track density observed in the detector is directly proportional to the uranium concentration. The specific advantages of this technique are: (1) only a small quantity of sample, typically 0.1–1 ml, is needed; (2) no sample concentration is necessary; (3) it is capable of providing analyses with a lower reporting limit of 1 μg per liter; and (4) the actual time spent on an analysis can be only a few minutes. This paper discusses and describes the method.

Journal of Geochemical Exploration↗

USGS1987

BOREHOLE NEUTRON ACTIVATION: THE RARE EARTHS.

Neutron-induced borehole gamma-ray spectroscopy has been widely used as a geophysical exploration technique by the petroleum industry, but its use for mineral exploration is not as common. Nuclear methods can be applied to mineral exploration, for determining stratigraphy and bed correlations, for mapping ore deposits, and for studying mineral concentration gradients. High-resolution detectors are essential for mineral exploration, and by using them an analysis of the major element concentrations in a borehole can usually be made. A number of economically important elements can be detected at typical ore-grade concentrations using this method. Because of the application of the rare-earth elements to high-temperature superconductors, these elements are examined in detail as an example of how nuclear techniques can be applied to mineral exploration.

IEEE Transactions on Nuclear Science↗

USGS1990

Base-flow-frequency characteristics of selected Pennsylvania streams

Streamflow hydrographs of 309 streamflow stations in Pennsylvania were analyzed by using three computer-assisted empirical methods--local-minimum , fixed-interval, and sliding-interval--to separate the ground-water and surface-runoff components. The 2-, 5-, 10-, and 25-year base-flow-recurrence intervals were determined for each station. The 50- and 100-year recurrence intervals were determined for stations with minimums of 25 and 50 years of record, respectively. All active and inactive continuous-recording Pennsylvania streamflow stations with 10 or more years of record through water year 1986 were analyzed. Stations on the Delaware River in New York and New Jersey also were included. Hydrograph analysis by computer provides consistency of results by removing the subjectivity inherent in manual analyses and considerably reduces the time required to make the analyses. Estimates of the 25-year base-flow-recurrence interval made by using the local-minimum technique, which gives the most conservative estimate, range from 0.069 to 0.888 million gallons per day per square mile. Base flows estimated by using the three computer-assisted techniques compared well with published base flows estimated by using manual methods for three studies in southeastern Pennsylvania. Examples of the effects of geology, climate, regulation, and urbanization on base flow are provided.

Pennsylvania↗

USGS2008

Comparison of two cell lysis procedures for recovery of microcystins in water samples from silver lake in Dover, Delaware, with microcystin producing cyanobacterial accumulations

A collaboration was developed between Abraxis, LLC, the State of Delaware Department of Natural Resources and Environmental Control Division of Water Resources Environmental Laboratory, the University of Delaware, and the United States Geological Survey to investigate the efficacy of the QuikLyse procedure developed by Abraxis, LLC as an alternative cell-lysis technique suitable for use with an existing liquid chromatography/tandem mass spectrometry research method developed at the United States Geological Survey Organic Geochemistry Research Laboratory to analyze cyanotoxins. A comparison of three sequential freeze/thaw cycles versus QuikLyse, a proprietary chemical lysis procedure was conducted on four water samples collected from Silver Lake in Dover, Delaware. Results from the Abraxis Microcystins-DM enzyme-linked immunosorbent assay and liquid chromatography/tandem mass spectrometry were tabulated as a function of the cell lysis technique. Stastical comparison of percent relative standard deviations showed no significant difference (alpha = 0.05) between both cell-lysis techniques when measured by enzyme-linked immunosorbent assay or liquid chromatography/tandem mass spectrometry for three of the four samples.

Delaware↗

USGS2012

Aerial surveys adjusted by ground surveys to estimate area occupied by black-tailed prairie dog colonies

Aerial surveys using line-intercept methods are one approach to estimate the extent of prairie dog colonies in a large geographic area. Although black-tailed prairie dogs ( Cynomys ludovicianus ) construct conspicuous mounds at burrow openings, aerial observers have difficulty discriminating between areas with burrows occupied by prairie dogs (colonies) versus areas of uninhabited burrows (uninhabited colony sites). Consequently, aerial line-intercept surveys may overestimate prairie dog colony extent unless adjusted by an on-the-ground inspection of a sample of intercepts. We compared aerial line-intercept surveys conducted over 2 National Grasslands in Colorado, USA, with independent ground-mapping of known black-tailed prairie dog colonies. Aerial line-intercepts adjusted by ground surveys using a single activity category adjustment overestimated colonies by ≥94% on the Comanche National Grassland and ≥58% on the Pawnee National Grassland. We present a ground-survey technique that involves 1) visiting on the ground a subset of aerial intercepts classified as occupied colonies plus a subset of intercepts classified as uninhabited colony sites, and 2) based on these ground observations, recording the proportion of each aerial intercept that intersects a colony and the proportion that intersects an uninhabited colony site. Where line-intercept techniques are applied to aerial surveys or remotely sensed imagery, this method can provide more accurate estimates of black-tailed prairie dog abundance and trends

Colorado↗

USGS2008

Field Techniques for Estimating Water Fluxes Between Surface Water and Ground Water

This report focuses on measuring the flow of water across the interface between surface water and ground water, rather than the hydrogeological or geochemical processes that occur at or near this interface. The methods, however, that use hydrogeological and geochemical evidence to quantify water fluxes are described herein. This material is presented as a guide for those who have to examine the interaction of surface water and ground water. The intent here is that both the overview of the many available methods and the in-depth presentation of specific methods will enable the reader to choose those study approaches that will best meet the requirements of the environments and processes they are investigating, as well as to recognize the merits of using more than one approach. This report is designed to make the reader aware of the breadth of approaches available for the study of the exchange between surface and ground water. To accomplish this, the report is divided into four chapters. Chapter 1 describes many well-documented approaches for defining the flow between surface and ground waters. Subsequent chapters provide an in-depth presentation of particular methods. Chapter 2 focuses on three of the most commonly used methods to either calculate or directly measure flow of water between surface-water bodies and the ground-water domain: (1) measurement of water levels in well networks in combination with measurement of water level in nearby surface water to determine water-level gradients and flow; (2) use of portable piezometers (wells) or hydraulic potentiomanometers to measure hydraulic gradients; and (3) use of seepage meters to measure flow directly. Chapter 3 focuses on describing the techniques involved in conducting water-tracer tests using fluorescent dyes, a method commonly used in the hydrogeologic investigation and characterization of karst aquifers, and in the study of water fluxes in karst terranes. Chapter 4 focuses on heat as a tracer in hydrological investigations of the near-surface environment.

Techniques and Methods↗

USGS2020

Expanding the feasibility of fish and wildlife assessments with close-kin mark–recapture

Close-kin mark–recapture (CKMR) is a powerful new method for the assessment of fish and wildlife population dynamics. Unlike traditional mark–recapture techniques, the use of kinship as an identifying mark is robust to many forms of capture heterogeneity including variation in gear efficiency and tagging-based effects such as loss and differential mortality. In addition, close-kin methods can be applied to a wider range of sampling designs than traditional methods (e.g., single-occasion surveys and lethal capture), can provide retrospective historical abundance estimates, and can produce survival estimates from as few as two sampling occasions. We evaluated the ability of CKMR to provide estimates of abundance and adult survival and then compared results to those from traditional mark–recapture. This analysis incorporated data from a three-year study of lake resident brook trout ( Salvelinus fontinalis ) where individuals were both physically (PIT) tagged and genotyped for 44 de novo developed microsatellites with high throughput sequencing. Traditional mark–recapture estimates were derived using Pollock’s Robust Design, relying upon three primary open sampling occasions and four secondary closed occasions. We found that close-kin methods produced contemporary estimates of adult abundance and survival that were similar to those produced by traditional mark–recapture in both magnitude and precision. Furthermore, CKMR provided abundance estimates for multiple years prior to sampling and, when restricted to data from a single year, still produced reliable abundance estimates for at least one and as many as three years. Retrospective abundance estimates corresponded with those from a separate historical two-sample mark–recapture dataset. This study provides support for the use of CKMR as a robust and sampling-efficient alternative to traditional mark–recapture methods of assessing population parameters.

New York↗

USGS1993

An objective replacement method for censored geochemical data

Geochemical data are commonly censored, that is, concentrations for some samples are reported as "less than" or "greater than" some value. Censored data hampers statistical analysis because certain computational techniques used in statistical analysis require a complete set of uncensored data. We show that the simple substitution method for creating an uncensored dataset, e.g., replacement by 3/4 times the detection limit, has serious flaws, and we present an objective method to determine the replacement value. Our basic premise is that the replacement value should equal the mean of the actual values represented by the qualified data. We adapt the maximum likelihood approach (Cohen, 1961) to estimate this mean. This method reproduces the mean and skewness as well or better than a simple substitution method using 3/4 of the lower detection limit or 3/4 of the upper detection limit. For a small proportion of "less than" substitutions, a simple-substitution replacement factor of 0.55 is preferable to 3/4; for a small proportion of "greater than" substitutions, a simple-substitution replacement factor of 1.7 is preferable to 4/3, provided the resulting replacement value does not exceed 100%. For more than 10% replacement, a mean empirical factor may be used. However, empirically determined simple-substitution replacement factors usually vary among different data sets and are less reliable with more replacements. Therefore, a maximum likelihood method is superior in general. Theoretical and empirical analyses show that true replacement factors for "less thans" decrease in magnitude with more replacements and larger standard deviation; those for "greater thans" increase in magnitude with more replacements and larger standard deviation. In contrast to any simple substitution method, the maximum likelihood method reproduces these variations. Using the maximum likelihood method for replacing "less thans" in our sample data set, correlation coefficients were reasonably accurately estimated in 90% of the cases for as much as 40% replacement and in 60% of the cases for 80% replacement. These results suggest that censored data can be utilized more than is commonly realized. ?? 1993 International Association for Mathematical Geology.

Mathematical Geology↗

USGS1958

Technique for the extraction and partial chemical analysis of fluid-filled inclusions from minerals

A method has been developed for the extraction and limited chemical analysis of the materials in solution in the fluid from the very minute fluid-filled inclusions such as commonly occur in whitish or milky quartz. The method may also be applied, with some reservations, to a variety of other minerals. As the amounts of substances in the fluid are small compared with possible contaminants, great care is needed in sample purification and cleaning; an electrolytic method has been found to be the only satisfactory final cleaning step. Following this, the inclusions are opened by ball milling of the cleaned sample, with deionized water, in an alumina ball mill using alumina grinding media. The ions present in the resultant slurry are separated from the ground quartz by electrodialysis and analyzed. Other methods, such as the decrepitation of a sample in an absorption train, are used to estimate the amount of H2O and CO2 in the inclusions. The most significant part of the analytical work has been to determine the ratios between the alkali metals. The materials in solution in the fluid-filled inclusions from 11 samples of quartz have been analyzed by the ball milling-electrodialysis method. Although there are large differences between samples, the average weights of the alkali metal ions found, for all samples, in milligrams per kilogram of quartz, are: Li+-0.92, Na+-99, K+-133, Rb+-0.45, Cs+-0.38 (atomic ratios, in the same sequence: 0.03/1.00/0.79/0.001/0.0007). In addition, 27 to 193 milligrams of CI", and 5 to 140 milligrams of SOr were found, per kilogram of quartz. H2O and COa were determined on only one sample. Six of the samples were from gold-quartz veins in the Grass Valley district, California. In these six the Na+/K+ ratios were all very similar, but the amounts of Li+, Rb+ and Cs+ found varied greatly. Although there are serious limitations to this and to all other techniques developed, it is felt that the results presented are sufficiently encouraging to warrant further study and possible application to specific geologic problems, such as the identification of epochs of quartz deposition

Economic Geology↗