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USGS2012

Multivariate statistical approach to estimate mixing proportions for unknown end members

A multivariate statistical method is presented, which includes principal components analysis (PCA) and an end-member mixing model to estimate unknown end-member hydrochemical compositions and the relative mixing proportions of those end members in mixed waters. PCA, together with the Hotelling T 2 statistic and a conceptual model of groundwater flow and mixing, was used in selecting samples that best approximate end members, which then were used as initial values in optimization of the end-member mixing model. This method was tested on controlled datasets (i.e., true values of estimates were known a priori) and found effective in estimating these end members and mixing proportions. The controlled datasets included synthetically generated hydrochemical data, synthetically generated mixing proportions, and laboratory analyses of sample mixtures, which were used in an evaluation of the effectiveness of this method for potential use in actual hydrological settings. For three different scenarios tested, correlation coefficients ( R 2 ) for linear regression between the estimated and known values ranged from 0.968 to 0.993 for mixing proportions and from 0.839 to 0.998 for end-member compositions. The method also was applied to field data from a study of end-member mixing in groundwater as a field example and partial method validation.

Journal of Hydrology↗

USGS2016

Testing the suitability of geologic frameworks for extrapolating hydraulic properties across regional scales

The suitability of geologic frameworks for extrapolating hydraulic conductivity ( K ) to length scales commensurate with hydraulic data is difficult to assess. A novel method is presented for evaluating assumed relations between K and geologic interpretations for regional-scale groundwater modeling. The approach relies on simultaneous interpretation of multiple aquifer tests using alternative geologic frameworks of variable complexity, where each framework is incorporated as prior information that assumes homogeneous K within each model unit. This approach is tested at Pahute Mesa within the Nevada National Security Site (USA), where observed drawdowns from eight aquifer tests in complex, highly faulted volcanic rocks provide the necessary hydraulic constraints. The investigated volume encompasses 40 mi 3 (167 km 3 ) where drawdowns traversed major fault structures and were detected more than 2 mi (3.2 km) from pumping wells. Complexity of the five frameworks assessed ranges from an undifferentiated mass of rock with a single unit to 14 distinct geologic units. Results show that only four geologic units can be justified as hydraulically unique for this location. The approach qualitatively evaluates the consistency of hydraulic property estimates within extents of investigation and effects of geologic frameworks on extrapolation. Distributions of transmissivity are similar within the investigated extents irrespective of the geologic framework. In contrast, the extrapolation of hydraulic properties beyond the volume investigated with interfering aquifer tests is strongly affected by the complexity of a given framework. Testing at Pahute Mesa illustrates how this method can be employed to determine the appropriate level of geologic complexity for large-scale groundwater modeling.

Nevada↗

USGS1993

A pressure-packer system for conducting rising head tests in water table wells

The pressure system developed for fully-saturated well screens has been modified for conducting rising head tests in water table wells installed in highly permeable aquifers. The pressure system consists of a compressed air source and 1 inch diameter PVC piping with a packer attached at the end. The pressure system was evaluated in a series of rising head tests conducted in a well at a Superfund site in New England. The well was tested with slugs and with the pressure system. Within each technique, estimates of hydraulic conductivity showed no difference. Comparison of hydraulic conductivity estimates between techniques (slug test vs. pressure test) showed differences due to stratigraphy. The interval tested using slug tests crossed two stratigraphic units; the pressure system tested only one of these units. We conclude that the pressure system may be used to characterize the vertical hydraulic conductivity distribution in a series of successive tests by changing the packer position and the screened interval tested.

Journal of Hydrology↗

USGS2018

U.S. Geological Survey science for the Wyoming Landscape Conservation Initiative—2016 annual report

This is the ninth annual report highlighting U.S. Geological Survey (USGS) science and decision-support activities conducted for the Wyoming Landscape Conservation Initiative (WLCI). The activities address specific management needs identified by WLCI partner agencies. In fiscal year (FY) 2016, there were 26 active USGS WLCI science-based projects. Of these 26 projects, one project was new for FY2016, and three were completed by the end of the fiscal year (though final products were still in preparation or review). USGS WLCI projects were grouped under five categories: (1) Baseline Synthesis, (2) Long-Term Monitoring, (3) Effectiveness Monitoring, (4) Mechanistic Studies of Wildlife, and (5) Data and Information Management. Each of these topic areas is designed to address WLCI management needs: identifying key drivers of change, identifying the condition and distribution of key wildlife species and habitats and of species’ habitat requirements, development of an integrated inventory and monitoring strategy, use of emerging technologies and development and testing of innovative methods for maximizing the efficiency and efficacy of monitoring efforts, evaluating the effectiveness of habitat treatment projects, evaluating the responses of wildlife to development, and developing a data clearinghouse and information management framework to support and provide access to results of most USGS WLCI projects. In FY2016, we assisted with updating the WLCI Conservation Action Plan and associated databases as part of the Comprehensive Assessment, and we also assisted with the Bureau of Land Management 2015 WLCI annual report. By the end of FY2016, we completed or had nearly completed assessments of WLCI energy and mineral resources and had submitted a manuscript on modeled effects of oil and gas development on wildlife to a peer-reviewed journal. We also initiated a study on the effects of wind energy on wildlife in the WLCI region. A USGS circular on WLCI long-term monitoring was in review at the end of the fiscal year, and seven projects monitoring water and vegetation (including changes in sagebrush cover and patterns of sagebrush mortality) continued through the year. USGS scientists continued many projects in FY2016 that evaluate the effectiveness of habitat conservation actions (including sagebrush, cheatgrass, and aspen habitat treatments) and provide tools in support of mechanistic studies of wildlife. In FY2016, USGS scientists, along with university and State partners, continued work on five focal wildlife species/communities (pygmy rabbits [ Brachylagus idahoensis ], greater sage grouse , mule deer, sagebrush songbirds, and native fish). In FY2016, the USGS Information Management Team presented information to WLCI scientists on how USGS tools and resources can be used to fulfill the requirements of new USGS policies regarding data release, data management, and data visualization.

Wyoming↗

USGS2010

Prevalence of antibodies to type A influenza virus in wild avian species using two serologic assays

Serologic testing to detect antibodies to avian influenza (AI) virus has been an underused tool for the study of these viruses in wild bird populations, which traditionally has relied on virus isolation and reverse transcriptase-polymerase chain reaction (RT-PCR). In a preliminary study, a recently developed commercial blocking enzyme-linked immunosorbent assay (bELISA) had sensitivity and specificity estimates of 82% and 100%, respectively, for detection of antibodies to AI virus in multiple wild bird species after experimental infection. To further evaluate the efficacy of this commercial bELISA and the agar gel immunodiffusion (AGID) test for AI virus antibody detection in wild birds, we tested 2,249 serum samples collected from 62 wild bird species, representing 10 taxonomic orders. Overall, the bELISA detected 25.4% positive samples, whereas the AGID test detected 14.8%. At the species level, the bELISA detected as many or more positive serum samples than the AGID in all 62 avian species. The majority of positive samples, detected by both assays, were from species that use aquatic habitats, with the highest prevalence from species in the orders Anseriformes and Charadriiformes. Conversely, antibodies to AI virus were rarely detected in the terrestrial species. The serologic data yielded by both assays are consistent with the known epidemiology of AI virus in wild birds and published reports of host range based on virus isolation and RT-PCR. The results of this research are also consistent with the aforementioned study, which evaluated the performance of the bELISA and AGID test on experimental samples. Collectively, the data from these two studies indicate that the bELISA is a more sensitive serologic assay than the AGID test for detecting prior exposure to AI virus in wild birds. Based on these results, the bELISA is a reliable species-independent assay with potentially valuable applications for wild bird AI surveillance.

Alaska, California, Delaware, Georgia, Michigan, M↗

USGS2020

Behavioural responses of female lake trout Salvelinus namaycush to male chemical stimuli and prostaglandin F2α

Male olfactory cues may guide aggregation on spawning reefs, mate evaluation, and synchronized gamete release in lake trout Salvelinus namaycush, but a lack of information on the source and identity of the cues precludes direct tests of their function. Using a two-channel flume assay, we found female lake trout increased time spent in the channel treated with male-conditioned water, urine, and bile but not synthesized prostaglandin F2α. We suggest future efforts to characterize male olfactory cues focus on urine and postulate that bile acids contribute to its behavioural activity.

Journal of Fish Biology↗

USGS2006

Detection and quantification of Renibacterium salmoninarum DNA in salmonid tissues by real-time quantitative polymerase chain reaction analysis

Renibacterium salmoninarum is an important salmonid pathogen that is difficult to culture. We developed and assessed a real-time, quantitative, polymerase chain reaction (qPCR) assay for the detection and enumeration of R. salmoninarum. The qPCR is based on TaqMan technology and amplifies a 69-base pair (bp) region of the gene encoding the major soluble antigen (MSA) of R. salmoninarum. The qPCR assay consistently detected as few as 5 R. salmoninarum cells per reaction in kidney tissue. The specificity of the qPCR was confirmed by testing the DNA extracts from a panel of microorganisms that were either common fish pathogens or reported to cause false-positive reactions in the enzyme-linked immunosorbent assay (ELISA). Kidney samples from 38 juvenile Chinook salmon (Oncorhynchus tshawytscha) in a naturally infected population were examined by real-time qPCR, a nested PCR, and ELISA, and prevalences of R. salmoninarum detected were 71, 66, and 71%, respectively. The qPCR should be a valuable tool for evaluating the R. salmoninarum infection status of salmonids.

Journal of Veterinary Diagnostic Investigation↗

USGS1972

Effect of certain anesthetic agents on mallard ducks

Four anesthetic agents used in human or veterinary medicine and 3 experimental anesthetic preparations were evaluated for effectiveness in inducing narcosis when administered orally to game-farm mallard ducks (Anas platyrhynchos).Tribromoethanol was the only compound to satisfy criteria of initial tests. Mean duration of the induction, immobilization, and recovery periods was 2.4 minutes, 8.7 minutes, and 1.3 hours, respectively, at the median effective dosage for immobilization (ED50; 100 mg./kg. of body weight). The median lethal dosage (LD50) was 400 mg./kg. of body weight.Tribromoethanol was also tested on mallards during the reproductive season. Effects on the hatchability of eggs or the survival of young were not detected.

Journal of the American Veterinary Medical Associa↗

USGS2003

Modeling flow and transport in unsaturated fractured rock: An evaluation of the continuum approach

Because the continuum approach is relatively simple and straightforward to implement, it has been commonly used in modeling flow and transport in unsaturated fractured rock. However, the usefulness of this approach can be questioned in terms of its adequacy for representing fingering flow and transport in unsaturated fractured rock. The continuum approach thus needs to be evaluated carefully by comparing simulation results with field observations directly related to unsaturated flow and transport processes. This paper reports on such an evaluation, based on a combination of model calibration and prediction, using data from an infiltration test carried out in a densely fractured rock within the unsaturated zone of Yucca Mountain, Nevada. Comparisons between experimental and modeling results show that the continuum approach may be able to capture important features of flow and transport processes observed from the test. The modeling results also show that matrix diffusion may have a significant effect on the overall transport behavior in unsaturated fractured rocks, which can be used to estimate effective fracture-matrix interface areas based on tracer transport data. While more theoretical, numerical, and experimental studies are needed to provide a conclusive evaluation, this study suggests that the continuum approach is useful for modeling flow and transport in unsaturated, densely fractured rock. ?? 2002 Elsevier Science B.V. All rights reserved.

Journal of Contaminant Hydrology↗

USGS2017

Long-term monitoring data provide evidence of declining species richness in a river valued for biodiversity conservation

Free-flowing river segments provide refuges for many imperiled aquatic biota that have been extirpated elsewhere in their native ranges. These biodiversity refuges are also foci of conservation concerns because species persisting within isolated habitat fragments may be particularly vulnerable to local environmental change. We have analyzed long-term (14- and 20-y) survey data to assess evidence of fish species declines in two southeastern U.S. rivers where managers and stakeholders have identified potentially detrimental impacts of current and future land uses. The Conasauga River (Georgia and Tennessee) and the Etowah River (Georgia) form free-flowing headwaters of the extensively dammed Coosa River system. These rivers are valued in part because they harbor multiple species of conservation concern, including three federally endangered and two federally threatened fishes. We used data sets comprising annual surveys for fish species at multiple, fixed sites located at river shoals to analyze occupancy dynamics and temporal changes in species richness. Our analyses incorporated repeated site-specific surveys in some years to estimate and account for incomplete species detection, and test for species-specific (rarity, mainstem-restriction) and year-specific (elevated frequencies of low- or high-flow days) covariates on occupancy dynamics. In the Conasauga River, analysis of 26 species at 13 sites showed evidence of temporal declines in colonization rates for nearly all taxa, accompanied by declining species richness. Four taxa (including one federally endangered species) had reduced occupancy across the Conasauga study sites, with three of these taxa apparently absent for at least the last 5 y of the study. In contrast, a similar fauna of 28 taxa at 10 sites in the Etowah River showed no trends in species persistence, colonization, or occupancy. None of the tested covariates showed strong effects on persistence or colonization rates in either river. Previous studies and observations identified contaminants, nutrient loading, or changes in benthic habitat as possible causes for fish species declines in the Conasauga River. Our analysis provides baseline information that could be used to assess effectiveness of future management actions in the Conasauga or Etowah rivers, and illustrates the use of dynamic occupancy models to evaluate evidence of faunal decline from time-series data.

Georgia↗

USGS2008

Detection of spring viraemia of carp virus (SVCV) by loop-mediated isothermal amplification (LAMP) in koi carp, Cyprinus carpio L

Spring viraemia of carp virus (SVCV) is a rhabdovirus associated with systemic illness and mortality in cyprinids. Several diagnostic tests are available for detection of SVCV. However, most of these tests are time consuming and are not well adapted for field-based diagnostics. In this study, a diagnostic tool for SVCV detection based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) has been developed. Based on the nucleotide sequence of the glycoprotein (G) gene of SVCV North Carolina (NC) isolate, four sets (each set containing two outer and two inner) of primers were designed. Temperature and time conditions were optimized to 65 ??C and 60 min, respectively, for LAMP and RT-LAMP using one primer set. In vitro specificity was evaluated using four different strains of fish rhabdoviruses and RT-LAMP was found to be specific to SVCV. Serial dilutions of SVCV NC isolate was used to evaluate the in vitro sensitivity of RT-LAMP. Sensitivity of the assays was similar to RT-PCR and detected SVCV even at the lowest dilution of 10 1 TCID50 mL-1. The ability of RT-LAMP to detect SVCV from infected carp was also tested and the assay detected SVCV from all infected fish. The isothermal temperature requirements, high specificity and sensitivity, and short incubation time of the RT-LAMP assay make it an excellent choice as a field diagnostic test for SVCV. ?? 2008 The Authors.

Journal of Fish Diseases↗

USGS2024

Effects of release strategy, source population, and age on reintroduced scaled quail reproduction

Translocation is one strategy to reestablish populations of scaled quail ( Callipepla squamata ). Initial reproductive success post-translocation is important for establishing short-lived species such as quail, but factors influencing reproductive success are poorly understood. We evaluated the effect of source population and variation in delayed release strategy (1−9 weeks) on nest initiation and nest survival of wild-caught, translocated scaled quail. We trapped and translocated scaled quail in 2016–2017 from source populations in the Edwards Plateau and Rolling Plains ecoregions of Texas, USA, to a large contiguous (>40,000 ha) release site in Knox County, Texas. We used a multi-state mark-recapture model with state uncertainty to test for effects of release treatment, source population, age, release location, and year on nest initiation and survival. Increased length of holding time decreased re-nesting effort. Yearlings were more likely to initiate nests than adults and the probability of re-nesting was lower during the year with drought conditions. There was no effect of source population on any of the parameters we evaluated. Future scaled quail reintroduction efforts may benefit from prioritizing translocation of yearlings and conducting translocations when drought conditions are not forecasted.

Texas↗

USGS1995

Detection and identification of aquatic birnaviruses by PCR assay

A reverse transcriptase polymerase chain reaction (RT-PCR) assay was developed for the detection and identification of aquatic birnaviruses. The four sets of primers (PrA, PrB, PrC, and PrD) that we used are specific for regions of cDNA coded by genome segment A of aquatic birnaviruses. PrA identifies a large fragment (1,180 bp) within the pVP2-coding region, and PrB identifies a 524-bp fragment within the sequence amplified by PrA. Primer set PrC frames a genome fragment (339 bp) within the NS-VP3-coding region, and PrD identifies a 174-bp sequence within the fragment identified by PrC. PrB and PrD amplified cDNAs from all nine recognized serotypes of aquatic birnavirus serogroup A as well as the N1 isolate that may represent a 10th serotype. These results indicate that these three primer sequences are highly conserved and can be used in PCR assays for group identification of these viruses. PrA routinely produced amplification products from eight serotypes but exhibited variable results with one serotype, and primer PrC identified 6 of the 11 virus isolates tested. The qualitative sensitivity of the RT-PCR assay was evaluated by comparison of the results with those of cell culture isolation assays. With the exception of one sample, the RT-PCR assay with primer PrD was as accurate as cell culture isolation for detecting virus in kidney and spleen tissues from naturally infected, asymptomatic carrier fish. These results indicate that the RT-PCR assay can be a rapid and reliable substitute for cell culture methods for the detection of aquatic birnaviruses.

Journal of Clinical Microbiology↗

USGS2017

Forecasting the probability of future groundwater levels declining below specified low thresholds in the conterminous U.S.

We present a logistic regression approach for forecasting the probability of future groundwater levels declining or maintaining below specific groundwater-level thresholds. We tested our approach on 102 groundwater wells in different climatic regions and aquifers of the United States that are part of the U.S. Geological Survey Groundwater Climate Response Network. We evaluated the importance of current groundwater levels, precipitation, streamflow, seasonal variability, Palmer Drought Severity Index, and atmosphere/ocean indices for developing the logistic regression equations. Several diagnostics of model fit were used to evaluate the regression equations, including testing of autocorrelation of residuals, goodness-of-fit metrics, and bootstrap validation testing. The probabilistic predictions were most successful at wells with high persistence (low month-to-month variability) in their groundwater records and at wells where the groundwater level remained below the defined low threshold for sustained periods (generally three months or longer). The model fit was weakest at wells with strong seasonal variability in levels and with shorter duration low-threshold events. We identified challenges in deriving probabilistic-forecasting models and possible approaches for addressing those challenges.

Journal of the American Water Resources Associatio↗

USGS2019

Understanding conservation decisions of agriculture producers

Most land in the United States (US) is privately owned and used for agriculture. To address the effect of agriculture on wildlife, conservation professionals and organizations need to understand the land use decisions made by farmers and ranchers. We developed a tool for categorizing farmers and ranchers by their conservation land use values (LUVs) to understand how those values affect their land use motivations and resultant decisions. We defined land as the whole natural environment including soil, water, plants, fish, and wildlife. We used principal axis factoring and reliability analysis to identify statements representing human-centered values and nature-centered values of farmers and ranchers. We tested the validity of the combined statements with a survey of South Dakota’s private landowners (N = 4,000, [Jan through May 2016]) resulting in the LUV scale. Crossing the average scores on the human-centered and nature-centered statements identified 4 LUV types: humans first (20%), nature first (29%), interconnected (29%), and disconnected (22%). Analysis of variance and chi-square tests showed that, compared to the humans first and disconnected LUV types, the nature first and interconnected LUV types reported significantly greater importance of the following: most categories of types of wildlife in their land use decisions; conservation-related motivations for participating in a United States Farm Bill Conservation Program; conservation-related motivations for land use decisions; and participation in conservation-related behaviors. Conservation professionals and organizations may use the LUV scale to better understand landowners’ land use decisions to evaluate and inform conservation policy, programs, messaging, and improve conservation outcomes.

Journal of Wildlife Management↗

USGS2011

Comparison of Bayesian clustering and edge detection methods for inferring boundaries in landscape genetics

Recently, techniques available for identifying clusters of individuals or boundaries between clusters using genetic data from natural populations have expanded rapidly. Consequently, there is a need to evaluate these different techniques. We used spatially-explicit simulation models to compare three spatial Bayesian clustering programs and two edge detection methods. Spatially-structured populations were simulated where a continuous population was subdivided by barriers. We evaluated the ability of each method to correctly identify boundary locations while varying: (i) time after divergence, (ii) strength of isolation by distance, (iii) level of genetic diversity, and (iv) amount of gene flow across barriers. To further evaluate the methods’ effectiveness to detect genetic clusters in natural populations, we used previously published data on North American pumas and a European shrub. Our results show that with simulated and empirical data, the Bayesian spatial clustering algorithms outperformed direct edge detection methods. All methods incorrectly detected boundaries in the presence of strong patterns of isolation by distance. Based on this finding, we support the application of Bayesian spatial clustering algorithms for boundary detection in empirical datasets, with necessary tests for the influence of isolation by distance

International Journal of Molecular Sciences↗

USGS2006

Simulation of solute transport across low-permeability barrier walls

Low-permeability, non-reactive barrier walls are often used to contain contaminants in an aquifer. Rates of solute transport through such barriers are typically many orders of magnitude slower than rates through the aquifer. Nevertheless, the success of remedial actions may be sensitive to these low rates of transport. Two numerical simulation methods for representing low-permeability barriers in a finite-difference groundwater-flow and transport model were tested. In the first method, the hydraulic properties of the barrier were represented directly on grid cells and in the second method, the intercell hydraulic-conductance values were adjusted to approximate the reduction in horizontal flow, allowing use of a coarser and computationally efficient grid. The alternative methods were tested and evaluated on the basis of hypothetical test problems and a field case involving tetrachloroethylene (PCE) contamination at a Superfund site in New Hampshire. For all cases, advective transport across the barrier was negligible, but preexisting numerical approaches to calculate dispersion yielded dispersive fluxes that were greater than expected. A transport model (MODFLOW-GWT) was modified to (1) allow different dispersive and diffusive properties to be assigned to the barrier than the adjacent aquifer and (2) more accurately calculate dispersion from concentration gradients and solute fluxes near barriers. The new approach yields reasonable and accurate concentrations for the test cases.

Journal of Contaminant Hydrology↗

USGS1986

Regional method to assess offshore slope stability.

The slope stability of some offshore environments can be evaluated by using only conventional acoustic profiling and short-core sampling, followed by laboratory consolidation and strength testing. The test results are synthesized by using normalized-parameter techniques. The normalized data are then used to calculate the critical earthquake acceleration factors or the wave heights needed to initiate failure. These process-related parameters provide a quantitative measure of the relative stability for locations from which short cores were obtained. The method is most applicable to offshore environments of gentle relief and simple subsurface structure and is not considered a substitute for subsequent site-specific analysis. -from ASCE Publications Information

Journal of Geotechnical Engineering↗