USGS Science⌕ Search

SEARCH · USGS Science

Results for “Current Protocols”

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

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 145 records · Page 8Linked to original sources
USGS2015

A reply to Iversen et al.'s comment “Monitoring of animal abundance by environmental DNA - An increasingly obscure perspective”

We appreciate the conversation put forward by Iversen et al. (2015) in their response to our article “Quantification of eDNA shedding rates from invasive bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix ” in the 2015 environmental DNA special issue of Biological Conservation. We agree with Iversen et al.'s concern about overly optimistic conclusions that could be drawn from the current eDNA literature. One hope for eDNA technology is that it can be used in estimating abundance or population density. Evidence suggests that eDNA measurements correlate with total biomass (Takahara et al., 2012) rather than abundance. We demonstrate a similar relationship between biomass and eDNA shedding rates. Nevertheless, without field testing of these methods and specific survey protocols, we cannot make strong conclusions regarding the technique's field applicability. In our manuscript, we attempted to point out areas in which more research is needed.

Biological Conservation↗
USGS2005

Occurrence of fecal-indicator bacteria and protocols for identification of fecal-contamination sources in selected reaches of the West Branch Brandywine Creek, Chester County, Pennsylvania

The presence of fecal-indicator bacteria indicates the potential presence of pathogens originating from the fecal matter of warm-blooded animals. These pathogens are responsible for numerous human diseases ranging from common diarrhea to meningitis and polio. The detection of fecal-indicator bacteria and interpretation of the resultant data are, therefore, of great importance to water-resource managers. Current (2005) techniques used to assess fecal contamination within the fluvial environment primarily assess samples collected from the water column, either as grab samples or as depth- and (or) width-integrated samples. However, current research indicates approximately 99 percent of all bacteria within nature exist as attached, or sessile, bacteria. Because of this condition, most current techniques for the detection of fecal contamination, which utilize bacteria, assess only about 1 percent of the total bacteria within the fluvial system and are, therefore, problematic. Evaluation of the environmental factors affecting the occurrence and distribution of bacteria within the fluvial system, as well as the evaluation and modification of alternative approaches that effectively quantify the larger population of sessile bacteria within fluvial sediments, will present water-resource managers with more effective tools to assess, prevent, and (or) eliminate sources of fecal contamination within pristine and impaired watersheds. Two stream reaches on the West Branch Brandywine Creek in the Coatesville, Pa., region were studied between September 2002 and August 2003. The effects of sediment particle size, climatic conditions, aquatic growth, environmental chemistry, impervious surfaces, sediment and soil filtration, and dams on observed bacteria concentrations were evaluated. Alternative approaches were assessed to better detect geographic sources of fecal contamination including the use of turbidity as a surrogate for bacteria, the modification and implementation of sandbag bacteria samplers, and the use of optical brighteners. For the purposes of this report, sources of bacteria were defined as geographic locations where elevated concentrations of bacteria are observed within, or expected to enter, the main branch of the West Branch Brandywine Creek. Biologic sources (for example, waterfowl) were noted where applicable; however, no specific study of biologic sources (such as bacterial source tracking) was conducted. Data indicated that specific bacterial populations within fluvial sediments could be related to specific particle-size ranges. This relation is likely the result of the reduced porosity and permeability associated with finer sediments and the ability of specific bacteria to tolerate particular environments. Escherichia coli (E. coli) showed a higher median concentration (2,160 colonies per gram of saturated sediment) in the 0.125 to 0.5-millimeter size range of natural sediments than in other ranges, and enterococcus bacteria showed a higher median concentration (61,830 colonies per gram of saturated sediment) in the 0.062 to 0.25-millimeter size range of natural sediments than in other ranges. There were insufficient data to assess the particle-size relation to fecal coliform bacteria and (or) fecal streptococcus bacteria. Climatic conditions were shown to affect bacteria concentrations in both the water column and fluvial sediments. Drought conditions in 2002 resulted in lower overall bacteria concentrations than the more typically wet year of 2003. E. coli concentrations in fluvial sediment along the Coatesville study reach in 2002 had a median concentration of 92 colonies per gram of saturated sediment; in 2003, the median concentration had risen to 4,752 colonies per gram of saturated sediment. Symbiotic relations between bacteria and aquatic growth were likely responsible for increased bacteria concentrations observed within an impoundment area on the Coatesville study reach. This reach showed evidence of elevated aquatic growth and sharp increases in E. coli concentrations from upstream to downstream through the impoundment area in both 2002 and 2003. In 2003, E. coli concentrations within the waters column increased from 940 colonies per 100 milliliters upstream to 6,000 colonies per 100 milliliters at the dam crest. Given that these bacteria likely resulted from natural bacterial regrowth, the use of E. coli as an indicator of fecal contamination was severely impaired. Variable environmental conditions along the West Branch Brandywine Creek made the common field-chemical parameters of specific conductance, temperature, pH, and dissolved oxygen ineffective and (or) impossible to use for the determination of inputs of fecal contamination. Extreme variations in chemical gradients commonly were related to the urban/industrial signature of the watershed. For example, during base-flow sampling in 2002, specific-conductance values exceeding 1,000 microsiemens per centimeter observed in effluent from a local steel mill. This effluent raised the specific conductance within the West Branch Brandywine from just above 200 microsiemens per centimeter upstream from the outfall to just below 500 microsiemens per centimeter downstream from the outfall. These chemical gradients also, likely, had an effect on the initial colonization of bacteria, the formation of biofilms, and the persistence of certain types of bacteria along the study reach. Data collected in 2003 indicated that nutrients increased during both base-flow and stormflow conditions along the Coatesville study reach. For example, during base-flow sampling in 2003, 20 pounds of phosphorus was shown to enter the West Branch Brandywine Creek along the Coatesville study reach. The largest contributors to this base-flow nutrient load were likely two wastewater-treatment facilities adjacent to the study reach. During stormflow sampling in 2003, 480 pounds of phosphorus was shown to enter the West Branch Brandywine Creek along the Coatesville study reach. Data, along with other research, indicated the largest contributor to this stormflow nutrient load was likely remobilized sediment originating from a large dam impoundment. These elevated nutrient concentrations were considered sufficient to promote accelerated aquatic growth along the reach. Data collected in 2003 showed that wastewater constituents entered the West Branch Brandywine Creek largely from urban storm-sewer systems. Samples from the primary storm sewer for the city of Coatesville had detections for 20 of 69 wastewater constituents. These constituents included both strong and weak indicators of fecal contamination and generally indicated the storm-sewer system along the Coatesville study reach was a likely source of fecal-indicator bacteria and fecal contamination under base-flow conditions. By comparison, 5 constituents were detected in samples from the upstream end of the reach, and 10 constituents were detected in samples from the downstream end of the reach. During stormflow, numbers of detections were similar along the entire length of the study reach-five in samples from the upstream end, eight in samples from the center of the reach, and seven in samples from the downstream end of the reach. These data indicate that point sources (such as culverts and pipes, septic systems, and wastewater-treatment facilities) are not likely the origin of bacteria contamination during stormflow. The bacteria concentrations observed during stormflow events probably result from remobilized sessile bacteria stored within fluvial sediments. In this case, these bacteria should not be considered indicators of current fecal contamination. Impervious surfaces were found to increase bacteria concentrations along the West Branch Brandywine Creek because contaminated runoff from impervious areas generally flows into, and is concentrated within, the confines of the local storm-sewer system. During 2002, storm-sewer outfalls draining impervious areas were associated with all major locations of elevated bacterial concentrations (greater than 1,200 colonies per gram of saturated sediment) in fluvial sediments. During 2003, wetter conditions and overall bacteria concentrations higher than in 2002 resulted in point sources of bacterial contamination becoming less pronounced; however, the storm-sewer system, draining adjacent impervious areas, was still observed to be the primary source of bacteria along the reach. Where stormwater and (or) other runoff from these areas was allowed to infiltrate and (or) flow through wetland and riparian buffers, bacteria concentrations were not observed to be elevated above background levels commonly observed throughout similar areas of the same reach. Two run-of-the-river dams along the Coatesville study reach were evaluated for their effects on observed bacterial concentrations. These dams were shown to have greater or lesser effects on bacterial concentrations depending on the size of the structure and the capacity of the structure to impede flows. The smaller upstream dam had an approximate height of 3 feet and showed little observed effect on measured turbidity values; these data indicated that the dam did not effectively impede the flow of water or sediment within the West Branch Brandywine Creek. Consequently, this small dam did not show any observed effect on bacterial concentrations either upstream or downstream of the structure. The larger dam, near the middle of the reach, had an approximate height of 20 feet and showed greater effects on both turbidity and bacteria concentrations. The capacity of the larger dam to impede flows, combined with nutrients entering the reach, resulted in increased biologic activity throughout the impoundment area. Within this larger impoundment, enterococcus bacteria populations were observed to decrease sharply and E. coli bacteria populations were observed to increase sharply as flow approached the dam crest. All bacteria levels were then observed to drop to background levels, in both the water column and fluvial sediment, immediately downstream from the dam crest. Additional study is required to determine the cause for this rapid die off. Turbidity was assessed as a potential surrogate for E. coli bacteria. Regression analysis indicated higher turbidity levels usually can indicate higher concentrations of bacteria (R2 = 0.67), but the relation was too sporadic on the West Branch Brandywine Creek to use turbidity as a surrogate for estimated bacteria concentrations. Evaluation of data from individual base-flow and stormflow events resulted in variable and generally poor statistical relations between E. coli bacteria and turbidity (R2 values ranged from 0.02 to 0.94). Sandbag samplers were used in 2003 to determine their suitability for the assessment of fecal contamination. Sandbag samplers rely on the ability of bacteria to attach to surfaces and use the larger sessile bacteria populations instead of the more commonly used planktonic bacteria populations. E. coli bacteria concentrations observed in the sandbag samplers, after 1 week in place, were similar to those found within natural sediments collected concurrently. Enterococcus bacteria concentrations within the same sandbag samplers were not similar, and were generally lower, than those observed within the natural sediments. This discrepancy was likely because sand within the samplers was sieved to a size that was likely too coarse for enterococcus bacteria to persist. Optical-brightener samplers were installed along with each sandbag sampler. Optical brighteners are additives used in common household detergents; therefore, detection of optical brighteners, along with elevated fecal-indicator bacteria concentrations, strongly indicates a link to humans. Positive results for optical brighteners were detected only at the outfalls of two sewage-treatment facilities; because of treatment of the effluent from these facilities, these samples did not have elevated bacteria concentrations. The lack of additional positive results was largely because this method is not sensitive to low concentrations of optical brighteners.

Pennsylvania↗
USGS2016

The National Wind Erosion Research Network: Building a standardized long-term data resource for aeolian research, modeling and land management

The National Wind Erosion Research Network was established in 2014 as a collaborative effort led by the United States Department of Agriculture’s Agricultural Research Service and Natural Resources Conservation Service, and the United States Department of the Interior’s Bureau of Land Management, to address the need for a long-term research program to meet critical challenges in wind erosion research and management in the United States. The Network has three aims: (1) provide data to support understanding of basic aeolian processes across land use types, land cover types, and management practices, (2) support development and application of models to assess wind erosion and dust emission and their impacts on human and environmental systems, and (3) encourage collaboration among the aeolian research community and resource managers for the transfer of wind erosion technologies. The Network currently consists of thirteen intensively instrumented sites providing measurements of aeolian sediment transport rates, meteorological conditions, and soil and vegetation properties that influence wind erosion. Network sites are located across rangelands, croplands, and deserts of the western US. In support of Network activities, http://winderosionnetwork.org was developed as a portal for information about the Network, providing site descriptions, measurement protocols, and data visualization tools to facilitate collaboration with scientists and managers interested in the Network and accessing Network products. The Network provides a mechanism for engaging national and international partners in a wind erosion research program that addresses the need for improved understanding and prediction of aeolian processes across complex and diverse land use types and management practices.

Arizona, California, Colorado, Idaho, North Dakota↗
USGS2009

The reintroduction of the Andean condor into Colombia, South America: 1989-1991

From 1989 to 1991,22 captive-reared Andean condors Vultur gryphus were released into three protected areas in the Andes of Colombia, South America. The goals of this reintroduction programme were to re-establish populations of these birds in protected habitat where the species had been extirpated, and to train local biologists in the conservation techniques necessary to recover their native condor. All birds were hatched, reared and released according to the protocols established by the US Fish and Wildlife Service and the California Department of Fish and Game for the California condor Gymnogyps californianus. At the time of release, the birds ranged in age from 11 to 26 months. Each bird was fitted with individually numbered wing tags and wing-mounted radio transmitters. Of the 22 released animals, 19 currently survive – a substantial increase to the wild population in Colombia, which had been estimated by Colombian biologists to number only 20 individuals.

Oryx↗
USGS2022

A scalable model-independent iterative data assimilation tool for sequential and batch estimation of high dimensional model parameters and states

Ensemble-based data assimilation (DA) methods have displayed strong potential to improve model state and parameter estimation across several disciplines due to their computational efficiency, scalability, and ability to estimate uncertainty in the dynamic states and the parameters. However, a barrier to adoption of ensemble DA methods remains. Namely, there is currently a lack of available tools that enable efficient and scalable DA in a non-intrusive fashion and that support implementation flexibility. This paper presents an open-source software tool (PESTPP-DA) that implements a range of data assimilation methods—Ensemble Kalman filter, Ensemble Kalman Smoother and Ensemble Smoother—using the widely known PEST model-interface protocols, to interact with any model. Two iterative solutions can be used for nonlinear and/or non-Gaussian assimilation problems. To demonstrate the broad range of PESTPP-DA applications, two synthetic case studies are presented: (1) the Lorenz model and (2) a groundwater pumping test in the presence of a non-Gaussian hydraulic conductivity field.

Environmental Modelling & Software↗
USGS2003

Framework for a ground-water quality monitoring and assessment program for California

The State of California uses more ground water than any other State in the Nation. With a population of over 30 million people, an agricultural economy based on intensive irrigation, large urban industrial areas, and naturally elevated concentrations of some trace elements, there is a wide range of contaminant sources that have the potential to contaminate ground water and limit its beneficial uses. In response to the many-and different-potential sources of ground-water contamination, the State of California has evolved an extensive set of rules and programs to protect ground-water quality, and agencies to implement the rules and programs. These programs have in common a focus on compliance with regulations governing chemical use and (or) ground-water quality. Although appropriate for, and successful at, their specific missions, these programs do not at present provide a comprehensive view of ground-water quality in the State of California. In October 2001, The California Assembly passed a bill, AB 599, establishing the Ground-Water- Quality Monitoring Act of 2001.' The goal of AB 599 is to improve Statewide comprehensive ground-water monitoring and increase availability of information about ground-water quality to the public. AB 599 requires the State Water Resources Control Board (SWRCB), in collaboration with an interagency task force (ITF) and a public advisory committee (PAC), to develop a plan for a comprehensive ground-water monitoring program. AB 599 specifies that the comprehensive program should be capable of assessing each ground-water basin in the State through direct and other statistically reliable sampling approaches, and that the program should integrate existing monitoring programs and design new program elements, as necessary. AB 599 also stresses the importance of prioritizing ground-water basins that provide drinking water. The United States Geological Survey (USGS), in cooperation with the SWRCB, and in coordination with the ITF and PAC, has developed a framework for a comprehensive ground-water-quality monitoring and assessment program for California. The proposed framework relies extensively on previous work conducted by the USGS through its National Water-Quality Assessment (NAWQA) program. In particular, the NAWQA program defines three types of ground-water assessment: (1) status, the assessment of the current quality of the ground-water resource; (2) trends, the detection of changes in water quality, and (3) understanding, assessing the human and natural factors that affect ground-water quality. A Statewide, comprehensive ground-water quality-monitoring and assessment program is most efficiently accomplished by applying uniform and consistent study-design and data-collection protocols to the entire State. At the same time, a comprehensive program should be relevant at a variety of scales, and therefore needs to retain flexibility to address regional and local issues. Consequently, many of the program components include a predominant element that will be consistently applied in all basins, and a secondary element that may be applied in specific basins where local conditions warrant attention.

Water-Resources Investigations Report↗
USGS2025

Field test of the self-preserving eDNA filter and the importance of calibration when changing methods during long-term monitoring

Filtering water is currently the primary field method used for collecting aquatic environmental DNA (eDNA). One of the drawbacks of filtering is the need to transfer the filter from the filter housing to a preservative-filled container in the field. New products are being developed to avoid this handling step, but comparative studies are needed to ensure that the results produced by new protocols are transferable within and across eDNA monitoring programs. To meet this need, we evaluated two filter preservation methods (self-preserving filter housing vs. ethanol) of the 5.0-μm polyethersulfone (PES) filter membrane in a field trial typical of stream fisheries eDNA sampling. We compared DNA detection and yield for free-swimming rainbow trout, Oncorhynchus mykiss (Walbaum, 1792), from streams in Washington, United States, and British Columbia, Canada, while accounting for the effects of two environmental covariates: stream discharge and water temperature. As these streams were part of an ongoing fisheries eDNA monitoring program, we also compared these methods to the original protocol, which used a 0.45-μm cellulose nitrate (CN) filter membrane and ethanol preservative. We found that the self-preserving filter housings collected and preserved eDNA well and provided similar results to identical filters preserved in ethanol. The 5.0-μm PES filters preserved in ethanol significantly outperformed the original protocol in terms of both DNA detection and yield, highlighting the importance of calibration of eDNA results when changing sampling methods during an ongoing monitoring program.

british Columbia, Washington↗
USGS2020

Case Study 4: NABat acoustic monitoring allows inferences about bat populations at multiple scales

North American bats face unprecedented risks from continuing and emerging threats including white-nose syndrome, wind energy development, and habitat loss. Many species of bats are thought to be recently experiencing unparalleled population declines unlike any previously observed (O’Shea et al. 2016). The North American Bat Monitoring Program (NABat) was conceived to better understand the true ecological consequences of these large-scale population reductions (Loeb et al. 2015). NABat aims is to improve the state of conservation science for the 47 species of bats shared by Canada, United States, and Mexico. To meet this objective, NABat offers standardize protocols and a unifying sample design facilitating a multi-agency, multinational, collaborative monitoring effort. A key element of NABat is cross-boundary partner coordination and sharing of limited resources for the collection of bat echolocation data. Here we provide three compelling examples of how NABat provides a convenient framework for using acoustic data to assess the potential impacts of current and future threats to North American bats across multiple spatial scales.

Oregon↗
USGS2014

Routine screening of harmful microorganisms in beach sands: implications to public health

Beaches worldwide provide recreational opportunities to hundreds of millions of people and serve as important components of coastal economies. Beach water is often monitored for microbiological quality to detect the presence of indicators of human sewage contamination so as to prevent public health outbreaks associated with water contact. However, growing evidence suggests that beach sand can harbor microbes harmful to human health, often in concentrations greater than the beach water. Currently, there are no standards for monitoring, sampling, analyzing, or managing beach sand quality. In addition to indicator microbes, growing evidence has identified pathogenic bacteria, viruses, and fungi in a variety of beach sands worldwide. The public health threat associated with these populations through direct and indirect contact is unknown because so little research has been conducted relating to health outcomes associated with sand quality. In this manuscript, we present the consensus findings of a workshop of experts convened in Lisbon, Portugal to discuss the current state of knowledge on beach sand microbiological quality and to develop suggestions for standardizing the evaluation of sand at coastal beaches. The expert group at the “Microareias 2012” workshop recommends that 1) beach sand should be screened for a variety of pathogens harmful to human health, and sand monitoring should then be initiated alongside regular water monitoring; 2) sampling and analysis protocols should be standardized to allow proper comparisons among beach locations; and 3) further studies are needed to estimate human health risk with exposure to contaminated beach sand. Much of the manuscript is focused on research specific to Portugal, but similar results have been found elsewhere, and the findings have worldwide implications.

Science of the Total Environment↗
USGS2015

Environmental DNA sampling protocol - filtering water to capture DNA from aquatic organisms

Environmental DNA (eDNA) analysis is an effective method of determining the presence of aquatic organisms such as fish, amphibians, and other taxa. This publication is meant to guide researchers and managers in the collection, concentration, and preservation of eDNA samples from lentic and lotic systems. A sampling workflow diagram and three sampling protocols are included as well as a list of suggested supplies. Protocols include filter and pump assembly using: (1) a hand-driven vacuum pump, ideal for sample collection in remote sampling locations where no electricity is available and when equipment weight is a primary concern; (2) a peristaltic pump powered by a rechargeable battery-operated driver/drill, suitable for remote sampling locations when weight consideration is less of a concern; (3) a 120-volt alternating current (AC) powered peristaltic pump suitable for any location where 120-volt AC power is accessible, or for roadside sampling locations. Images and detailed descriptions are provided for each step in the sampling and preservation process.

Techniques and Methods↗
USGS2022

The potential of semi-structured citizen science data as a supplement for conservation decision-making: Validating the performance of eBird against targeted avian monitoring efforts

Methods are being developed to capitalize on citizen science data for research and monitoring, but these data are rarely used within established decision-making frameworks of wildlife agencies. Citizen science data are often collected at higher resolution and extent than targeted monitoring programs, and may provide complementary information. Here, we demonstrate that carefully filtered semi-structured citizen science observations, when paired with targeted survey data, can produce ecological predictions at higher resolution and extent than targeted surveys alone, and both datasets can represent complementary aspects of species' ecology. We present case studies demonstrating how citizen science data can enhance or supplement decision-making of government and conservation organizations. First, we show how the continuous spatial coverage of citizen science projects, when coupled with targeted surveys, can improve estimates of metrics used by the U.S. Fish and Wildlife Service in regulatory processes to estimate population size, and inform take limits of federally managed species nationwide. Second, we show that the spatial coverage of citizen science accommodates dynamic avian space use patterns during key times of the year, relative to standardized monitoring protocols carried out by the Illinois Natural History Survey. Lastly, we demonstrate that citizen science information can replicate estimates of migratory chronologies for the Illinois Natural History Survey and the U.S. Fish and Wildlife Service for some waterfowl species, and in some contexts can supplement missing data on abundance. These findings illustrate the value of integrating validated information from semi-structured citizen science into the current evidence base used to justify, inform, and evaluate conservation decision-making.

California, Illinois, Iowa, Missouri↗
USGS2022

A model-independent tool for evolutionary constrained multi-objective optimization under uncertainty

An open-source tool has been developed to facilitate constrained single- and multi-objective optimization under uncertainty (CMOU) analyses. The tool uses the well-known PEST interface protocols to communicate with the underlying forward simulation, making it non-intrusive. The tool contains a built-in parallel run manager to make use of heterogeneous and distributed computing resources. Several popular and well-known evolutionary algorithms are implemented and can be combined with a range of approaches to represent uncertainty in model-derived constraint/objective values. These attributes serve to address the current barrier to adopt advanced CMOU analyses for a wide range of decision-support problems across the environmental modeling spectrum. We demonstrate the capabilities of the CMOU tool on a well-known analytical benchmark problem that we augmented to include uncertainty, as well as on a synthetic density-dependent coastal groundwater management benchmark problem. Both demonstrations highlight the importance of explicitly accounting for uncertainty to convey risk and reliability in pareto-optimal design.

Environmental Modelling & Software↗
USGS2023

Characterizing lung particulates using quantitative microscopy in coal miners with severe pneumoconiosis

Context.— Current approaches for characterizing retained lung dust using pathologists' qualitative assessment or scanning electron microscopy with energy-dispersive spectroscopy (SEM/EDS) have limitations. Objective.— To explore polarized light microscopy coupled with image-processing software, termed quantitative microscopy–particulate matter (QM-PM), as a tool to characterize in situ dust in lung tissue of US coal miners with progressive massive fibrosis. Design.— We developed a standardized protocol using microscopy images to characterize the in situ burden of birefringent crystalline silica/silicate particles (mineral density) and carbonaceous particles (pigment fraction). Mineral density and pigment fraction were compared with pathologists' qualitative assessments and SEM/EDS analyses. Particle features were compared between historical (born before 1930) and contemporary coal miners, who likely had different exposures following changes in mining technology. Results.— Lung tissue samples from 85 coal miners (62 historical and 23 contemporary) and 10 healthy controls were analyzed using QM-PM. Mineral density and pigment fraction measurements with QM-PM were comparable to consensus pathologists' scoring and SEM/EDS analyses. Contemporary miners had greater mineral density than historical miners (186 456 versus 63 727/mm 3 ; P = .02) and controls (4542/mm 3 ), consistent with higher amounts of silica/silicate dust. Contemporary and historical miners had similar particle sizes (median area, 1.00 versus 1.14 μm 2 ; P = .46) and birefringence under polarized light (median grayscale brightness: 80.9 versus 87.6; P = .29). Conclusions.— QM-PM reliably characterizes in situ silica/silicate and carbonaceous particles in a reproducible, automated, accessible, and time/cost/labor-efficient manner, and shows promise as a tool for understanding occupational lung pathology and targeting exposure controls.

Archives of Pathology and Laboratory Medicine↗
USGS2014

Monitoring Hawaiian waterbirds: evaluation of sampling methods to produce reliable estimates

We conducted field trials to assess several different methods of estimating the abundance of four endangered Hawaiian waterbirds: the Hawaiian duck ( Anas wyvilliana ), Hawaiian coot ( Fulica alai ), Hawaiian common moorhen ( Gallinula chloropus sandvicensis ) and Hawaiian stilt ( Himantopus mexicanus knudseni ). At two sites on Oʽahu, James Campbell National Wildlife Refuge and Hamakua Marsh, we conducted field trials where both solitary and paired observers counted birds and recorded the distance to observed birds. We then compared the results of estimates using the existing simple count, distance estimates from both point- and line-transect surveys, paired observer count estimates, bounded count, and Overton estimators. Comparing covariate recorded values among simultaneous observations revealed inconsistency between observers. We showed that the variation among simple counts means the current direct count survey, even if interpreted as a proportional index of abundance, incorporates many sources of uncertainty that are not taken into account. Analysis revealed violation of model assumptions that allowed us to discount distance-based estimates as a viable estimation technique. Among the remaining methods, point counts by paired observers produced the most precise estimates while meeting model assumptions. We present an example sampling protocol using paired observer counts. Finally, we suggest further research that will improve abundance estimates of Hawaiian waterbirds.

Hawai'i↗
USGS2026

Improving the use of expert opinion in disease risk analysis for conservation translocations

Conservation translocations are subject to considerable uncertainty and risk, of which disease is one of the most recognized. To address disease risks, several protocols for qualitative disease risk analysis (qDRA) exist and are used for responsible conservation translocation planning. Existing qDRA protocols usually rely on expert judgment, but they lack quantitative aggregation of elicited estimates, transparent treatment of uncertainty, and explicit comparison of alternative disease risk management pathways. We added these factors to a qDRA for translocation of a charismatic species that is extinct in the wild, the sihek (Guam kingfisher) ( Todiramphus cinnamominus ). We asked a panel of seven independent experts to quantify their judgment of risks of pathogen release, exposure, and consequences for seven pathogen hazards under three translocation management scenarios. Experts suggested that implementing a full biosecurity protocol would reduce risk for several pathogen hazards but would have variable effectiveness (11–65% depending on the hazard). There was substantial uncertainty associated with individual experts and noise among different experts, showing the potential for error if decisions are based on single-point judgments (i.e., providing judgment of a central tendency without accounting for uncertainty) from one expert or on collaborative consensus of multiple experts, as is current practice.

Conservation Biology↗
USGS2012

Evaluating a fish monitoring protocol using state-space hierarchical models

Using data collected from three river reaches in Montana, we evaluated our ability to detect population trends and predict fish future fish abundance. Data were collected as part of a long-term monitoring program conducted by Montana Fish, Wildlife and Parks to primarily estimate rainbow (Oncorhynchus mykiss) and brown trout (Salmo trutta) abundance in numerous rivers across Montana. We used a hierarchical Bayesian mark-recapture model to estimate fish abundance over time in each of the three river reaches. We then fit a state-space Gompertz model to estimate current trends and future fish populations. Density dependent effects were detected in 1 of the 6 fish populations. Predictions of future fish populations displayed wide credible intervals. Our simulations indicated that given the observed variation in the abundance estimates, the probability of detecting a 30% decline in fish populations over a five-year period was less than 50%. We recommend a monitoring program that is closely tied to management objectives and reflects the precision necessary to make informed management decisions.

Montana↗
USGS2016

Flexible risk metrics for identifying and monitoring conservation-priority species

Region-specific conservation programs should have objective, reliable metrics for species prioritization and progress evaluation that are customizable to the goals of a program, easy to comprehend and communicate, and standardized across time. Regional programs may have vastly different goals, spatial coverage, or management agendas, and one-size-fits-all schemes may not always be the best approach. We propose a quantitative and objective framework for generating metrics for prioritizing species that is straightforward to implement and update, customizable to different spatial resolutions, and based on readily available time-series data. This framework is also well-suited to handling missing-data and observer error. We demonstrate this approach using North American Breeding Bird Survey (NABBS) data to identify conservation priority species from a list of over 300 landbirds across 33 bird conservation regions (BCRs). To highlight the flexibility of the framework for different management goals and timeframes we calculate two different metrics. The first identifies species that may be inadequately monitored by NABBS protocols in the near future (TMT, time to monitoring threshold), and the other identifies species likely to decline significantly in the near future based on recent trends (TPD, time to percent decline). Within the individual BCRs we found up to 45% (mean 28%) of the species analyzed had overall declining population trajectories, which could result in up to 37 species declining below a minimum NABBS monitoring threshold in at least one currently occupied BCR within the next 50 years. Additionally, up to 26% (mean 8%) of the species analyzed within the individual BCRs may decline by 30% within the next decade. Conservation workers interested in conserving avian diversity and abundance within these BCRs can use these metrics to plan alternative monitoring schemes or highlight the urgency of those populations experiencing the fastest declines. However, this framework is adaptable to many taxa besides birds where abundance time-series data are available.

Ecological Indicators↗
USGS2014

U.S. Geological Survey Science for the Wyoming Landscape Conservation Initiative - 2013 Annual Report

This is the sixth report produced by the U.S. Geological Survey (USGS) for the Wyoming Landscape Conservation Initiative (WLCI) to detail annual activities conducted by USGS for addressing specific management needs identified by WLCI partners. In FY2013, there were 25 ongoing and new projects conducted by the USGS. These projects fall into 8 major categories: (1) synthesizing and analyzing existing data to describe (model and map) current conditions on the landscape; (2) developing models for projecting past and future landscape conditions; (3) monitoring indicators of ecosystem conditions and the effectiveness of on-the-ground habitat projects; (4) conducting research to elucidate the mechanisms underlying wildlife and habitat responses to changing land uses; (5) managing and making accessible the large number of databases, maps, and other products being developed; (6) helping to integrate WLCI outcomes with future habitat enhancement and research projects; (7) coordinating efforts among WLCI partners; and (8) providing support to WLCI decision-makers and assisting with overall evaluation of the WLCI program. The two new projects initiated in FY2013 address (1) important agricultural lands in southwestern Wyoming, and (2) the influence of energy development on native fish communities. The remaining activities entailed our ongoing efforts to compile data, model landscape conditions, monitor trends in habitat conditions, conduct studies of wildlife responses to energy development, and upgrade Web-based products in support of both individual and overall WLCI efforts. Milestone FY2013 accomplishments included completing the development of a WLCI inventory and monitoring framework and the associated monitoring strategies, protocols, and analytics; and initial development of an Interagency Inventory and Monitoring Database, which will be accessible through the Monitoring page of the WLCI Web site at http://www.wlci.gov/monitoring. We also completed the initial phase of the mountain shrub-mapping project in the Big Piney-La Barge mule deer winter range. Finally, a 3-year survey of pygmy rabbits in four major gas-field areas was completed and used to validate the pygmy rabbit habitat model/map developed earlier in the project. Important products that became available for use by WLCI partners included publication of USGS Data Series report (http://pubs.usgs.gov/ds/800/pdf/ds800.pdf) that compiles our WLCI land cover and land use data, which depict current and historical patterns of sage-grouse habitat in relation to energy development and will be used to pose “what-if” scenarios to evaluate possible outcomes of alternative land-use strategies and practices on habitat and wildlife. Another important FY2013 product was a journal article (http://aapgbull.geoscienceworld.org/content/97/6/899.full) that describes the Mowry Shale and Frontier formation, which harbors coalbed methane and shale gas resources in Wyoming, Colorado, and Utah, for use in future scenario-building work. We also produced maps and databases that depict the structure and condition of aspen stands in the Little Mountain Ecosystem, and then presented this information to the Bureau of Land Management, Wyoming Game and Fish Department, and other interested entities for supporting aspen-management objectives.

Open-File Report↗