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USGS1983

Methods for estimating peak discharge and flood boundaries of streams in Utah

Equations for estimating 2-, 5-, 10-, 25-, 50-, and 100-year peak discharges and flood depths at ungaged sites in Utah were developed using multiple-regression techniques. Ratios of 500- to 100-year values also were determined. The peak discharge equations are applicable to unregulated streams and the flood depth equations are applicable to the unregulated flow in natural stream channels. The flood depth data can be used to approximate flood prone areas. Drainage area and mean basin elevation are the two basin characteristics needed to use these equations. The standard error of estimate ranges from 38% to 74% for the 100-year peak discharge and from 23% to 33% for the 100-year flood depth. Five different flood mapping methods are described. Streams are classified into four categories as a basis for selecting a flood mapping method. Procedures for transferring flood depths obtained from the regression equations to a flood boundary map are outlined. Also, previous detailed flood mapping by government agencies and consultants is summarized to assist the user in quality control and to minimize duplication of effort. Methods are described for transferring flood frequency data from gaged to ungaged sites on the same stream. Peak discharge and flood depth frequency relations and selected basin characteristics data, updated through the 1980 water year, are tabulated for more than 300 gaging stations in Utah and adjoining states. In addition, weighted estimates of peak discharge relations based on the station data and the regression estimates are provided for each gaging station used in the regression analysis. (Author 's abstract)

Water-Resources Investigations Report↗

USGS2012

Coordinated bird monitoring: Technical recommendations for military lands

The Department of Defense (DoD) is subject to several rules and regulations establishing responsibilities for monitoring migratory birds. The Sikes Act requires all military installations with significant natural resources to prepare and implement Integrated Natural Resources Management Plans (INRMPs). These plans guide the conservation and long-term management of natural resources on military lands in a manner that is compatible with and sustains the military mission. An INRMP also supports compliance with all legal requirements and guides the military in fulfilling its obligation to be a good steward of public land.The management and conservation of migratory birds is addressed in installation INRMPs. The National Environmental Policy Act (NEPA) requires federal agencies to evaluate and disclose the potential environmental impacts of their proposed actions. More recently, DoD signed an MOU (http://www.dodpif.org/downloads/EO13186_MOU-DoD.pdf) for migratory birds, under Executive Order 13186, with the US Fish and Wildlife Service (USFWS) in July 2006 and a Migratory Bird Rule (http://www.dodpif.org/downloads/MigBirdFINALRule_FRFeb2007.pdf) was passed by Congress in February 2007. The Migratory Bird Rule addresses the potential impacts of military readiness activities on populations of migratory birds and establishes a process to implement conservation measures if and when a military readiness activity is expected to have a significant adverse impact on a population of migratory bird species (as determined through the NEPA process). The MOU states that for nonmilitary readiness activities, prior to initiating any activity likely to affect populations of migratory birds DoD shall (1) identify the migratory bird species likely to occur in the area of the proposed action and determine if any species of concern could be affected by the activity, and (2) assess and document, using NEPA when applicable, the effect of the proposed action on species of concern. By following these procedures, DoD will minimize the possibility for a proposed action to unintentionally take migratory birds at a level that would violate any of the migratory bird treaties and potentially impact mission activities. In addition, implementing conservation and monitoring programs for migratory birds supports the ecosystem integrity necessary to sustain DoD's natural resources for the military mission.Non-compliance with the procedural requirements of the MBTA could result in a private party lawsuit under the Administrative Procedures Act (APA). A lawsuit filed under APA involving a Navy bombing range is the basis for a court ruling that unintentional take of migratory birds applies to federal actions. Ensuring the necessary data is available to adequately assess impacts of a proposed action will help avoid lawsuits or help ensure such lawsuits have no grounds. The data gathered in a bird monitoring program will provide the best scientific data available to assess the expected impacts of a proposed action on migratory bird species through the NEPA process. This report presents recommendations developed by the U.S. Geological Survey (USGS) for the Department of Defense (DoD) on establishing a "Coordinated Bird Monitoring (CBM) Plan." The CBM Plan is intended to ensure that DoD meets its conservation and regulatory responsibilities for monitoring birds (Chapter 1). The report relies heavily on recommendations in the report, "Opportunities for improving avian monitoring" (http://www.nabci-us.org/aboutnabci/monitoringreportfinal0307.pdf), by the U.S. North American Bird Conservation Initiative (U.S. NABCI Monitoring Subcommittee, 2007) and on a review of 358 current DoD bird monitoring programs carried out as part of this project (Chapter 2). This report contains 12 recommendations which, if followed, would result in a comprehensive, efficient, and useful approach to bird monitoring. The recommendations are based on the entire report but are presented together at the end of Chapter 1. DoD has agreed to consider implementing these recommendations; however, final decisions will be based upon such factors as the availability of resources and military mission considerations. These recommendations from USGS can be summarized into 6 major themes: A major report on monitoring was released in 2007 by the U.S. North American Bird Conservation Initiative (http://www.nabci-us.org/main2.html). DoD can be consistent with this report by establishing policy that monitoring will be explicitly acknowledged as an integral element of bird management and conservation (Recommendation 1). The design of monitoring and assessment programs for birds should include the following steps: Preparation of a document describing the program's goals, objectives, and methods similar to a format we provide (Recommendation 2, Chapter 4). Selection of field methods using an "expert system" developed in this project (Recommendation 3, Chapter 5) or another well-documented system. Preparation and storage of metadata describing the monitoring program in the Natural Resources Monitoring Partnership (NRMP), and other appropriate databases Recommendation 4, Chapter 6). Entry of the survey data using eBird (http://ebird.org/content/dod) or the Coordinated Bird Monitoring Database (CBMD) and long-term storage of the data in the CBMD and the Avian Knowledge Network (AKN; Recommendation 5, Chapter 6; http://www.avianknowledge.net/). Submission of major results from the monitoring program for publication in a peer reviewed journal (Recommendation 6). The DoD Legacy Resource Management Program (Legacy; https://www.dodlegacy.org), Environmental Security Technology Certification Program (ESTCP; http://www.serdp.org/), and Strategic Environmental Research and Development Program (SERDP; http://www.serdp.org/) should be encouraged to continue their significant contributions to the foundations of bird monitoring (Recommendation 7, Chapters 1 and 3). Appropriate monitoring should be conducted to identify species of concern on installations. A year-round, one-time survey of birds on installations with habitat for migratory birds would provide the most information to assist compliance with the MOU, the Final Rule, and the NEPA analyses of proposed actions. However, less intensive survey efforts can still be conducted to yield useful information. We describe how various levels of survey effort might be organized and conducted. In addition, continuing surveys, as feasible, would further assist in documenting effects of military readiness and non-readiness activities on species of concern (SOC) (Recommendation 8, Chapter 7). Participation in well-designed, large-scale surveys [(e.g., North American Breeding Bird Survey (BBS; http://www.pwrc.usgs.gov/bbs/), Monitoring Avian Productivity and Survivorship (MAPS; http://www.birdpop.org/maps.htm)] on land that DoD manages or on lands where the results will be of high interest to DoD, will provide DoD and other NABCI members with information important to bird conservation (Recommendation 9, Chapter 8). Review and implementation of the CBM Plan should involve both higher level management and installation-level natural resources managers (Recommendation 11), be implemented through cooperative partnerships (Recommendation 12), and be followed on U.S territory lands and Army Corps of Engineers projects (Recommendation 10).Additional recommendations that pertain to implementing the DoD CBM Plan are discussed in Chapter 9.

Open-File Report↗

USGS2019

Methods for estimating the magnitude and frequency of peak streamflows for unregulated streams in Oklahoma developed by using streamflow data through 2017

The U.S. Geological Survey (USGS), in cooperation with the Oklahoma Department of Transportation, updated peak-streamflow regression equations for estimating flows with annual exceedance probabilities from 50 to 0.2 percent for the State of Oklahoma. These regression equations incorporate basin characteristics to estimate peak-streamflow magnitude and frequency throughout the State by use of a generalized least-squares regression analysis. The most statistically significant independent variables required to estimate peak-streamflow magnitude and frequency for unregulated streams in Oklahoma are contributing drainage area, mean-annual precipitation, and main-channel slope. The regression equations are applicable for stream basins with drainage areas less than 2,510 square miles that are not affected by regulation. The standard model error ranged from 31.28 to 49.32 percent for the different annual exceedance probabilities that were computed. Annual-maximum peak flows observed at 212 USGS streamgages through water year 2017 were used for the regression analysis, excluding the Oklahoma Panhandle region. The USGS StreamStats web application was used to obtain the independent variables required for the peak-streamflow regression equations. Limitations on the use of the regression equations and the reliability of regression estimates for natural unregulated streams are described. Log-Pearson Type III analysis information, basin and climate characteristics, and the peak-streamflow frequency estimates for the 212 streamgages in and near Oklahoma are provided in this report. This report contains descriptions of the methods that can be used to estimate peak streamflows at ungaged sites by using estimates from streamgages on unregulated streams. For ungaged sites on urban streams and streams regulated by small floodwater-retarding structures, an adjustment of the statewide regression equations for natural unregulated streams can be used to estimate peak-streamflow magnitude and frequency.

Arkansas, Kansas, Missouri, Oklahoma, Texas↗

USGS2005

Effects of spray-irrigated municipal wastewater on a small watershed in Chester County, Pennsylvania

Spray irrigation is a method for disposing of secondary treated municipal wastewater by spraying it on the land surface (fig. 1). The sprayed wastewater either evaporates into the air, soaks into the soil, or percolates through the soil and recharges the ground water. Land application of wastewater has advantages over conventional means of disposal by direct discharge to streams because the wastewater recharges the ground-water system and increases base flow in streams. Additional benefits are derived from the "natural" treatment of the wastewater that takes place in the soil when plants and other biota remove some nutrients (nitrogen and phosphorus) from the wastewater (Pennsylvania Department of Environmental Protection, 2003). The removal of nutrients is one advantage spray irrigation has to conventional disposal methods like instream discharge.

Fact Sheet↗

USGS2007

Tag return models allowing for harvest and catch and release: Evidence of environmental and management impacts on striped bass fishing and natural mortality rates

Catch-and-release fisheries have become very important in the management of overexploited recreational fish stocks. Tag return studies, where the tag is removed regardless of fish disposition, have been used to assess the effectiveness of restoration efforts for these fisheries. We extend the instantaneous rate formulation of tag return models to allow for catch and release as well as harvest. The key point of our methods is that, given an estimate of the tag reporting rate, the fishing mortality rate (F) is separated into two components: the mortality on harvested fish and the "mortality" on tags (because the lags are removed) of fish released alive. The total fishing mortality rate for untagged fish is the sum of the Fs due to harvest and hooking mortality suffered by fish released alive. Natural mortality rates can also be estimated. Both age-independent models and age-dependent models are constructed, and the age-dependent models are illustrated by application to data from a study of striped bass Morone saxatilis in Chesapeake Bay from 1991 to 2003 by the Maryland Department of Natural Resources. By fitting models of the natural mortality rate with limited age and year dependence, we demonstrate an overall decrease in natural mortality rates as fish age and provide evidence of an increase in natural mortality beginning in the late 1990s, when an outbreak of the disease mycobacteriosis is thought to have begun. Our results indicate that fishing mortality is age dependent; selectivity increases up to age 6, when fish appear to be fully recruited to the fishery. There is also evidence of an increase in fishing mortality since 1995, when regulations were relaxed. ?? Copyright by the American Fisheries Society 2007.

North American Journal of Fisheries Management↗

USGS2026

Uncertainty quantification of geologic energy storage in depleted gas reservoirs using material balance equations embedded in a hierarchical errors-in-variables model

The storage potential for gas in geologic settings, such as depleted hydrocarbon reservoirs and solution-mined salt caverns, is becoming salient to future energy infrastructure planning. Technologies such as carbon capture, utilization, and storage, carbon dioxide-enhanced oil recovery, and natural gas and hydrogen storage help meet growing energy demands, reduce carbon emissions to meet climate goals, and provide energy security amid geopolitical uncertainties. Therefore, estimates of underground gas storage capacity could be useful for efficiently navigating the energy transitions. Material balance is a fundamental method in reservoir engineering for estimating original gas in place and potential storage capacity at the scale necessary for national assessments of subsurface pore space resources. However, the deterministic method cannot accommodate multiple data sources or quantify uncertainty in predictions. In this study, a method that embeds material balance equations within a hierarchical errors-in-variables model is proposed which allows the estimation of the distributions of reservoir properties needed for assessments. Uncertainties associated with these reservoir properties have traditionally been expert-elicited, whereas the uncertainty estimates from the proposed models are data-driven. Capacity and uncertainty estimates can be used in a probabilistic resource assessment, supplementing information traditionally used by assessors or even replacing this expert elicitation step when data are unavailable. Various regression models are compared in a case study of the Michigan Basin, a large contributor to the United States’ current natural gas storage capacity. In particular, errors-in-variables models help ameliorate regression dilution and can quantify uncertainty in predictions of pressure in addition to storage capacity. Overfitting is addressed by quantifying generalization error and model averaging in simple and stratified cross-validation against reported working gas capacity, representing the varying quality and quantity of available data. Incorporating a statistical framework into existing numerical methods in reservoir engineering can improve the quality of estimation, and in particular, this method brings rigor to uncertainty quantification as part of a larger effort by the U.S. Geological Survey to assess domestic energy gas storage resources in depleted hydrocarbon reservoirs.

Mathematical Geosciences↗

USGS2018

Simulation of less‐mobile porosity dynamics in contrasting sediment water interface porous media

Considering heterogeneity in porous media pore size and connectivity is essential to predicting reactive solute transport across interfaces. However, exchange with less‐mobile porosity is rarely considered in surface water/groundwater recharge studies. Previous research indicates that a combination of pore‐fluid sampling and geoelectrical measurements can be used to quantify less‐mobile porosity exchange dynamics using the time‐varying relation between fluid and bulk electrical conductivity. For this study, we use macro‐scale (10 s of cm) advection–dispersion solute transport models linked with electrical conduction in COMSOL Multiphysics to explore less‐mobile porosity dynamics in two different types of observed sediment water interface porous media. Modeled sediment textures contrast from strongly layered streambed deposits to poorly sorted lakebed sands and cobbles. During simulated ionic tracer perturbations, a lag between fluid and bulk electrical conductivity, and the resultant hysteresis, is observed for all simulations indicating differential loading of pore spaces with tracer. Less‐mobile exchange parameters are determined graphically from these tracer time series data without the need for inverse numerical model simulation. In both sediment types, effective less‐mobile porosity exchange parameters are variable in response to changes in flow direction and fluid flux. These observed flow‐dependent effects directly impact local less‐mobile residence times and associated contact time for biogeochemical reaction. The simulations indicate that for the sediment textures explored here, less‐mobile porosity exchange is dominated by variable rates of advection through the domain, rather than diffusion of solute, for typical low‐to‐moderate rate (approximately 3–40 cm/day) hyporheic fluid fluxes. Overall, our model‐based results show that less‐mobile porosity may be expected in a range of natural hyporheic sediments and that changes in flowpath orientation and magnitude will impact less‐mobile exchange parameters. These temporal dynamics can be assessed with the geoelectrical experimental tracer method applied at laboratory and field scales.

Hydrological Processes↗

USGS2011

Estimating the Cumulative Ecological Effect of Local Scale Landscape Changes in South Florida

Ecosystem restoration in south Florida is a state and national priority centered on the Everglades wetlands. However, urban development pressures affect the restoration potential and remaining habitat functions of the natural undeveloped areas. Land use (LU) planning often focuses at the local level, but a better understanding of the cumulative effects of small projects at the landscape level is needed to support ecosystem restoration and preservation. The South Florida Ecosystem Portfolio Model (SFL EPM) is a regional LU planning tool developed to help stakeholders visualize LU scenario evaluation and improve communication about regional effects of LU decisions. One component of the SFL EPM is ecological value (EV), which is evaluated through modeled ecological criteria related to ecosystem services using metrics for (1) biodiversity potential, (2) threatened and endangered species, (3) rare and unique habitats, (4) landscape pattern and fragmentation, (5) water quality buffer potential, and (6) ecological restoration potential. In this article, we demonstrate the calculation of EV using two case studies: (1) assessing altered EV in the Biscayne Gateway area by comparing 2004 LU to potential LU in 2025 and 2050, and (2) the cumulative impact of adding limestone mines south of Miami. Our analyses spatially convey changing regional EV resulting from conversion of local natural and agricultural areas to urban, industrial, or extractive use. Different simulated local LU scenarios may result in different alterations in calculated regional EV. These case studies demonstrate methods that may facilitate evaluation of potential future LU patterns and incorporate EV into decision making.

Florida↗

USGS2007

Separation of copper, iron, and zinc from complex aqueous solutions for isotopic measurement

The measurement of Cu, Fe, and Zn isotopes in natural samples may provide valuable information about biogeochemical processes in the environment. However, the widespread application of stable Cu, Fe, and Zn isotope chemistry to natural water systems remains limited by our ability to efficiently separate these trace elements from the greater concentrations of matrix elements. In this study, we present a new method for the isolation of Cu, Fe, and Zn from complex aqueous solutions using a single anion-exchange column with hydrochloric acid media. Using this method we are able to quantitatively separate Cu, Fe, and Zn from each other and from matrix elements in a single column elution. Elution of the elements of interest, as well as all other elements, through the anion-exchange column is a function of the speciation of each element in the various concentrations of HCl. We highlight the column chemistry by comparing our observations with published studies that have investigated the speciation of Cu, Fe, and Zn in chloride solutions. The functionality of the column procedure was tested by measuring Cu, Fe, and Zn isotopes in a variety of stream water samples impacted by acid mine drainage. The accuracy and precision of Zn isotopic measurements was tested by doping Zn-free stream water with the Zn isotopic standard. The reproducibility of the entire column separation process and the overall precision of the isotopic measurements were also evaluated. The isotopic results demonstrate that the Cu, Fe, and Zn column separates from the tested stream waters are of sufficient purity to be analyzed directly using a multicollector inductively coupled plasma mass spectrometer (MC-ICP-MS), and that the measurements are fully-reproducible, accurate, and precise. Although limited in scope, these isotopic measurements reveal significant variations in δ 65 Cu (− 1.41 to + 0.30‰), δ 56 Fe (− 0.56 to + 0.34‰), and δ 66 Zn (0.31 to 0.49‰) among samples collected from different abandoned mines within a single watershed. Hence, Cu, Fe, and Zn isotopic measurements may be a powerful tool for fingerprinting specific metal sources and/or examining biogeochemical reactions within fresh water systems.

Chemical Geology↗

USGS2023

A model integrating satellite-derived shoreline observations for predicting fine-scale shoreline response to waves and sea-level rise across large coastal regions

Satellite-derived shoreline observations combined with dynamic shoreline models enable fine-scale predictions of coastal change across large spatiotemporal scales. Here, we present a satellite-data-assimilated, “littoral-cell”-based, ensemble Kalman-filter shoreline model to predict coastal change and uncertainty due to waves, sea-level rise (SLR), and other natural and anthropogenic processes. We apply the developed ensemble model to the entire California coastline (approximately 1,760 km), much of which is sparsely monitored with traditional survey methods (e.g., Lidar/GPS). Water-level-corrected, satellite-derived shoreline observations (obtained from the CoastSat toolbox) offer a nearly unbiased representation of in situ surveyed shorelines (e.g., mean sea-level elevation contours) at Ocean Beach, San Francisco. We demonstrate that model calibration with satellite observations during a 20-year hindcast period (1995–2015) provides nearly equivalent model forecast accuracy during a validation period (2015–2020) compared to model calibration with monthly in situ observations at Ocean Beach. When comparing model-predicted shoreline positions to satellite-derived observations, the model achieves an accuracy of <10 m RMSE for nearly half of the entire California coastline for the validation period. The calibrated/validated model is then applied for multi-decadal simulations of shoreline change due to projected wave and sea-level conditions, while holding the model parameters fixed. By 2100, the model estimates that 24%–75% of California's beaches may become completely eroded due to SLR scenarios of 1.0–3.0 m, respectively. The satellite-data-assimilated modeling system presented here is generally applicable to a variety of coastal settings around the world owing to the global coverage of satellite imagery.

JGR Earth Surface↗

USGS2010

Use of chlorofluorocarbons (CCl3F and CCl2F2) as hydrologic tracers and age‐dating tools: The alluvium and terrace system of central Oklahoma

The use of Chlorofluorocarbons (CFCs) as an age‐dating tool and tracer in shallow groundwaters has been investigated. New methodology for field sampling and preserving groundwaters containing parts per trillion concentrations of the CFCs, F‐1l and F‐12, is presented. Samples are analyzed by purge‐and‐trap gas chromatography with an electron capture detector. Physical and chemical processes that can alter natural concentrations (air‐water equilibrium) of CFCs were investigated to assess dating uncertainties. CFC model recharge ages appear to be defined within 2 years under optimum conditions. The method was applied to central Oklahoma to demonstrate the usefulness of CFCs as (1) an age‐dating tool of shallow groundwaters, (2) a tracer of sewage effluent in surface and shallow groundwaters, and (3) a tracer of shallow groundwater. Results of dating indicate two primary recharge periods in central Oklahoma over the past 45 years that correspond to the wet periods 1945–1960 and 1967–1975.

Water Resources Research↗

USGS2025

A global dataset of terrestrial biological nitrogen fixation

Biological nitrogen fixation (BNF) is the main natural source of new nitrogen inputs in terrestrial ecosystems, supporting terrestrial productivity, carbon uptake, and other Earth system processes. We assembled a comprehensive global dataset of field measurements of BNF in all major N-fixing niches across natural terrestrial biomes derived from the analysis of 376 BNF studies. The dataset comprises 32 variables, including site location, biome type, N-fixing niche, sampling year, quantification method, BNF rate (kg N ha −1 y −1 ), the percentage of nitrogen derived from the atmosphere (%N dfa ), N fixer or N-fixing substrate abundance, BNF rate per unit of N fixer abundance, and species identity. Overall, the dataset combines 1,207 BNF rates for trees, shrubs, herbs, soil, leaf litter, woody litter, dead wood, mosses, lichens, and biocrusts, 152 herb %N dfa values, 1,005 measurements of N fixer or N-fixing substrate abundance, and 762 BNF rates per unit of N fixer abundance for a total of 424 species across 66 countries. This dataset facilitates synthesis, meta-analysis, upscaling, and model benchmarking of BNF fluxes at multiple spatial scales.

Scientific Data↗

USGS2004

Demographic estimation methods for plants with unobservable life-states

Demographic estimation of vital parameters in plants with an unobservable dormant state is complicated, because time of death is not known. Conventional methods assume that death occurs at a particular time after a plant has last been seen aboveground but the consequences of assuming a particular duration of dormancy have never been tested. Capture–recapture methods do not make assumptions about time of death; however, problems with parameter estimability have not yet been resolved. To date, a critical comparative assessment of these methods is lacking. We analysed data from a 10 year study of Cleistes bifaria , a terrestrial orchid with frequent dormancy, and compared demographic estimates obtained by five varieties of the conventional methods, and two capture–recapture methods. All conventional methods produced spurious unity survival estimates for some years or for some states, and estimates of demographic rates sensitive to the time of death assumption. In contrast, capture–recapture methods are more parsimonious in terms of assumptions, are based on well founded theory and did not produce spurious estimates. In Cleistes , dormant episodes lasted for 1–4 years (mean 1.4, SD 0.74). The capture–recapture models estimated ramet survival rate at 0.86 (SE∼0.01), ranging from 0.77–0.94 (SEs≤0.1) in any one year. The average fraction dormant was estimated at 30% (SE 1.5), ranging 16–47% (SEs≤5.1) in any one year. Multistate capture–recapture models showed that survival rates were positively related to precipitation in the current year, but transition rates were more strongly related to precipitation in the previous than in the current year, with more ramets going dormant following dry years. Not all capture–recapture models of interest have estimable parameters; for instance, without excavating plants in years when they do not appear aboveground, it is not possible to obtain independent time-specific survival estimates for dormant plants. We introduce rigorous computer algebra methods to identify the parameters that are estimable in principle. As life-states are a prominent feature in plant life cycles, multistate capture–recapture models are a natural framework for analysing population dynamics of plants with dormancy.

Oikos↗

USGS2018

Adaptive population divergence and directional gene flow across steep elevational gradients in a climate‐sensitive mammal

The American pika is a thermally sensitive, alpine lagomorph species. Recent climate-associated population extirpations and genetic signatures of reduced population sizes range-wide indicate the viability of this species is sensitive to climate change. To test for potential adaptive responses to climate stress, we sampled pikas along two elevational gradients (each ~470 to 1640 m) and employed three outlier detection methods, BAYESCAN, LFMM, and BAYPASS, to scan for genotype-environment associations in samples genotyped at 30,763 SNP loci. We resolved 173 loci with robust evidence of natural selection detected by either two independent analyses or replicated in both transects. A BLASTN search of these outlier loci revealed several genes associated with metabolic function and oxygen transport, indicating natural selection from thermal stress and hypoxia. We also found evidence of directional gene flow primarily downslope from large high-elevation populations and reduced gene flow at outlier loci, a pattern suggesting potential impediments to the upward elevational movement of adaptive alleles in response to contemporary climate change. Finally, we documented evidence of reduced genetic diversity associated the south-facing transect and an increase in corticosterone stress levels associated with inbreeding. This study suggests the American pika is already undergoing climate-associated natural selection at multiple genomic regions. Further analysis is needed to determine if the rate of climate adaptation in the American pika and other thermally sensitive species will be able to keep pace with rapidly changing climate conditions.

Washington↗

USGS2024

Validation of a real-time quaking-induced conversion (RT-QuIC) assay protocol to detect chronic wasting disease using rectal mucosa of naturally infected, pre-clinical white-tailed deer (Odocoileus virginianus)

Chronic wasting disease (CWD) is a fatal prion disease of cervids spreading across North America. More effective mitigation efforts may require expansion of the available toolkit to include new methods that provide earlier antemortem detection, higher throughput, and less expense than current immunohistochemistry (IHC) methods. The rectal mucosa near the rectoanal junction is a site of early accumulation of CWD prions and is safely sampled in living animals by pinch biopsy. A fluorescence-based, 96-well format, protein-aggregation assay-the real-time quaking-induced conversion (RT-QuIC) assay-is capable of ultra-sensitive detection of CWD prions. Notably, the recombinant protein substrate is crucial to the assay's performance and is now commercially available. In this blinded independent study, the preclinical diagnostic performance of a standardized RT-QuIC protocol using a commercially sourced substrate (MNPROtein) and a laboratory-produced substrate was studied using mock biopsy samples of the rectal mucosa from 284 white-tailed deer ( Odocoileus virginianus ). The samples were from a frozen archive of intact rectoanal junctions collected at depopulations of farmed herds positive for CWD in the United States. All deer were pre-clinical at the time of depopulation and infection status was established from the regulatory record, which evaluated the medial retropharyngeal lymph nodes (MRPLNs) and obex by CWD-IHC. A pre-analytic sample precipitation step was found to enhance the protocol's detection limit. Performance metrics were influenced by the choice of RT-QuIC diagnostic cut points (minimum number of positive wells and assay time) and by deer attributes (preclinical infection stage and prion protein genotype). The peak overall diagnostic sensitivities of the protocol were similar for both substrates (MNPROtein, 76.8%; laboratory-produced, 73.2%), though each was achieved at different cut points. Preclinical infection stage and prion protein genotype at codon 96 (G = glycine, S = serine) were primary predictors of sensitivity. The diagnostic sensitivities in late preclinical infections (CWD-IHC positive MPRLNs and obex) were similar, ranging from 96% in GG96 deer to 80% in xS96 deer (x = G or S). In early preclinical infections (CWD-IHC positive MRPLNs only), the diagnostic sensitivity was 64-71% in GG96 deer but only 25% in xS96 deer. These results demonstrate that this standardized RT-QuIC protocol for rectal biopsy samples using a commercial source of substrate produced stratified diagnostic sensitivities similar to or greater than those reported for CWD-IHC but in less than 30 hours of assay time and in a 96-well format. Notably, the RT-QuIC protocol used herein represents a standardization of protocols from several previous studies. Alignment of the sensitivities across these studies suggests the diagnostic performance of the assay is robust given quality reagents, optimized diagnostic criteria, and experienced staff.

PLoS ONE↗

USGS2021

Watersheds and drainage networks

This topic is an overview of basic concepts about how the distribution of water on the Earth, with specific regard to watersheds, stream and river networks, and waterbodies are represented by geographic data. The flowing and non-flowing bodies of water on the earth’s surface vary in extent largely due to seasonal and annual changes in climate and precipitation. Consequently, modeling the detailed representation of surface water using geographic information is important. The area of land that collects surface runoff and other flowing water and drains to a common outlet location defines a watershed. Terrain and surface features can be naturally divided into watersheds of various sizes. Drainage networks are important data structures for modeling the distribution and movement of surface water over the terrain. Numerous tools and methods exist to extract drainage networks and watersheds from digital elevation models (DEMs). The cartographic representations of surface water are referred to as hydrographic features and consist of a snapshot at a specific time. Hydrographic features can be assigned general feature types, such as lake, pond, river, and ocean. Hydrographic features can be stored, maintained, and distributed for use through vector geospatial databases, such as the National Hydrography Dataset (NHD) for the United States.

Book chapter↗

USGS2014

Comments on the Yule Marble Haines block: Potential replacement, Tomb of the Unknown Soldier, Arlington National Cemetery

Marble for the Tomb of the Unknown Soldier at Arlington National Cemetery was cut from the Colorado Yule Marble Quarry in 1931. Although anecdotal reports suggest that cracks were noticed in the main section of the monument shortly after its installation at the Arlington National Cemetery in Arlington, Virginia, detailed documentation of the extent of cracking did not appear until 1963. Although debate continues as to whether the main section of the Tomb of the Unknowns monument should be repaired or replaced, Mr. John S. Haines of Glenwood Springs, Colorado, in anticipation of the permanent closing of the Yule Quarry, donated a 58-ton block of Yule Marble, the so-called Haines block, as a potential backup. The brief study reported here was conducted during mid-summer 2009 at the behest of the superintendent of Arlington National Cemetery. The field team entered the subterranean Yule Marble Quarry with the Chief Extraction Engineer in order to contrast the method used for extraction of the Haines block with the method that was probably used to extract the marble block that is now cracked. Based on surficial inspection and shallow coring of the Haines block, and on the nature of crack propagation in Yule Marble as judged by close inspection of a large collection of surrogate Yule Marble blocks, the team found the block to be structurally sound and cosmetically equivalent to the marble used for the current monument. If the Haines block were needed, it would be an appropriate replacement for the existing cracked section of the Tomb of the Unknown Soldier Monument.

Virginia↗

USGS2019

National assessment of shoreline change — Historical shoreline change along the north coast of Alaska, Icy Cape to Cape Prince of Wales

Beach erosion is a persistent problem along most open-ocean shores of the United States. Along the Arctic coast of Alaska, coastal erosion is widespread and threatens communities, defense and energy-related infrastructure, and coastal habitat. As coastal populations continue to expand and infrastructure and habitat are increasingly threatened by erosion, there is increased demand for accurate information regarding past and present trends and rates of shoreline movement. Shoreline change was evaluated by comparing three to four historical shoreline positions derived from 1950s-era topographic surveys and black and white aerial photography, 1980s-era color-infrared Alaska High-Altitude Aerial Photography, 2003 natural color aerial photography, and 2010s-era natural color aerial photography. Long-term (1950s–2010s) and short-term (1980s–2010s) shoreline change rates were calculated using linear-regression and end-point methods, respectively, at transects spaced approximately every 50 meters along both the mainland and barrier island coasts. Shoreline change rates calculated on more than 24,000 individual transects indicate that between 1948 and 2016 the northern coast of Alaska between Icy Cape and Cape Prince of Wales was slightly erosional, with 68 percent of the total transects showing shoreline retreat over the long term and 63 percent over the short term. However, only 9 percent of the total transects showed shoreline retreat greater than 1 meter per year (m/yr) over the long and short term, respectively. Mean rates of shoreline change of −0.2±0.1 and −0.2±0.3 m/yr, were calculated for the long and short term, respectively. Many rates measured were near the limit of our shoreline change uncertainty estimates. Erosion and accretion rates on individual transects ranged from −8.3 to +9.6 m/yr over the long term and −16.0 to +20.0 m/yr over the short-term analysis periods. The highest rates of erosion and accretion were associated with the formation and migration of inlets along barrier island coasts. The highest erosional rates of change were measured in the southern part of the study area between Sullivan Lake and Cape Prince of Wales. The highest accretional rates of change were measured in the northern part of the study area on the open-ocean coast of barrier islands fronting Kasegaluk Lagoon. Open-ocean exposed shorelines compose 85 percent of all transects and 70 percent were erosional over the long term. Sheltered mainland-lagoon shorelines compose 15 percent of all transects in the study area and 58 percent were erosional over the long term. Although mean shoreline change rates were quite low along all coasts, exposed shorelines retreated at twice the rate (−0.2±0.1 m/yr) of sheltered shorelines (−0.1±0.1 m/yr). Barrier shoreline transects (includes barrier islands, spits, and beaches) compose 49 percent of the total transects and 56 percent of all exposed shoreline transects. Mean shoreline change rates on exposed barrier shorelines were only slightly greater than exposed mainland shorelines (−0.3±0.1 and −0.2±0.1 m/yr, respectively). Mean shoreline change rates on sheltered barrier shorelines were similar to sheltered mainland shorelines (−0.1±0.3 m/yr). In contrast to the majority of the Nation’s shorelines, for all but three months of the year (July–September), the north coast of Alaska has historically been protected by landfast sea ice from processes such as waves, winds, and currents that typically drive coastal change on beaches in more temperate regions of the world. Projected and observed increases in periods of sea-ice-free conditions, as sea ice melts earlier and forms later in the year, particularly in the autumn, when large storms are more common in the Arctic, suggest that Arctic coasts will be more vulnerable to storm surge and wave energy, potentially resulting in accelerated shoreline erosion and terrestrial habitat loss in the future. Increases in air and sea water temperatures may also increase erosion of the ice-rich, coastal permafrost bluffs present along much of Alaska’s Arctic coast. More frequent shoreline change data collection and analysis in this rapidly changing environment should be considered in order to evaluate shoreline change trends in the future.

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