SEARCH · USGS Science

Results for “Nature Methods”

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

SourceResearch connectionFrom yearThrough year

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

At least 793 records · Page 44Linked to original sources

USGS2003

Determining temperature and thermal properties for heat-based studies of surface-water ground-water interactions: Appendix A of Heat as a tool for studying the movement of ground water near streams (Cir1260)

Advances in electronics leading to improved sensor technologies, large-scale circuit integration, and attendant miniaturization have created new opportunities to use heat as a tracer of subsurface flow. Because nature provides abundant thermal forcing at the land surface, heat is particularly useful in studying stream-groundwater interactions. This appendix describes methods for obtaining the thermal data needed in heat-based investigations of shallow subsurface flow.

Report↗

USGS2021

Effectiveness of rapid 'ōhi'a death management strategies at a focal disease outbreak on Hawai'i Island

The ongoing spread of rapid ‘ōhi‘a death (ROD) in the Hawaiian Islands threatens the long-term sustainability of ‘ōhi‘a lehua (Metrosideros polymorpha) forests throughout the state. First identified in the Puna district of Hawai‘i Island in 2014, the disease caused by the novel fungi Ceratocystis lukuohia and Ceratocystis huliohia has now spread island-wide and was recently detected on Kaua‘i, O‘ahu, and Maui. The leading hypothesis for the spread of ROD is through airborne ambrosia beetle frass particles that contain viable Ceratocystis propagules, thus management efforts focus on containing this frass. At the time of this study (2017–2018), the Waipunalei site was the northernmost outbreak of ROD on Hawai‘i Island. The focal nature of the outbreak and accessibility of the location provided the opportunity to monitor the effectiveness of two types of proposed management methods to reduce the airborne spread of potentially infective ambrosia beetle frass: tree felling and insecticide treatments. We placed 23 passive environmental samplers (PES), which monitored for airborne frass and wood particles containing C. lukuohia and C. huliohia in a grid that spanned the outbreak area over 22 weeks. Cross-vane panel traps with 1:1 methanol:ethanol lures were attached to nine of the PES to document wood-boring ambrosia and cerambycid beetle populations during the latter three months of the study. Monitoring with PES began three weeks before management and continued for one month after the last infected trees were felled. Glass microscope slides from the 23 PES were examined for airborne ambrosia beetle frass and wood particles by microscopy. DNA was extracted from the slides and tested by qPCR (quantitative polymerase chain reaction) for C. lukuohia and C. huliohia. We also investigated the correlation of beetle gallery counts with tree height and tested the efficacy of Bifen I/T insecticide (active ingredient: bifenthrin 7.9%) for preventing beetle attacks on the cut surface of ‘ōhi‘a bolts (tree stem sections). Beetle trapping data revealed that the area supports a diverse community of wood-boring beetles, some of which likely attack ‘ōhi‘a and may facilitate the spread of ROD. The number of beetle galleries on felled ‘ōhi‘a trees decreased linearly as tree height increased. We also observed significantly fewer beetle attacks on Bifen I/T treated ‘ōhi‘a bolts than non-treated bolts, but gallery formation nearly ceased in both treated and control bolts by week three. Ceratocystis lukuohia DNA was detected twenty-six times and C. huliohia was detected five times in the PES throughout this study. DNA detections were correlated to frass and wood counts, and the number of felled trees were correlated to wood particle counts but not frass counts. Both the timing and distribution of detections across the sampling grid indicate that tree felling may have reduced airborne detections of Ceratocystis DNA soon after tree felling was completed. A subsequent increase in detections after tree felling ceased may indicate that incomplete removal of infected trees and the appearance of new infections in previously asymptomatic trees could have allowed airborne detections of potentially infectious fungal propagules to once again increase.

Hawaii↗

USGS2021

Investigation of otolith microstructure and composition for identification of rearing strategies and associated Baker Lake sockeye salmon (Oncorhynchus nerka) smolt production, Washington, 2016–17

Baker River (Washington, USA) sockeye salmon (Oncorhynchus nerka) are a recovering Puget Sound stock that are aided by trap-and-haul and hatchery programs to mitigate for the presence of a high head dam. The relative contribution of hatchery and natural adults to overall production of smolts and recruits is unknown. The ability to identify three different sockeye production groups (natural production, artificial incubation, and artificial spawning beach) within the Baker system is crucial to moving forward with management goals. The examination of otoliths was proposed as a technical tool for improved understanding and management of Baker sockeye rebuilding efforts. Otoliths were chosen as they provide a chronological record on an individual fish basis and have been shown to identify fish origin through both otolith microstructure and chemistry. The goal of this pilot project was to determine the feasibility of assigning sockeye to their production source based on otolith analysis. A variety of methods were employed and compared for accuracy of group assignment. The maximum overall accuracy capable of attainment was 88.57 percent, however complete confidence (100 percent) in the separation of natural production from artificial production was reached through the analysis of trace elements alone. Some segregation of the two artificial production groups was reached through analysis of a few specific trace elements (magnesium, manganese, and zinc). This confidence in assignment for the artificial production groups was aided by a two-step process of combining trace elements with microstructure. The Sr isotope ratios supported the trace element findings but did not help to boost the overall level of confidence in the separation of production groups. Based upon the results from this preliminary investigation, one could choose a statistically sound, efficient, and cost-effective use of otoliths as a tool for discriminating between the sockeye production groups of the Baker Lake system.

Washington↗

USGS2007

Hydrogeologic characteristics of the St. Croix River basin, Minnesota and Wisconsin: Implications for the susceptibility of ground water to potential contamination

Population growth in the St. Croix River Basin in Minnesota and Wisconsin has intensified concerns of county resource managers and the National Park Service, which is charged with protecting the St. Croix National Scenic Riverway, about the potential for ground-water contamination in the basin. This report describes a previously developed method that was adapted to illustrate potential ground-water-contamination susceptibility in the St. Croix River Basin. The report also gives an estimate of ground-water-residence time and surface-water/ground-water interaction as related to natural attenuation and movement of contaminants in five tributary basins. A ground-water-contamination-susceptibility map was adapted from a state-wide map of Wisconsin to the St. Croix River Basin by use of well-driller construction records and regional maps of aquifer properties in Minnesota and Wisconsin. Measures of various subsurface properties were combined to generate a spatial index of susceptibility. The subjective index method developed for the State of Wisconsin by Schmidt (1987) 1 was not derived from analyses of water-quality data or physical processes. Nonetheless, it was adapted for this report to furnish a seamless map across state boundaries that would be familiar to many resource managers. Following this method, areas most susceptible to contamination appear to have coarse-grained sediments (sands or gravels) and shallow water tables or are underlain by carbonate-bedrock aquifers. The least susceptible areas appear to have fine-grained sediments and deep water tables. If an aquifer becomes contaminated, the ground-water-residence time can affect potential natural attenuation along the ground-water-flow path. Mean basin ground-water-residence times were computed for the Apple, Kettle, Kinnickinnic, Snake and Sunrise River Basins, which are tributary basins to the St. Croix Basin, by use of average aquifer properties of saturated thickness, porosity, and recharge rates. The Apple River Basin had the shortest mean ground-water-residence times (20–120 years), owing largely to the moderate saturated thickness and high recharge rate in the basin. The Kinnickinnic and Sunrise River Basins had the longest mean residence times (60–350 and 70–390 years, respectively) chiefly because of the relatively large saturated thickness of the basins. Owing to limitations of the residence-time calculations, actual ground-water-residence times will vary around the mean values within each basin and may range from days or weeks in karst carbonate aquifers to millennia in deep confined sandstone aquifers. Areas of relatively short residence time (less than the median residence time in each basin) were identified by use of ground-water-flow models for each of the five tributary basins. Results of simulations show that these areas, in which contaminants may have relatively less time for natural attenuation along the short flow paths, generally occur near streams and rivers where ground water discharges to the surface. Finally, the ground-water-flow models were used to simulate ground-water/surface-water interaction in the five tributary basins. Results of simulations show that some lakes and reservoirs leak surface water into the ground-water-flow system on their downgradient side, where the surface-water outflow has been restricted by a dam or a naturally constricted outlet. These locations are noteworthy because contaminated surface waters could potentially enter the ground-water-flow system at these locations.

Minnesota, Wisconsin↗

USGS2017

Methods for estimating selected low-flow frequency statistics and mean annual flow for ungaged locations on streams in North Georgia

The U.S. Geological Survey, in cooperation with the Georgia Department of Natural Resources, Environmental Protection Division, developed regional regression equations for estimating selected low-flow frequency and mean annual flow statistics for ungaged streams in north Georgia that are not substantially affected by regulation, diversions, or urbanization. Selected low-flow frequency statistics and basin characteristics for 56 streamgage locations within north Georgia and 75 miles beyond the State’s borders in Alabama, Tennessee, North Carolina, and South Carolina were combined to form the final dataset used in the regional regression analysis. Because some of the streamgages in the study recorded zero flow, the final regression equations were developed using weighted left-censored regression analysis to analyze the flow data in an unbiased manner, with weights based on the number of years of record. The set of equations includes the annual minimum 1- and 7-day average streamflow with the 10-year recurrence interval (referred to as 1Q10 and 7Q10), monthly 7Q10, and mean annual flow. The final regional regression equations are functions of drainage area, mean annual precipitation, and relief ratio for the selected low-flow frequency statistics and drainage area and mean annual precipitation for mean annual flow. The average standard error of estimate was 13.7 percent for the mean annual flow regression equation and ranged from 26.1 to 91.6 percent for the selected low-flow frequency equations. The equations, which are based on data from streams with little to no flow alterations, can be used to provide estimates of the natural flows for selected ungaged stream locations in the area of Georgia north of the Fall Line. The regression equations are not to be used to estimate flows for streams that have been altered by the effects of major dams, surface-water withdrawals, groundwater withdrawals (pumping wells), diversions, or wastewater discharges. The regression equations should be used only for ungaged sites with drainage areas between 1.67 and 576 square miles, mean annual precipitation between 47.6 and 81.6 inches, and relief ratios between 0.146 and 0.607; these are the ranges of the explanatory variables used to develop the equations. An attempt was made to develop regional regression equations for the area of Georgia south of the Fall Line by using the same approach used during this study for north Georgia; however, the equations resulted with high average standard errors of estimates and poorly predicted flows below 0.5 cubic foot per second, which may be attributed to the karst topography common in that area. The final regression equations developed from this study are planned to be incorporated into the U.S. Geological Survey StreamStats program. StreamStats is a Web-based geographic information system that provides users with access to an assortment of analytical tools useful for water-resources planning and management, and for engineering design applications, such as the design of bridges. The StreamStats program provides streamflow statistics and basin characteristics for U.S. Geological Survey streamgage locations and ungaged sites of interest. StreamStats also can compute basin characteristics and provide estimates of streamflow statistics for ungaged sites when users select the location of a site along any stream in Georgia.

Georgia↗

USGS2025

Fluvial sediment dynamics in the Shoshone River and tributaries around Willwood Dam, Park County, Wyoming

Sedimentation affects many of the aging reservoirs in the United States. Dams and water diversions from rivers have been central elements of infrastructure supporting agricultural irrigation in the arid and semiarid regions of the Western United States for more than a century. The Willwood Irrigation District diversion dam (hereafter referred to as “Willwood Dam”) in Park County, Wyoming, is approximately 12 miles northeast of Cody, Wyo.; has a structural height of 70 feet; and impounds the Shoshone River for diversion into the Willwood Canal. Willwood Dam is part of a larger irrigation scheme supported by water storage in the much larger Buffalo Bill Dam, which is approximately 20 miles upstream. In October 2016, renovation construction activities at Willwood Dam and the Willwood Canal caused an unplanned evacuation of nearly 96,000 cubic yards of fine sediment. The fine sediment release in 2016 raised concerns that ongoing sediment management at Willwood Dam could impose limits on the long-term health of the aquatic ecosystem and fish populations. The U.S. Geological Survey, in cooperation with Wyoming Department of Environmental Quality and Willwood Work Groups 2 and 3, initiated an investigation of the dynamics of sediment transport in the Shoshone River and selected tributaries between Buffalo Bill Dam and Willwood Dam. The goal of the study was to quantify sediment transport into and out of Willwood Dam on an annual, seasonal, and event basis to better understand the relative quantities of sediment coming from natural sources and human activities on the landscape. The study ran from March 2019 through October 2021 and used observations of streamflow, turbidity, and acoustic backscatter collected at streamgages upstream and downstream from Willwood Dam to quantify suspended-sediment loads into and out of the dam during irrigation and fallow seasons, precipitation-runoff events, and deliberate sediment releases. Each tributary’s relative contribution to the sediment load upstream from Willwood Dam was examined using discrete measurements of suspended-sediment concentration and bedload during irrigation and fallow seasons, precipitation events, and stable conditions. Analysis of daily precipitation and temperature data indicated that conditions in the study area during the 2019 agricultural year were wetter and colder than period of record normal, and drier and near normal temperatures for the 2020 and 2021 agricultural years. Not all sediment load records between 2019 and 2021 are complete because of rejected observations (outliers), instrument failures or fouling, and instrument removal for calibrations. Statistical modeling of suspended-sediment concentration using paired values of turbidity and acoustic backscatter produced four models that, after refinement, had coefficients of determination indicating that more than 84 percent of the variance was explained by either turbidity or acoustic backscatter. A system of rules was developed to select the model predictions based on the seasonal operations of Willwood Dam, assumptions about the grain sizes mobilized during these operations, and assumed accuracy of the models at the downstream streamgage (Shoshone River below Willwood Dam, near Ralston, Wyo. [streamgage 06284010]) under different operational conditions. The sediment budget between upstream and downstream estimates of loads was interpreted using the mean predicted values bound by their respective model prediction intervals. When mean predicted loads of one streamgage were contained in the prediction intervals of the other streamgage, and vice-versa, difference in the sediment budget were interpreted as “indeterminate.” Modeled sediment load balances demonstrated the depositional and erosional behaviors expected from the conceptual model of dam operations whereby sediment tends to accumulate during irrigation seasons when the dam is spilling over the top, and sediment tends to evacuate during the fallow seasons when it is flowing through the sluice gates at the base of the dam. The sediment load calculations using the rules-based model criteria indicated that between 14,200 and 380,000 tons of suspended sediment moved through the Shoshone River around Willwood Dam during the irrigation seasons of 2019, 2020, and 2021; 380,000 tons of suspended sediment were transported during the cool, wet year of 2019, and 14,200 tons of suspended sediment were transported in 2020, which was relatively dry. During fallow seasons 2019, 2020, and 2021, which had fewer complete records, between 1,140 and 106,000 tons of suspended sediment was estimated to have moved through the river. For all seasons except fallow season 2022, the models estimated that more sediment was released from the dam than entered the dam, but the modeled mean loads at each streamgage were nearly always within the prediction intervals of each other, making the sediment balance indeterminant. Examination of suspended-sediment loads during irrigation seasons indicated that between 65 and 85 percent of fine sediment was transported during annual high flows and storm events, with the remainder transported during steady, lower streamflows. Examination of suspended loads during fallow seasons indicated that deliberate sediment releases through Willwood Dam accounted for between 39 and 67 percent of the total sediment moved during the fallow seasons. Deliberate sediment releases from Willwood Dam had estimated net exports of between 1,360 and 22,400 tons. Between August 2017 and July 2023, suspended-sediment concentration and bedload sediment samples were collected from 9 tributaries to the Shoshone River during 137 sampling events, including stable and precipitation-runoff conditions. During irrigation season precipitation events, the mean total sediment yields ranged from 0.33 to 9.51 tons per day per square mile; during fallow season precipitation events, the mean total yields ranged from 0.04 to 0.95 ton per day per square mile. The mean total sediment yield per unit area across all samples at each tributary site ranged from 0.26 to 3.08 tons per day per square mile. Bedload was a minor fraction of the total load, constituting a mean of 4 percent across all samples; 3 and 6 percent for events and nonevents, respectively, during irrigation season; and 3 and 1 percent for events and nonevents, respectively, during the fallow season. With the exception of one tributary, Dry Creek, these mean yield values were within the range of watershed-scale background sediment yield values estimated from reservoir surveys and previous suspended-sediment studies. Imagery from irrigation seasons 2012, 2015, 2017, 2019, and 2022 was used to determine the planimetric backwater extent of the pool area in the Shoshone River behind Willwood Dam to identify any changes in sediment storage. Active river channel widths in the Shoshone River upstream from Willwood Dam were all similar between years except 2015, which was determined to be statistically different from all other years. Bathymetric data taken in the pool behind Willwood Dam during three different surveys between November 2017 and April 2022 indicated no statistically significant differences in bed elevations between the years. Results from the planimetric and bathymetric survey data provide multiple lines of evidence indicating that sediment did not accumulate behind the dam within the error of the methods used. Examination of how precipitation affects sediment transport in the Shoshone River upstream from Willwood Dam indicated that accumulated rainfall from the natural runoff events captured during the study period varied from a trace to as much as 4.26 inches, with associated predicted suspended-sediment loads varying from 112 to 232,000 tons of suspended sediment. The behavior of the sediment loads relative to accumulated precipitation did not appear to change depending on irrigation or fallow season. A model of suspended-sediment concentrations relative to the 2-day accumulated precipitation indicated that suspended-sediment concentrations in the Shoshone River upstream from Willwood Dam increased exponentially for accumulations of 0.3 inch or more; such storms accounted for 10 percent or less of precipitation events observed during the 1981 to 2018 period of record. The gaps in records, precision of the instrumentation, and large variation in grain sizes in suspended-sediment mixtures downstream from the dam made closing the sediment budgets for most seasons unattainable. The biggest recent change in sediment storage measured using the planimetric area of deposits behind Willwood Dam took place between 2015 and 2017. The main event between these two measurements was the installation of new Willwood Canal gates in October 2016, which resulted in the large unplanned sediment release. Because the sediment budgets were nearly always indeterminate and the planimetric and bathymetric data indicated little change in the bed and bank material, it is likely that the change in sediment storage behind the dam during the study period was small relative to the precision of the statistical models and other uncertainties. This body of evidence suggests that, averaged during the 3-year study period, no major changes in storage took place, and that the current operations may be keeping storage at near-equilibrium. This condition could have been initiated because the middle sluice gate has now been operational since 2014, and the sediment release in October 2016 evacuated a large amount of legacy sediment from storage. Although the uncertainties are large, sluicing events allow for controlled releases of sediment that contributed to the near equilibrium conditions observed over an annual basis during this study.

Wyoming↗

USGS2015

Climate change and wildfire risk in an expanding wildland–urban interface: a case study from the Colorado Front Range Corridor

Context Wildfire is a particular concern in the wildland–urban interface (WUI) of the western United States where human development occurs close to flammable natural vegetation. Objectives (1) Assess the relative influences of WUI expansion versus climate-driven fire regime change on spatial and temporal patterns of burned WUI, and (2) determine whether WUI developed in the future will have higher or lower wildfire risk than existing WUI. Methods We projected the spatial pattern of the WUI and its associated wildfire risk from 2005 to 2050 at 90-m spatial resolution and 5-year intervals in Colorado Front Range using CHANGE, a landscape change model that simulates land cover and land use change, natural vegetation dynamics, and wildfire in a unified framework. A total of four scenarios from a factorial design with static versus changing WUI and static versus changing fire regimes were simulated to examine the effects of WUI expansion and climate-driven fire regime change on burned area in the WUI. Results Both WUI expansion and fire regime change contributed to the increase of burned WUI, but fire regime change had a stronger influence. The effects of WUI expansion and fire regime change had a combined influence greater than the sum of their individual effects. This interaction was a result of projected WUI expansion into regions of higher wildfire risk than existing WUI. Conclusions The human footprint will continue to expand into wildland areas and must be considered along with climate effects when assessing the impacts of changing fire regimes in future landscapes.

Landscape Ecology↗

USGS2006

A review of the population estimation approach of the North American landbird conservation plan

As part of their development of a continental plan for monitoring landbirds (Rich et al. 2004), Partners in Flight (PIF) applied a new method to make preliminary estimates of population size for all 448 species of landbirds present in the continental United States and Canada (Table 1). Estimation of the global population size of North American landbirds was intended to (1) identify the degree of vulnerability of each species, (2) provide estimates of the current population size for each species, and (3) provide a starting point for estimating population sizes in states, provinces, territories, and Bird Conservation Regions (Rich et al. 2004). A method proposed by Rosenberg and Blancher (2005) was used to derive population estimates from available survey data. To enhance the credibility of these estimates, PIF organized a review of the methodology used to estimate North American landbird population sizes. A planning committee selected members from the ornithological and biometrical communities (hereafter “the panel”), with the aim of selecting individuals from academia, state natural-resource agencies, and the U.S. and Canadian federal governments, including the Canadian Wildlife Service, the U.S. Geological Survey, and the U.S. Department of Agriculture Forest Service. The panel addressed three questions: (1) Were the methods of population estimation proposed by PIF reasonable? (2) What actions could be taken to improve the data or analyses on which the PIF population estimates were based? and (3) How should the PIF population estimates be interpreted?

The Auk↗

USGS2020

Tests in a semi-natural environment suggest that bait and switch strategy could be used to control invasive Common Carp

Common Carp ( Cyprinus carpio Linnaeus, 1758), is a highly invasive species that has had profound effects on biodiversity and ecosystem services. Many Carp management methods have been applied including physical removal, pesticide treatments of whole lakes, and water drawdowns. Herein, we tested key elements of a potential “bait and switch” approach in which corn could be used to induce feeding aggregations of Carp and then switched for corn pellets with a pesticide Antimycin-A (ANT-A) to selectively target the Carp. First, laboratory experiments were used to determine if addition of lethal concentrations of ANT-A to corn pellets deterred Carp from eating corn-based food pellets. Second, a pond experiment tested if a corn-based bait containing ANT-A functioned as a species-specific Carp management tool in a semi-natural environment with three common native fishes: White Sucker ( Catostomus commersonii Lacepède, 1803), Yellow Perch ( Perca flavescens Mitchill, 1814), and Bluegill ( Lepomis macrochirus Rafinesque, 1819). The use of baited sites by Carp and native species was monitored using passive integrated transponder (PIT) tags. Mortality of each species and presence of corn in their digestive tracts was also monitored. Our laboratory experiment showed that presence of ANT-A did not deter Carp from consuming the pellets. The pond experiment showed that only Carp perished in significant numbers once toxic bait was applied. Further, only Carp increased their use of baited sites once baiting began, and only Carp had corn in their digestive tracts. Overall, our results indicate that corn might function as a species-specific Carp attractant in systems of North American Midwest and that corn-based bait can be used to effectively conceal a lethal dose of ANT-A. Further research is necessary to refine this potential management tool, specifically investigating the behavioral and social dynamics of Carp aggregating at sites baited with corn to enhance the temporal and spatial specificity of pesticide application.z

Management of Biological Invasions↗

USGS2000

Regional evaluation of evapotranspiration in the Everglades

Nine sites in the Florida Everglades were selected and instrumented for collection of data necessary for evapotranspiration-determination using the Bowen-ratio energy-budget method. The sites were selected to represent the sawgrass or cattail marshes, wet prairie, and open-water areas that constitute most of the natural Everglades system. At each site, measurements necessary for evapotranspiration (ET) calculation and modeling were automatically made and stored on-site at 15- or 30-minute intervals. Data collected included air temperature and humidity at two heights, wind speed and direction, incoming solar radiation, net solar radiation, water level and temperature, soil moisture content, soil temperature, soil heat flux, and rainfall. Data summarized in this report were collected from January 1996 through December 1997, and the development of site-specific and regional models of ET for this period is described. Latent heat flux is the energy flux density equivalent of the ET rate. Modified Priestley-Taylor models of latent heat flux as a function of selected independent variables were developed at each site. These models were used to fill in periods of missing latent heat flux measurement, and to develop regional models of the entire Everglades region. The regional models may be used to estimate ET in wet prairie, sawgrass or cattail marsh, and open-water portions of the natural Everglades system. The models are not applicable to forested areas or to the brackish areas adjacent to Florida Bay. Two types of regional models were developed. One type of model uses measurements of available energy at a site, together with incoming solar energy and water depth, to estimate hourly ET. This available-energy model requires site data for net radiation, water heat storage, and soil heat flux, as well as data for incoming solar radiation and water depth. The other type of model requires only incoming solar energy, air temperature, and water depth data to provide estimates of hourly ET. The second model thus uses data that are more readily available than the data required for the available-energy model. Computed ET mean annual totals for all nine sites for the 1996-97 period ranged from 42.4 inches per year at a site where the water level is below land surface for several months each year to 57.4 inches per year at an open-water site with no emergent vegetation. Although the density of photosynthetically-active plant leaves has been shown to relate directly to ET in some studies, it does not appear to relate directly to ET in the Everglades, based on comparison of annual ET data with leaf-area index, defined as the Normalized Difference Vegetation Index (NDVI), data from satellite imagery. NDVI and ET appear to be inversely related in the Everglades. The greatest ET rates occurred at open-water sites where the NDVI data indicated the lowest leaf-area index. Among the remaining vegetated sites, there is no clear relation between ET and NDVI, though the highest ET rate corresponded to the lowest NDVI and one of the lowest ET rates corresponded to the highest NDVI value. The variation in ET follows a seasonal pattern, with lowest monthly ET totals occurring in December through February, and highest ET occurring in May through August. The greatest range in monthly ET among all nine sites for the 2-year period occurred at site 3: from 1.81 inches in December 1997 to 6.84 inches in July 1996. A study to compare the Bowen-ratio/energy balance method of ET measurement with the eddy-correlation method was done at one site from June 22, 1998, through September 28, 1998. This comparison indicated that both methods gave comparable values of the Bowen ratio, but there was a considerable difference in available energy measured by the two methods. The mean of all 30-minute measured turbulent heat fluxes from the eddy-correlation apparatus for June 22 through September 29, 1998, was 137.4 watts per square meter, and the mean of the corresponding measured energy was 163.6 watts per square meter, or about 20 percent greater. The disagreement in mean energy fluxes measured by the two methods is problematical and is not fully understood. Although the difference seems to be related to friction velocity, and is practically non-existent at values of friction velocity greater than 0.3 meter per second, the "correctness" of either method cannot be determined with the data available.

Florida↗

USGS2019

Case studies in groundwater contaminant fate and transport

A case study of groundwater contamination is a detailed study of a single site contaminated with a chemical or mixture that is known to be a problem at many sites. The goal of case studies is to provide insights into the physical, chemical, and biological processes controlling migration, natural attenuation, or remediation of common groundwater contaminants. Ideally, processes occurring at a case study site are representative of other sites so that knowledge gained from these intensive studies can be applied at thousands of sites where fewer data are available. Several characteristics of case studies contribute to their value. First, they may have tens to hundreds of monitoring wells, compared to fewer than ten wells at some contaminated sites. Second, some case studies continue for many years or even decades, providing insights into temporal progression of slow processes. Third, analytical methods prohibitively expensive for routine use or under development may be tested at case study sites. Finally, the ongoing characterization typical of case study sites builds a foundation of knowledge that facilitates sophisticated experimental design and testing of new methods. This article is divided into sections based on the contaminant type because the chemical and biological processes required for remediation vary for each contaminant. Most importantly, some contaminants can be biodegraded whereas metals and radionuclides cannot be destroyed but can be immobilized or rendered less toxic. The emphasis is on case studies of natural processes that control the fate and transport of contaminants in groundwater rather than on active remediation methods. The principles learned from these studies may form the basis for design of remedial strategies. The organic contaminants are divided into: petroleum hydrocarbons, fuel oxygenates, coal tar and wastes from manufactured gas plants, and chlorinated solvents. The inorganic contaminants covered are metals and radionuclides, arsenic, and nitrate. Case studies of mixed waste plumes from landfills are also described. Experimental sites where contaminants have been introduced into an aquifer as an emplaced source or a controlled release may not meet the above definition of case studies, but some are included because the overall goal is to impart lessons learned from detailed field studies. It is impossible to cover all case studies in this short format. Conversely, focusing on one or two does not convey the breadth of research results in entire range of case studies. Instead, the strategy is to describe the evolution of knowledge for each contaminant class while providing citations of relevant case studies. Much of the progress in understanding of the fate of contaminants in groundwater is based on laboratory studies; thus whenever possible, papers that included both field and laboratory results have been included among the citations. Two topics of growing importance have not been covered. These are the fate of pharmaceuticals in groundwater and discharge of contaminant plumes to surface water. These topics merit coverage in the future as knowledge grows and case studies increase in number.

Environmental Science↗

USGS2022

Scat as a source of DNA for population monitoring

Sampling fecal droppings (scat) to genetically identify individual animals is an established method for monitoring mammal populations and could be highly useful for monitoring reptile populations. Whereas existing protocols for obtaining DNA from reptile scat focus on analyses of whole, fresh scat deposited during animal handling, the collection of scat naturally deposited by reptiles in situ, as required for non-invasive population monitoring, requires protocols to extract highly degraded DNA. Using surface swabs from such scats can reduce PCR inhibition, ecological impacts of removing scat, and zoonotic risks. We report on three related but independently designed studies of DNA analyses from scat swabs of herbivorous reptiles under natural desert conditions: two free-ranging desert tortoise species (Agassiz's desert tortoise, Gopherus agassizii , California, US, and Morafka's desert tortoise, G. morafkai , Arizona, US) and the common chuckwalla (Sauromalus atar ) (Arizona, US, and Sonora, MX). We analyzed samples from both tortoise species with the same set of 16 microsatellites and chuckwalla samples with four mtDNA markers; studies also varied in swab preservation medium and DNA extraction method. Microsatellite amplification success per sample, defined as ≥9 loci with amplification, varied between studies, with 15% for Agassiz's desert tortoise and 42% Morafka's desert tortoise. For chuckwallas, we successfully amplified and sequenced 50% of samples. We recovered fragments up to 400 bp for tortoises and 980 bp for chuckwallas from scat swab samples. This study demonstrates that genotypes can successfully be obtained from swabs of herbivorous reptile scat collected in the field under natural environmental conditions and emphasizes that repeat amplifications are necessary for genetic identification of individuals from non-invasive samples.

Arizona, California↗

USGS2013

Identification of metrics to monitor salt marsh integrity on National Wildlife Refuges in relation to conservation and management objectives

Executive Summary Most salt marshes in the US have been degraded by human activities, and threats from physical alterations, surrounding land-use, species invasions, and global climate change persist. Salt marshes are unique and highly productive ecosystems with high intrinsic value to wildlife, and many National Wildlife Refuges (NWRs) have been established in coastal areas to protect large tracts of salt marsh and wetland-dependent species. Various management practices are employed routinely on coastal NWRs to restore and enhance marsh integrity and ensure ecosystem sustainability. Prioritizing NWR salt marshes for application of management actions and choosing among multiple management options requires scientifically-based methods for assessing marsh condition. Monitoring is integral to structured decision-making (SDM), a formal process for decomposing a decision into its essential elements. Within a natural resource context, SDM involves identifying management objectives, alternative management actions, and expected management outcomes. The core of SDM is a set of criteria for measuring system performance and evaluating management responses. Therefore, use of SDM to frame natural resource decisions leads to logical selection of monitoring attributes that are linked explicitly to management needs. We used SDM to guide selection of variables for monitoring the ecological integrity of salt marshes within the National Wildlife Refuge System (NWRS). Our objectives were to identify indicators of salt marsh integrity that are effective across large geographic regions, responsive to a wide range of threats, and feasible to implement within funding and staffing constraints of the NWRS. In April, 2008, we engaged interdisciplinary experts in a week-long rapid prototyping SDM workshop to define the essential elements of salt marsh management decisions on refuges throughout the northeastern, southwestern, and northwestern US, corresponding to respective Regions 5, 2, and 1 of the US Fish and Wildlife Service (FWS). Through this process we identified measurable attributes for monitoring salt marsh ecosystems that are integrated into conservation practice and target management objectives. The following salt marsh attributes were identified through the SDM process either for describing state condition to determine management needs or for evaluating the achievement of management objectives: historical condition and geomorphic setting; ditch density; surrounding land use; ratio of open water area to vegetation area; rate of pesticide application; environmental contaminant concentration; change in marsh surface elevation relative to sea level rise; tidal range and groundwater level; surface topography; salinity; and species composition and abundance of vegetation, invasive species, invertebrates, nekton, and breeding and wintering birds. The identified attributes were too broadly defined to serve as operational monitoring variables. Therefore, we tested specific metrics for quantifying most of these attributes in summers of 2008 and 2009. The first four attributes in the above list can be characterized by office-based analysis of existing GIS data layers. The remaining attributes require field-based methods for assessment. We were forced to exclude a small number of attributes from field tests due to inconsistent data (pesticide application rate, environmental contaminant concentrations) or requirements that exceeded the scope of this project (change in marsh surface elevation; surface topography; benthic invertebrates; wintering birds). We evaluated potential metrics for evaluating all remaining field attributes. In partnership with NWRS biologists, we tested rapid versus intensive metrics for monitoring field attributes (tidal range and groundwater level; marsh surface elevation; salinity; and species composition and abundance of vegetation, invasive species, nekton, and breeding birds) at coastal refuges throughout FWS Region 5. Seven refuges participated in metric testing in 2008: Rachel Carson (ME), Parker River (MA), Wertheim (NY), E. B. Forsythe (NJ), Bombay Hook (DE), Prime Hook (DE), and Eastern Shore of Virginia Complex (VA). These seven and two additional refuges participated in metric testing in 2009: Rhode Island Complex (RI) and Stewart B. McKinney (CT). We based all field metrics on existing protocols for salt marsh assessment. Sampling locations were determined randomly within delineated marsh study units (MSUs) at each refuge. Detailed field methods are provided in appendices to this report. Measurements for individual metrics were averaged across samples within MSUs during each year of sampling. Each year, correlation or regression analysis was conducted on average measurements across MSUs within each attribute set to identify redundant metrics. Statistical redundancy between a pair of metrics within an attribute set (i.e., correlation or regression slopes with p-values < 0.05) was considered justification for eliminating one of the pair from the regional set of monitoring metrics. Decisions regarding metric elimination versus retention were based on feasibility of monitoring, considering such factors as sampling time, resources required, and potential for regional standardization in implementation. The result of these tests is a reduced suite of monitoring metrics that targets NWRS management decisions and is practicable for implementing on a regional scale. Based on these tests, we recommend the following list of metrics for monitoring integrity of NWRS salt marshes (marsh attribute category is in parentheses): (historical condition and geomorphic setting) position of marsh in the landscape, marsh shape, degree of fill and/or fragmentation, degree of tidal flushing, amount of aquatic edge; (ditch density) ranking of ditch density from none to severe; (surrounding land use) relative proportion of agricultural land in a 150-m buffer around the marsh, relative proportion of natural land in a 150-m buffer around the marsh, relative proportion of natural land in a 1-km buffer around the marsh; (ratio of open water area to vegetation area) ratio of open water to emergent herbaceous wetlands within the marsh; (marsh surface elevation) elevation referenced to NAVD88 in a representative area of the marsh; (tidal range and groundwater level) percent of time the marsh surface is flooded during deployment of a continuous water-level monitor at a representative marsh location, mean depth of surface flooding as measured by a continuous water-level monitor at a representative location; (salinity) salinity measured in surface water; (vegetation community) vegetation species richness using the point-intercept method in 100-m diameter survey plots, percent cover of various marsh community types within 100-m diameter survey plots; (invasive species abundance) percent cover of invasive plant species measured using the point-intercept method in 100-m diameter survey plots; (nekton community) nekton density, nekton species richness, length of Fundulus heteroclitus ; (breeding bird community) abundance of Willets counted per point during standard call-broadcast surveys, summed abundance of tidal marsh obligate species (Clapper Rail, Willet, Saltmarsh Sparrow, Seaside Sparrow) counted per point during standard call-broadcast surveys. Metrics describing the historical condition, geomorphic setting, and broad landscape features can be assessed using existing GIS databases. Our results support use of rapid methods to assess the majority of field metrics; only those used to describe the nekton community must be measured using intensive methods (throw traps or ditch nets, dependant on habitat configuration). Implementation of these metrics for quantitative assessment of NWRS salt marsh integrity in FWS Region 5 requires developing sampling designs for each refuge. Additionally, it is important to determine how the monitoring information will be used within a management context. SDM should be used to complete the analysis of salt marsh management decisions. The next steps would involve 1) prioritizing and weighting the management objectives; 2) predicting responses to individual management actions in terms of objectives and metrics; 3) using multiattribute utility theory to convert all measurable attributes to a common utility scale; 4) determining the total management benefit of each action by summing utilities across objectives; and 5) maximizing the total management benefits within cost constraints for each refuge. This process would allow the optimum management decisions for NWRS salt marshes to be selected and implemented based directly on monitoring data and current understanding of marsh responses to management actions. Monitoring the outcome of management actions would then allow new monitoring data to be incorporated into subsequent decisions.

Connecticut, Delaware, Maine, Massachusetts, New J↗

USGS1996

Measuring and monitoring biological diversity: Standard methods for mammals

Measuring and Monitoring Biological Diversity: Standard Methods for Mammals provides a comprehensive manual for designing and implementing inventories of mammalian biodiversity anywhere in the world and for any group, from rodents to open-country grazers. The book emphasizes formal estimation approaches, which supply data that can be compared across habitats and over time. Beginning with brief natural histories of the twenty-six orders of living mammals, the book details the field techniques—observation, capture, and sign interpretation—appropriate to different species. The contributors provide guidelines for study design, discuss survey planning, describe statistical techniques, and outline methods of translating field data into electronic formats. Extensive appendixes address such issues as the ethical treatment of animals in research, human health concerns, preserving voucher specimens, and assessing age, sex, and reproductive condition in mammals. Useful in both developed and developing countries, this volume and the Biological Diversity Handbook Series as a whole establish essential standards for a key aspect of conservation biology and resource management.

Book↗

USGS2018

Relationships between landscape constraints and a crayfish assemblage with consideration of competitor presence

Aim Crayfish are globally diverse and one of the most important taxa in North American streams. Despite their importance, many species are of conservation concern and efforts to improve conditions are limited. Here, we address two major impediments to improving conditions: (a) our lack of knowledge of the interplay among natural landscape and human-induced changes; and (b) a very limited understanding of how species interactions affect overall crayfish distributions. Location Ozark Highlands ecoregion, USA. Methods We used both existing data and field-collected data to examine the relationships between 12 Faxonius species and physicochemical variables at multiple spatial scales. Data were analysed using a generalized linear mixed model. After fitting our environmental variables, we also considered possible relationships between species considered strong competitors and species occurrence. Results Our results indicated that elevation, lithology, an interaction between drainage area and anthropogenic disturbance, and the presence of strong competitors were associated with Faxonius occurrences. Faxonius occurrences were associated with assemblage-structuring variables: lithology and elevation. More interestingly, we found several patterns of interactions between drainage area and disturbance. The most common pattern among several species was a decline in occurrence in larger drainages when disturbance was high; however, longpincered crayfish ( Faxonius longidigitus ) was more likely to occupy large drainages as disturbance increased. Additionally, the presence of species considered strong competitors resulted in lower occurrence probability for many species, including two of the species classified as competitors. Main conclusions In addition to identifying the relationships between native species and assemblage-structuring variables, we show how the probability of species occurrences relate to interactions between disturbance and natural landscape features. Further, our results suggest competitor presence also plays a role in structuring distributions at the stream segment scale. Our findings emphasize the value of considering both competitor presence and interactions among landscape variables and disturbances in structuring crayfish assemblages.

Arkansas, Missouri↗

USGS2014

Viral fitness does not correlate with three genotype displacement events involving infectious hematopoietic necrosis virus

Viral genotype displacement events are characterized by the replacement of a previously dominant virus genotype by a novel genotype of the same virus species in a given geographic region. We examine here the fitness of three pairs of infectious hematopoietic necrosis virus (IHNV) genotypes involved in three major genotype displacement events in Washington state over the last 30 years to determine whether increased virus fitness correlates with displacement. Fitness was assessed using in vivo assays to measure viral replication in single infection, simultaneous co-infection, and sequential superinfection in the natural host, steelhead trout. In addition, virion stability of each genotype was measured in freshwater and seawater environments at various temperatures. By these methods, we found no correlation between increased viral fitness and displacement in the field. These results suggest that other pressures likely exist in the field with important consequences for IHNV evolution.

Washington↗

USGS2005

Perchlorate isotope forensics

Perchlorate has been detected recently in a variety of soils, waters, plants, and food products at levels that may be detrimental to human health. These discoveries have generated considerable interest in perchlorate source identification. In this study, comprehensive stable isotope analyses ( 37 Cl/ 35 Cl and 18 O/ 17 O/ 16 O) of perchlorate from known synthetic and natural sources reveal systematic differences in isotopic characteristics that are related to the formation mechanisms. In addition, isotopic analyses of perchlorate extracted from groundwater and surface water demonstrate the feasibility of identifying perchlorate sources in contaminated environments on the basis of this technique. Both natural and synthetic sources of perchlorate have been identified in water samples from some perchlorate occurrences in the United States by the isotopic method.

Analytical Chemistry↗

USGS2000

Using structural equation modeling to investigate relationships among ecological variables

Structural equation modeling is an advanced multivariate statistical process with which a researcher can construct theoretical concepts, test their measurement reliability, hypothesize and test a theory about their relationships, take into account measurement errors, and consider both direct and indirect effects of variables on one another. Latent variables are theoretical concepts that unite phenomena under a single term, e.g., ecosystem health, environmental condition, and pollution (Bollen, 1989). Latent variables are not measured directly but can be expressed in terms of one or more directly measurable variables called indicators. For some researchers, defining, constructing, and examining the validity of latent variables may be the end task of itself. For others, testing hypothesized relationships of latent variables may be of interest. We analyzed the correlation matrix of eleven environmental variables from the U.S. Environmental Protection Agency's (USEPA) Environmental Monitoring and Assessment Program for Estuaries (EMAP-E) using methods of structural equation modeling. We hypothesized and tested a conceptual model to characterize the interdependencies between four latent variables-sediment contamination, natural variability, biodiversity, and growth potential. In particular, we were interested in measuring the direct, indirect, and total effects of sediment contamination and natural variability on biodiversity and growth potential. The model fit the data well and accounted for 81% of the variability in biodiversity and 69% of the variability in growth potential. It revealed a positive total effect of natural variability on growth potential that otherwise would have been judged negative had we not considered indirect effects. That is, natural variability had a negative direct effect on growth potential of magnitude -0.3251 and a positive indirect effect mediated through biodiversity of magnitude 0.4509, yielding a net positive total effect of 0.1258. Natural variability had a positive direct effect on biodiversity of magnitude 0.5347 and a negative indirect effect mediated through growth potential of magnitude -0.1105 yielding a positive total effects of magnitude 0.4242. Sediment contamination had a negative direct effect on biodiversity of magnitude -0.1956 and a negative indirect effect on growth potential via biodiversity of magnitude -0.067. Biodiversity had a positive effect on growth potential of magnitude 0.8432, and growth potential had a positive effect on biodiversity of magnitude 0.3398. The correlation between biodiversity and growth potential was estimated at 0.7658 and that between sediment contamination and natural variability at -0.3769.

Environmental and Ecological Statistics↗