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USGS2016

Removing sun glint from optical remote sensing images of shallow rivers

Sun glint is the specular reflection of light from the water surface, which often causes unusually bright pixel values that can dominate fluvial remote sensing imagery and obscure the water-leaving radiance signal of interest for mapping bathymetry, bottom type, or water column optical characteristics. Although sun glint is ubiquitous in fluvial remote sensing imagery, river-specific methods for removing sun glint are not yet available. We show that existing sun glint-removal methods developed for multispectral images of marine shallow water environments over-correct shallow portions of fluvial remote sensing imagery resulting in regions of unreliable data along channel margins. We build on existing marine glint-removal methods to develop a river-specific technique that removes sun glint from shallow areas of the channel without overcorrection by accounting for non-negligible water-leaving near-infrared radiance. This new sun glint-removal method can improve the accuracy of spectrally-based depth retrieval in cases where sun glint dominates the at-sensor radiance. For an example image of the gravel-bed Snake River, Wyoming, USA, observed-vs.-predicted R 2 values for depth retrieval improved from 0.66 to 0.76 following sun glint removal. The methodology presented here is straightforward to implement and could be incorporated into image processing workflows for multispectral images that include a near-infrared band.

Earth Surface Processes and Landforms↗

USGS2019

Demographic factors affecting population growth in giant gartersnakes

Demographic models provide insight into which vital rates and life stages contribute most to population growth. Integral projection models (IPMs) offer flexibility in matching model structure to a species’ demography. For many rare species, data are lacking for key vital rates, and uncertainty might dissuade researchers from attempting to build a demographic model. We present work that highlights how the implications of uncertainties and unknowns can be explored by building and analyzing alternative models. We constructed IPMs for the threatened giant gartersnake ( Thamnophis gigas ) based on published studies to determine where management efforts could be targeted to have the greatest effect on population persistence and what unknowns remain for future research. Given uncertainty in the survival of snakes during their first year, and in the form of the size‐survival relationship, we modeled a range of scenarios and evaluated where models agree about factors influencing population growth and where discrepancies exist. For most scenarios, the survival of large adult females had the greatest influence on population growth, but the relative importance of juvenile versus adult somatic growth for population growth was dependent on the recruitment probability and the shape of the size‐survival function. More data on temporal variation and covariance among vital rates would improve stochastic models for the giant gartersnake. This paper demonstrates the effectiveness of IPMs for studying the demography of reptiles and the value of the model‐building process for formalizing what is known and unknown about the demography of rare species. Published 2019. This article is a U.S. Government work and is in the public domain in the USA.

California↗

USGS2023

Bobcat occupancy, tree islands, and invasive Burmese pythons in an Everglades conservation area

Bobcats ( Lynx rufus ) are terrestrial mammals that also inhabit tree islands (i.e., topographically elevated patches of forested land) embedded in the subtropical Everglades wetlands, which serve as a dry refuge habitat during the wet season in this region of Florida, USA. The Comprehensive Everglades Restoration Plan seeks to restore Everglades water flow to pre-drainage conditions, but little is known about how water levels or other landscape-level factors may influence mammalian occurrence, such as bobcats, on the tree islands in this ecosystem. We used game camera records and occupancy modeling to test for effects of static habitat variables and dynamic hydrologic variables. We hypothesized that deep water levels would limit the accessibility of tree islands to bobcats; therefore, we predicted that bobcat occupancy would decline with higher water levels. We also tested for the effect of an expanding invasive snake (i.e., Burmese python [ Python molarus bivittatus ]) using output from a model constructed to predict density and spread of Burmese pythons across southern Florida. We hypothesized that increases in Burmese pythons on the landscape would influence the food resources of bobcats, resulting in reduced bobcat occupancy at higher predicted densities of pythons. We built detection histories using 1,855 bobcat images from game cameras set on 87 tree islands in an Everglades conservation area from 2005–2019. Bobcat occupancy was significantly diminished when predicted Burmese python densities exceeded approximately 3 Burmese pythons/km 2 . Bobcat occupancy probability also increased with tree-island density around the focal tree island. Although water depth and hydroperiod surrounding tree islands appeared in our top 3 candidate models, the hydrologic variables had weak effects on bobcat occupancy. Our results suggest that while hydrologic dynamics may play a role, the invasive Burmese python has stronger influences on bobcat occupancy of tree islands in this Everglades conservation area.

Florida↗

USGS2023

Drawdown, habitat, and kokanee populations in a western U.S. reservoir

Greater drought frequency and severity due to climate change will result in greater drawdown of water storage reservoirs. However, changes to oxythermal regimes due to drawdown are reservoir specific and interface with fish species-specific habitat requirements, producing varying effects on coldwater fish populations. We examined the effect of drawdown on the oxythermal habitat and relative abundance of kokanee Oncorhynchus nerka , a coldwater salmonid, in Island Park Reservoir on the Henrys Fork of the Snake River, Idaho. A measure of relative kokanee abundance was negatively, exponentially related to drawdown. Oxythermal patterns measured in the reservoir during 2021, a severe drought year, revealed that drawdown reduced kokanee habitat by increasing water temperatures and decreasing dissolved oxygen concentrations. Oxythermal refugia for kokanee appeared to relate to inflow from the spring-fed Henrys Fork and other groundwater inflows. However, we did not quantify groundwater flow or connections, and we did not study kokanee population demographics or mortality. Reducing these sources of uncertainty is a priority for future study. Still, our study highlights a potential mechanism connecting reservoir drawdown to fish populations and the unique yet predictable mechanisms by which reservoir drawdown interacts with reservoir morphometry to affect fish habitat availability.

Idaho↗

USGS2005

Application of wavelet analysis for monitoring the hydrologic effects of dam operation: Glen canyon dam and the Colorado River at lees ferry, Arizona

Wavelet analysis is a powerful tool with which to analyse the hydrologic effects of dam construction and operation on river systems. Using continuous records of instantaneous discharge from the Lees Ferry gauging station and records of daily mean discharge from upstream tributaries, we conducted wavelet analyses of the hydrologic structure of the Colorado River in Grand Canyon. The wavelet power spectrum (WPS) of daily mean discharge provided a highly compressed and integrative picture of the post-dam elimination of pronounced annual and sub-annual flow features. The WPS of the continuous record showed the influence of diurnal and weekly power generation cycles, shifts in discharge management, and the 1996 experimental flood in the post-dam period. Normalization of the WPS by local wavelet spectra revealed the fine structure of modulation in discharge scale and amplitude and provides an extremely efficient tool with which to assess the relationships among hydrologic cycles and ecological and geomorphic systems. We extended our analysis to sections of the Snake River and showed how wavelet analysis can be used as a data mining technique. The wavelet approach is an especially promising tool with which to assess dam operation in less well-studied regions and to evaluate management attempts to reconstruct desired flow characteristics. Copyright ?? 2005 John Wiley & Sons, Ltd.

River Research and Applications↗

USGS2023

Survey optimization for invasive Burmese pythons informed by camera traps

The Burmese python ( Python bivittatus ) is an invasive predator responsible for broad mammal declines in South Florida, United States. Despite their large size, pythons remain cryptic and require multifaceted approaches for detection. We evaluated a novel technique by deploying camera traps at known locations of radiotagged pythons in the Florida Keys. We estimated daily detection probabilities of snakes and plotted diel activity patterns. Our results suggest camera traps can effectively survey pythons but seasonality and camera trigger mechanisms affect utility. Pythons were most detectable with time-lapse camera traps and more detectable in winter. The diel activity pattern of pythons peaked midday through early afternoon, indicating an optimal survey time for other search methods. Artificial intelligence can alleviate photo volume, so we recommend a combination of motion detection and time-lapse with shorter time (1 min) intervals for python-specific surveys and where camera traps are deployed to monitor mammals to improve passive python detection.

Florida↗

USGS2025

Observability of eastern massasauga (Sistrurus catenatus) during visual encounter surveys in Michigan, USA

Visual encounter surveys are commonly used to document site occupancy for the eastern massasauga ( Sistrurus catenatus ; EMR). Efficacy of surveys depends on visual and auditory cues, with basking behavior and burrow use strongly affecting detection. Our goal was to predict body exposure and probability of burrow use from telemetered EMR to better inform implementation of visual encounter surveys. We collected body exposure and burrow use from 23 EMR (14 females [12 gravid], 9 males) from April through September (i.e., active season) at 2 sites in south central Michigan, USA, 2020–2022. Average body exposure for observed snakes was 42% (SE = 3%) and ranged from 0–100%. Percent body exposure during the active season was positively influenced by air temperature, where body exposure increased from ~25% at ~15°C to ~50% at ~35°C. We did not find an effect of cloud cover, hour of day, humidity, or sex on EMR body exposure. Of 176 observations of EMR during the active season, we found EMR using burrows 20 times (~11% of observations). Julian date and air temperature affected the probability of EMR burrow use early in the active season. Probability of EMR burrow use was <0.10 from the end of May through the end of October and was almost 0.00 after mid-July. The probability of using a burrow was generally low (i.e., <0.25) across the range of air temperatures measured in our study, but approached 0.00 as temperatures exceeded 30°C. We did not find an effect of cloud cover, time of day, humidity, or sex on probability of EMR burrow use. Our results indicated that EMR observability in southern Michigan was greatest when air temperatures were 30°C to 35°C, corresponding to when EMR were visible and aboveground.

Michigan↗

USGS2017

Comparison of conventional K-Ar and 40Ar/39Ar dating of young mafic volcanic rocks

K-Ar and 40Ar/39Ar ages have been measured on nine mafic volcanic rocks younger than 1 myr from the Snake River Plain (Idaho), Mount Adams (Washington), and Crater Lake (Oregon). The K-Ar ages were calculated from Ar measurements made by isotope dilution and K2O measurements by flame photometry. The 40Ar/39Ar ages are incremental-heating experiments using a low-blank resistance-heated furnace. The results indicate that high-quality ages can be measured on young, mafic volcanic rocks using either the K-Ar or the 40Ar/39Ar technique. The precision of an 40Ar/39Ar plateau age generally is better than the precision of a K-Ar age because the plateau age is calculated by pooling the ages of several gas increments. The precision of a plateau age generally is better than the precision of an isotope correlation (isochron) age for the same sample. For one sample the intercept of the isochron yielded an 40Ar/36Ar value significantly different from the atmospheric value of 295.5. Recalculation of increment ages using the isochron intercept for the composition of nonradiogenic Ar in the sample resulted in much better agreement of ages for this sample. The results of this study also indicate that, given suitable material and modern equipment, precise K-Ar and 40Ar/39Ar ages can be measured on volcanic rocks as young as the latest Pleistocene, and perhaps even the Holocene.

Quaternary Research↗

USGS2023

Amphibians and reptiles

Amphibians and reptiles are a diverse group of ectothermic vertebrates that occupy a variety of habitats in rangelands of North America, from wetlands to the driest deserts. These two classes of vertebrates are often referred to as herpetofauna and are studied under the field of herpetology. In U.S. rangelands, there are approximately 66 species of frogs and toads, 58 salamanders, 98 lizards, 111 snakes, and 27 turtles and tortoises. Herpetofauna tend to be poorly studied compared with other vertebrates, which creates a challenge for biologists and landowners who are trying to manage rangeland activities for this diverse group of animals and their habitats. Degradation of habitats from human land use and alteration of natural processes, like wildfire, are primary threats to herpetofauna populations. Disease, non-native predators, collection for the pet trade, and persecution are also conservation concerns for some species. Properly managed livestock grazing is generally compatible with herpetofauna conservation, and private and public rangelands provide crucial habitat for many species. Climate change also poses a threat to herpetofauna, but we have an incomplete understanding of the potential effects on species. Dispersal and adaptation could provide some capacity for species to persist on rangelands as climates, disturbance regimes, and habitats change. However, inadequate information and considerable uncertainty will make climate mitigation planning difficult for the foreseeable future. Planning for and mitigating effects of climate change, and interactions with other stressors, is an urgent area for research. Maintaining large, heterogeneous land areas as rangelands will certainly be an important part of the conservation strategy for herpetofauna in North America.

Book chapter↗

USGS1996

Predictive techniques for river channel evolution and maintenance

Predicting changes in alluvial channel morphology associated with anthropogenic and natural changes in flow and/or sediment supply is a critical part of the management of riverine systems. Over the past few years, advances in the understanding of the physics of sediment transport in conjunction with rapidly increasing capabilities in computational fluid dynamics have yielded now approaches to problems in river mechanics. Techniques appropriate for length scales ranging from reaches to bars and bedforms are described here. Examples of the use of these computational approaches are discussed for three cases: (1) the design of diversion scenarios that maintain channel morphology in steep cobble-bedded channels in Colorado, (2) determination of channel maintenance flows for the preservation of channel islands in the Snake River in Idaho, and (3) prediction of the temporal evolution of deposits in lateral separation zones for future assessment of the impacts of various dam release scenarios on lateral separation deposits in the Colorado River in Grand Canyon. With continued development of their scientific and technical components, the methodologies described here can provide powerful tools for the management of river environments in the future.

Water, Air, & Soil Pollution↗

USGS1985

Metals in riparian wildlife of the lead mining district of southeastern Missouri

Five species of riparian vertebrates (425 individuals) primarily representing upper trophic levels were collected from the Big River and Black River drainages in two lead mining districts of southeastern Missouri, 1981–82. Big River is subject to metal pollution via erosion and seepage from large tailings piles from inactive lead mines. Black River drains part of a currently mined area. Bullfrogs ( Rana catesbeiana ), muskrats ( Ondatra zibethicus ), and green-backed herons ( Butorides striatus ) collected downstream from the source of metal contamination to Big River had significantly (ANOVA, P<0.05) higher lead and cadmium levels than specimens collected at either an uncontaminated upstream site or on Black River. Northern water snakes ( Nerodia sipedon ) had elevated lead levels below the tailings source, but did not seem to accumulate cadmium. Levels of lead, cadmium, or zinc in northern rough-winged swallows ( Stelgidopteryx serripennis ) were not related to collecting locality. Carcasses of ten bank swallows ( Riparia riparia ) collected from a colony nesting in a tailings pile along the Big River had lead concentrations of 2.0–39 ppm wet weight. Differences between zinc concentrations in vertebrates collected from contaminated and uncontaminated sites were less apparent than differences in lead and cadmium. There was little relationship between metal concentrations in the animals studied and their trophic levels. Bullfrogs are the most promising species examined for monitoring environmental levels of lead, cadmium, and zinc. Downstream from the source of tailings, bullfrogs had markedly higher levels of these metals in most of their tissues. The species is also widely distributed in North America, easily caught, and relatively sedentary.

Missouri↗

USGS2012

Mercury and selenium concentrations in biofilm, macroinvertebrates, and fish collected in the Yankee Fork of the Salmon River, Idaho, USA, and their potential effects on fish health

The Yankee Fork is a large tributary of the Salmon River located in central Idaho, USA, with an extensive history of placer and dredge-mining activities. Concentrations of selenium (Se) and mercury (Hg) in various aquatic trophic levels were measured in the Yankee Fork during 2001 and 2002. Various measurements of fish health were also performed. Sites included four on the mainstem of the Yankee Fork and two off-channel sites in partially reclaimed dredge pools used as rearing habitat for cultured salmonid eggs and fry. Hg concentrations in whole mountain whitefish and shorthead sculpin ranged from 0.28 to 0.56 μg/g dry weight (dw), concentrations that are generally less than those reported to have significant impacts on fish. Biofilm and invertebrates ranged from 0.05 to 0.43 μg Hg/g dw. Se concentrations measured in biota samples from the Yankee Fork were greater than many representative samples collected in the Snake and Columbia watersheds and often exceeded literature-based toxic thresholds. Biofilm and invertebrates ranged from 0.58 to 4.66 μg Se/g dw. Whole fish ranged from 3.92 to 7.10 μg Se/g dw, and gonads ranged from 6.91 to 31.84 μg Se/g dw. Whole-body Se concentrations exceeded reported toxicological thresholds at three of four sites and concentrations in liver samples were mostly greater than concentrations shown to have negative impacts on fish health. Histological examinations performed during this study noted liver abnormalities, especially in shorthead sculpin, a bottom-dwelling species.

Idaho↗

USGS2001

Determination of variables in the prediction of strontium distribution coefficients for selected sediments

Idaho State University and the US Geological Survey, in cooperation with the US Department of Energy, conducted a study to determine and evaluate strontium distribution coefficients (Kds) of subsurface materials at the Idaho National Engineering and Environmental Laboratory (INEEL). The Kds were determined to aid in assessing the variability of strontium Kds and their effects on chemical transport of strontium-90 in the Snake River Plain aquifer system. Data from batch experiments done to determine strontium Kds of five sediment-infill samples and six standard reference material samples were analyzed by using multiple linear regression analysis and the stepwise variable-selection method in the statistical program, Statistical Product and Service Solutions, to derive an equation of variables that can be used to predict strontium Kds of sediment-infill samples. The sediment-infill samples were from basalt vesicles and fractures from a selected core at the INEEL; strontium Kds ranged from ???201 to 356 ml g-1. The standard material samples consisted of clay minerals and calcite. The statistical analyses of the batch-experiment results showed that the amount of strontium in the initial solution, the amount of manganese oxide in the sample material, and the amount of potassium in the initial solution are the most important variables in predicting strontium Kds of sediment-infill samples.

Environmental Geology↗

USGS2016

Geochemistry and hydrology of perched groundwater springs: assessing elevated uranium concentrations at Pigeon Spring relative to nearby Pigeon Mine, Arizona (USA)

The processes that affect water chemistry as the water flows from recharge areas through breccia-pipe uranium deposits in the Grand Canyon region of the southwestern United States are not well understood. Pigeon Spring had elevated uranium in 1982 (44 μg/L), compared to other perched springs (2.7–18 μg/L), prior to mining operations at the nearby Pigeon Mine. Perched groundwater springs in an area around the Pigeon Mine were sampled between 2009 and 2015 and compared with material from the Pigeon Mine to better understand the geochemistry and hydrology of the area. Two general groups of perched groundwater springs were identified from this study; one group is characterized by calcium sulfate type water, low uranium activity ratio 234 U/ 238 U (UAR) values, and a mixture of water with some component of modern water, and the other group by calcium-magnesium sulfate type water, higher UAR values, and radiocarbon ages indicating recharge on the order of several thousand years ago. Multivariate statistical principal components analysis of Pigeon Mine and spring samples indicate Cu, Pb, As, Mn, and Cd concentrations distinguished mining-related leachates from perched groundwater springs. The groundwater potentiometric surface indicates that perched groundwater at Pigeon Mine would likely flow toward the northwest away from Pigeon Spring. The geochemical analysis of the water, sediment and rock samples collected from the Snake Gulch area indicate that the elevated uranium at Pigeon Spring is likely related to a natural source of uranium upgradient from the spring and not likely related to the Pigeon Mine.

Arizona↗

USGS2016

Preferential flow, diffuse flow, and perching in an interbedded fractured-rock unsaturated zone

Layers of strong geologic contrast within the unsaturated zone can control recharge and contaminant transport to underlying aquifers. Slow diffuse flow in certain geologic layers, and rapid preferential flow in others, complicates the prediction of vertical and lateral fluxes. A simple model is presented, designed to use limited geological site information to predict these critical subsurface processes in response to a sustained infiltration source. The model is developed and tested using site-specific information from the Idaho National Laboratory in the Eastern Snake River Plain (ESRP), USA, where there are natural and anthropogenic sources of high-volume infiltration from floods, spills, leaks, wastewater disposal, retention ponds, and hydrologic field experiments. The thick unsaturated zone overlying the ESRP aquifer is a good example of a sharply stratified unsaturated zone. Sedimentary interbeds are interspersed between massive and fractured basalt units. The combination of surficial sediments, basalts, and interbeds determines the water fluxes through the variably saturated subsurface. Interbeds are generally less conductive, sometimes causing perched water to collect above them. The model successfully predicts the volume and extent of perching and approximates vertical travel times during events that generate high fluxes from the land surface. These developments are applicable to sites having a thick, geologically complex unsaturated zone of substantial thickness in which preferential and diffuse flow, and perching of percolated water, are important to contaminant transport or aquifer recharge.

Idaho↗

USGS2023

To remediate or not? Source identification in an acid mine drainage stream, Warden Gulch, Colorado

A synoptic water quality study was implemented in Warden Gulch, a headwater stream affected by metals that are contributed by both natural and mining-impacted sources. Warden Gulch is a tributary to Peru Creek (Colorado, USA), where emplacement of a mine tunnel bulkhead and other remedial actions have improved water quality upstream of Warden Gulch. The goal of this study was to identify individual source contributions to Warden Gulch and determine if additional remedial actions were warranted. To this end, trace metal loading was quantified from various sources including an actively draining mine. Although highly concentrated waste streams from mining-impacted sites degrade water quality, natural contributions from unmined areas within the Warden Gulch watershed are the dominant sources of metal loading. Further, some mining-impacted sources are associated with diffuse groundwater inflows that may not be amenable to clean up, due to the diffuse nature of the sources and the associated cost. Mining-impacted sources that are amenable to clean up may therefore represent a small portion of the overall metal loading to Warden Gulch. Remedial measures directed at these sources may not substantially improve the water quality of Peru Creek and the larger Snake River watershed.

Colorado↗

USGS2014

Indirect effects of biocontrol of an invasive riparian plant ( Tamarix ) alters habitat and reduces herpetofauna abundance

The biological control agent (tamarisk leaf beetle, Diorhabda spp.) is actively being used to defoliate exotic saltcedar or tamarisk ( Tamarix spp.) in riparian ecosystems in western USA. The Virgin River in Arizona and Nevada is a system where tamarisk leaf beetle populations are spreading. Saltcedar biocontrol, like other control methods, has the potential to affect non-target species. Because amphibians and reptiles respond to vegetation changes in habitat and forage in areas where beetles are active, herpetofauna are model taxa to investigate potential impacts of biocontrol defoliation. Our objectives related herpetofauna abundance to vegetation cover and indices (normalized difference vegetation index, NDVI; enhanced vegetation index, EVI) and timing of biocontrol defoliation. We captured herpetofauna and ground-dwelling arthropods in trap arrays and measured vegetation using remotely sensed images and on-the-ground measurements at 16–21 sites 2 years before (2009–2010) and 2 years following (2011–2012) biocontrol defoliation. Following defoliation, riparian stands (including stands mixed with native and exotic trees and stands of monotypic exotic saltcedar) had significantly lower NDVI and EVI values and fewer captures of marked lizards. Total captures of herpetofauna (toads, lizards, and snakes) were related to higher vegetation cover and sites with a lower proportion of saltcedar. Our results suggest that effects of biocontrol defoliation are likely to be site-specific and depend upon the proportion of native riparian trees established prior to biocontrol introduction and defoliation. The mechanisms by which habitat structure, microclimate, and ultimately vertebrate species are affected by exotic plant biocontrol riparian areas should be a focus of natural-resource managers.

Mojave Desert↗

USGS2010

A population genetic analysis of the midget faded rattlesnake in Wyoming

Little is known about the population biology of midget faded rattlesnakes, a sensitive subspecies of the Western Rattlesnake, despite conservation efforts to protect them. We conducted a molecular genetic study of midget faded rattlesnakes in southwestern Wyoming to investigate population genetic structure in this area, particularly with reference to Flaming Gorge Reservoir and its associated human activities, and to document levels of genetic diversity. We genotyped 229 snakes from 11 sampling sites using 9 microsatellite loci. We found significant levels of genetic structure among sites that were better explained by geographic region and isolation by distance than by position relative to waterways. Sites on either side of the reservoir at its widest point were not significantly different. Six of the sites showed signatures of a population bottleneck using an alpha value of 0.05. Three of these bottlenecked sites (the three most northern) were the most genetically distinct and occur in areas of greatest impact from human activity.

Wyoming↗