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At least 1,009 records · Page 56Linked to original sources

USGS2014

Inferences about population dynamics from count data using multi-state models: A comparison to capture-recapture approaches

Wildlife populations consist of individuals that contribute disproportionately to growth and viability. Understanding a population's spatial and temporal dynamics requires estimates of abundance and demographic rates that account for this heterogeneity. Estimating these quantities can be difficult, requiring years of intensive data collection. Often, this is accomplished through the capture and recapture of individual animals, which is generally only feasible at a limited number of locations. In contrast, N-mixture models allow for the estimation of abundance, and spatial variation in abundance, from count data alone. We extend recently developed multistate, open population N-mixture models, which can additionally estimate demographic rates based on an organism's life history characteristics. In our extension, we develop an approach to account for the case where not all individuals can be assigned to a state during sampling. Using only state-specific count data, we show how our model can be used to estimate local population abundance, as well as density-dependent recruitment rates and state-specific survival. We apply our model to a population of black-throated blue warblers ( Setophaga caerulescens ) that have been surveyed for 25 years on their breeding grounds at the Hubbard Brook Experimental Forest in New Hampshire, USA. The intensive data collection efforts allow us to compare our estimates to estimates derived from capture–recapture data. Our model performed well in estimating population abundance and density-dependent rates of annual recruitment/immigration. Estimates of local carrying capacity and per capita recruitment of yearlings were consistent with those published in other studies. However, our model moderately underestimated annual survival probability of yearling and adult females and severely underestimates survival probabilities for both of these male stages. The most accurate and precise estimates will necessarily require some amount of intensive data collection efforts (such as capture–recapture). Integrated population models that combine data from both intensive and extensive sources are likely to be the most efficient approach for estimating demographic rates at large spatial and temporal scales.

New Hampshire↗

USGS2019

Integrating behavior and physiology into strategies for amphibian conservation

The amphibian decline crisis has been challenging to address because of the complexity of factors—and their multitude of interactive effects—that drive this global issue. Dissecting such complexity could benefit from strategies that integrate multiple disciplines and address the mechanistic underpinnings of population declines and extirpations. We examine how the disciplines of behavior and physiology could be used to develop conservation strategies for amphibians and identify eight research gaps that provide future directions for the emerging fields of conservation behavior and conservation physiology. We present two case studies on imperiled salamanders that show how studies of behavior and physiology may support amphibian conservation efforts. We found several applications of stress physiology to amphibian conservation, but long-term studies are needed to understand how stress ultimately affects individual fitness and population resilience. Additionally, multiple measures of physiological health are needed to provide a more holistic assessment of an individual’s overall condition. Previous behavioral and physiological studies have been instrumental for understanding how amphibians respond to habitat modification, pathogens and parasites, contaminants, and invasive species. Some behavior-based approaches to mitigating invasive species issues have been successful in short-term studies with individual species. However, widespread application of these tactics has not yet been integrated into conservation and management strategies for ecologically-similar species. A diversity of modeling approaches has enhanced understanding of how climate change may impact amphibian populations, but model predictions need empirical tests to provide conservation managers with workable approaches to multiple perturbations associated with global environmental change. We illustrate that behavior and physiology can have broad utility for amphibian conservation, but evidence is scant that such studies have actually been used to inform strategies for amphibian conservation and management.

Frontiers in Ecology and Evolution↗

USGS2015

Effects of changing climate on aquatic habitat and connectivity for remnant populations of a wide-ranging frog species in an arid landscape

Amphibian species persisting in isolated streams and wetlands in desert environments can be susceptible to low connectivity, genetic isolation, and climate changes. We evaluated the past (1900–1930), recent (1981–2010), and future (2071–2100) climate suitability of the arid Great Basin (USA) for the Columbia spotted frog ( Rana luteiventris ) and assessed whether changes in surface water may affect connectivity for remaining populations. We developed a predictive model of current climate suitability and used it to predict the historic and future distribution of suitable climates. We then modeled changes in surface water availability at each time period. Finally, we quantified connectivity among existing populations on the basis of hydrology and correlated it with interpopulation genetic distance. We found that the area of the Great Basin with suitable climate conditions has declined by approximately 49% over the last century and will likely continue to decline under future climate scenarios. Climate conditions at currently occupied locations have been relatively stable over the last century, which may explain persistence at these sites. However, future climates at these currently occupied locations are predicted to become warmer throughout the year and drier during the frog's activity period (May – September). Fall and winter precipitation may increase, but as rain instead of snow. Earlier runoff and lower summer base flows may reduce connectivity between neighboring populations, which is already limited. Many of these changes could have negative effects on remaining populations over the next 50–80 years, but milder winters, longer growing seasons, and wetter falls might positively affect survival and dispersal. Collectively, however, seasonal shifts in temperature, precipitation, and stream flow patterns could reduce habitat suitability and connectivity for frogs and possibly other aquatic species inhabiting streams in this arid region.

Ecology and Evolution↗

USGS2022

Decision support for aquatic restoration based on species-specific responses to disturbance

Disturbances to aquatic habitats are not uniformly distributed within the Great Lakes and acute effects can be strongest in nearshore areas where both landscape and within lake effects can have strong influence. Furthermore, different fish species respond to disturbances in different ways. A means to identify and evaluate locations and extent of disturbances that affect fish is needed throughout the Great Lakes. We used partial Canonical Correspondence Analysis to separate “natural” effects on nearshore assemblages from disturbance effects. Species-specific quadratic models of fish abundance as functions of in-lake disturbance or watershed-derived disturbance were developed separately for each of 35 species and lakewide predictions mapped for Lake Erie. Most responses were unimodal and more species decreased in abundance with increasing watershed disturbance than increased. However, eight species increased in abundance with current in-lake disturbance conditions. Optimum Yellow Perch ( Perca flavescens ) abundance occurred at in-lake disturbance values less than the gradient mean, but decreased continuously from minimum watershed disturbance to higher values. Bands of optimum in-lake conditions occurred throughout the eastern and western portions of the Lake Erie nearshore zone; some areas were less disturbed than desirable. However, watershed-derived disturbance conditions were generally poor for Yellow Perch throughout the lake. In contrast, optimum Smallmouth Bass ( Micropterus dolomieu ) abundance occurred at in-lake disturbance values greater than the gradient mean and continuously increased with increasing watershed disturbance. Smallmouth Bass responses to disturbance indicated that most of the nearshore zone was less disturbed than is desirable and were most abundant in areas that the Yellow Perch response indicated were highly disturbed. Mapping counts of species response models that agreed on the disturbance level in each spatial unit of the nearshore zone showed a fine-scale mosaic of areas in which habitat restoration may benefit many or few species. This tool may assist managers in prioritizing conservation and restoration efforts and evaluating environmental conditions that may be improved.

Great Lakes↗

USGS2023

Living on the edge: Predicting songbird response to management and environmental changes across an ecotone

Effective wildlife management requires robust information regarding population status, habitat requirements, and likely responses to changing resource conditions. Single-species management may inadequately conserve communities and result in undesired effects to non-target species. Thus, management can benefit from understanding habitat relationships for multiple species. Pinyon pine and juniper ( Pinus spp. and Juniperus spp.) are expanding into sagebrush-dominated ( Artemisia spp.) ecosystems within North America and mechanical removal of these trees is frequently conducted to restore sagebrush ecosystems and recover Greater Sage-grouse ( Centrocercus urophasianus ). However, pinyon-juniper removal effects on non-target species are poorly understood, and changing pinyon-juniper woodland dynamics, climate, and anthropogenic development may obscure conservation priorities. To better predict responses to changing resource conditions, evaluate non-target effects of pinyon-juniper removal, prioritize species for conservation, and inform species recovery within pinyon-juniper and sagebrush ecosystems, we modeled population trends and density-habitat relationships for four sagebrush-associated, four pinyon-juniper-associated, and three generalist songbird species with respect to these ecosystems. We fit hierarchical population models to point count data collected throughout the western United States from 2008 to 2020. We found regional population changes for 10 of 11 species investigated; 6 of which increased in the highest elevation region of our study. Our models indicate pinyon-juniper removal will benefit Brewer's Sparrow ( Spizella breweri ), Green-tailed Towhee ( Pipilo chlorurus ), and Sage Thrasher ( Oreoscoptes montanus ) densities. Conversely, we predict largest negative effects of pinyon-juniper removal for species occupying early successional pinyon-juniper woodlands: Bewick's Wren ( Thryomanes bewickii ), Black-throated Gray Warblers ( Setophaga nigrescens ), Gray Flycatcher ( Empidonax wrightii ), and Juniper Titmouse ( Baeolophus ridgwayi ). Our results highlight the importance of considering effects to non-target species before implementing large-scale habitat manipulations. Our modeling framework can help prioritize species and regions for conservation action, infer effects of management interventions and a changing environment on wildlife, and help land managers balance habitat requirements across ecosystems.

Ecology and Evolution↗

USGS2009

Quality characteristics of ground water in the Ozark aquifer of northwestern Arkansas, southeastern Kansas, southwestern Missouri and northeastern Oklahoma, 2006-07

Because of water quantity and quality concerns within the Ozark aquifer, the State of Kansas in 2004 issued a moratorium on most new appropriations from the aquifer until results were made available from a cooperative study between the U.S. Geological Survey and the Kansas Water Office. The purposes of the study were to develop a regional ground-water flow model and a water-quality assessment of the Ozark aquifer in northwestern Arkansas, southeastern Kansas, southwestern Missouri, and northeastern Oklahoma (study area). In 2006 and 2007, water-quality samples were collected from 40 water-supply wells completed in the Ozark aquifer and spatially distributed throughout the study area. Samples were analyzed for physical properties, dissolved solids and major ions, nutrients, trace elements, and selected isotopes. This report presents the results of the water-quality assessment part of the cooperative study. Water-quality characteristics were evaluated relative to U.S. Environmental Protection Agency drinking-water standards. Secondary Drinking-Water Regulations were exceeded for dissolved solids (11 wells), sulfate and chloride (2 wells each), fluoride (3 wells), iron (4 wells), and manganese (2 wells). Maximum Contaminant Levels were exceeded for turbidity (3 wells) and fluoride (1 well). The Maximum Contaminant Level Goal for lead (0 milligrams per liter) was exceeded in water from 12 wells. Analyses of isotopes in water from wells along two 60-mile long ground-water flow paths indicated that water in the Ozark aquifer was at least 60 years old but the upper age limit is uncertain. The source of recharge water for the wells along the flow paths appeared to be of meteoric origin because of isotopic similarity to the established Global Meteoric Water Line and a global precipitation relation. Additionally, analysis of hydrogen-3 (3H) and carbon-14 (14C) indicated that there was possible leakage of younger ground water into the lower part of the Ozark aquifer. This may be caused by cracks or fissures in the confining unit that separates the upper and lower parts of the aquifer, poorly constructed or abandoned wells, or historic mining activities. Analyses of major ions in water from wells along the flow paths indicated a transition from freshwater in the east to saline water in the west. Generally, ground water along flow paths evolved from a calcium magnesium bicarbonate type to a sodium calcium bicarbonate or a sodium calcium chloride bicarbonate type as water moved from recharge areas in Missouri into Kansas. Much of this evolution occurred within the last 20 to 25 miles of the flow paths along a water-quality transition zone near the Kansas-Missouri State line and west. The water quality of the Kansas part of the Ozark aquifer is degraded compared to the Missouri part. Geophysical and well-bore flow information and depth-dependent water-quality samples were collected from a large-capacity (1,900-2,300 gallons per minute) municipal-supply well to evaluate vertical ground-water flow accretion and variability in water-quality characteristics at different levels. Although the 1,050-foot deep supply well had 500 feet of borehole open to the Ozark aquifer, 77 percent of ground-water flow entering the borehole came from two 20-foot thick rock layers above the 1,000-foot level. For the most part, water-quality characteristics changed little from the deepest sample to the well-head sample, and upwelling of saline water from deeper geologic formations below the well was not evident. However, more saline water may be present below the bottom of the well.

Arkansas, Kansas, Missouri, Oklahoma↗

USGS1989

Geology of the Arabian Peninsula; shield area of western Saudi Arabia

Western Arabia lies within the low-latitude desert of north Africa and the Middle East, the core being the Arabian segment of the African Shield. The core of complex basement rocks accounts for about 670,000 km 2 , or one-third of the Arabian Peninsula. Reconnaissance mapping of these crystalline rocks, together with bordering sedimentary rocks and volcanic flows, begun in 1950, resulted during the next 13 years in a series of geologic and geographic maps without extensive texts. The maps served as general guides for development of natural resources, including water supplies, ore deposits, and building materials. An intensive exploration program that began in 1963 and involved numerous geologists has vastly increased geologic information. Rainfall in Arabia is meager and episodic, and vegetation is sparse except in isolated copses on the crest of the Hejaz Range. Comparison of flora with similar species in the Sudan, where records of rainfall have long been kept, allows evaluation of mean annual precipitation. Wandering bedouin following fodder created a delicate balance between population and water supply-now disturbed by wells drilled in alluvium and lava fields. A trapezoidal region of Precambrian crystalline rocks lies along the northeast flank of the Red Sea, with two long prongs extending northwest and southeast for a total of 1,800 km. These basement rocks of the Arabian Shield are well exposed on the uplands, scarp mountains, and coastal pediments where the Phanerozoic cover rocks have been stripped as a result of Paleozoic epeirogeny and Tertiary ramping. The shield outcrops are divided into three tectonic provinces by N. 45°W.- trending shear zones of the Najd fault system of latest Proterozoic and possibly earliest Paleozoic time. The southwestern province, the 'Asir1 upland, was sharply uplifted and tilted to the northeast during the Neogene. The northwestern province, consisting of the Ash Shifa'- Hisma upland as well as Jabal Shammar farther east, similarly was uplifted and tilted. These two provinces are separated by the flat-lying median N ajd province, which is chiefly bounded by the principal Najd faults. The outcrops of the shield rocks are of the Late Proterozoic Eonupper Riphean to Vendian or Infracambrian epochs, including the Ediacarian System. The most reliable isotopic ages range from about 900 to 560 m.y., but some Middle Proterozoic rocks may be present in the easternmost shield. The rocks are divided into six lithostratigraphic sequences, two plutonic suites, and an ophiolitic suite. The mafic and ultramafic volcanic and plutonic rocks of the ophiolitic suite everywhere were emplaced tectonically and are probably of different ages in different places. Some ophiolite occurs as obducted blocks, but most is highly deformed and altered to serpentinite in fault zones that mostly define sutures between different tectonic blocks or terranes within the shield. Three of the lithostratigraphic sequences consist of mafic to silicic volcanic rocks and volcanic-derived clastic rocks which, with their subvolcanic plutonic rocks of a dioritic suite, probably formed in oceanic island arcs during convergent plate tectonism. These rocks make up the primary, or first-formed, crust of the shield. Chemical analyses show that the primary shield rocks, regardless of age, are principally calc-alkalic with some associated tholeiitic varieties. Most of the layered rocks are andesitic, but they range from basalt to dacite and in places contain intercalated pillow basalt, marble, chert, and carbonaceous or graphitic schist. Most of the plutonic rocks of the dioritic suite are dioritic, but they range from gabbro to trondhjemite and rarely contain potassium feldspar. The sequences and an associated dioritic suite become younger toward the eastern shield, that is, the primary crust of the shield youngs toward the east. Two western sequences consist of the Jiddah (Samran) and BaishBahah Groups and range in radiometric age from about 900 to 800 m.y.; the eastern sequence consists of the Halaban (Hulayfah) Group and ranges from 800 to about 700 m.y. During subsequent orogeny, most of the rocks were intensely deformed and mostly metamorphosed to upper greenschist facies, but rising in places to the almandine-amphibolite facies. Two other lithostratigraphic sequences with an associated plutonic granitic suite are the products of two mountain-building episodes during which the primary crust was greatly thickened and converted into craton. The two sequences, including largely the Ablah (Al Ays) and Murdama (Shammar) Groups, consist of abundant sedimentary rocks, commonly arkosic, that are the erosional products of the orogenic mountains. They are several thousand meters thick. Less abundant calc-alkalic to alkalic volcanic rocks, commonly dacitic and rhyolitic, are intercalated with the sedimentary rocks. The plutonic rocks of the granitic suite in association with both sequences have syntectonic and posttectonic phases, are products of the orogenies, and are the principal new ingredients making up the craton. Gneiss domes were a significant part of these cratonization orogenies. In association with orogenic crustal heating, some of the low-density, more silicic tonalitic and trondhjemitic rocks of the primary crust rose as gneiss domes. Partial melting in the middle or lower crust below the gneiss domes produced large volumes of granitic magma that intruded the gneiss domes as granodioritic batholiths. The Ablah Group and the older part of the granitic suite are about 775 to 740 Ma old and are associated with the Ablah orogeny and early cratonization in the western and earlier formed half of the shield. The Murdama (Shammar) Group and the younger part of the granitic suite are about 660 to 580 Ma old and are associated with the culminant orogeny and late cratonization that was shieldwide. The granitic suite during both orogenies consists of early, syntectonic granodiorite batholiths associated with the gneiss domes and late, posttectonic monzogranite plutons. Only during the culminant orogeny, late magmatic evolution produced syenogranite and alkali-feldspar granite commonly in circular and ring-structured plutons and with associated explosive volcanic deposits (Shammar Group); final products, some of which have economic potential, were peralkalic and peraluminous. The late plutonism of the culminant orogeny was distinctly bimodal in that subordinate gabbroic rocks are associated with the granites. Various building blocks or terranes of the andesitic and dioritic primary crust were collisionally agglomerated during the Ablah orogeny, early cratonization, whereas the entire shield as currently exposed was further collisionally accreted and compressionally consolidated during the culminant orogeny, final cratonization. Thousands of kilometers of oceanic crust had to be subducted in about 300 m.y. to form the large primary crust of the Arabian Shield. The inevitable collisional events during consumption of such a large volume of oceanic crust invariably led to numerous collisional orogenies that collectively encompass the widely known Pan African tectonic episode. The youngest lithostratigraphic sequence, the Jubaylah Group, is essentially postcratonic, although it is the end product of the collisional culminant orogeny. Final east-west compression of the entire shield from about 580 to 560 m.y. caused the craton to fracture along the large northwest-trending, left-lateral faults and elsewhere along lesser, northeast-trending, right-lateral, conjugate faults of the N ajd fault system. Erosional products of this more localized deformation were the sedimentary rocks of the Jubaylah Group, which also includes intercalated andesitic to basaltic volcanic rocks of a mafic alkalic compositional trend. The collisional edge of an old continental plate (or tectonic fragments thereof), suspected on the eastern edge of the Arabian Shield, has not been shown with certainty to be exposed. Presumably, widespread contamination from such an old continental crust affects U/Pb, Sm/Nd, Rb/Sr, and common lead ratios in the young plutonic rocks of the easternmost shield. One mass of anorthosite near Jabal Khida' on the central eastern edge of the shield may be a fragment of this old continental plate in that associated granodiorite may be as old as 1,600 to 1,800 Ma. Epeirogenic uplift, erosion, and cooling of the uppermost shield during Early and Middle Cambrian time is indicated by an average fission track age of 510±52 m.y., on sphene from diorite (hornblende K-Ar age of 615±12 m.y.) in the southwestern part of the shield. The hiatus was followed by extensive deposition of the Cambro-Ordovician Saq Sandstone in the north and northeast and the Wajid Sandstone in the southeast and south of the shield. The Cambrian Siq Sandstone had already been deposited in the northern part. During the middle and late Paleozoic, broad epeirogeny caused further erosion of the shield until marine transgression deposited the Upper Permian Khuff Formation at least in the eastern part of the shield. In the southwestern shield, the nonmarine Upper Triassic Khums Sandstone was deposited variably on Wajid or Precambrian rocks and is overlain by limestone of the middle Upper Jurassic Amran Formation. Except for shallow marine sandstone of problematic Cretaceous age deposited on the Amran Formation in the south.western shield and on Precambrian rocks in the northwestern shield, the younger beds on the shield are Paleocene and younger, with the possibility that the lowermost are upper Maestrichtian. The early Tertiary beds contain vertebrate fossils of coastal marine or estuarine environment 250 km east of the Red Sea in the central shield. Marginal marine sediments were deposited in a western tongue of the latest Tethys Sea as late as Eocene on the western shield and at least as far south as Jiddah. The great harrats of flood basalt erupted on th~ western shield during late Oligocene and early Miocene at the same time a 2,000-kmlong continental rift valley developed along the future Red Sea axis. Within this rift valley, Baid freshwater tuffaceous lakebeds were deposited between mafic and silicic volcanoes. During late early Miocene time, the Red Sea opened at a rate of 4.4 cm/yr in a firststage movement while continental dikes and swarms of oceanic tholeiitic dikes, gabbro, and granophyre plutonic rocks were intruded into the rift sedimentary and volcanic rocks at the newly formed continental margin. The continental margin was deformed and greatly extended at this time. About 14 or 15 m.y., as the first-stage spreading stopped, the Red Sea Escarpment rose; its erosion caused deposition of coarse conglomerate of the Bathan Formation. About 3,000 m of evaporite was deposited on the young Red Sea oceanic crust during the late Miocene desiccation crisis. A second stage of sea-floor spreading about 4-5 m.y. produced the Red Sea axial trough, consisting of oceanic crust, as well as renewed uplift and tilting of the three tectonic provinces in response to compression from counterclockwise rotation against the Dead Sea Rift. This late movement caused widespread major stream capture, especially along the wadis that formerly drained southwesterly or northwesterly, the channels turning westward through narrow gorges to the coastal plain and the Red Sea.

Professional Paper↗

USGS2022

Optimizing trilateration estimates for tracking fine-scale movement of wildlife using automated radio telemetry networks

A major advancement in the use of radio telemetry has been the development of automated radio tracking systems (ARTS), which allow animal movements to be tracked continuously. A new ARTS approach is the use of a network of simple radio receivers (nodes) that collect radio signal strength (RSS) values from animal-borne radio transmitters. However, the use of RSS-based localization methods in wildlife tracking research is new, and analytical approaches critical for determining high-quality location data have lagged behind technological developments. We present an analytical approach to optimize RSS-based localization estimates for a node network designed to track fine-scale animal movements in a localized area. Specifically, we test the application of analytical filters (signal strength, distance among nodes) to data from real and simulated node networks that differ in the density and configuration of nodes. We evaluate how different filters and network configurations (density and regularity of node spacing) may influence the accuracy of RSS-based localization estimates. Overall, the use of signal strength and distance-based filters resulted in a 3- to 9-fold increase in median accuracy of location estimates over unfiltered estimates, with the most stringent filters providing location estimates with a median accuracy ranging from 28 to 73 m depending on the configuration and spacing of the node network. We found that distance filters performed significantly better than RSS filters for networks with evenly spaced nodes, but the advantage diminished when nodes were less uniformly spaced within a network. Our results not only provide analytical approaches to greatly increase the accuracy of RSS-based localization estimates, as well as the computer code to do so, but also provide guidance on how to best configure node networks to maximize the accuracy and capabilities of such systems for wildlife tracking studies.

Ecology and Evolution↗

USGS2018

Quantitative acoustic differentiation of cryptic species illustrated with King and Clapper rails

Reliable species identification is vital for survey and monitoring programs. Recently, the development of digital technology for recording and analyzing vocalizations has assisted in acoustic surveying for cryptic, rare, or elusive species. However, the quantitative tools that exist for species differentiation are still being refined. Using vocalizations recorded in the course of ecological studies of a King Rail ( Rallus elegans ) and a Clapper Rail ( Rallus crepitans ) population, we assessed the accuracy and effectiveness of three parametric (logistic regression, discriminant function analysis, quadratic discriminant function analysis) and six nonparametric (support vector machine, CART, Random Forest, k ‐nearest neighbor, weighted k ‐nearest neighbor, and neural networks) statistical classification methods for differentiating these species by their kek mating call. We identified 480 kek notes of each species and quantitatively characterized them with five standardized acoustic parameters. Overall, nonparametric classification methods outperformed parametric classification methods for species differentiation (nonparametric tools were between 57% and 81% accurate, parametric tools were between 57% and 60% accurate). Of the nine classification methods, Random Forest was the most accurate and precise, resulting in 81.1% correct classification of kek notes to species. This suggests that the mating calls of these sister species are likely difficult for human observers to tell apart. However, it also implies that appropriate statistical tools may allow reasonable species‐level classification accuracy of recorded calls and provide an alternative to species classification where other capture‐ or genotype‐based survey techniques are not possible.

Ecology and Evolution↗

USGS2011

Modeling of hydroecological feedbacks predicts distinct classes of landscape pattern, process, and restoration potential in shallow aquatic ecosystems

It is widely recognized that interactions between vegetation and flow cause the emergence of channel patterns that are distinct from the standard Schumm classification of river channels. Although landscape pattern is known to be linked to ecosystem services such as habitat provision, pollutant removal, and sustaining biodiversity, the mechanisms responsible for the development and stability of different landscape patterns in shallow, vegetated flows have remained poorly understood. Fortunately, recent advances have made possible large-scale models of flow through vegetated environments that can be run over a range of environmental variables and over timescales of millennia. We describe a new, quasi-3D cellular automata model that couples simulations of shallow-water flow, bed shear stresses, sediment transport, and vegetation dynamics in an efficient manner. That efficiency allowed us to apply the model widely in order to determine how different hydroecological feedbacks control landscape pattern and process in various types of wetlands and floodplains. Distinct classes of landscape pattern were uniquely associated with specific types of allogenic and autogenic drivers in wetland flows. Regular, anisotropically patterned wetlands were dominated by allogenic processes (i.e., processes driven by periodic high water levels and flow velocities that redistribute sediment), relative to autogenic processes (e.g., vegetation production, peat accretion, and gravitational erosion). These anistropically patterned wetlands are therefore particularly prone to hydrologic disturbance. Other classes of wetlands that emerged from simulated interactions included maze-patterned, amorphous, and topographically noisy marshes, open marsh with islands, banded string-pool sequences perpendicular to flow, parallel deep and narrow channels flanked by marsh, and ridge-and-slough patterned marsh oriented parallel to flow. Because vegetation both affects and responds to the balance between the transport capacity of the flow and sediment supply, these vegetated systems exhibit a feedback that is not dominant in most rivers. Consequently, unlike in most rivers, it is not possible to predict the “channel pattern” of a vegetated landscape based only on discharge characteristics and sediment supply; the antecedent vegetation pattern and vegetation dynamics must also be known. In general, the stability of different wetland pattern types is most strongly related to factors controlling the erosion and deposition of sediment at vegetation patch edges, the magnitude of sediment redistribution by flow, patch elevation relative to water level, and the variability of erosion rates in vegetation patches with low flow-resistance. As we exemplify in our case-study of the Everglades ridge and slough landscape, feedback between flow and vegetation also causes hysteresis in landscape evolution trajectories that will affect the potential for landscape restoration. Namely, even if the hydrologic conditions that historically produced higher flows are restored, degraded portions of the ridge and slough landscape are unlikely to revert to their former patterning. As wetlands and floodplains worldwide become increasingly threatened by climate change and urbanization, the greater mechanistic understanding of landscape pattern and process that our analysis provides will improve our ability to forecast and manage the behavior of these ecosystems.

Florida↗

USGS2018

Dynamic occupancy modeling of temperate marine fish in area-based closures

Species distribution models (SDMs) are commonly used to model the spatial structure of species in the marine environment, however, most fail to account for detectability of the target species. This can result in underestimates of occupancy, where nondetection is conflated with absence. The site occupancy model (SOM) overcomes this failure by treating occupancy as a latent variable of the model and incorporates a detection submodel to account for variability in detection rates. These have rarely been applied in the context of marine fish and never for the multiseason dynamic occupancy model (DOM). In this study, a DOM is developed for a designated species of concern, cusk ( Brosme brosme ), over a four-season period. Making novel use of a high-resolution 3-dimensional hydrodynamic model, detectability of cusk is considered as a function of current speed and algae cover. Algal cover on the seabed is measured from video surveys to divide the study area into two distinct regions: those with canopy forming species of algae and those without (henceforth bottom types). Modeled estimates of the proportion of sites occupied in each season are 0.88, 0.45, 0.74, and 0.83. These are significantly greater than the proportion of occupied sites measured from underwater video observations which are 0.57, 0.28, 0.43, and 0.57. Individual fish are detected more frequently with increasing current speed in areas lacking canopy and less frequently with increasing current speed in areas with canopy. The results indicate that, where possible, SDM studies for all marine species should take account of detectability to avoid underestimating the proportion of sites occupied at a given study area. Sampling closed areas or areas of conservation often requires the use of nonphysical, low impact sampling methods like camera surveys. These methods inherently result in detection probabilities less than one, an issue compounded by time-varying features of the environment that are rarely accounted for marine studies. This work highlights the use of modeled hydrodynamics as a tool to correct some of this imbalance.

Gulf of Maine↗

USGS2019

Effects of invasive plants on fire regimes and postfire vegetation diversity in an arid ecosystem

We assessed the impacts of co‐occurring invasive plant species on fire regimes and postfire native communities in the Mojave Desert, western USA. We analyzed the distribution and co‐occurrence patterns of three invasive annual grasses (Bromus rubens, Bromus tectorum, and Schismus spp.) known to alter fuel conditions and community structure, and an invasive forb (Erodium cicutarium) which dominates postfire sites. We developed species distribution models (SDMs) for each of the four taxa and analyzed field plot data to assess the relationship between invasives and fire frequency, years postfire, and the impacts on postfire native herbaceous diversity. Most of the Mojave Desert is highly suitable for at least one of the four invasive species, and 76% of the ecoregion is predicted to have high or very high suitability for the joint occurrence of B. rubens and B. tectorum and 42% high or very high suitability for the joint occurrence of the two Bromus species and E. cicutarium. Analysis of cover from plot data indicated two or more of the species occurred in 77% of the plots, with their cover doubling with each additional species. We found invasive cover in burned plots increased for the first 20 years postfire and recorded two to five times more cover in burned than unburned plots. Analysis also indicated that native species diversity and evenness as negatively associated with higher levels of relative cover of the four invasive taxa. Our findings revealed overlapping distributions of the four invasives; a strong relationship between the invasives and fire frequency; and significant negative impacts of invasives on native herbaceous diversity in the Mojave. This suggests predicting the distributions of co‐occurring invasive species, especially transformer species, will provide a better understanding of where native‐dominated communities are most vulnerable to transformations following fire or other disturbances.

California, Nevada↗

USGS2021

Linking behavioral states to landscape features for improved conservation management

A central theme for conservation is understanding how animals differentially use, and are affected by change in, the landscapes they inhabit. However, it has been challenging to develop conservation schemes for habitat-specific behaviors. Here we use behavioral change point analysis to identify behavioral states of golden eagles ( Aquila chrysaetos ) in the Sonoran and Mojave Deserts of the southwestern United States, and we identify, for each behavioral state, conservation-relevant habitat associations. We modeled behavior using 186,859 GPS points from 48 eagles and identified 2,851 distinct segments comprising four behavioral states. Altitude above ground level (AGL) best differentiated behavioral states, with two clusters of short-distance movement behaviors characterized by low AGL (state 1 AGL = 14 m (median); state 2 AGL = 11 m) and two associated with longer-distance movement behaviors and characterized by higher AGL (state 3 AGL = 108 m; state 4 AGL = 450 m). Behaviors such as perching and low-altitude hunting were associated with short-distance movements in updraft-poor environments, at higher elevations, and over steeper and more north-facing terrain. In contrast, medium-distance movements such as hunting and transiting were over gentle and south-facing slopes. Long-distance transiting occurred over the desert habitats that generate the best updraft. This information can guide management of this species, and our approach provides a template for behavior-specific habitat associations for other species of management concern.

California↗

USGS2017

Imperfect pathogen detection from non-invasive skin swabs biases disease inference

1. Conservation managers rely on accurate estimates of disease parameters, such as pathogen prevalence and infection intensity, to assess disease status of a host population. However, these disease metrics may be biased if low-level infection intensities are missed by sampling methods or laboratory diagnostic tests. These false negatives underestimate pathogen prevalence and overestimate mean infection intensity of infected individuals. 2. Our objectives were two-fold. First, we quantified false negative error rates of Batrachochytrium dendrobatidis on non-invasive skin swabs collected from an amphibian community in El Copé, Panama. We swabbed amphibians twice in sequence, and we used a recently developed hierarchical Bayesian estimator to assess disease status of the population. Second, we developed a novel hierarchical Bayesian model to simultaneously account for imperfect pathogen detection from field sampling and laboratory diagnostic testing. We evaluated the performance of the model using simulations and varying sampling design to quantify the magnitude of bias in estimates of pathogen prevalence and infection intensity. 3. We show that Bd detection probability from skin swabs was related to host infection intensity, where Bd infections < 10 zoospores have < 95% probability of being detected. If imperfect Bd detection was not considered, then Bd prevalence was underestimated by as much as 16%. In the Bd-amphibian system, this indicates a need to correct for imperfect pathogen detection caused by skin swabs in persisting host communities with low-level infections. More generally, our results have implications for study designs in other disease systems, particularly those with similar objectives, biology, and sampling decisions. 4. Uncertainty in pathogen detection is an inherent property of most sampling protocols and diagnostic tests, where the magnitude of bias depends on the study system, type of infection, and false negative error rates. Given that it may be difficult to know this information in advance, we advocate that the most cautious approach is to assume all errors are possible and to accommodate them by adjusting sampling designs. The modeling framework presented here improves the accuracy in estimating pathogen prevalence and infection intensity.

Methods in Ecology and Evolution↗

USGS2016

The source of groundwater and solutes to Many Devils Wash at a former uranium mill site in Shiprock, New Mexico

The Shiprock Disposal Site is the location of the former Navajo Mill (Mill), a uranium ore-processing facility, located on a terrace overlooking the San Juan River in the town of Shiprock, New Mexico. Following the closure of the Mill, all tailings and associated materials were encapsulated in a disposal cell built on top of the former Mill and tailings piles. The milling operations, conducted at the site from 1954 to 1968, created radioactive tailings and process-related wastes that are now found in the groundwater. Elevated concentrations of constituents of concern—ammonium, manganese, nitrate, selenium, strontium, sulfate, and uranium—have also been measured in groundwater seeps in the nearby Many Devils Wash arroyo, leading to the inference that these constituents originated from the Mill. These constituents have also been reported in groundwater that is associated with Mancos Shale, the bedrock that underlies the site. The objective of this report is to increase understanding of the source of water and solutes to the groundwater beneath Many Devils Wash and to establish the background concentrations for groundwater that is in contact with the Mancos Shale at the site. This report presents evidence on three working hypotheses: (1) the water and solutes in Many Devils Wash originated from the operations at the former Mill, (2) groundwater in deep aquifers is upwelling under artesian pressure to recharge the shallow groundwater beneath Many Devils Wash, and (3) the groundwater beneath Many Devils Wash originates as precipitation that infiltrates into the shallow aquifer system and discharges to Many Devils Wash in a series of springs on the east side of the wash. The solute concentrations in the shallow groundwater of Many Devils Wash would result from the interaction of the water and the Mancos Shale if the source of water was upwelling from deep aquifers or precipitation. In order to compare the groundwater from various wells to groundwater that has been affected by Mill activities, a classification system was developed to determine which wells were most likely to have been affected. Affects to groundwater by the Mill were determined by using the reported uranium alpha activity ratios measured in groundwater samples, along with the concentration of the uranium and the location of the wells relative to the Mill. Activity ratios of 1.2 or less were determined to be the most reliable indicator of Mill-affected groundwater. Wells with samples that had a reported activity ratio of 1.2 or less were classified as Mill affected. To compare groundwater with background water-quality, data from groundwater seeps and springs in the Upper Eagle Nest Arroyo and Salt Creek Wash, located north of the San Juan River, are also presented and analyzed. Based on groundwater elevations and tritium concentrations measured in wells located between the disposal cell and Many Devils Wash, Mill water is not likely to reach Many Devils Wash. The tritium concentrations also indicate that groundwater from the Mill has not substantially affected Many Devils Wash in the past. Upwelling from deep aquifers was also determined to be an unlikely source, primarily by comparing the composition of the stable isotopes of water in the shallow groundwater with those reported in groundwater samples from the deeper aquifers. The stable-isotope compositions of the shallow groundwater around the site are enriched relative to the San Juan River and local meteoric lines, which suggests that most of the shallow groundwater has been influenced by evaporation and therefore was recharged at the surface. Several observations indicate that focused recharge is the likely source of groundwater in the area of Many Devils Wash. The visible erosional features in Many Devils Wash provide evidence of piping and groundwater sapping, and the distribution and type of vegetation in Many Devils Wash suggest that the focused recharge of precipitation is occurring. The estimated recharge from precipitation was calculated to be 0.0008 inches per year (in/yr) by using the mass-balance approach from reported seep discharge and 0.0011 in/yr using the chloride mass-balance approach. A conceptual model of groundwater quality beneath Many Devils Wash is presented to explain the source of solutes in the groundwater beneath Many Devils Wash. The major-ion concentrations and geochemical evolution in the groundwater beneath Many Devils Wash and across the study area support the conceptual model that the underlying Mancos Shale is the source of solutes. Differences in the major-ion composition between groundwater samples collected around the site, result from the degree of weathering to the Mancos Shale. The cation distribution appears to be an indicator of effects from the Mill, with samples from the Mill-affected wells largely having a calcium/magnesium-sulfate composition that resembles the reported compositions of more weathered shale; however, that composition could change if the Mill-processed water flowed into areas where the Mancos Shale was less weathered. On the basis of the widespread presence of uranium in the Mancos Shale and the distribution of aqueous uranium in the analog sites and other sites in the region, it appears likely that uranium in the groundwater of Many Devils Wash is naturally sourced from the Mancos Shale.

New Mexico↗

USGS2025

Development of a genotyping-in-thousands by sequencing (GT-seq) panel for identifying individuals and estimating relatedness among Alaska black bears (Ursus americanus)

The management and conservation of large mammals, such as black bears ( Ursus americanus ), have long been informed by genetic estimates of population size and individual dispersal. Amplicon sequencing methods, also known as ‘genotyping-in-thousands-by sequencing’ (GT-seq), now enable the efficient and cost-effective genotyping of hundreds of loci and individuals in the same sequencing run. Here, we develop a GT-seq panel for individual identification and kinship inference in Alaska black bears. Using genomic data from restriction site-associated DNA sequencing of hunter-harvested bears from Southcentral Alaska ( n = 85), we identified 170 microhaplotype and single nucleotide polymorphism (SNP) loci that were highly heterozygous in local populations. To enable sexing of individuals, we also included a previously published sex-linked locus in the GT-seq panel. We empirically validated the GT-seq panel using samples collected at different spatial scales. These samples included tissues ( n = 82) obtained from bears within a small geographic area in Anchorage, Alaska, which were likely to be relatives as well as the hunter-harvested samples collected from geographically widespread locations throughout Southcentral Alaska. Empirical validation indicated high genotyping success and genotype reproducibility across replicate subsamples. Computer simulations demonstrated that the GT-seq panel had ample statistical power for distinguishing distinct individuals and first-order relatives (parent-offspring and full-sibling pairs) from unrelated individuals. As a final proof of concept, the panel was used to identify individual bears and close kin sampled from urban and wild habitats in Anchorage, Alaska. We anticipate that the GT-seq panel will be a useful genomic resource for the monitoring and management of Alaska black bear populations. ons.

Alaska↗

USGS2014

Accounting for tagging-to-harvest mortality in a Brownie tag-recovery model by incorporating radio-telemetry data

The Brownie tag-recovery model is useful for estimating harvest rates but assumes all tagged individuals survive to the first hunting season; otherwise, mortality between time of tagging and the hunting season will cause the Brownie estimator to be negatively biased. Alternatively, fitting animals with radio transmitters can be used to accurately estimate harvest rate but may be more costly. We developed a joint model to estimate harvest and annual survival rates that combines known-fate data from animals fitted with transmitters to estimate the probability of surviving the period from capture to the first hunting season, and data from reward-tagged animals in a Brownie tag-recovery model. We evaluated bias and precision of the joint estimator, and how to optimally allocate effort between animals fitted with radio transmitters and inexpensive ear tags or leg bands. Tagging-to-harvest survival rates from >20 individuals with radio transmitters combined with 50–100 reward tags resulted in an unbiased and precise estimator of harvest rates. In addition, the joint model can test whether transmitters affect an individual's probability of being harvested. We illustrate application of the model using data from wild turkey, Meleagris gallapavo, to estimate harvest rates, and data from white-tailed deer, Odocoileus virginianus, to evaluate whether the presence of a visible radio transmitter is related to the probability of a deer being harvested. The joint known-fate tag-recovery model eliminates the requirement to capture and mark animals immediately prior to the hunting season to obtain accurate and precise estimates of harvest rate. In addition, the joint model can assess whether marking animals with radio transmitters affects the individual's probability of being harvested, caused by hunter selectivity or changes in a marked animal's behavior.

Ecology and Evolution↗

USGS2024

Behavioral trade-offs and multitasking by elk in relation to predation risk from Mexican gray wolves

Predator non-consumptive effects (NCE) can alter prey foraging time and habitat use, potentially reducing fitness. Prey can mitigate NCEs by increasing vigilance, chewing-vigilance synchronization, and spatiotemporal avoidance of predators. We quantified the relationship between Mexican wolf ( Canis lupus baileyi ) predation risk and elk ( Cervus canadensis ) behavior. We conducted behavioral observations on adult female elk and developed predation risk indices using GPS collar data from Mexican wolves, locations of elk killed by wolves, and landscape covariates. We compared a priori models to determine the best predictors of adult female behavior and multitasking. Metrics that quantified both spatial and temporal predation risk were the most predictive. Vigilance was positively associated with increased predation risk. The effect of predation risk on foraging and resting differed across diurnal periods. During midday when wolf activity was lower, the probability of foraging increased while resting decreased in high-risk areas. During crepuscular periods when elk and wolves were most active, increased predation risk was associated with increased vigilance and slight decreases in foraging. Our results suggest elk are temporally avoiding predation risk from Mexican wolves by trading resting for foraging, a trade-off often not evaluated in behavioral studies. Probability of multitasking depended on canopy openness and an interaction between maternal period and predation risk; multitasking decreased prior to parturition and increased post parturition in high-risk areas. Openness was inversely related to multitasking. These results suggest adult female elk are altering the type of vigilance used depending on resource availability/quality, current energetic needs, and predation risk. Our results highlight potentially important, but often-excluded behaviors and trade-offs prey species may use to reduce the indirect effects of predation and contribute additional context to our understanding of predator–prey dynamics.

Ecology and Evolution↗