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USGS2002

Desert Tortoise (Gopherus agassizii)

The desert tortoise is widely distributed throughout major portions of the Mojave and Sonoran deserts of California, Nevada, Utah, Arizona, Sonora, and Sinaloa. Genetic, morphological, ecological, and behavioral features suggest an evolutionary divergence between the tortoises found south and east of the Colorado River (“Sonoran population”), and those found north and west of the river (“Mojave population;” Lamb et al. 1989). The latter is the population Federally and State-listed as threatened. This population will be referred to in the remainder of this account. The majority of animals in the Mojave population occur at variable densities in six distinct population segments (i.e., evolutionarily significant units), each identified in the Recovery Plan for desert tortoises as separate Recovery Units (USFWS 1994).

Report↗

USGS2017

Microhabitat and biology of Sphaerium striatinum in a central New York stream

In many lotic systems, drastic declines in freshwater bivalve populations, including fingernail clams (Sphaeriidae), have created concerns about biodiversity and future ecosystem services. We examined the local occurrence of the historically common fingernail clam, Sphaerium striatinum , in a central New York stream. We sampled the density of sphaeriids and measured the associated habitat variables (substrate, depth, water flow) to test within-stream multivariate benthic microhabitat association. Size distribution, density, and diel feeding periodicity were measured as focal aspects of fingernail clam biology and ecology. S. striatinum tended to be found in microhabitats that had harder substrates and faster flow. The Labrador Creek fingernail clam local population had positive indicators (size distribution, density). There was significant diel periodicity in feeding behavior. The clams fed most actively during the 0400–0800 h periods. This kind of behavioral periodicity can indicate a significant ecological interaction between predators and bivalve prey. Increased understanding of the behavioral ecology of small native freshwater bivalves in an unimpacted headwater stream is a fundamental building block for development of overall ecological conservation goals for freshwater bivalves and their lotic habitats.

New York↗

USGS2020

Linking land and sea through an ecological-economic model of coral reef recreation

Coastal zones are popular recreational areas that substantially contribute to social welfare. Managers can use information about specific environmental features that people value, and how these might change under different management scenarios, to spatially target actions to areas of high current or potential value. We explored how snorkelers’ experience would be affected by separate and combined land and marine management actions in West Maui, Hawaiʻi, using a Bayesian Belief Network (BBN) and a spatially explicit ecosystem services model. The BBN simulates the attractiveness of a site for recreation by combining snorkeler preferences for coastal features with expert opinions on ecological dynamics, snorkeler behavior, and management actions. A choice experiment with snorkelers elucidated their preferences for sites with better ecological and water-quality conditions. Linking the economic elicitation to the spatially explicit BBN to evaluate land-sea management scenarios provides specific guidance on where and how to act in West Maui to maximize ecosystem service returns. Improving coastal water quality through sediment runoff and cesspool effluent reductions (land management), and enhancing coral reef ecosystem conditions (marine management) positively affected overall snorkeling attractiveness across the study area, but with differential results at specific sites. The highest improvements were attained through joint land-sea management, driven by strong efforts to increase fish abundance and reduced sediment; however, the effects of management at individual beaches varied.

Hawaii↗

USGS2023

Virtual snow stakes: a new method for snow depth measurement at remote camera stations

Remote cameras are used to study demographics, ecological processes, and behavior of wildlife populations. Cameras have also been used to measure snow depth with physical snow stakes. However, concerns that physical instruments at camera sites may influence animal behavior limit installation of instruments to facilitate collecting such data. Given that snow depth data are inherently contained within images, potential insights that could be made using these data are lost. To facilitate camera-based snow depth observations without additional equipment installation, we developed a method implemented in an R package called edger to superimpose virtual measurement devices onto images. The virtual snow stakes can be used to derive snow depth measurements. We validated the method for snow depth estimation using camera data from Latah County, Idaho, USA in winter 2020–2021. Mean bias error between the virtual snow stake and a physical snow stake was 5.8 cm; the mean absolute bias error was 8.8 cm. The mean Nash Sutcliffe Efficiency score comparing the fit of the 2 sets of measurements within each camera was 0.748, indicating good agreement. The edger package provides researchers with a means to take critical measurements for ecological studies without the use of physical objects that could alter animal behavior, and snow data at finer scales can complement other snow data sources that have coarser spatial and temporal resolution.

Idaho↗

USGS2020

Analysis of movement recursions to detect reproductive events and estimate their fate in central place foragers

Recursive movement patterns have been used to detect behavioral structure within individual movement trajectories in the context of foraging ecology, home-ranging behavior, and predator avoidance. Some animals exhibit movement recursions to locations that are tied to reproductive functions, including nests and dens; while existing literature recognizes that, no method is currently available to explicitly target different types of revisited locations. Moreover, the temporal persistence of recursive movements to a breeding location can carry information regarding the fate of breeding attempts, but it has never been used as a metric to quantify recursive movement patterns. Here, we introduce a method to locate breeding attempts and estimate their fate from GPStracking data of central place foragers. We tested the performance of our method in three bird species differing in breeding ecology (wood stork (Mycteria americana), lesser kestrel (Falco naumanni), Mediterranean gull (Ichthyaetus melanocephalus)) and implemented it in the R package ‘nestR’. Methods: We identified breeding sites based on the analysis of recursive movements within individual tracks. Using trajectories with known breeding attempts, we estimated a set of species-specific criteria for the identification of nest sites, which we further validated using non-reproductive individuals as controls. We then estimated individual nest survival as a binary measure of reproductive fate (success, corresponding to fledging of at least one chick, or failure) from nest-site revisitation histories during breeding attempts, using a Bayesian hierarchical modeling approach that accounted for temporally variable revisitation patterns, probability of visit detection, and missing data. Results: Across the three species, positive predictive value of the nest-site detection algorithm varied between 87 and 100% and sensitivity between 88 and 92%, and we correctly estimated the fate of 86–100% breeding attempts.

Movement Ecology↗

USGS2025

DNA metabarcoding and video camera collars yield different inferences about the summer diet of an arctic ungulate

The diets of wild ungulates are a foundational component of their ecology, influencing their behavior, body condition, and demography. With changing environmental conditions, there is a significant need to identify important forage items for ungulates, but this has often proved challenging. Declines in several barren-ground caribou herds across the North American Arctic have raised concerns about the influence of climate change on caribou forage conditions. Shifts in plant phenology, biomass, quality, and composition may be influencing caribou diets and subsequently affecting their body condition and demographic rates. Although forage is a primary driver of barren-ground caribou behavior and population dynamics, there is limited recent information about the specific foods they consume, and uncertainty about appropriate methods for identifying those foods. Investigators are increasingly using fecal DNA metabarcoding and video camera collars to assess ungulate diets, but comparative studies of these approaches are lacking. To examine the summer diets of barren-ground caribou, we used both fecal metabarcoding and video camera collars to identify forage used by the Porcupine caribou herd, which spans the Alaska–Yukon border. In 2021, we sampled the diets of adult females by collecting fecal samples and observing collar videos during 4 sampling occasions. We found that caribou consumed very specific forage items, and those items varied markedly across the growing season. Caribou predominantly consumed graminoids and lichens during early summer, and shrubs and forbs later in the season. Metabarcoding and video data provided significantly different estimates of diet for all taxonomic levels we evaluated, and inferences from the two approaches were often disparate. Metabarcoding failed to detect some items frequently consumed in videos, such as lichens, and indicated high use of other items rarely consumed, such as mosses. We found that video data provided greater taxonomic diversity and resolution for vascular plants and lichens, and more closely aligned with past research and biological expectations than data from fecal metabarcoding. Additional research is needed to be able to use these methods to identify the biomass of different forage items consumed.

Alaska, Yukon↗

USGS2011

Pathology and failure in the design and implementation of adaptive management

The conceptual underpinnings for adaptive management are simple; there will always be inherent uncertainty and unpredictability in the dynamics and behavior of complex ecological systems as a result non-linear interactions among components and emergence, yet management decisions must still be made. The strength of adaptive management is in the recognition and confrontation of such uncertainty. Rather than ignore uncertainty, or use it to preclude management actions, adaptive management can foster resilience and flexibility to cope with an uncertain future, and develop safe to fail management approaches that acknowledge inevitable changes and surprises. Since its initial introduction, adaptive management has been hailed as a solution to endless trial and error approaches to complex natural resource management challenges. However, its implementation has failed more often than not. It does not produce easy answers, and it is appropriate in only a subset of natural resource management problems. Clearly adaptive management has great potential when applied appropriately. Just as clearly adaptive management has seemingly failed to live up to its high expectations. Why? We outline nine pathologies and challenges that can lead to failure in adaptive management programs. We focus on general sources of failures in adaptive management, so that others can avoid these pitfalls in the future. Adaptive management can be a powerful and beneficial tool when applied correctly to appropriate management problems; the challenge is to keep the concept of adaptive management from being hijacked for inappropriate use.

Journal of Environmental Management↗

USGS2025

Alternating movement strategies of a tropical raptor

The majority of raptor species reside in the tropics, yet very little is known about their movement ecology. However, quantifying movement behavior can provide otherwise elusive information on resource needs, habitat selection, and ecological constraints, which is important for understanding ecological patterns and the management of species of conservation concern. On the Island of Hawai‘i, Hawai‘i, USA, the endemic ‘Io, or Hawaiian Hawk ( Buteo solitarius ), is a species of conservation concern that little is known of their movement ecology, yet they are dependent on a fragmented and rapidly changing environment. We tracked 15 individuals for up to 18 months across a diverse landscape on the eastern side of the island. We found that all ‘Io occupied a relatively small geographic area, their place of residency, where they spent all or most of their time. However, 10 individuals also exhibited an alternative movement pattern, where individuals repeatedly commuted back and forth between their place of residency to another, geographically disjunct location. These commuter periods, which could last from 24–180 days, were characterized by frequent (9–259) movements, with individual trips lasting 4–77 h away from their place of residency and 12–47 h in between commuter trips. In most cases, individuals went to the same non-contiguous commuting destination, even across multiple commuting sessions, indicating high fidelity to commuting locations. The ‘Io is a forest adapted Buteo but occurs across a diverse landscape from forest to agriculture lands to urban areas. Habitat selection analysis indicated high individual variation among different birds, but generally a preference for forest patches at localized levels. The discovery of the alternative commuting strategy for many ‘Io represents a cryptic movement pattern in the species, demonstrating the power of small, long-lived Global Position System tracking devices to track movement and providing important insights into the ecology of a tropical island raptor.

Hawaii↗

USGS2001

Mapping wildland fuels for fire management across multiple scales: integrating remote sensing, GIS, and biophysical modeling

Fuel maps are essential for computing spatial fire hazard and risk and simulating fire growth and intensity across a landscape. However, fuel mapping is an extremely difficult and complex process requiring expertise in remotely sensed image classification, fire behavior, fuels modeling, ecology, and geographical information systems (GIS). This paper first presents the challenges of mapping fuels: canopy concealment, fuelbed complexity, fuel type diversity, fuel variability, and fuel model generalization. Then, four approaches to mapping fuels are discussed with examples provided from the literature: (1) field reconnaissance; (2) direct mapping methods; (3) indirect mapping methods; and (4) gradient modeling. A fuel mapping method is proposed that uses current remote sensing and image processing technology. Future fuel mapping needs are also discussed which include better field data and fuel models, accurate GIS reference layers, improved satellite imagery, and comprehensive ecosystem models.

International Journal of Wildland Fire↗

USGS2013

Broad-scale patterns of Brook Trout responses to introduced Brown Trout in New York

Brook Trout Salvelinus fontinalis and Brown Trout Salmo trutta are valuable sport fish that coexist in many parts of the world due to stocking introductions. Causes for the decline of Brook Trout within their native range are not clear but include competition with Brown Trout, habitat alteration, and repetitive stocking practices. New York State contains a large portion of the Brook Trout's native range, where both species are maintained by stocking and other management actions. We used artificial neural network models, regression, principal components analysis, and simulation to evaluate the effects of Brown Trout, environmental conditions, and stocking on the distribution of Brook Trout in the center of their native range. We found evidence for the decline of Brook Trout in the presence of Brown Trout across many watersheds; 22% of sampled reaches where both species were expected to occur contained only Brown Trout. However, a model of the direct relationship between Brook Trout and Brown Trout abundance explained less than 1% of data variation. Ordination showed extensive overlap of Brook Trout and Brown Trout habitat conditions, with only small components of the hypervolume (multidimensional space) being distinctive. Subsequent analysis indicated higher abundances of Brook Trout in highly forested areas, while Brown Trout were more abundant in areas with relatively high proportions of agriculture. Simulation results indicated that direct interactions and habitat conditions were relatively minor factors compared with the effects of repeated stocking of Brown Trout into Brook Trout habitat. Intensive annual stocking of Brown Trout could eliminate resident Brook Trout in less than a decade. Ecological differences, harvest behavior, and other habitat changes can exacerbate Brook Trout losses. Custom stocking scenarios with Brown Trout introductions at relatively low proportions of resident Brook Trout populations may be able to sustain healthy populations of both species within their present range.

New York↗

USGS2020

A synthesis of the biology and ecology of sculpin species in the Laurentian Great Lakes and implications for the adaptive capacity of the benthic ecosystem

The Laurentian Great Lakes have experienced recent ecosystem changes that could lead to reductions in adaptive capacity and ultimately a loss of biodiversity and production throughout the food web. Observed changes in Great Lakes benthic communities include declines of native species and widespread success of invasive species like dreissenid mussels in all but Lake Superior. Understanding the ecology of native benthic deepwater preyfish and the reasons for their declines is important for predicting future losses in adaptive capacity and diversity, as well as managing the Great Lakes ecosystem to avoid such losses. Native sculpin species ( Cottus bairdii , C. cognatus , C. ricei , Myoxocephalus thompsonii ) historically were among the most abundant of the Great Lakes native deepwater benthic preyfish community and are an important link between offshore benthic and pelagic food webs. With one exception, these species have declined in abundance throughout the Great Lakes in recent years, but relatively little is known about their biology and ecology. This review synthesizes the available knowledge for the Great Lakes sculpin species and provides suggestions for future research efforts, which include understanding reproductive ecology and spawning behavior, connectivity and dispersal of populations, early life history, and influences of interactions with native and non-native species.

Great Lakes↗

USGS2024

Potential use of poultry farms by wild waterfowl in California's Central Valley varies across space, times of day, and species: implications for influenza transmission risk

Interactions between wildlife and livestock can lead to cross-species disease transmission, which incurs economic costs and threatens wildlife conservation. Wild waterfowl are natural hosts of avian influenza viruses (AIVs), are often abundant near poultry farms, and have been linked to outbreaks of AIVs in poultry. Interspecific and seasonal variation in waterfowl movement and habitat use means that the risk of disease transmission between wild birds and poultry inevitably varies across species, space, and time. Here, we used GPS telemetry data from 10 waterfowl species in and near California's Central Valley, a region where both wild waterfowl and domestic poultry are abundant, to study selection of poultry farms by waterfowl across diel, seasonal, and annual cycles. We found that waterfowl selected for wetlands, open water, protected areas, and croplands, which meant that they generally avoided habitats that were likely to be used for poultry farming. These selection patterns were linked to species' ecology and diel behavioral patterns, such that avoidance of poultry habitats was stronger for local or partial migrants than for long-distance migrants, and stronger during daytime than at night. We then combined these habitat selection results with data on poultry farm locations to map risk of waterfowl–poultry contact across the Central Valley. Average selection strength at poultry farms was low, suggesting that current placement of poultry farms is generally effective for limiting risk of contact with wild birds. When we combined these habitat selection results with data on species' abundances and AIV infection prevalence, we found dramatic variation in potential AIV transmission risk among species. These results could be used to prioritize surveillance and biosecurity efforts for regions and times of relatively high risk. More generally, these results highlight that fine-scale movement data can help identify interspecific, seasonal, and diel patterns in animal behaviors that affect wildlife and poultry health.

California↗

USGS2015

The effects of heterospecifics and climatic conditions on incubation behavior within a mixed-species colony

Parental incubation behavior largely influences nest survival, a critical demographic process in avian population dynamics, and behaviors vary across species with different life history breeding strategies. Although research has identified nest survival advantages of mixing colonies, behavioral mechanisms that might explain these effects is largely lacking. We examined parental incubation behavior using video-monitoring techniques on Alcatraz Island, California, of black-crowned night-heron Nycticorax nycticorax (hereinafter, night-heron) in a mixed-species colony with California gulls Larus californicus and western gulls L. occidentalis . We first quantified general nesting behaviors (i.e. incubation constancy, and nest attendance), and a suite of specific nesting behaviors (i.e. inactivity, vigilance, preening, and nest maintenance) with respect to six different daily time periods. We employed linear mixed effects models to investigate environmental and temporal factors as sources of variation in incubation constancy and nest attendance using 211 nest days across three nesting seasons (2010–2012). We found incubation constancy (percent of time on the eggs) and nest attendance (percent of time at the nest) were lower for nests that were located < 3 m from one or more gull nest, which indirectly supports the predator protection hypothesis, whereby heterospecifics provide protection allowing more time for foraging and other self-maintenance activities. To our knowledge, this is the first empirical evidence of the influence of one nesting species on the incubation behavior of another. We also identified distinct differences between incubation constancy and nest attentiveness, indicating that these biparental incubating species do not share similar energetic constraints as those that are observed for uniparental species. Additionally, we found that variation in incubation behavior was a function of temperature and precipitation, where the strength of these effects was dependent on the time of day. Overall, these findings strengthen our understanding of incubation behavior and nest ecology of a colonial-nesting species.

California↗

USGS1989

Regionwide polygyny in willow flycatchers

Most species of North American flycatchers (Tyranidae) are believed to be normally monogamous (Skutch 1960, Verner and Willson 1969). Some instances of bigamy are known for the Eastern Phoebe ( Sayornis phoebe ; Sherman 1952), Eastern Wood-Pewee ( Contopus virens ; W. J. Smith, cited in Eckhardt 1976), Western Wood-Pewee ( C. sordidulus ; Eckhardt 1976), and Acadian Flycatcher ( Empidonax viriscens ; Mumford 1964). Recently, local incidences of polygyny have also been reported for the Least ( E. minimus ; Briskie and Sealy 1987) and Willow ( E. traillii ; Prescott 1986) flycatchers. Here, we present details on two additional instances of polygyny in Willow Flycatchers in different regions of North America, including information on the behavior and nesting ecology of polygynous trios.

The Condor↗

USGS2022

Positively selected genes in the hoary bat (Lasiurus cinereus) lineage: Prominence of thymus expression, immune and metabolic function, and regions of ancient synteny

Background Bats of the genus Lasiurus occur throughout the Americas and have diversified into at least 20 species among three subgenera. The hoary bat ( Lasiurus cinereus ) is highly migratory and ranges farther across North America than any other wild mammal. Despite the ecological importance of this species as a major insect predator, and the particular susceptibility of lasiurine bats to wind turbine strikes, our understanding of hoary bat ecology, physiology, and behavior remains poor. Methods To better understand adaptive evolution in this lineage, we used whole-genome sequencing to identify protein-coding sequence and explore signatures of positive selection. Gene models were predicted with Maker and compared to seven well-annotated and phylogenetically representative species. Evolutionary rate analysis was performed with PAML. Results Of 9,447 single-copy orthologous groups that met evaluation criteria, 150 genes had a significant excess of nonsynonymous substitutions along the L. cinereus branch ( P < 0.001 after manual review of alignments). Selected genes as a group had biased expression, most strongly in thymus tissue. We identified 23 selected genes with reported immune functions as well as a divergent paralog of Steep1 within suborder Yangochiroptera. Seventeen genes had roles in lipid and glucose metabolic pathways, partially overlapping with 15 mitochondrion-associated genes; these adaptations may reflect the metabolic challenges of hibernation, long-distance migration, and seasonal variation in prey abundance. The genomic distribution of positively selected genes differed significantly from background expectation by discrete Kolmogorov–Smirnov test ( P < 0.001). Remarkably, the top three physical clusters all coincided with islands of conserved synteny predating Mammalia, the largest of which shares synteny with the human cat-eye critical region (CECR) on 22q11. This observation coupled with the expansion of a novel Tbx1 -like gene family may indicate evolutionary innovation during pharyngeal arch development: both the CECR and Tbx1 cause dosage-dependent congenital abnormalities in thymus, heart, and head, and craniodysmorphy is associated with human orthologs of other positively selected genes as well.

PeerJ↗

USGS1999

Snake species of the world: A taxonomic and geographic reference. v. 1

Given the absence of a current source on snake diversity and nomenclature and the expressed global need to understand better the diversity of our biota, we think that a catalogue of the world snake fauna complete with synonymies at the familial, generic, and specific levels is essential. We provide that here beginning with publication of the first volume. This compendium will facilitate comparative studies on the ecology, genetics, and behavior of snakes and, we hope, contribute to their conservation. At the very least, this work, when completed, will provide a readily available reference to the current taxonomic statuses and geographic distributions of snakes on a global scale. No comprehensive, up-to-date catalogue of snake species exists, and it is obvious that a detailed and inclusive treatment is long overdue. Snake Species of the World provides a comprehensive treatment of 31 families, 450 genera, and more than 2500 species of living snakes. The magnitude of the compilation requires publication in several volumes. This volume, the first of three, covers 682 species. A primary goal of this synthesis is to provide interested readers with a means for tracking scientific names that have been applied to a snake and determining the currently accepted name of that species. A secondary goal is to alert those interested in snakes as research subjects that in general many species are poorly known, that some have limited distributions, and that several are characterized by taxonomic problems.

Book↗

USGS2017

Identifying ecologically relevant scales of habitat selection: diel habitat selection in elk

Although organisms make resource selection decisions at multiple spatiotemporal scales, not all scales are ecologically relevant to any given organism. Ecological patterns and rhythms such as behavioral and climatic patterns may provide a consistent method for identifying ecologically relevant scales of habitat selection. Using elk ( Cervus canadensis ) as an example species, we sought to test the ability of behavioral patterns to empirically partition diel scales for modeling habitat selection. We used model selection to partition diel scales by shifts in dominant behavior and then used resource selection probability functions to model elk habitat selection hierarchically at diel scales within seasons. Model selection distinguished four diel temporal partitions following elk crepuscular behavioral patterns: dawn, midday, dusk, and night. Across seasons, model‐averaged coefficients indicated that elk shifted from selecting grassland cover at dawn/dusk, to selecting for greater canopy and forest cover at midday, and then to areas with greater herbaceous biomass at night. Top models changed between diel intervals in spring and fall but stayed the same across diel intervals in winter and summer. In winter, elk selected for southern aspects during midday, for unburned areas at dawn/dusk, and for areas burned within 1–3 yr at dawn/dusk and night. In spring, elk selected for northern aspects and for areas burned within 1–3 yr at midday, for areas farther from roads at dawn/dusk and midday, and for areas farther from water at midday. In summer, elk changed diel preferences for fewer covariates: At dawn/dusk and midday, elk selected for areas farther from water and avoided forest cover, and at night, elk selected for areas burned within 1–3 yr. In fall, elk selected for areas burned the previous year at dawn/dusk and night, for higher elevations at midday, and for areas closer water at night. Using behavioral patterns to identify ecologically relevant scales can help identify overlooked habitat requirements such as diel changes in preference for fire history, forage availability, and cover. We show that the ecological relevancy of a given scale (e.g., a diel temporal scale) can change throughout a given extent (e.g., across seasons).

New Mexico↗

USGS2016

Research on Golden-winged Warblers: Recent progress and current needs

Considerable advances have been made in knowledge about Golden-winged Warblers ( Vermivora chrysoptera ) in the past decade. Recent employment of molecular analysis, stable-isotope analysis, telemetry-based monitoring of survival and behavior, and spatially explicit modeling techniques have added to, and revised, an already broad base of published knowledge. Here, we synthesize findings primarily from recent peer-reviewed literature on Golden-winged Warblers, from this volume and elsewhere, and we identify some of the substantial remaining research needs. We have organized this synthesis by stages of the Golden-winged Warbler annual cycle. First, we discuss the relatively well-studied breeding-grounds ecology including nesting and post-fledging ecology and hybridization with closely related Blue-winged Warblers ( Vermivora cyanoptera ). Second, we discuss the much-less-studied, non-breeding-grounds ecology, including the first empirical studies of non-breeding-grounds cover-type associations and spatial and social behavioral ecology. Third, we address migratory connectivity and migration ecology, for which little is known and research has only just begun. Last, we close with cautious optimism that current knowledge is adequate to inform initial conservation and management plans for Golden-winged Warblers, and with a sobering acknowledgement of the quantity of research still needed.

Studies in Avian Biology↗