Geology Reports⌕ Search

SEARCH · Geology Reports

Results for “Journal of Animal Ecology”

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

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

At least 127 records · Page 7Linked to original sources
USGS2009

Trend estimation in populations with imperfect detection

1. Trends of animal populations are of great interest in ecology but cannot be directly observed owing to imperfect detection. Binomial mixture models use replicated counts to estimate abundance, corrected for detection, in demographically closed populations. Here, we extend these models to open populations and illustrate them using sand lizard Lacerta agilis counts from the national Dutch reptile monitoring scheme. 2. Our model requires replicated counts from multiple sites in each of several periods, within which population closure is assumed. Counts are described by a hierarchical generalized linear model, where the state model deals with spatio-temporal patterns in true abundance and the observation model with imperfect counts, given that true state. We used WinBUGS to fit the model to lizard counts from 208 transects with 1–10 (mean 3) replicate surveys during each spring 1994–2005. 3. Our state model for abundance contained two independent log-linear Poisson regressions on year for coastal and inland sites, and random site effects to account for unexplained heterogeneity. The observation model for detection of an individual lizard contained effects of region, survey date, temperature, observer experience and random survey effects. 4. Lizard populations increased in both regions but more steeply on the coast. Detectability increased over the first few years of the study, was greater on the coast and for the most experienced observers, and highest around 1 June. Interestingly, the population increase inland was not detectable when the observed counts were analysed without account of detectability. The proportional increase between 1994 and 2005 in total lizard abundance across all sites was estimated at 86% (95% CRI 35–151). 5. Synthesis and applications . Open-population binomial mixture models are attractive for studying true population dynamics while explicitly accounting for the observation process, i.e. imperfect detection. We emphasize the important conceptual benefit provided by temporal replicate observations in terms of the interpretability of animal counts.

Journal of Applied Ecology↗
USGS2025

Using distance sampling with camera traps to estimate densities of ungulates on tropical oceanic islands

Reliable population estimates are one of the most elementary needs for the management of wildlife, particularly for introduced ungulates on oceanic islands. We aimed to produce accurate and precise density estimates of Philippine deer ( Rusa marianna ) and wild pigs ( Sus scrofa ) on Guam using motion-triggered cameras combined with distance sampling to estimate densities from observations of unmarked animals while accounting for imperfect detection. We used an automated digital data processing pipeline for species recognition and to estimate the distance to detected species. Our density estimates were slightly lower than published estimates, consistent with management to reduce populations. We estimated the number of camera traps needed to obtain a 0.1 coefficient of variation was substantial, requiring > ten-fold increase in camera traps, while estimates with precision of 0.2 or 0.3 were more achievable, requiring doubling to quadrupling the number of camera traps. We provide best practices for establishing and conducting distance sampling with camera trap surveys for density estimation based on lessons learned during this study. Future studies should consider distance sampling with camera traps to efficiently survey and monitor unmarked animals, particularly medium-sized ungulates, in tropical, oceanic island ecosystems.

Journal of Tropical Ecology↗
USGS2003

A new pterosaur tracksite from the Jurassic Summerville formation, near Ferron, Utah

Pterosaur tracks (cf. Pteraichnus ) from the Summerville Formation of the Ferron area of central Utah add to the growing record of Pteraichnus tracksites in the Late Jurassic Summerville Formation and time-equivalent, or near time-equivalent, deposits. The site is typical in revealing high pterosaur track densities, but low ichnodiversity suggesting congregations or “flocks” of many individuals. Footprint length varies from 2.0 to 7.0 cms. The ratio of well-preserved pes:manus tracks is about 1:3.4. This reflects a bias in favor of preservation of manus tracks due to the greater weight-bearing role of the front limbs, as noted in other pterosaur track assemblages. The sample also reveals a number of well-preserved trackways including one suggestive of pes-only progression that might be associated with take off or landing, and another that shows pronounced lengthening of stride indicating acceleration. One well-preserved medium-sized theropod trackway ( Therangospodus ) and other larger theropod track casts (cf. Megalosauripus ) are associated with what otherwise appears to be a nearly monospecific pterosaur track assemblage. However, traces of a fifth pes digit suggest some tracks are of rhamphorynchoid rather than pterodactyloid origin, as usually inferred for Pteraichnus . The tracks occur at several horizons in a thin stratigraphic interval of ripple marked sandstones and siltstones. Overall the assemblage is similar to others found in the same time interval in the Western Interior from central and eastern Utah through central and southern Wyoming, Colorado, northeastern Arizona, and western Oklahoma. This vast “ Pteraichnus ichnofacies,” with associated saurischian tracks, remains the only ichnological evidence of pre-Cretaceous pterosaurs in North America and sheds important light on the vertebrate ecology of the Summerville Formation and contiguous deposits.

Utah↗
USGS2010

Susceptibility of three stocks of pacific herring to viral hemorrhagic septicemia

Laboratory challenges using specific-pathogen-free Pacific herring Clupea pallasii from three distinct populations indicated that stock origin had no effect on susceptibility to viral hemorrhagic septicemia (VHS). All of the populations were highly susceptible to the disease upon initial exposure, with significantly greater cumulative mortalities occurring in the exposed treatment groups (56.3-64.3%) than in the unexposed control groups (0.8-9.0%). Interstock differences in cumulative mortality were not significant. The virus loads in the tissues of fish experiencing mortality were 10-10,000 times higher during the acute phase of the epizootics (day 13 postexposure) than during the recovery phase (days 30-42). Survivors of the epizootics were refractory to subsequent VHS, with reexposure of VHS survivors resulting in significantly less cumulative mortality (1.2-4.0%) than among positive controls (38.1-64.4%); interstock differences in susceptibility did not occur after reexposure. These results indicate that data from experiments designed to understand the ecology of VHS virus in a given stock of Pacific herring are broadly applicable to stocks throughout the northeastern Pacific.

Journal of Aquatic Animal Health↗
USGS2026

Advances and applications of Unoccupied Aerial Systems (UAS) research in landscape ecology

Landscape ecologists have long depended on satellite and aerial remote sensing to address questions about landscape pattern and process, structure, and change (Foody 2023 ). Unoccupied aerial systems/vehicles (UAS/UAV, a.k.a. drones) technology is becoming an increasingly popular research tool in environmental sciences allowing scientists to generate low-cost, high-quality, and high-resolution imagery on demand that can be tailored to specific research questions. While satellite data are of a fixed resolution and temporal interval, UAS offer researchers control and flexibility to design studies and collect data at resolutions and scales that provide ecologically relevant information at finer spatial resolutions (e.g., < 30 cm) than what is currently available from satellite platforms (typically > 3m), thus helping capture objects such as individual plant canopies, micro-topography, and individual animals. Unlike satellites with fixed orbits, UAS can be deployed at more optimal temporal frequencies for ecological monitoring. We organized the special collection “Advances and Applications of Unoccupied Aerial Systems (UAS) Research in Landscape Ecology” to showcase the many ways that UAS tools and technologies are currently applied to advance landscape ecological research. When we announced the collection in 2023, only 11 papers published in the journal Landscape Ecology used UAS data, which was a notably small number compared to many other general ecology, environmental science and remote sensing journals. In an attempt to understand why UAS were not more widely used in landscape ecology and provide possible solutions, we published a review article (Villarreal et al. 2025) that identified the challenges, knowledge gaps, and obstacles for the adoption of UAS technologies in landscape ecology research. The main issues we identified include: (1) an abundance of UAS methods papers in the existing literature, with comparatively few studies demonstrating how UAS can be applied to address ecological questions; (2) a perceived scale mismatch between the geographic extent of UAS data collection (local) compared to larger study areas (landscapes) and a need to design robust scaling approaches to connect fine-scale UAS data with broader ecological patterns; and (3) a need for improved integration of UAS data with other commonly used remote sensing datasets including historical high resolution aerial imagery. Additionally, researchers new to UAS remote sensing may be discouraged or overwhelmed by the general lack of scientific consensus and standardized protocols for typical tasks such as data collection, vegetation classification, and change detection, as well as restrictive and/or confusing policy, regulatory, and legal issues surrounding UAS operations (Villarreal et al. 2025).

Landscape Ecology↗
USGS1966

Contamination of the freshwater ecosystem by pesticides

A large part of our disquieting present-day pesticide problem is intimately tied to the freshwater ecosystem. Economic poisons are used in so many types of terrain to control so many kinds of organisms that almost all lakes and streams are likely to be contaminated. In addition to accidental contamination many pesticides are deliberately applied directly to fresh waters for suppression of aquatic animals or plants. The problem is intensified because of the extreme susceptibility of freshwater organisms. The complexity of freshwater environments and their variety makes it difficult to comprehend the total effect of pesticides.

Journal of Applied Ecology↗
USGS2005

Thiamine status in adult salmonines in the Great Lakes

In 1996 and again in 1999, hatchery personnel noted that some Lake Michigan coho salmon Oncorhynchus kisutch from fall spawning runs on the Platte River weir exhibited abnormal wiggling behavior that was similar to the behavior exhibited by thiamine-deficient Atlantic salmon Salmo salar , from the Baltic Sea. Samples of eggs or gonads, muscle, and liver from salmon and lake trout Salvelinus namaycush exhibiting abnormal behaviors were collected to determine the extent to which the behaviors were related to a thiamine deficiency. We compared these values with those found in normally behaving fish that produced offspring with high embryonic survival. In all adult fish exhibiting abnormal behavior, tissue residues of thiamine were among the lowest observed in the Great Lakes. Where embryonic survival was assessed, abnormal adult behavior was also associated with very high levels of offspring mortality due to early mortality syndrome. While the overall ecological significance remains to be determined, it appears that adult fish also exhibit neurological dysfunction and mortality associated with thiamine deficiency.

Journal of Aquatic Animal Health↗
USGS1975

Blood analyses of wolf pups and their ecological and metabolic interpretation

Blood samples were obtained from 32 wolf ( Canis lupus ) pups live-trapped over a three-year period in northern Minnesota. The results of 21 laboratory analyses of hematology and blood chemistry are tabulated and analyzed in terms of study area, age, sex, and year of collection. Mean values are compared to those reported for dogs in the same age group. The numerous differences between dog and wolf pups are interpreted in terms of nutritional levels and dietary composition with the suggestion that the wolves are not achieving their full growth potential. Individual abnormal test results are tabulated and possible interpretations are suggested. Abnormal results were observed in 13 animals including 10 of 11 animals sampled in 1972. The results in the 1972 animals indicated a poorer nutrition. This preponderance of abnormal test results in pups from 1972 is correlated with ecological studies on this wolf population indicating decreased survival. The potential value of such long-term integrated field and laboratory studies for providing a more complete understanding of changes in the dynamics of natural populations in terms of the responses of individual animals is demonstrated.

Minnesota↗
USGS2014

Standardized phenology monitoring methods to track plant and animal activity for science and resource management applications

Phenology offers critical insights into the responses of species to climate change; shifts in species’ phenologies can result in disruptions to the ecosystem processes and services upon which human livelihood depends. To better detect such shifts, scientists need long-term phenological records covering many taxa and across a broad geographic distribution. To date, phenological observation efforts across the USA have been geographically limited and have used different methods, making comparisons across sites and species difficult. To facilitate coordinated cross-site, cross-species, and geographically extensive phenological monitoring across the nation, the USA National Phenology Network has developed in situ monitoring protocols standardized across taxonomic groups and ecosystem types for terrestrial, freshwater, and marine plant and animal taxa. The protocols include elements that allow enhanced detection and description of phenological responses, including assessment of phenological “status”, or the ability to track presence–absence of a particular phenophase, as well as standards for documenting the degree to which phenological activity is expressed in terms of intensity or abundance. Data collected by this method can be integrated with historical phenology data sets, enabling the development of databases for spatial and temporal assessment of changes in status and trends of disparate organisms. To build a common, spatially, and temporally extensive multi-taxa phenological data set available for a variety of research and science applications, we encourage scientists, resources managers, and others conducting ecological monitoring or research to consider utilization of these standardized protocols for tracking the seasonal activity of plants and animals.

International Journal of Biometeorology↗
USGS2016

Combining citizen science species distribution models and stable isotopes reveals migratory connectivity in the secretive Virginia rail

Stable hydrogen isotope (δD) methods for tracking animal movement are widely used yet often produce low resolution assignments. Incorporating prior knowledge of abundance, distribution or movement patterns can ameliorate this limitation, but data are lacking for most species. We demonstrate how observations reported by citizen scientists can be used to develop robust estimates of species distributions and to constrain δD assignments. We developed a Bayesian framework to refine isotopic estimates of migrant animal origins conditional on species distribution models constructed from citizen scientist observations. To illustrate this approach, we analysed the migratory connectivity of the Virginia rail Rallus limicola , a secretive and declining migratory game bird in North America. Citizen science observations enabled both estimation of sampling bias and construction of bias-corrected species distribution models. Conditioning δD assignments on these species distribution models yielded comparably high-resolution assignments. Most Virginia rails wintering across five Gulf Coast sites spent the previous summer near the Great Lakes, although a considerable minority originated from the Chesapeake Bay watershed or Prairie Pothole region of North Dakota. Conversely, the majority of migrating Virginia rails from a site in the Great Lakes most likely spent the previous winter on the Gulf Coast between Texas and Louisiana. Synthesis and applications . In this analysis, Virginia rail migratory connectivity does not fully correspond to the administrative flyways used to manage migratory birds. This example demonstrates that with the increasing availability of citizen science data to create species distribution models, our framework can produce high-resolution estimates of migratory connectivity for many animals, including cryptic species. Empirical evidence of links between seasonal habitats will help enable effective habitat management, hunting quotas and population monitoring and also highlight critical knowledge gaps.

Journal of Applied Ecology↗
USGS2008

Importance of sampling design and analysis in animal population studies: a comment on Sergio et al

1. The use of predators as indicators and umbrellas in conservation has been criticized. In the Trentino region, Sergio et al. (2006; hereafter SEA) counted almost twice as many bird species in quadrats located in raptor territories than in controls. However, SEA detected astonishingly few species. We used contemporary Swiss Breeding Bird Survey data from an adjacent region and a novel statistical model that corrects for overlooked species to estimate the expected number of bird species per quadrat in that region. 2. There are two anomalies in SEA which render their results ambiguous. First, SEA detected on average only 6.8 species, whereas a value of 32 might be expected. Hence, they probably overlooked almost 80% of all species. Secondly, the precision of their mean species counts was greater in two-thirds of cases than in the unlikely case that all quadrats harboured exactly the same number of equally detectable species. This suggests that they detected consistently only a biased, unrepresentative subset of species. 3. Conceptually, expected species counts are the product of true species number and species detectability p. Plenty of factors may affect p, including date, hour, observer, previous knowledge of a site and mobbing behaviour of passerines in the presence of predators. Such differences in p between raptor and control quadrats could have easily created the observed effects. Without a method that corrects for such biases, or without quantitative evidence that species detectability was indeed similar between raptor and control quadrats, the meaning of SEA's counts is hard to evaluate. Therefore, the evidence presented by SEA in favour of raptors as indicator species for enhanced levels of biodiversity remains inconclusive. 4. Synthesis and application. Ecologists should pay greater attention to sampling design and analysis in animal population estimation. Species richness estimation means sampling a community. Samples should be representative for the community studied and the sampling fraction among communities compared should be the same on average, otherwise formal estimation approaches must be applied to avoid misleading inference.

Journal of Applied Ecology↗
USGS2003

Analysis of ecological context for identifying vegetation and animal conservation planning foci: An example from the arid South-western USA

In developing conservation strategies, it is important to maximize effects of conservation within a specified land tract and to maximize conservation effects on surrounding area (ecological context). The authors proposed two criteria to select biotic entities for conservation foci: (1) the relative occurrence of fauna or flora in a tract is greater than that of an ecological context region; and (2) occurrence of the fauna or flora is relatively limited in the ecological context region. Using extensive spatial data on vegetation and wildlife habitat distribution, the authors identified strategic vegetation and fauna conservation foci for the 400 000 ha Fort Bliss military reservation in New Mexico and Texas relative to a 164 km radius ecological context region intersecting seven ecological zones and the predicted habitat distribution of 616 animal species. The authors set two specific criteria: (1) predicted area of a species' occurrence is <50% of the ecological context region; and (2) percentage of Fort Bliss intersecting the species' or vegetation community predicted areas in the ecological context region is >5% (Fort Bliss is 4.2% of the region). These criteria selected one vegetation class and 40 animal species. Further, these vegetation and animal foci were primarily located in two areas of Fort Bliss. Sensitivity analyses with other analytical radii corroborated the context radius used. Conservation of the two areas and associated taxa will maximize the contribution of Fort Bliss's conservation efforts in its ecological proximity. This relatively simple but information-rich process represents economical and defensible preliminary contextual analysis for detailed conservation planning.

Journal of Environmental Planning and Management↗
USGS2015

Cyclic avian mass mortality in the northeastern United States is associated with a novel orthomyxovirus

Since 1998, cyclic mortality events in common eiders ( Somateria mollissima ), numbering in the hundreds to thousands of dead birds, have been documented along the coast of Cape Cod, Massachusetts, USA. Although longitudinal disease investigations have uncovered potential contributing factors responsible for these outbreaks, detecting a primary etiological agent has proven enigmatic. Here we identify a novel orthomyxovirus, tentatively named Wellfleet Bay virus (WFBV), as a potential causative agent of these outbreaks. Genomic analysis of WFBV revealed that it is most closely related to members of the Quaranjavirus genus within the family Orthomyxoviridae . Similar to other members of the genus, WFBV contains an alphabaculovirus gp64-like glycoprotein, which was demonstrated to have fusion activity, and also tentatively suggests that ticks (and/or insects) may vector the virus in nature. However, in addition to the six RNA segments encoding the prototypical structural proteins identified in other quaranjaviruses, a previously unknown RNA segment (segment 7) encoding a novel protein designated as VP7 was discovered in WFBV. Although WFBV shows low to moderate levels of sequence similarity to Quaranfil virus and Johnston Atoll virus , the original members of the Quaranjavirus genus, additional antigenic and genetic analyses demonstrated that it is closely related to the recently identified Cygnet River virus (CyRV) from South Australia, suggesting that WFBV and CyRV may be geographic variants of the same virus. Although the identification of WFBV in part may resolve the enigma of these mass mortality events, the details of the ecology and epidemiology of the virus remain to be determined. Importance The emergence or reemergence of viral pathogens resulting in large-scale outbreaks of disease in humans and/or animals is one of the most important challenges facing biomedicine. For example, understanding how orthomyxoviruses such as novel influenza A virus reassortants and/or mutants emerge to cause epidemic or pandemic disease is at the forefront of current global health concerns. Here we describe the emergence of a novel orthomyxovirus, Wellfleet Bay virus (WFBV), which has been associated with cyclic large-scale bird die-offs in the northeastern United States. This initial characterization study provides a foundation for further research into the evolution, epidemiology, and ecology of newly emerging orthomyxoviruses, such as WFBV, and their potential impacts on animal and/or human health.

Massachusets↗
USGS2022

Priorities for translating goodwill between movement ecologists and conservation practitioners into effective collaboration

Addressing ongoing biodiversity loss requires collaboration between conservation scientists and practitioners. However, such collaboration has proved challenging. Despite the potential importance of tracking animal movements for conservation, reviews of the tracking literature have identified a gap between the academic discipline of movement ecology and its application to biodiversity conservation. Through structured conversations with movement ecologists and conservation practitioners, we aimed to understand whether the identified gap is also perceived in practice, and if so, what factors hamper collaboration and how these factors can be remediated. We found that both groups are motivated and willing to collaborate. However, because their motivations differ, there is potential for misunderstandings and miscommunications. In addition, external factors such as funder requirements, academic metrics, and journal scopes may limit the applicability of scientific results in a conservation setting. Potential solutions we identified included improved communication and better presentation of results, acknowledging each other's motivations and desired outputs, and adjustment of funder priorities. Addressing gaps between science and implementation can enhance collaboration and support conservation action to address the global biodiversity crisis more effectively.

Conservation Science and Practice↗
USGS2018

Population ecology of Roosevelt elk: Conservation and management in Redwood National and State Parks. Butch Weckerly. 2017. University of Nevada Press, Reno, Nevada, USA. 224 pp. $54.95 hardback. ISBN 978- 1943859504.

Long-term research on large ungulate populations typically conjures perceptions of extensive (and expensive) animal capture and telemetry work, and subsequent advanced modeling of resource selection and population dynamics that inform management decisions. In contrast, studies lacking a telemetry component are often limited to animal behavior or natural history. Although compelling from a standpoint of advancing understanding of ecological and evolutionary processes, results from the latter can be unfairly labeled as esoteric because they are not easily transferable to resource managers or may not provide exceptional interest to a general public drawn to these charismatic megafuana. Such dichotomies are not predetermined, however, because study conditions exist where dedicated academic researchers on tight budgets can achieve results relevant to ecology and management.

Journal of Wildlife Management↗
USGS1976

Feeding ecology of breeding gadwalls on saline wetlands

The feeding ecology of breeding gadwalls ( Anas strepera ) from saline wetlands in North Dakota was examined in relation to sex, pair mates, reproductive status, food availability, and wetland type during the spring and summer of 1971 and 1972. Esophagi of males and females contained 40.4 and 48.2 percent animal food, respectively, between 17 April and 25 August. Animal foods consumed by paired females varied with reproductive condition and were independent of their mates. Invertebrates increased from 47.7 i?? 17.4 percent in the diet during prelaying to 72.0 i?? 18.4 percent during laying and declined to 46.3 i?? 30.0 percent during postlaying. Aquatic insects dominated the diet during egg-laying and were selected disproportionately relative to their availability. Esophageal contents indicated that diversity of plant and animal foods in the diet varied inversely with specific conductance. Major factors influencing food selection of the breeding birds are discussed as interactions among their physiological status, their anatomical and behavioral characteristics, and the abundance and behavior of food organisms as influenced by chemical and physical features of the environment. The data suggested that these interrelated ecological factors act simultaneously to control the phenology of events and determine the foods utilized.

North Dakota↗
USGS2009

Maintaining the competitiveness of the American Fisheries Society journals: An assessment based on influence and cost-effectiveness

Recent changes in the landscape of scientific publishing prompted the Publications Overview Committee of the American Fisheries Society (AFS) to review the Society's portfolio of scientific journals. We evaluated journals based on metrics in two categories: (1) citation-based measures of the influence of a journal on the scientific literature, and (2) measures of the cost-effectiveness of a journal (citation rate adjusted for subscription cost). Over the long-term, we found that ecology journals had far stronger citation-based influence than fisheries and aquatic sciences journals, and that journals publishing primarily basic research had stronger influence than journals publishing applied research (including four AFS journals and Fisheries magazine). In evaluating the current status of fisheries and aquatic sciences journals, we found that metrics of influence and cost-effectiveness provided considerably different portrayals of journals relative to their peers. In terms of citation-based influence, we found that the AFS journal Transactions of the American Fisheries Society (TAFS) and Fisheries magazine were competitive with highly regarded peer fisheries journals, but that North American Journal of Aquaculture (NAJA) and Journal of Aquatic Animal Health (JAAH) were less influential than their peers. The citation-based influence of North American Journal of Fisheries Management (NAJFM) was intermediate between TAFS/Fisheries and NAJA/JAAH . For journals like NAJFM and NAJA , we expect that much of the scientific influence on policy and management is not captured by citations in the primary literature, and alternative methods of evaluation may be needed. All of the AFS journals ranked highly with regard to cost-effectiveness because their subscription costs are low, and these rankings are in accordance with membership needs and the strategic mission of AFS to provide broad and timely dissemination of scientific information. We conclude by suggesting ways to increase the influence of AFS journals without compromising their accessibility and affordability, and offer advice about methods and frequency for future journal evaluations.

Fisheries↗