SEARCH · Geology Reports

Results for “Animals”

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

SourceResearch connectionFrom yearThrough year

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

At least 685 records · Page 38Linked to original sources

USGS2012

Adaptive breeding habitat selection: Is it for the birds?

The question of why animals choose particular habitats has important implications for understanding behavioral evolution and distribution of organisms in the wild and for delineating between habitats of different quality for conservation and management. Habitats chosen by animals can influence fitness outcomes via the costs (e.g., predation risk) and benefits (e.g., food availability) of habitat use. Habitat preferences should therefore be under selection to favor those that confer fitness advantages (Clark and Shutler 1999). Indeed, prevailing theory suggests that the habitat preferences of animals should be adaptive, such that fitness is higher in preferred habitats (Hildén 1965, Southwood 1977, Martin 1998). However, studies have often identified apparent mismatches between observed habitat preferences and fitness outcomes across a wide variety of taxa (Valladares and Lawton 1991, Mayhew 1997, Kolbe and Janzen 2002, Arlt and Pärt 2007, Mägi et al. 2009). Certainly, one limitation of studies may be that assessment of “fitness” is typically constrained to fitness surrogates such as nest success rather than lifetime reproductive success or classic Fisherian fitness (Endler 1986). Nevertheless, important habitat choices such as nest sites influence the probability that temporarily sedentary, dependent young are discovered by enemies such as predators and parasites. We therefore expect, on average, to see congruence between evolved habitat preferences and relevant components of fitness (e.g., nest success). Here, we (1) review the prevalence of apparent mismatches between avian breeding-habitat preferences and fitness outcomes using nest-site selection as a focus; (2) describe several potential mechanisms for such mismatches, including anthropogenic, methodological, and ecological–evolutionary; and (3) suggest a framework for understanding the contexts in which habitat preferences represent adaptive decisions, with a primary focus on ecological information theory. We largely focus on habitat selection as a behavioral process at the scale of individuals (e.g., Robertson and Hutto 2006), rather than at the scale of population-level patterns (Fretwell and Lucas 1970, Morris 2003, Johnson 2007). However, these two scales cannot be wholly divorced from one another, as we will discuss.

The Auk↗

USGS1965

A review of advances in the study of diseases of fish: 1954-1964

STUDY OF DISEASE IN ANIMALS, INCLUDING MAN, has progressed rapidly in the past decade. Looking back, we find amazing success in the study of man's diseases and possibly only a little less success in studies of diseases of domesticated homeothermic animals. We who are interested in the poikilothermic animals may feel at times that we have not advanced so rapidly in our field. The reason for this may be closely associated with economics. The market for drugs and therapeutic agents is greater for domestic livestock than for cultured fishes. A larger income is derived from rearing domestic livestock. Therefore, more public funds are available for study of diseases of man and domestic livestock, while such funds are limited for the study of diseases of fish. The Federal and State fish-cultural systems, as well as colleges and universities, have been most active in research on fish disease and probably will continue to be so.

Progressive Fish-Culturist↗

USGS1995

Evidence for lack of homing by sea lampreys

Recently metamorphosed sea lampreys Petromyzon marinus were captured in the Devil River, a tributary to Lake Huron, during summer and autumn 1990. They were tagged with a coded wire tag and returned to the river to continue their migration to Lake Huron to begin the parasitic (juvenile) phase of their life. During the spawning run in spring 1992 when the tagged animals were expected to mature and return to spawn, sea lampreys were trapped in nine tributaries to Lake Huron, including the Devil River; 47,946 animals were examined for coded wire tags, and 41 tagged animals were recovered. None of the 45 mature sea lampreys captured in the Devil River in 1992 were tagged, a proportion (0%) significantly lower than the proportion of the recently metamorphosed sea lampreys tagged in 1990. The distribution of tag recoveries among streams lakewide, however, was proportional to catch. Tagged sea lampreys did not appear to home, but instead seemed to select spawning streams through innate attraction to other sensory cues.

Transactions of the American Fisheries Society↗

USGS2018

Movements and dive patterns of pygmy killer whales (Feresa attenuata) released in the Gulf of Mexico following rehabilitation

The habits and habitats of pygmy killer whales ( Feresa attenuata ) in the Gulf of Mexico (GoM) are poorly known outside of strandings and line-transect surveys. Two adult male pygmy killer whales were found live-stranded in the state of Mississippi (USA) on 1 September 2015 and were subsequently rehabilitated and returned to the offshore waters of the GoM on 11 July 2016. To monitor the animals post-release, both were tagged with satellite-linked location and dive behavior tags. Tags were programed to record and transmit dive duration and depth (when dives were ≥ 30 m deep for ≥ 30 s), duration of time spent above 30 m depth, and estimate locations using the Argos system. The tags transmitted for 15 and 88 days, respectively, providing a total of 1,027 filtered locations and 3,150 dive duration and maximum depth records. The animals began diving after two and four days, respectively, post-release. More than 96% of dives occurred at night. The longest recorded dive was more than 9 min in duration, and the deepest was to 368 m. More than 98% of the locations were over the GoM shelf break, spanning water 200 to 1,200 m deep. Diving patterns indicate that this species is most active at night in the GoM, suggesting its prey species are likely diel migrators that are below reachable depths during daylight hours. Near simultaneous location data from both animals confirmed that they stayed in close proximity but did not dive synchronously. Success of the rehabilitation and release was inconclusive for pygmy killer whale ID 30IMMS, whereas 31IMMS met the established criteria for success with ≥ 6 weeks of documented post-release survival. Follow-up monitoring through satellite-linked telemetry provided not only important data for evaluating the success of the rehabilitation but also for documenting the activity and habitat use of these seldom-observed cetaceans.

Aquatic Mammals↗

USGS2014

A hierarchical model combining distance sampling and time removal to estimate detection probability during avian point counts

Imperfect detection during animal surveys biases estimates of abundance and can lead to improper conclusions regarding distribution and population trends. Farnsworth et al. (2005) developed a combined distance-sampling and time-removal model for point-transect surveys that addresses both availability (the probability that an animal is available for detection; e.g., that a bird sings) and perceptibility (the probability that an observer detects an animal, given that it is available for detection). We developed a hierarchical extension of the combined model that provides an integrated analysis framework for a collection of survey points at which both distance from the observer and time of initial detection are recorded. Implemented in a Bayesian framework, this extension facilitates evaluating covariates on abundance and detection probability, incorporating excess zero counts (i.e. zero-inflation), accounting for spatial autocorrelation, and estimating population density. Species-specific characteristics, such as behavioral displays and territorial dispersion, may lead to different patterns of availability and perceptibility, which may, in turn, influence the performance of such hierarchical models. Therefore, we first test our proposed model using simulated data under different scenarios of availability and perceptibility. We then illustrate its performance with empirical point-transect data for a songbird that consistently produces loud, frequent, primarily auditory signals, the Golden-crowned Sparrow ( Zonotrichia atricapilla ); and for 2 ptarmigan species ( Lagopus spp.) that produce more intermittent, subtle, and primarily visual cues. Data were collected by multiple observers along point transects across a broad landscape in southwest Alaska, so we evaluated point-level covariates on perceptibility (observer and habitat), availability (date within season and time of day), and abundance (habitat, elevation, and slope), and included a nested point-within-transect and park-level effect. Our results suggest that this model can provide insight into the detection process during avian surveys and reduce bias in estimates of relative abundance but is best applied to surveys of species with greater availability (e.g., breeding songbirds).

The Auk↗

USGS2000

Comparisons of methods for determining dominance rank in male and female prairie voles ( Microtus ochrogastor )

Dominance ranks in male and female prairie voles ( Microtus ochrogaster ) were determined from 6 measurements that mimicked environmental situations that might be encountered by prairie voles in communal groups, including agonistic interactions resulting from competition for food and water and encounters in burrows. Male and female groups of 6 individuals each were tested against one another in pairwise encounters (i.e., dyads) for 5 of the measurements and together as a group in a 6th measurement. Two types of response variables, aggressive behaviors and possession time of a limiting resource, were collected during trials, and those data were used to determine cardinal ranks and principal component ranks for all animals within each group. Cardinal ranks and principal component ranks seldom yielded similar rankings for each animal across measurements. However, dominance measurements that were conducted in similar environmental contexts, regardless of the response variable recorded, ranked animals similarly. Our results suggest that individual dominance measurements assessed situation- or resource-specific responses. Our study demonstrates problems inherent in determining dominance rankings of individuals within groups, including choosing measurements, response variables, and statistical techniques. Researchers should avoid using a single measurement to represent social dominance until they have first demonstrated that a dominance relationship between 2 individuals has been learned (i.e., subsequent interactions show a reduced response rather than an escalation), that this relationship is relatively constant through time, and that the relationship is not context dependent. Such assessments of dominance status between all dyads then can be used to generate dominance rankings within social groups.

Journal of Mammalogy↗

USGS2019

Optimizing walking pace to maximize snake detection rate: A visual encounter survey experiment

Visual encounter survey efforts can be defined and constrained by duration, distance, or both duration and distance simultaneously. This study examines the optimal walking pace that will maximize the number of animal detections within a limited time frame. We predicted that animal sighting rate per unit of distance would decline with increasing pace, but that maximal sighting rate per unit of time would occur at some intermediate pace because walking faster means covering more ground and passing more animals that could potentially be detected. We conducted a controlled experiment during which we searched for Brown Treesnakes ( Boiga irregularis ) while walking 220-m-long transects at three different speeds. For transects inside the forest, detection rate per unit distance decreased (nonlinearly) with increasing pace. When considering catch per unit time, however, we found 5% more snakes at the medium pace compared with the slow pace, and 63% more snakes at the fast pace compared with the slow pace. The pattern appeared different for surveys along forest edges with higher vegetation density, in which snakes might be more difficult to spot. Surprisingly, pace had no detectable effect on the body sizes or perch heights of snakes successfully detected. Finding the optimal search pace for a particular study organism in a focal habitat has the potential to substantially increase survey cost-efficacy.

Herpetologica↗

USGS1997

Estimating temporary emigration using capture-recapture data with Pollock's robust design

Statistical inference for capture–recapture studies of open animal populations typically relies on the assumption that all emigration from the studied population is permanent. However, there are many instances in which this assumption is unlikely to be met. We define two general models for the process of temporary emigration: completely random and Markovian. We then consider effects of these two types of temporary emigration on Jolly–Seber estimators and on estimators arising from the full-likelihood approach to robust design data. Capture–recapture data arising from Pollock’s robust design provide the basis for obtaining unbiased estimates of demographic parameters in the presence of temporary emigration, and for estimating the probability of temporary emigration. We present a likelihood-based approach to dealing with temporary emigration that permits estimation under different models of temporary emigration and yields tests for completely random and Markovian emigration. In addition, we use the relationship between capture probability estimates based on closed and open models under completely random temporary emigration to derive three ad hoc estimators for the probability of temporary emigration. Two of these should be especially useful in situations where capture probabilities are heterogeneous among individual animals. Ad hoc and full-likelihood estimators are illustrated for small-mammal capture–recapture data sets. We believe that these models and estimators will be useful for testing hypotheses about the process of temporary emigration, for estimating demographic parameters in the presence of temporary emigration, and for estimating probabilities of temporary emigration. These latter estimates are frequently of ecological interest as indicators of animal movement and, in some sampling situations, as direct estimates of breeding probabilities and proportions.

Ecology↗

USGS2000

Estimation of contributions to population growth: A reverse-time capture-recapture approach

We consider methods for estimating the relative contributions of different demographic components, and their associated vital rates, to population growth. We identify components of the population at time i (including a component for animals not in the population at i ). For each such component we ask the following question: “What is the probability that an individual randomly selected from the population at time i + 1 was a member of this component at i ?” The estimation methods for these probabilities (γ i ) are based on capture–recapture studies of marked animal populations and use reverse-time modeling. We consider several different sampling situations and present example analyses for meadow voles, Microtus pennsylvanicus. The relationship between these γ i parameters and elasticities (and other parameters based on projection matrix asymptotics) is noted and discussed. We conclude by suggesting that model-based asymptotics be viewed as demographic theory and that direct estimation approaches be used to test this theory with data from sampled populations with marked animals.

Ecology↗

USGS2004

Estimating survival and breeding probability for pond-breeding amphibians: a modified robust design

Many studies of pond-breeding amphibians involve sampling individuals during migration to and from breeding habitats. Interpreting population processes and dynamics from these studies is difficult because (1) only a proportion of the population is observable each season, while an unknown proportion remains unobservable (e.g., non-breeding adults) and (2) not all observable animals are captured. Imperfect capture probability can be easily accommodated in capture-recapture models, but temporary transitions between observable and unobservable states, often referred to as temporary emigration, is known to cause problems in both open- and closed-population models. We develop a multistate mark-recapture (MSMR) model, using an open-robust design that permits one entry and one exit from the study area per season. Our method extends previous temporary emigration models (MSMR with an unobservable state) in two ways. First, we relax the assumption of demographic closure (no mortality) between consecutive (secondary) samples, allowing estimation of within-pond survival. Also, we add the flexibility to express survival probability of unobservable individuals (e.g., ‘ ‘non-breeders’ ’ ) as a function of the survival probability of observable animals while in the same, terrestrial habitat. This allows for potentially different annual survival probabilities for observable and unobservable animals. We apply our model to a relictual population of eastern tiger salamanders ( Ambystoma tigrinum tigrinum ). Despite small sample sizes, demographic parameters were estimated with reasonable precision. We tested several a priori biological hypotheses and found evidence for seasonal differences in pond survival. Our methods could be applied to a variety of pond-breeding species and other taxa where individuals are captured entering or exiting a common area (e.g., spawning or roosting area, hibernacula).

Ecology↗

USGS2009

Modeling misidentification errors in capture-recapture studies using photographic identification of evolving marks

Misidentification of animals is potentially important when naturally existing features (natural tags) are used to identify individual animals in a capture-recapture study. Photographic identification (photoID) typically uses photographic images of animals' naturally existing features as tags (photographic tags) and is subject to two main causes of identification errors: those related to quality of photographs (non-evolving natural tags) and those related to changes in natural marks (evolving natural tags). The conventional methods for analysis of capture-recapture data do not account for identification errors, and to do so requires a detailed understanding of the misidentification mechanism. Focusing on the situation where errors are due to evolving natural tags, we propose a misidentification mechanism and outline a framework for modeling the effect of misidentification in closed population studies. We introduce methods for estimating population size based on this model. Using a simulation study, we show that conventional estimators can seriously overestimate population size when errors due to misidentification are ignored, and that, in comparison, our new estimators have better properties except in cases with low capture probabilities (<0.2) or low misidentification rates (<2.5%). ?? 2009 by the Ecological Society of America.

Ecology↗

USGS2011

Use of the superpopulation approach to estimate breeding population size: An example in asynchronously breeding birds

Many populations of animals are fluid in both space and time, making estimation of numbers difficult. Much attention has been devoted to estimation of bias in detection of animals that are present at the time of survey. However, an equally important problem is estimation of population size when all animals are not present on all survey occasions. Here, we showcase use of the superpopulation approach to capture–recapture modeling for estimating populations where group membership is asynchronous, and where considerable overlap in group membership among sampling occasions may occur. We estimate total population size of long‐legged wading bird (Great Egret and White Ibis) breeding colonies from aerial observations of individually identifiable nests at various times in the nesting season. Initiation and termination of nests were analogous to entry and departure from a population. Estimates using the superpopulation approach were 47–382% larger than peak aerial counts of the same colonies. Our results indicate that the use of the superpopulation approach to model nesting asynchrony provides a considerably less biased and more efficient estimate of nesting activity than traditional methods. We suggest that this approach may also be used to derive population estimates in a variety of situations where group membership is fluid.

Florida↗

USGS2001

Food webs including parasites, biomass, body sizes, and life stages for three California/Baja California estuaries

This data set presents food webs for three North American Pacific coast estuaries and a “Metaweb” composed of the species/stages compiled from all three estuaries. The webs have four noteworthy attributes: (1) parasites (infectious agents), (2) body-size information, (3) biomass information, and (4) ontogenetic stages of many animals with complex life cycles. The estuaries are Carpinteria Salt Marsh, California (CSM); Estero de Punta Banda, Baja California (EPB); and Bahía Falsa in Bahía San Quintín, Baja California (BSQ). Most data on species assemblages and parasitism were gathered via consistent sampling that acquired body size and biomass information for plants and animals larger than ∼1 mm, and for many infectious agents (mostly metazoan parasites, but also some microbes). We augmented this with information from additional published sources and by sampling unrepresented groups (e.g., plankton). We estimated free-living consumer–resource links primarily by extending a previously published version of the CSM web (which the current CSM web supplants) and determined most parasite consumer–resource links from direct observation. We recognize 21 possible link types including four general interactions: predators consuming prey, parasites consuming hosts, predators consuming parasites, and parasites consuming parasites. While generally resolved to the species level, we report stage-specific nodes for many animals with complex life cycles. We include additional biological information for each node, such as taxonomy, lifestyle (free-living, infectious, commensal, mutualist), mobility, and residency. The Metaweb includes 500 nodes, 314 species, and 11 270 links projected to be present given appropriate species' co-occurrences. Of these, 9247 links were present in one or more of the estuarine webs. The remaining 2023 links were not present in the estuaries but are included here because they may occur in other places or times. Initial analyses have examined and are examining the interrelationships among consumer strategy, body size, abundance, biomass, trophic level, life stages, and food-web structure and dynamics. Further use of these data may enable a more general exploration how infectious processes and parasites impact communities and ecosystems. Additionally, we present the data and metadata in a standardized format, attempting to provide a system-neutral template for future food-web assembly and publication.

Ecology↗

USGS1998

Estimating population change from count data: Application to the North American Breeding Bird Survey

For birds and many other animal taxa, surveys that collect count data form a primary source of information on population change. Because counts are only indices to population size, care must be taken in using them in analyses of population change. Temporal or geographic differences in the proportion of animals counted can be misinterpreted as differences in population size. Therefore, temporally or geographically varying factors that influence the proportion of animals counted must be incorporated as covariables in the analysis of population parameters from count data. We describe the North American Breeding Bird Survey (BBS) for illustration. The BBS is a major, landscape-level survey of birds in North America; it is typical of many count surveys, in that the same sample units (survey routes) are sampled each year, and change is modeled on these routes over time. We identify covariables related to observer ability, the omission of which can bias estimation of population change from BBS data. Controlling for observer effects or other potential sources of confounding requires the specification of models relating counts to population size. We begin with a partial model specification relating expected counts to population sizes; we describe estimators currently in use in relation to this partial specification. Additional assumptions lead to a class of over-dispersed multinomial models, for which we describe estimators of population change and procedures for parsimonious model selection. We illustrate the use of over-dispersed multinomial models by an application to data for Carolina Wren (Thryothorus ludovicianus).

Ecological Applications↗

USGS2012

Density estimation in tiger populations: combining information for strong inference

A productive way forward in studies of animal populations is to efficiently make use of all the information available, either as raw data or as published sources, on critical parameters of interest. In this study, we demonstrate two approaches to the use of multiple sources of information on a parameter of fundamental interest to ecologists: animal density. The first approach produces estimates simultaneously from two different sources of data. The second approach was developed for situations in which initial data collection and analysis are followed up by subsequent data collection and prior knowledge is updated with new data using a stepwise process. Both approaches are used to estimate density of a rare and elusive predator, the tiger, by combining photographic and fecal DNA spatial capture–recapture data. The model, which combined information, provided the most precise estimate of density (8.5 ± 1.95 tigers/100 km 2 [posterior mean ± SD]) relative to a model that utilized only one data source (photographic, 12.02 ± 3.02 tigers/100 km 2 and fecal DNA, 6.65 ± 2.37 tigers/100 km 2 ). Our study demonstrates that, by accounting for multiple sources of available information, estimates of animal density can be significantly improved.

Ecology↗

USGS2013

Practical guidance on characterizing availability in resource selection functions under a use-availability design

Habitat selection is a fundamental aspect of animal ecology, the understanding of which is critical to management and conservation. Global positioning system data from animals allow fine-scale assessments of habitat selection and typically are analyzed in a use-availability framework, whereby animal locations are contrasted with random locations (the availability sample). Although most use-availability methods are in fact spatial point process models, they often are fit using logistic regression. This framework offers numerous methodological challenges, for which the literature provides little guidance. Specifically, the size and spatial extent of the availability sample influences coefficient estimates potentially causing interpretational bias. We examined the influence of availability on statistical inference through simulations and analysis of serially correlated mule deer GPS data. Bias in estimates arose from incorrectly assessing and sampling the spatial extent of availability. Spatial autocorrelation in covariates, which is common for landscape characteristics, exacerbated the error in availability sampling leading to increased bias. These results have strong implications for habitat selection analyses using GPS data, which are increasingly prevalent in the literature. We recommend researchers assess the sensitivity of their results to their availability sample and, where bias is likely, take care with interpretations and use cross validation to assess robustness.

Ecology↗

USGS1999

Health status and relative exposure of mule deer and white-tailed deer to soil contaminants at the rocky mountain arsenal

We evaluated the health of 18 radio-collared deer [13 mule deer ( Odocoileus hemionus ) and 5 white-tailed deer ( O. virginianus )] from the Rocky Mountain Arsenal, near Denver, Colorado, USA, a Superfund site contaminated with a variety of materials, including organochlorine pesticides, metals, and nerve gas production by-products. Radio-collared deer were tracked for 1 to 3 years (1989–1992) to identify relative exposure to contaminants based on telemetry locations plotted on grid maps depicting known soil contaminant concentrations. At the end of the study, all animals were in fair or good body condition at the time of necropsy. Mean ages of mule deer and white-tailed deer were 7.4 (range 4–12) and 10.6 years (range 5–17), respectively. At necropsy, tissues were collected from the deer for serology, histopathology, and analysis for eight chlorinated hydrocarbons and two metals. Detectable residues of mercury were found in the kidneys of 10 deer (range 0.055–0.096 μg/g), dieldrin was found in fat ( n = 9) (range 0.02–0.72 μg/g), liver ( n = 4) (range 0.017–0.12 μg/g), and brain ( n = 1, 0.018 μg/g), and DDE was found in the muscle of one animal (0.02 μg/g). Relative exposure estimates derived from telemetry and soil contamination data were correlated with tissue levels of dieldrin ( p < 0.001) and mercury ( p = 0.05). Two mule deer had severe testicular atrophy, and one of these animals also had antler deformities. The prevalence of antibodies against epizootic hemorrhagic disease serotype 2 was 85%.

Colorado↗

USGS2019

One Health: A perspective from wildlife and environmental health sectors

Loss of biodiversity, habitat fragmentation and pollution, and subsequent degradation of natural environments threaten the range of ecosystem services that support all life on this planet. These changes, among others, are also driving the emergence of infectious diseases, with negative health outcomes for humans, animals, and our shared environment. Historically, interventions aimed at human and agricultural health issues did not always integrate wildlife or environmental health as part of the solution, which has resulted in unintended consequences. One Health recognises the interdependence of humans, animals and their shared environment, and provides a conceptual framework for developing interventions that optimise outcomes for human, animal and environmental health. However, there is a need to clearly articulate the core values, goals, and objectives of One Health for all relevant sectors in order to maximise synergies for communication, coordination, collaboration, and, ultimately, for joint actions on disease control and prevention. Application of systems and harm reduction approaches, focusing on the socio-economic and environmental determinants of health, and ensuring good governance and effective leadership will also maximise the opportunities to develop ‘win-win-win’ solutions to global health and environmental challenges. These solutions would help propel One Health forward to reach its full potential and truly optimise health outcomes for all.

Scientific and Technical Review↗