Geology topics

Larissa L. Bailey

Publications and source records attributed to Larissa L. Bailey.

53 records · Page 3Linked to original sources

USGS2015

Performance of species occurrence estimators when basic assumptions are not met: a test using field data where true occupancy status is known

Populations are rarely censused. Instead, observations are subject to incomplete detection, misclassification and detection heterogeneity that result from human and environmental constraints. Though numerous methods have been developed to deal with observational uncertainty, validation under field conditions is rare because truth is rarely known in these cases. We present the most comprehensive test of occupancy estimation methods to date, using more than 33 000 auditory call observations collected under standard field conditions and where the true occupancy status of sites was known. Basic occupancy estimation approaches were biased when two key assumptions were not met: that no false positives occur and that no unexplained heterogeneity in detection parameters occurs. The greatest bias occurred for dynamic parameters (i.e. local colonization and extinction), and in many cases, the degree of inaccuracy would render results largely useless. We examined three approaches to increase adherence or relax these assumptions: modifying the sampling design, employing estimators that account for false-positive detections and using covariates to account for site-level heterogeneity in both false-negative and false-positive detection probabilities. We demonstrate that bias can be substantially reduced by modifications to sampling methods and by using estimators that simultaneously account for false-positive detections and site-level covariates to explain heterogeneity. Our results demonstrate that even small probabilities of misidentification and among-site detection heterogeneity can have severe effects on estimator reliability if ignored. We challenge researchers to place greater attention on both heterogeneity and false positives when designing and analysing occupancy studies. We provide 9 specific recommendations for the design, implementation and analysis of occupancy studies to better meet this challenge.

Methods in Ecology and Evolution↗

USGS2014

Animal reintroductions: an innovative assessment of survival

Quantitative evaluations of reintroductions are infrequent and assessments of milestones reached before a project is completed, or abandoned due to lack of funding, are rare. However, such assessments, which are promoted in adaptive management frameworks, are critical. Quantification can provide defensible estimates of biological success, such as the number of survivors from a released cohort, with associated cost per animal. It is unlikely that the global issues of endangered wildlife and population declines will abate, therefore, assurance colonies and reintroductions are likely to become more common. If such endeavors are to be successful biologically or achieve adequate funding, implementation must be more rigorous and accountable. We use a novel application of a multistate, robust design capture-recapture model to estimate survival of reintroduced tadpoles through metamorphosis (i.e., the number of individuals emerging from the pond) and thereby provide a quantitative measure of effort and success for an "in progress" reintroduction of toads. Our data also suggest that tadpoles released at later developmental stages have an increased probability of survival and that eggs laid in the wild hatched at higher rates than eggs laid by captive toads. We illustrate how an interim assessment can identify problems, highlight successes, and provide information for use in adjusting the effort or implementing a Decision-Theoretic adaptive management strategy.

Biological Conservation↗

USGS2014

Demography of a reintroduced population: moving toward management models for an endangered species, the whooping crane

The reintroduction of threatened and endangered species is now a common method for reestablishing populations. Typically, a fundamental objective of reintroduction is to establish a self-sustaining population. Estimation of demographic parameters in reintroduced populations is critical, as these estimates serve multiple purposes. First, they support evaluation of progress toward the fundamental objective via construction of population viability analyses (PVAs) to predict metrics such as probability of persistence. Second, PVAs can be expanded to support evaluation of management actions, via management modeling. Third, the estimates themselves can support evaluation of the demographic performance of the reintroduced population, e.g., via comparison with wild populations. For each of these purposes, thorough treatment of uncertainties in the estimates is critical. Recently developed statistical methods - namely, hierarchical Bayesian implementations of state-space models - allow for effective integration of different types of uncertainty in estimation. We undertook a demographic estimation effort for a reintroduced population of endangered whooping cranes with the purpose of ultimately developing a Bayesian PVA for determining progress toward establishing a self-sustaining population, and for evaluating potential management actions via a Bayesian PVA-based management model. We evaluated individual and temporal variation in demographic parameters based upon a multi-state mark-recapture model. We found that survival was relatively high across time and varied little by sex. There was some indication that survival varied by release method. Survival was similar to that observed in the wild population. Although overall reproduction in this reintroduced population is poor, birds formed social pairs when relatively young, and once a bird was in a social pair, it had a nearly 50% chance of nesting the following breeding season. Also, once a bird had nested, it had a high probability of nesting again. These results are encouraging considering that survival and reproduction have been major challenges in past reintroductions of this species. The demographic estimates developed will support construction of a management model designed to facilitate exploration of management actions of interest, and will provide critical guidance in future planning for this reintroduction. An approach similar to what we describe could be usefully applied to many reintroduced populations.

Ecological Applications↗

USGS2013

Trends in amphibian occupancy in the United States

Though a third of amphibian species worldwide are thought to be imperiled, existing assessments simply categorize extinction risk, providing little information on the rate of population losses. We conducted the first analysis of the rate of change in the probability that amphibians occupy ponds and other comparable habitat features across the United States. We found that overall occupancy by amphibians declined 3.7% annually from 2002 to 2011. Species that are Red-listed by the International Union for Conservation of Nature (IUCN) declined an average of 11.6% annually. All subsets of data examined had a declining trend including species in the IUCN Least Concern category. This analysis suggests that amphibian declines may be more widespread and severe than previously realized.

PLoS ONE↗

USGS2013

Factors influencing survival and mark retention in postmetamorphic boreal chorus frogs

The ability to track individual animals is crucial in many field studies and often requires applying marks to captured individuals. Toe clipping has historically been a standard marking method for wild amphibian populations, but more recent marking methods include visual implant elastomer and photo identification. Unfortunately, few studies have investigated the influence and effectiveness of marking methods for recently metamorphosed individuals and as a result little is known about this life-history phase for most amphibians. Our focus was to explore survival probabilities, mark retention, and mark migration in postmetamorphic Boreal Chorus Frogs ( Psuedacris maculata ) in a laboratory setting. One hundred forty-seven individuals were assigned randomly to two treatment groups or a control group. Frogs in the first treatment group were marked with visual implant elastomer, while frogs in the second treatment group were toe clipped. Growth and mortality were recorded for one year and resulting data were analyzed using known-fate models in Program MARK. Model selection results suggested that survival probabilities of frogs varied with time and showed some variation among marking treatments. We found that frogs with multiple toes clipped on the same foot had lower survival probabilities than individuals in other treatments, but individuals can be marked by clipping a single toe on two different feet without any mark loss or negative survival effects. Individuals treated with visual implant elastomer had a mark migration rate of 4% and mark loss rate of 6%, and also showed very little negative survival impacts relative to control individuals.

Copeia↗

USGS2012

Experimental investigation of false positive errors in auditory species occurrence surveys

False positive errors are a significant component of many ecological data sets, which in combination with false negative errors, can lead to severe biases in conclusions about ecological systems. We present results of a field experiment where observers recorded observations for known combinations of electronically broadcast calling anurans under conditions mimicking field surveys to determine species occurrence. Our objectives were to characterize false positive error probabilities for auditory methods based on a large number of observers, to determine if targeted instruction could be used to reduce false positive error rates, and to establish useful predictors of among-observer and among-species differences in error rates. We recruited 31 observers, ranging in abilities from novice to expert, that recorded detections for 12 species during 180 calling trials (66,960 total observations). All observers made multiple false positive errors and on average 8.1% of recorded detections in the experiment were false positive errors. Additional instruction had only minor effects on error rates. After instruction, false positive error probabilities decreased by 16% for treatment individuals compared to controls with broad confidence interval overlap of 0 (95% CI: -46 to 30%). This coincided with an increase in false negative errors due to the treatment (26%; -3 to 61%). Differences among observers in false positive and in false negative error rates were best predicted by scores from an online test and a self-assessment of observer ability completed prior to the field experiment. In contrast, years of experience conducting call surveys was a weak predictor of error rates. False positive errors were also more common for species that were played more frequently, but were not related to the dominant spectral frequency of the call. Our results corroborate other work that demonstrates false positives are a significant component of species occurrence data collected by auditory methods. Instructing observers to only report detections they are completely certain are correct is not sufficient to eliminate errors. As a result, analytical methods that account for false positive errors will be needed, and independent testing of observer ability is a useful predictor for among-observer variation in observation error rates.

Ecological Applications↗

USGS2011

Inference for occupancy and occupancy dynamics

This chapter deals with the estimation of occupancy as a state variable to assess the status of, and track changes in, species distributions when sampling with camera traps. Much of the recent interest in occupancy estimation and modeling originated from the models developed by MacKenzie et al. (2002, 2003), although similar methods were developed independently (Azuma et al. 1990; Bayley and Petersen 2001; Nichols and Karanth, 2002; Tyre et al. 2003), all of which deal with species occurrence information and imperfect detection. Less than a decade after these publications, the modeling and estimation of species occurrence and occupancy dynamics have increased significantly. Special features of scientific journals have explored innovative uses of detection–nondetection data with occupancy models (Vojta 2005), and an entire volume has synthesized the use and application of occupancy estimation methods (MacKenzie et al. 2006). Reviews of the topical concepts, philosophical considerations, and various sampling designs that can be used for occupancy estimation are now readily available for a range of audiences (MacKenzie and Royle 2005; MacKenzie et al. 2006; Bailey et al. 2007; Royle and Dorazio 2008; Conroy and Carroll 2009; Kendall and White 2009; Hines et al. 2010; Link and Barker 2010). As a result, it would be pointless here to recast all that these publications have so eloquently articulated, but that said, a review of any scientific topic requires sufficient context and relevant background information, especially when relatively new methodologies and techniques such as occupancy estimation and camera traps are involved. This is especially critical in a digital age where new information is published at warp speed, making it increasingly difficult to stay abreast of theoretical advances and research developments.

Book chapter↗

USGS2011

Using multilevel spatial models to understand salamander site occupancy patterns after wildfire

Studies of the distribution of elusive forest wildlife have suffered from the confounding of true presence with the uncertainty of detection. Occupancy modeling, which incorporates probabilities of species detection conditional on presence, is an emerging approach for reducing observation bias. However, the current likelihood modeling framework is restrictive for handling unexplained sources of variation in the response that may occur when there are dependence structures such as smaller sampling units that are nested within larger sampling units. We used multilevel Bayesian occupancy modeling to handle dependence structures and to partition sources of variation in occupancy of sites by terrestrial salamanders (family Plethodontidae) within and surrounding an earlier wildfire in western Oregon, USA. Comparison of model fit favored a spatial N ‐mixture model that accounted for variation in salamander abundance over models that were based on binary detection/non‐detection data. Though catch per unit effort was higher in burned areas than unburned, there was strong support that this pattern was due to a higher probability of capture for individuals in burned plots. Within the burn, the odds of capturing an individual given it was present were 2.06 times the odds outside the burn, reflecting reduced complexity of ground cover in the burn. There was weak support that true occupancy was lower within the burned area. While the odds of occupancy in the burn were 0.49 times the odds outside the burn among the five species, the magnitude of variation attributed to the burn was small in comparison to variation attributed to other landscape variables and to unexplained, spatially autocorrelated random variation. While ordinary occupancy models may separate the biological pattern of interest from variation in detection probability when all sources of variation are known, the addition of random effects structures for unexplained sources of variation in occupancy and detection probability may often more appropriately represent levels of uncertainty.

Ecology↗

USGS2010

Using occupancy models to understand the distribution of an amphibian pathogen, Batrachochytrium dendrobatidis

Batrachochytrium dendrobatidis is a fungal pathogen that is receiving attention around the world for its role in amphibian declines. Study of its occurrence patterns is hampered by false negatives: the failure to detect the pathogen when it is present. Occupancy models are a useful but currently underutilized tool for analyzing detection data when the probability of detecting a species is <1. We use occupancy models to evaluate hypotheses concerning the occurrence and prevalence of B. dendrobatidis and discuss how this application differs from a conventional occupancy approach. We found that the probability of detecting the pathogen, conditional on presence of the pathogen in the anuran population, was related to amphibian development stage, day of the year, elevation, and human activities. Batrachochytrium dendrobatidis was found throughout our study area but was only estimated to occur in 53.4% of 78 populations of native amphibians and 66.4% of 40 populations of nonnative Rana catesbeiana tested. We found little evidence to support any spatial hypotheses concerning the probability that the pathogen occurs in a population, but did find evidence of some taxonomic variation. We discuss the interpretation of occupancy model parameters, when, unlike a conventional occupancy application, the number of potential samples or observations is finite.

California, Oregon↗

USGS2010

Simultaneous modeling of habitat suitability, occupancy, and relative abundance: African elephants in Zimbabwe

The recent development of statistical models such as dynamic site occupancy models provides the opportunity to address fairly complex management and conservation problems with relatively simple models. However, surprisingly few empirical studies have simultaneously modeled habitat suitability and occupancy status of organisms over large landscapes for management purposes. Joint modeling of these components is particularly important in the context of management of wild populations, as it provides a more coherent framework to investigate the population dynamics of organisms in space and time for the application of management decision tools. We applied such an approach to the study of water hole use by African elephants in Hwange National Park, Zimbabwe. Here we show how such methodology may be implemented and derive estimates of annual transition probabilities among three dry-season states for water holes: (1) unsuitable state (dry water holes with no elephants); (2) suitable state (water hole with water) with low abundance of elephants; and (3) suitable state with high abundance of elephants. We found that annual rainfall and the number of neighboring water holes influenced the transition probabilities among these three states. Because of an increase in elephant densities in the park during the study period, we also found that transition probabilities from low abundance to high abundance states increased over time. The application of the joint habitat–occupancy models provides a coherent framework to examine how habitat suitability and factors that affect habitat suitability influence the distribution and abundance of organisms. We discuss how these simple models can further be used to apply structured decision-making tools in order to derive decisions that are optimal relative to specified management objectives. The modeling framework presented in this paper should be applicable to a wide range of existing data sets and should help to address important ecological, conservation, and management problems that deal with occupancy, relative abundance, and habitat suitability.

Hwange National Park↗

USGS2010

Unmodeled observation error induces bias when inferring patterns and dynamics of species occurrence via aural detections

The recent surge in the development and application of species occurrence models has been associated with an acknowledgment among ecologists that species are detected imperfectly due to observation error. Standard models now allow unbiased estimation of occupancy probability when false negative detections occur, but this is conditional on no false positive detections and sufficient incorporation of explanatory variables for the false negative detection process. These assumptions are likely reasonable in many circumstances, but there is mounting evidence that false positive errors and detection probability heterogeneity may be much more prevalent in studies relying on auditory cues for species detection (e.g., songbird or calling amphibian surveys). We used field survey data from a simulated calling anuran system of known occupancy state to investigate the biases induced by these errors in dynamic models of species occurrence. Despite the participation of expert observers in simplified field conditions, both false positive errors and site detection probability heterogeneity were extensive for most species in the survey. We found that even low levels of false positive errors, constituting as little as 1% of all detections, can cause severe overestimation of site occupancy, colonization, and local extinction probabilities. Further, unmodeled detection probability heterogeneity induced substantial underestimation of occupancy and overestimation of colonization and local extinction probabilities. Completely spurious relationships between species occurrence and explanatory variables were also found. Such misleading inferences would likely have deleterious implications for conservation and management programs. We contend that all forms of observation error, including false positive errors and heterogeneous detection probabilities, must be incorporated into the estimation framework to facilitate reliable inferences about occupancy and its associated vital rate parameters.

North Carolina↗

USGS2009

Modeling co-occurrence of northern spotted and barred owls: accounting for detection probability differences

Barred owls (Strix varia) have recently expanded their range and now encompass the entire range of the northern spotted owl (Strix occidentalis caurina). This expansion has led to two important issues of concern for management of northern spotted owls: (1) possible competitive interactions between the two species that could contribute to population declines of northern spotted owls, and (2) possible changes in vocalization behavior and detection probabilities of northern spotted owls induced by presence of barred owls. We used a two-species occupancy model to investigate whether there was evidence of competitive exclusion between the two species at study locations in Oregon, USA. We simultaneously estimated detection probabilities for both species and determined if the presence of one species influenced the detection of the other species. Model selection results and associated parameter estimates provided no evidence that barred owls excluded spotted owls from territories. We found strong evidence that detection probabilities differed for the two species, with higher probabilities for northern spotted owls that are the object of current surveys. Non-detection of barred owls is very common in surveys for northern spotted owls, and detection of both owl species was negatively influenced by the presence of the congeneric species. Our results suggest that analyses directed at hypotheses of barred owl effects on demographic or occupancy vital rates of northern spotted owls need to deal adequately with imperfect and variable detection probabilities for both species.

Oregon↗

USGS2008

Multi-scale occupancy estimation and modelling using multiple detection methods

Occupancy estimation and modelling based on detection–nondetection data provide an effective way of exploring change in a species’ distribution across time and space in cases where the species is not always detected with certainty. Today, many monitoring programmes target multiple species, or life stages within a species, requiring the use of multiple detection methods. When multiple methods or devices are used at the same sample sites, animals can be detected by more than one method. We develop occupancy models for multiple detection methods that permit simultaneous use of data from all methods for inference about method-specific detection probabilities. Moreover, the approach permits estimation of occupancy at two spatial scales: the larger scale corresponds to species’ use of a sample unit, whereas the smaller scale corresponds to presence of the species at the local sample station or site. We apply the models to data collected on two different vertebrate species: striped skunks Mephitis mephitis and red salamanders Pseudotriton ruber . For striped skunks, large-scale occupancy estimates were consistent between two sampling seasons. Small-scale occupancy probabilities were slightly lower in the late winter/spring when skunks tend to conserve energy, and movements are limited to males in search of females for breeding. There was strong evidence of method-specific detection probabilities for skunks. As anticipated, large- and small-scale occupancy areas completely overlapped for red salamanders. The analyses provided weak evidence of method-specific detection probabilities for this species. Synthesis and applications. Increasingly, many studies are utilizing multiple detection methods at sampling locations. The modelling approach presented here makes efficient use of detections from multiple methods to estimate occupancy probabilities at two spatial scales and to compare detection probabilities associated with different detection methods. The models can be viewed as another variation of Pollock's robust design and may be applicable to a wide variety of scenarios where species occur in an area but are not always near the sampled locations. The estimation approach is likely to be especially useful in multispecies conservation programmes by providing efficient estimates using multiple detection devices and by providing device-specific detection probability estimates for use in survey design.

Journal of Applied Ecology↗

USGS2008

Prevalence of the amphibian pathogen Batrachochytrium dendrobatidis in stream and wetland amphibians in Maryland, USA

The amphibian chytrid fungus Batrachochytrium dendrobatidis , responsible for the potentially fatal amphibian disease chytridiomycosis, is known to occur in a large and ever increasing number of amphibian populations around the world. However, sampling has been biased towards stream- and wetland-breeding anurans, with little attention paid to stream-associated salamanders. We sampled three frog and three salamander species in the Chesapeake and Ohio Canal National Historic Park, Maryland, by swabbing animals for PCR analysis to detect DNA of B. dendrobatidis . Using PCR, we detected B. dendrobatidis DNA in both stream and wetland amphibians, and report here the first occurrence of the pathogen in two species of stream-associated salamanders. Future research should focus on mechanisms within habitats that may affect persistence and dissemination of B. dendrobatidis among stream-associated salamanders

Maryland↗

USGS2007

Making great leaps forward: Accounting for detectability in herpetological field studies

Detecting individuals of amphibian and reptile species can be a daunting task. Detection can be hindered by various factors such as cryptic behavior, color patterns, or observer experience. These factors complicate the estimation of state variables of interest (e.g., abundance, occupancy, species richness) as well as the vital rates that induce changes in these state variables (e.g., survival probabilities for abundance; extinction probabilities for occupancy). Although ad hoc methods (e.g., counts uncorrected for detection, return rates) typically perform poorly in the face of no detection, they continue to be used extensively in various fields, including herpetology. However, formal approaches that estimate and account for the probability of detection, such as capture-mark-recapture (CMR) methods and distance sampling, are available. In this paper, we present classical approaches and recent advances in methods accounting for detectability that are particularly pertinent for herpetological data sets. Through examples, we illustrate the use of several methods, discuss their performance compared to that of ad hoc methods, and we suggest available software to perform these analyses. The methods we discuss control for imperfect detection and reduce bias in estimates of demographic parameters such as population size, survival, or, at other levels of biological organization, species occurrence. Among these methods, recently developed approaches that no longer require marked or resighted individuals should be particularly of interest to field herpetologists. We hope that our effort will encourage practitioners to implement some of the estimation methods presented herein instead of relying on ad hoc methods that make more limiting assumptions.

Journal of Herpetology↗

USGS2006

Estimating site occupancy and detection probability parameters for meso- and large mammals in a coastal eosystem

Large-scale, multispecies monitoring programs are widely used to assess changes in wildlife populations but they often assume constant detectability when documenting species occurrence. This assumption is rarely met in practice because animal populations vary across time and space. As a result, detectability of a species can be influenced by a number of physical, biological, or anthropogenic factors (e.g., weather, seasonality, topography, biological rhythms, sampling methods). To evaluate some of these influences, we estimated site occupancy rates using species-specific detection probabilities for meso- and large terrestrial mammal species on Cape Cod, Massachusetts, USA. We used model selection to assess the influence of different sampling methods and major environmental factors on our ability to detect individual species. Remote cameras detected the most species (9), followed by cubby boxes (7) and hair traps (4) over a 13-month period. Estimated site occupancy rates were similar among sampling methods for most species when detection probabilities exceeded 0.15, but we question estimates obtained from methods with detection probabilities between 0.05 and 0.15, and we consider methods with lower probabilities unacceptable for occupancy estimation and inference. Estimated detection probabilities can be used to accommodate variation in sampling methods, which allows for comparison of monitoring programs using different protocols. Vegetation and seasonality produced species-specific differences in detectability and occupancy, but differences were not consistent within or among species, which suggests that our results should be considered in the context of local habitat features and life history traits for the target species. We believe that site occupancy is a useful state variable and suggest that monitoring programs for mammals using occupancy data consider detectability prior to making inferences about species distributions or population change.

Journal of Wildlife Management↗

USGS2005

Amphibian Research and Monitoring Initiative (ARMI): A successful start to a national program in the United States

Most research to assess amphibian declines has focused on local-scale projects on one or a few species. The Amphibian Research and Monitoring Initiative (ARMI) is a national program in the United States mandated by congressional directive and implemented by the U.S. Department of the Interior (specifically the U.S. Geological Survey, USGS). Program goals are to monitor changes in populations of amphibians across U.S. Department of the Interior lands and to address research questions related to amphibian declines using a hierarchical framework of base-, mid- and apex-level monitoring sites. ARMI is currently monitoring 83 amphibian species (29% of species in the U.S.) at mid- and apex-level areas. We chart the progress of this 5-year-old program and provide an example of mid-level monitoring from 1 of the 7 ARMI regions.

Applied Herpetology↗