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Geology topics

James D. Nichols

Publications and source records attributed to James D. Nichols.

At least 91 records · Page 5Linked to original sources
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↗
USGS2011

Demographic consequences of migratory stopover: Linking red knot survival to horseshoe crab spawning abundance

Understanding how events during one period of the annual cycle carry over to affect survival and other fitness components in other periods is essential to understanding migratory bird demography and conservation needs. Previous research has suggested that western Atlantic red knot ( Calidris canutus rufa ) populations are greatly affected by horseshoe crab ( Limulus polyphemus ) egg availability at Delaware Bay stopover sites during their spring northward migration. We present a mass‐based multistate, capture‐recapture/resighting model linking (1) red knot stopover mass gain to horseshoe crab spawning abundance and (2) subsequent apparent annual survival to mass state at the time of departure from the Delaware Bay stopover area. The model and analysis use capture‐recapture/resighting data with over 16,000 individual captures and 13,000 resightings collected in Delaware Bay over a 12 year period from 1997–2008, and the results are used to evaluate the central management hypothesis that red knot populations can be influenced by horseshoe crab harvest regulations as part of a larger adaptive management effort. Model selection statistics showed support for a positive relationship between horseshoe crab spawning abundance during the stopover and the probability of red knots gaining mass (parameter coefficient from the top model b̂ = 1.71, = 0.46). Our analyses also supported the link between red knot mass and apparent annual survival, although average estimates for the two mass classes differed only slightly. The addition of arctic snow depth as a covariate influencing apparent survival improved the fit of the data to the models (parameter coefficient from the top model b̂ = 0.50, = 0.08). Our results indicate that managing horseshoe crab resources in the Delaware Bay has the potential to improve red knot population status.

Delaware, New Jersey↗
USGS2011

A Markov decision process for managing habitat for Florida scrub-jays

Florida scrub-jays Aphelocoma coerulescens are listed as threatened under the Endangered Species Act due to loss and degradation of scrub habitat. This study concerned the development of an optimal strategy for the restoration and management of scrub habitat at Merritt Island National Wildlife Refuge, which contains one of the few remaining large populations of scrub-jays in Florida. There are documented differences in the reproductive and survival rates of scrubjays among discrete classes of scrub height (<120 cm or "short"; 120-170 cm or "optimal"; .170 cm or "tall"; and a combination of tall and optimal or "mixed"), and our objective was to calculate a state-dependent management strategy that would maximize the long-term growth rate of the resident scrub-jay population. We used aerial imagery with multistate Markov models to estimate annual transition probabilities among the four scrub-height classes under three possible management actions: scrub restoration (mechanical cutting followed by burning), a prescribed burn, or no intervention. A strategy prescribing the optimal management action for management units exhibiting different proportions of scrub-height classes was derived using dynamic programming. Scrub restoration was the optimal management action only in units dominated by mixed and tall scrub, and burning tended to be the optimal action for intermediate levels of short scrub. The optimal action was to do nothing when the amount of short scrub was greater than 30%, because short scrub mostly transitions to optimal height scrub (i.e., that state with the highest demographic success of scrub-jays) in the absence of intervention. Monte Carlo simulation of the optimal policy suggested that some form of management would be required every year. We note, however, that estimates of scrub-height transition probabilities were subject to several sources of uncertainty, and so we explored the management implications of alternative sets of transition probabilities. Generally, our analysis demonstrated the difficulty of managing for a species that requires midsuccessional habitat, and suggests that innovative management tools may be needed to help ensure the persistence of scrub-jays at Merritt Island National Wildlife Refuge. The development of a tailored monitoring program as a component of adaptive management could help reduce uncertainty about controlled and uncontrolled variation in transition probabilities of scrub-height and thus lead to improved decision making.

Florida↗
USGS2011

Targeted surveillance for highly pathogenic avian influenza in migratory waterfowl across the conterminous United States: chapter 12

Introduction of Asian strain H5N1 Highly Pathogenic avian influenca via waterfowl migration is one potential route of entry into the United States. In conjunction with state, tribe, and laboratory partners, the United States Department of Agriculture collected and tested 124,603 wild bird samples in 2006 as part of a national surveillance effort. A sampling plan was devised to increase the probability fo detecting Asian strain H5N1 at a national scale. Band recovery data were used to identify and prioritize sampling for wild migratory waterfowl, resulting in spatially targeted sampling recommendations focused on reads with high numbers of recoveries. We also compared the spatial and temporal distribution of the 2006 cloacal and fecal waterfowl sampling effort to the bird banding recovery data and found concordance between the two .Finally, we present improvements made to the 2007 fecal sampling component of the surveillance plan and suggest further improvements for future sampling.

Book chapter↗
USGS2010

Modelling postfledging survival and age-specific breeding probabilities in species with delayed maturity: A case study of Roseate Terns at Falkner Island, Connecticut

We modeled postfledging survival and age-specific breeding probabilities in endangered Roseate Terns (Sterna dougallii) at Falkner Island, Connecticut, USA using capture-recapture data from 1988-1998 of birds ringed as chicks and as adults. While no individuals bred as 2-yr-olds during this period, about three-quarters of the young that survived and returned as 3-yr-olds nested, and virtually all surviving birds had begun breeding by the time they reached 5 years of age. We found no evidence of temporal variation in age of first breeding of birds from different cohorts. There was significant temporal variation in the annual survival of adults and the survival over the typical 3-yr maturation period of prebreeding birds, with extremely low values for both groups from the 1991 breeding season. The estimated overwinter survival rate (0.62) for adults from 1991-1992 was about three-quarters the usual rate of about 0.83, but the low survival of fledglings from 1991 resulted in less than 25% of the otherwise expected number of young from that cohort returning as breeding birds; this suggests that fledglings suffered a greater proportional decrease in survival than did adults. The survival estimates of young from 1989 and 1990 show that these cohorts were not negatively influenced by the events that decimated the young from 1991, and the young from 1992 and 1993 had above-average survival estimates. The apparent decrease since 1996 in development of fidelity of new recruits to this site is suspected due mainly to nocturnal disturbance and predation of chicks causing low productivity.

Connecticut↗
USGS2010

Approaches for the direct estimation of lambda, and demographic contributions to lambda, using capture-recapture data

We first consider the estimation of the finite rate of population increase or population growth rate, u i , using capture-recapture data from open populations. We review estimation and modelling of u i under three main approaches to modelling openpopulation data: the classic approach of Jolly (1965) and Seber (1965), the superpopulation approach of Crosbie & Manly (1985) and Schwarz & Arnason (1996), and the temporal symmetry approach of Pradel (1996). Next, we consider the contributions of different demographic components to u i using a probabilistic approach based on the composition of the population at time i + 1 (Nichols et al., 2000b). The parameters of interest are identical to the seniority parameters, n i , of Pradel (1996). We review estimation of n i under the classic, superpopulation, and temporal symmetry approaches. We then compare these direct estimation approaches for u i and n i with analogues computed using projection matrix asymptotics. We also discuss various extensions of the estimation approaches to multistate applications and to joint likelihoods involving multiple data types.

Journal of Applied Statistics↗
USGS2010

Investigations of potential bias in the estimation of lambda using Pradel's (1996) model for capture-recapture data

Pradel's (1996) temporal symmetry model permitting direct estimation and modelling of population growth rate, u i , provides a potentially useful tool for the study of population dynamics using marked animals. Because of its recent publication date, the approach has not seen much use, and there have been virtually no investigations directed at robustness of the resulting estimators. Here we consider several potential sources of bias, all motivated by specific uses of this estimation approach. We consider sampling situations in which the study area expands with time and present an analytic expression for the bias in u i We next consider trap response in capture probabilities and heterogeneous capture probabilities and compute large-sample and simulation-based approximations of resulting bias in u i . These approximations indicate that trap response is an especially important assumption violation that can produce substantial bias. Finally, we consider losses on capture and emphasize the importance of selecting the estimator for u i that is appropriate to the question being addressed. For studies based on only sighting and resighting data, Pradel's (1996) u i ' is the appropriate estimator.

Journal of Applied Statistics↗
USGS2010

Genetic introgression and the survival of Florida panther kittens

Estimates of survival for the young of a species are critical for population models. These models can often be improved by determining the effects of management actions and population abundance on this demographic parameter. We used multiple sources of data collected during 1982–2008 and a live-recapture dead-recovery modeling framework to estimate and model survival of Florida panther ( Puma concolor coryi ) kittens (age 0–1 year). Overall, annual survival of Florida panther kittens was 0.323 ± 0.071 (SE), which was lower than estimates used in previous population models. In 1995, female pumas from Texas ( P. c. stanleyana ) were released into occupied panther range as part of an intentional introgression program to restore genetic variability. We found that kitten survival generally increased with degree of admixture: F 1 admixed and backcrossed to Texas kittens survived better than canonical Florida panther and backcrossed to canonical kittens. Average heterozygosity positively influenced kitten and older panther survival, whereas index of panther abundance negatively influenced kitten survival. Our results provide strong evidence for the positive population-level impact of genetic introgression on Florida panthers. Our approach to integrate data from multiple sources was effective at improving robustness as well as precision of estimates of Florida panther kitten survival, and can be useful in estimating vital rates for other elusive species with sparse data.

Florida↗
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&ndash;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↗
USGS2009

A hierarchical model for estimating density in camera-trap studies

Estimating animal density using capture–recapture data from arrays of detection devices such as camera traps has been problematic due to the movement of individuals and heterogeneity in capture probability among them induced by differential exposure to trapping. We develop a spatial capture–recapture model for estimating density from camera-trapping data which contains explicit models for the spatial point process governing the distribution of individuals and their exposure to and detection by traps. We adopt a Bayesian approach to analysis of the hierarchical model using the technique of data augmentation. The model is applied to photographic capture–recapture data on tigers Panthera tigris in Nagarahole reserve, India. Using this model, we estimate the density of tigers to be 14·3 animals per 100 km 2 during 2004. Synthesis and applications. Our modelling framework largely overcomes several weaknesses in conventional approaches to the estimation of animal density from trap arrays. It effectively deals with key problems such as individual heterogeneity in capture probabilities, movement of traps, presence of potential ‘holes’ in the array and ad hoc estimation of sample area. The formulation, thus, greatly enhances flexibility in the conduct of field surveys as well as in the analysis of data, from studies that may involve physical, photographic or DNA-based ‘captures’ of individual animals.

Journal of Applied Ecology↗
USGS2009

Dynamic multistate site occupancy models to evaluate hypotheses relevant to conservation of Golden Eagles in Denali National Park, Alaska

The recent development of multistate site occupancy models offers great opportunities to frame and solve decision problems for conservation that can be viewed in terms of site occupancy. These models have several characteristics (e.g., they account for detectability) that make them particularly well suited for addressing management and conservation problems. We applied multistate site occupancy models to evaluate hypotheses related to the conservation and management of Golden Eagles (Aquila chrysaetos) in Denali National Park, Alaska, and provided estimates of transition probabilities among three occupancy states for nesting areas (occupied with successful reproduction, occupied with unsuccessful reproduction, and unoccupied). Our estimation models included the effect of potential recreational activities (hikers) and environmental covariates such as a snowshoe hare (Lepus americanus) index on transition probabilities among the three occupancy states. Based on the most parsimonious model, support for the hypothesis of an effect of potential human disturbance on site occupancy dynamics was equivocal. There was some evidence that potential human disturbance negatively affected local colonization of territories, but there was no evidence of an effect on reproductive performance parameters. In addition, models that assume a positive relationship between the hare index and successful reproduction were well supported by the data. The statistical approach that we used is particularly useful to parameterize management models that can then be used to make optimal decisions related to the management of Golden Eagles in Denali. Although in our case we were particularly interested in managing recreational activities, we believe that such models should be useful to for a broad class of management and conservation problems.

Alaska↗
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↗
USGS2009

Modeling individual animal histories with multistate capture–recapture models

Many fields of science begin with a phase of exploration and description, followed by investigations of the processes that account for observed patterns. The science of ecology is no exception, and recent decades have seen a focus on understanding key processes underlying the dynamics of ecological systems. In population ecology, emphasis has shifted from the state variable of population size to the demographic processes responsible for changes in this state variable: birth, death, immigration, and emigration. In evolutionary ecology, some of these same demographic processes, rates of birth and death, are also the determinants of fitness. In animal population ecology, the estimation of state variables and their associated vital rates is especially problematic because of the difficulties in sampling such populations and detecting individual animals. Indeed, early capture–recapture models were developed for the purpose of estimating population size, given the reality that all animals are not caught or detected at any sampling occasion. More recently, capture–recapture models for open populations were developed to draw inferences about survival in the face of these same sampling problems. The focus of this paper is on multi‐state mark–recapture models (MSMR), which first appeared in the 1970s but have undergone substantial development in the last 15 years. These models were developed to deal explicitly with biological variation, in that animals in different “states” (classes defined by location, physiology, behavior, reproductive status, etc.) may have different probabilities of survival and detection. Animal transitions between states are also stochastic and themselves of interest. These general models have proven to be extremely useful and provide a way of thinking about a remarkably wide range of important ecological processes. These methods are now at a stage of refinement and sophistication where they can readily be used by biologists to tackle a wide range of important issues in ecology. In this paper, we draw together information on the state of the art in multistate mark–recapture methods, explaining the models and illustrating their use. We provide a modeling philosophy and a series of general principles on how to conduct analyses. We cover key issues and features, and we anticipate the ways in which we expect the models to develop in the years ahead.

Advances in Ecological Research↗
USGS2009

Dynamic models for problems of species occurrence with multiple states

Recent extensions of occupancy modeling have focused not only on the distribution of species over space, but also on additional state variables (e.g., reproducing or not, with or without disease organisms, relative abundance categories) that provide extra information about occupied sites. These biologist-driven extensions are characterized by ambiguity in both species presence and correct state classification, caused by imperfect detection. We first show the relationships between independently published approaches to the modeling of multistate occupancy. We then extend the pattern-based modeling to the case of sampling over multiple seasons or years in order to estimate state transition probabilities associated with system dynamics. The methodology and its potential for addressing relevant ecological questions are demonstrated using both maximum likelihood (occupancy and successful reproduction dynamics of California Spotted Owl) and Markov chain Monte Carlo estimation approaches (changes in relative abundance of green frogs in Maryland). Just as multistate capture–recapture modeling has revolutionized the study of individual marked animals, we believe that multistate occupancy modeling will dramatically increase our ability to address interesting questions about ecological processes underlying population-level dynamics.

Ecology↗
USGS2009

Perturbation analysis for patch occupancy dynamics

Perturbation analysis is a powerful tool to study population and community dynamics. This article describes expressions for sensitivity metrics reflecting changes in equilibrium occupancy resulting from small changes in the vital rates of patch occupancy dynamics (i.e., probabilities of local patch colonization and extinction). We illustrate our approach with a case study of occupancy dynamics of Golden Eagle ( Aquila chrysaetos ) nesting territories. Examination of the hypothesis of system equilibrium suggests that the system satisfies equilibrium conditions. Estimates of vital rates obtained using patch occupancy models are used to estimate equilibrium patch occupancy of eagles. We then compute estimates of sensitivity metrics and discuss their implications for eagle population ecology and management. Finally, we discuss the intuition underlying our sensitivity metrics and then provide examples of ecological questions that can be addressed using perturbation analyses. For instance, the sensitivity metrics lead to predictions about the relative importance of local colonization and local extinction probabilities in influencing equilibrium occupancy for rare and common species.

Ecology↗
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

An inventory of terrestrial mammals at national parks in the Northeast Temperate Network and Sagamore Hill National Historic Site

An inventory of mammals was conducted during 2004 at nine national park sites in the Northeast Temperate Network (NETN): Acadia National Park (NP), Marsh-Billings-Rockefeller National Historical Park (NHP), Minute Man NHP, Morristown NHP, Roosevelt-Vanderbilt National Historic Site (NHS), Saint-Gaudens NHS, Saugus Iron Works NHS, Saratoga NHP, and Weir Farm NHS. Sagamore Hill NHS, part of the Northeast Coastal and Barrier Network (NCBN), was also surveyed. Each park except Acadia NP was sampled twice, once in the winter/spring and again in the summer/fall. During the winter/spring visit, indirect measure (IM) sampling arrays were employed at 2 to 16 stations and included sampling by remote cameras, cubby boxes (covered trackplates), and hair traps. IM stations were established and re-used during the summer/fall sampling period. Trapping was conducted at 2 to 12 stations at all parks except Acadia NP during the summer/fall period and consisted of arrays of small-mammal traps, squirrel-sized live traps, and some fox-sized live traps. We used estimation-based procedures and probabilistic sampling techniques to design this inventory. A total of 38 species was detected by IM sampling, trapping, and field observations. Species diversity (number of species) varied among parks, ranging from 8 to 24, with Minute Man NHP having the most species detected. Raccoon (Procyon lotor), Virginia Opossum (Didelphis virginiana), Fisher (Martes pennanti), and Domestic Cat (Felis silvestris) were the most common medium-sized mammals detected in this study and White-footed Mouse (Peromyscus leucopus), Northern Short-tailed Shrew (Blarina brevicauda), Deer Mouse (P. maniculatus), and Meadow Vole (Microtus pennsylvanicus) the most common small mammals detected. All species detected are considered fairly common throughout their range including the Fisher, which has been reintroduced in several New England states. We did not detect any state or federal endangered or threatened species.

Scientific Investigations Report↗