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James D. Nichols

Publications and source records attributed to James D. Nichols.

At least 109 records · Page 6Linked to original sources
USGS2008

Juvenile survival in a tropical population of roseate terns: Interannual variation and effect of tick parasitism

Many demographic studies on long-lived seabirds have focused on the estimation of adult survival, but much less is known about survival during the early years of life, especially in tropical species. We report analyses of a capture–recapture dataset of 685 roseate terns ringed as fledglings and adults between 1998 and 2005 on Aride Island, Seychelles, and recaptured/resighted at the same colony site over a 5 yr (2002 to 2006) period. A multistate model was used to estimate survival for different age classes, including juvenile (first-year) birds returning as non-breeding prospectors. The effect of infestation by parasites (ticks) on survival was also examined. Overall, the estimated return of first-year individuals to the natal colony was very variable, ranging from 2 to 22%. Conditioned on survival, the probability of returning from Age 2 yr onwards increased to 70%. Survival rates were best modeled as time-specific, with estimates varying from 0.02 to 1.00 (mean 0.69) in first-year birds with a marked negative effect of tick infestation. In older birds (minimum age of 2 yr), the annual estimates fell between 0.69 and 0.86 (mean 0.77). Using a components of variance approach for estimation of year-to-year variation, we found high temporal variability for first-year individuals (coefficient of variation [CV] = 65%) compared to much less variation in the survival rate of older birds (CV = 9%). These findings agree with the life-history prediction that demographic rates of juveniles are usually lower and more variable than those of older individuals. Our results are also consistent with the predicted negative effect of tick parasitism on juvenile survival. Compared with data from other roseate tern populations, survival over the first 2 yr (Age 0 to 2 yr) was 18 to 40% higher in this study, suggesting that a high ‘young’ survival rate may be an important demographic trait in this tropical population to compensate for the low annual reproductive success. Our data show that estimating survival of young individuals may be crucial to elucidating the demographic tactics of seabirds.

Marine Ecology Progress Series↗
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↗
USGS2005

Modelling occurrence and abundance of species when detection is imperfect

Relationships between species abundance and occupancy are of considerable interest in metapopulation biology and in macroecology. Such relationships may be described concisely using probability models that characterize variation in abundance of a species. However, estimation of the parameters of these models in most ecological problems is impaired by imperfect detection. When organisms are detected imperfectly, observed counts are biased estimates of true abundance, and this induces bias in stated occupancy or occurrence probability. In this paper we consider a class of models that enable estimation of abundance/occupancy relationships from counts of organisms that result from surveys in which detection is imperfect. Under such models, parameter estimation and inference are based on conventional likelihood methods. We provide an application of these models to geographically extensive breeding bird survey data in which alternative models of abundance are considered that include factors that influence variation in abundance and detectability. Using these models, we produce estimates of abundance and occupancy maps that honor important sources of spatial variation in avian abundance and provide clearly interpretable characterizations of abundance and occupancy adjusted for imperfect detection.

Oikos↗
USGS2005

Individual quality, survival variation and patterns of phenotypic selection on body condition and timing of nesting in birds

Questions about individual variation in “quality” and fitness are of great interest to evolutionary and population ecologists. Such variation can be investigated using either a random effects approach or an approach that relies on identifying observable traits that are themselves correlated with fitness components. We used the latter approach with data from 1,925 individual females of three species of ducks (tufted duck, Aythya fuligula ; common pochard, Aythya ferina ; northern shoveler, Anas clypeata ) sampled on their breeding grounds at Engure Marsh, Latvia, for over 15 years. Based on associations with reproductive output, we selected two traits, one morphological (relative body condition) and one behavioral (relative time of nesting), that can be used to characterize individual females over their lifetimes. We then asked whether these traits were related to annual survival probabilities of nesting females. We hypothesized quadratic, rather than monotonic, relationships based loosely on ideas about the likely action of stabilizing selection on these two traits. Parameters of these relationships were estimated directly using ultrastructural models embedded within capture-recapture-band-recovery models. Results provided evidence that both traits were related to survival in the hypothesized manner. For all three species, females that tended to nest earlier than the norm exhibited the highest survival rates, but very early nesters experienced reduced survival and late nesters showed even lower survival. For shovelers, females in average body condition showed the highest survival, with lower survival rates exhibited by both heavy and light birds. For common pochard and tufted duck, the highest survival rates were associated with birds of slightly above-average condition, with somewhat lower survival for very heavy birds and much lower survival for birds in relatively poor condition. Based on results from this study and previous work on reproduction, we conclude that nest initiation date and body condition covary with both reproductive and survival components of fitness. These associations lead to a positive covariance of these two fitness components within individuals and to the conclusion that these two traits are indeed correlates of individual quality.

Oecologia↗
USGS2005

Double-observer approach to estimating egg mass abundance of vernal pool breeding amphibians

Interest in seasonally flooded pools, and the status of associated amphibian populations, has initiated programs in the northeastern United States to document and monitor these habitats. Counting egg masses is an effective way to determine the population size of pool-breeding amphibians, such as wood frogs ( Rana sylvatica ) and spotted salamanders ( Ambystoma maculatum ). However, bias is associated with counts if egg masses are missed. Counts unadjusted for the proportion missed (i.e., without adjustment for detection probability) could lead to false assessments of population trends. We used a dependent double-observer method in 2002–2003 to estimate numbers of wood frog and spotted salamander egg masses at seasonal forest pools in 13 National Wildlife Refuges, 1 National Park, 1 National Seashore, and 1 State Park in the northeastern United States. We calculated detection probabilities for egg masses and examined whether detection probabilities varied by species, observers, pools, and in relation to pool characteristics (pool area, pool maximum depth, within-pool vegetation). For the 2 years, model selection indicated that no consistent set of variables explained the variation in data sets from individual Refuges and Parks. Because our results indicated that egg mass detection probabilities vary spatially and temporally, we conclude that it is essential to use estimation procedures, such as double-observer methods with egg mass surveys, to determine population sizes and trends of these species.

Maine, Maryland, Massachusetts, New Hampshire, New↗
USGS2005

Improving inferences in population studies of rare species that are detected imperfectly

For the vast majority of cases, it is highly unlikely that all the individuals of a population will be encountered during a study. Furthermore, it is unlikely that a constant fraction of the population is encountered over times, locations, or species to be compared. Hence, simple counts usually will not be good indices of population size. We recommend that detection probabilities (the probability of including an individual in a count) be estimated and incorporated into inference procedures. However, most techniques for estimating detection probability require moderate sample sizes, which may not be achievable when studying rare species. In order to improve the reliability of inferences from studies of rare species, we suggest two general approaches that researchers may wish to consider that incorporate the concept of imperfect detectability: (1) borrowing information about detectability or the other quantities of interest from other times, places, or species; and (2) using state variables other than abundance (e.g., species richness and occupancy). We illustrate these suggestions with examples and discuss the relative benefits and drawbacks of each approach.

Ecology↗
USGS2005

Comparative demography of new world populations of thrushes (Turdus spp.): Comment

Survival and fecundity are fundamental to the study of evolutionary ecology, as they are two of the key variables influencing the constrained optimization process we call natural selection. Likewise, population managers require accurate estimates of these parameters; along with dispersal, they govern population dynamics ( Lack 1954 ) and thus are essential for predicting population change and the effects of management actions. It can be frustrating, then, when survival is difficult to estimate for certain populations, as in some avian species that exhibit a substantial degree of dispersal.

Ecology↗
USGS2005

Using the North American Breeding Bird Survey as a tool for conservation: A critique of Bart et al. (2004)

Bart et al. (2004) develop methods for predicting needed samples for estimation of long-term trends from Count survey data, and they apply these methods to the North American Breeding Bird Survey (BBS). They recommend adding approximately 40% more survey routes ill the BBS to allow for estimation of long-term (i.e., 20 year) trends for a collection of species. We critique several aspects of their analysis and suggest that their focus on long-term trends and expansion of the present survey design will provide limited benefits for conservation because it fails to either enhance the credibility of the survey or better tie the survey to regional management activities. A primary innovation claimed by Bart et al. (2004) is the incorporation of bias in estimation of study planning. We question the value of this approach, as it requires reliable estimates of range of future bias. We show that estimates of bias used by Bart et al. (2004) are speculative. Failure to obtain better estimates of this bias is likely to compromise the credibility of future analyses of the survey. We also note that the generic analysis of population trends that they provide is of questionable validity and is unlikely to be relevant for regions and species of management concern.

Journal of Wildlife Management↗
USGS2002

Of bugs and birds: Markov Chain Monte Carlo for hierarchical modeling in wildlife research

Markov chain Monte Carlo (MCMC) is a statistical innovation that allows researchers to fit far more complex models to data than is feasible using conventional methods. Despite its widespread use in a variety of scientific fields, MCMC appears to be underutilized in wildlife applications. This may be due to a misconception that MCMC requires the adoption of a subjective Bayesian analysis, or perhaps simply to its lack of familiarity among wildlife researchers. We introduce the basic ideas of MCMC and software BUGS (Bayesian inference using Gibbs sampling), stressing that a simple and satisfactory intuition for MCMC does not require extraordinary mathematical sophistication. We illustrate the use of MCMC with an analysis of the association between latent factors governing individual heterogeneity in breeding and survival rates of kittiwakes ( Rissa tridactyla ). We conclude with a discussion of the importance of individual heterogeneity for understanding population dynamics and designing management plans.

Journal of Wildlife Management↗
USGS2000

Geographic analysis of species richness and community attributes of forest birds from survey data in the mid-Atlantic integrated assessment region

Species richness of local communities is a state variable commonly used in community ecology and conservation biology. Investigation of spatial and temporal variations in richness and identification of factors associated with these variations form a basis for specifying management plans, evaluating these plans, and for testing hypotheses of theoretical interest. However, estimation of species richness is not trivial: species can be missed by investigators during sampling sessions. Sampling artifacts can lead to erroneous conclusions on spatial and temporal variation in species richness. Here we use data from the North American Breeding Bird Survey to estimate parameters describing the state of bird communities in the Mid-Atlantic Assessment (MAIA) region: species richness, extinction probability, turnover and relative species richness. We use a recently developed approach to estimation of species richness and related parameters that does not require the assumption that all the species are detected during sampling efforts. The information presented here is intended to visualize the state of bird communities in the MAIA region. We provide information on 1975 and 1990. We also quantified the changes between these years. We summarized and mapped the community attributes at a scale of management interest (watershed units).

Delaware, Maryland, Pennsylvania, Virginia, West V↗
USGS2000

Annual survival and site fidelity of Stellar's Eiders molting along the Alaska Peninsula

Populations of Steller's eiders ( Polysticta stelleri ) molting and wintering along the Alaska Peninsula have declined since the 1960's. We captured and marked a large sample of Steller's eiders molting in 2 lagoons along the Alaska Peninsula between 1975-97. We used mark-recapture analysis techniques to estimate annual survival and movement probabilities within and among lagoons for male and female eiders. Estimates of annual survival (±SE) were 0.899 ± 0.032 for females and 0.765 ± 0.044 for males. Both sexes showed high rates of fidelity to specific molting locations (>95%) within lagoons; yet we found no evidence that annual probability of survival differed among groups molting in different locations either within or among lagoons. We found weak evidence that annual survival decreased between the periods 1975-81 and 1991-97. The lower survival of males compared to females is unusual for waterfowl and may result in a female-biased sex ratio. We conclude that a decrease in adult survival may have initiated the long-term population decline. Further, a shortage of males may be limiting reproductive potential.

Alaska↗
USGS1999

Modeling data from double-tagging experiments to estimate heterogeneous rates of tag shedding in lake trout (Salvelinus namaycush)

Data from mark-recapture studies are used to estimate population rates such as exploitation, survival, and growth. Many of these applications assume negligible tag loss, so tag shedding can be a significant problem. Various tag shedding models have been developed for use with data from double-tagging experiments, including models to estimate constant instantaneous rates, time-dependent rates, and type I and II shedding rates. In this study, we used conditional (on recaptures) multinomial models implemented using the program SURVIV (G.C. White. 1983. J. Wildl. Manage. 47: 716-728) to estimate tag shedding rates of lake trout (Salvelinus namaycush) and explore various potential sources of variation in these rates. We applied the models to data from several long-term double-tagging experiments with Lake Superior lake trout and estimated shedding rates for anchor tags in hatchery-reared and wild fish and for various tag types applied in these experiments. Estimates of annual tag retention rates for lake trout were fairly high (80-90%), but we found evidence (among wild fish only) that retention rates may be significantly lower in the first year due to type I losses. Annual retention rates for some tag types varied between male and female fish, but there was no consistent pattern across years. Our estimates of annual tag retention rates will be used in future studies of survival rates for these fish.

Canadian Journal of Fisheries and Aquatic Sciences↗
USGS1998

Higher temporal variability of forest breeding bird communities in fragmented landscapes

Understanding the relationship between animal community dynamics and landscape structure has become a priority for biodiversity conservation. In particular, predicting the effects of habitat destruction that confine species to networks of small patches is an important prerequisite to conservation plan development. Theoretical models that predict the occurrence of species in fragmented landscapes, and relationships between stability and diversity do exist. However, reliable empirical investigations of the dynamics of biodiversity have been prevented by differences in species detection probabilities among landscapes. Using long-term data sampled at a large spatial scale in conjunction with a capture-recapture approach, we developed estimates of parameters of community changes over a 22-year period for forest breeding birds in selected areas of the eastern United States. We show that forest fragmentation was associated not only with a reduced number of forest bird species, but also with increased temporal variability in the number of species. This higher temporal variability was associated with higher local extinction and turnover rates. These results have major conservation implications. Moreover, the approach used provides a practical tool for the study of the dynamics of biodiversity.

Proceedings of the National Academy of Sciences↗
USGS1998

Estimating species richness: The importance of heterogeneity in species detectability

Estimating species richness (i.e., the actual number of species present in a given area) is a basic objective of many field studies carried out in community ecology and is also of crucial concern when dealing with the conservation and management of biodiversity. In most studies, the total number of species recorded in an area at a given time is taken as a measure of species richness. Here we use a capture–recapture approach to species richness estimation with North American Breeding Bird Survey (BBS) data in order to estimate species detectability and thus gain insight about its importance. In particular, competing models making different assumptions about species detectability are available. We carried out analyses on all survey routes of four states, Arizona, Maryland, North Dakota, and Wisconsin, in two years, 1970 and 1990. These states were chosen to provide contrasting habitats, bird species composition, and survey quality. We investigated the effect of state, year, and observer ability on the proportions of different models selected, and on estimates of detectability and species richness. Our results indicate that model M h , which assumes heterogeneous detection probability among species, is frequently appropriate for estimating species richness from BBS data. Species detectability varied among states and was higher for the more skilled observers. These results emphasize the need to take into account potential heterogeneities in detectability among species in studies of factors affecting species richness.

Ecology↗
USGS1998

Estimation of temporal variability of survival in animal populations

Temporal variation of demographic characteristics for animal populations is of interest to both ecologists and biological modelers. The standard deviation of a series of estimated parameter values (e.g., estimated population size) or some function thereof (e.g., log of the estimated parameters) is commonly used as a measure of temporal variability. These measures of temporal variation overestimate the true temporal variation by not accounting for sampling variability inherent to the estimation of unknown population parameters. Using a variance-components approach to partitioning the total variability of an estimated parameter, we demonstrate the ease with which sampling variation can be removed from the observed total variation of parameter estimates. Estimates of temporal variability of survival are given after removal of sampling variation for three bird species: the federally listed Roseate Tern ( Sterna dougallii ), Black-capped Chickadees ( Parus atricapillus ), and Mallard ducks ( Anas platyrhynchos ). Sampling variation accounted for the majority of the total variation in the survival estimates for nearly all of the populations studied. Substantial differences in observed significance levels were observed when testing for demographic differences in temporal variation using temporal variance estimates adjusted and unadjusted for sampling variance.

Ecology↗
USGS1998

Estimation of tiger densities in India using photographic captures and recaptures

The tiger ( Panthera tigris ) is an endangered, large felid whose demographic status is poorly known across its distributional range in Asia. Previously applied methods for estimating tiger abundance, using total counts based on tracks, have proved unreliable. Lack of reliable data on tiger densities not only has constrained our ability to understand the ecological factors shaping communities of large, solitary felids, but also has undermined the effective conservation of these animals. In this paper, we describe the use of a field method proposed by Karanth (1995), which combines camera-trap photography, to identify individual tigers, with theoretically well-founded capture–recapture models. We developed a sampling design for camera-trapping and used the approach to estimate tiger population size and density in four representative tiger habitats in different parts of India. The field method worked well and provided data suitable for analysis using closed capture–recapture models. The results suggest the potential for applying this methodology to rigorously estimate abundances, survival rates, and other population parameters for tigers and other low-density, secretive animal species in which individuals can be identified based on natural markings. Estimated probabilities of photo-capturing tigers present in the study sites ranged from 0.75 to 1.00. Estimated densities of tigers >1 yr old ranged from 4.1 ± 1.31 to 16.8 ± 2.96 tigers/100 km 2 (mean ± 1 se ). Simultaneously, we used line-transect sampling to determine that mean densities of principal tiger prey at these sites ranged from 56.1 to 63.8 ungulates/km 2 . Tiger densities appear to be positively associated with prey densities, except at one site influenced by tiger poaching. Our results generally support the prediction that relative abundances of large felid species may be governed primarily by the abundance and structure of their prey communities.

National Parks of Pench, Kanha, Kaziranga, and Nag↗
USGS1998

Are adult nonbreeders prudent parents? The kittiwake model

Understanding evolutionary consequences of intermittent breeding (nonbreeding in individuals that previously bred) requires investigation of the relationships between adult breeding state and two demographic parameters: survival probability and subsequent breeding probability. One major difficulty raised by comparing the demographic features of breeders and nonbreeders as estimated from capture–recapture data is that breeding state is often suspected to influence recapture or resighting probability. We used multistate capture–recapture models to test the hypothesis of equal recapture probabilities for breeding and nonbreeding Kittiwakes and found no evidence of an effect of breeding state on this parameter. The same method was used to test whether reproductive state affects survival probability. Nonbreeding individuals have lower survival rates than breeders. Moreover, nonbreeders have a higher probability of being nonbreeders the following year than do breeders. State-specific survival rates and transition probabilities vary from year to year, but temporal variations of survival and transition probabilities of breeders and nonbreeders are in parallel (on a logit scale). These inferences led us to conclude that nonbreeders tend to be lower quality individuals. The effect of sex was also investigated: males and females do not differ with respect to survival probabilities when reproductive state is taken into account. Similarly, there is no effect of sex on transition probabilities between reproductive states.

Ecology↗