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James D. Nichols

Publications and source records attributed to James D. Nichols.

At least 73 records · Page 4Linked to original sources

Relaxing the closure assumption in single-season occupancy models: staggered arrival and departure times

Occupancy statistical models that account for imperfect detection have proved very useful in several areas of ecology, including species distribution and spatial dynamics, disease ecology, and ecological responses to climate change. These models are based on the collection of multiple samples at each of a number of sites within a given season, during which it is assumed the species is either absent or present and available for detection while each sample is taken. However, for some species, individuals are only present or available for detection seasonally. We present a statistical model that relaxes the closure assumption within a season by permitting staggered entry and exit times for the species of interest at each site. Based on simulation, our open model eliminates bias in occupancy estimators and in some cases increases precision. The power to detect the violation of closure is high if detection probability is reasonably high. In addition to providing more robust estimation of occupancy, this model permits comparison of phenology across sites, species, or years, by modeling variation in arrival or departure probabilities. In a comparison of four species of amphibians in Maryland we found that two toad species arrived at breeding sites later in the season than a salamander and frog species, and departed from sites earlier.

Ecology

Resilience thinking and a decision-analytic approach to conservation: strange bedfellows or essential partners?

There has been some tendency to view decision science and resilience theory as opposing approaches, or at least as contending perspectives, for natural resource management. Resilience proponents have been especially critical of optimization in decision science, at least for those cases where it is focused on the aggressive pursuit of efficiency. In general, optimization of resource systems is held to reduce spatial, temporal, or organizational heterogeneity that would otherwise limit efficiency, leading to homogenization of a system and making it less able to cope with unexpected changes or disturbances. For their part, decision analysts have been critical of resilience proponents for not providing much practical advice to decision makers. We believe a key source of tension between resilience thinking and application of decision science is the pursuit of efficiency in the latter (i.e., choosing the “best” management action or strategy option to maximize productivity of one or few resource components), vs. a desire in the former to keep options open (i.e., maintaining and enhancing diversity). It seems obvious, however, that with managed natural systems, there must be a principle by which to guide decision making, which at a minimumallows for a comparison of projected outcomes associated with decision alternatives. This is true even if the primary concern of decision making is the preservation of system resilience. We describe how a careful framing of conservation problems, especially in terms of management objectives and predictive models, can help reduce the purported tension between resiliencethinking and decision analysis. In particular, objective setting in conservation problems needs to be more attuned to the dynamics of ecological systems and to the possibility of deep uncertainties that underlie the risk of unintended, if not irreversible, outcomes. Resilience thinking also leads to the suggestion that model development should focus more on process rather than pattern, on multiple scales of influence, and on phenomena that can create alternative stability regimes. Although we acknowledge the inherent difficulties in modeling ecological processes, we stress that formulation of useful models need not depend on a thorough mechanistic understanding or precise parameterization, assuming that uncertainty is acknowledged and treated in a systematic manner.

Ecology and Society

Presence-only modeling using MAXENT: when can we trust the inferences?

1. Recently, interest in species distribution modelling has increased following the development of new methods for the analysis of presence-only data and the deployment of these methods in user-friendly and powerful computer programs. However, reliable inference from these powerful tools requires that several assumptions be met, including the assumptions that observed presences are the consequence of random or representative sampling and that detectability during sampling does not vary with the covariates that determine occurrence probability. 2. Based on our interactions with researchers using these tools, we hypothesized that many presence-only studies were ignoring important assumptions of presence-only modelling. We tested this hypothesis by reviewing 108 articles published between 2008 and 2012 that used the MAXENT algorithm to analyse empirical (i.e. not simulated) data. We chose to focus on these articles because MAXENT has been the most popular algorithm in recent years for analysing presence-only data. 3. Many articles (87%) were based on data that were likely to suffer from sample selection bias; however, methods to control for sample selection bias were rarely used. In addition, many analyses (36%) discarded absence information by analysing presence–absence data in a presence-only framework, and few articles (14%) mentioned detection probability. We conclude that there are many misconceptions concerning the use of presence-only models, including the misunderstanding that MAXENT, and other presence-only methods, relieve users from the constraints of survey design. 4. In the process of our literature review, we became aware of other factors that raised concerns about the validity of study conclusions. In particular, we observed that 83% of articles studies focused exclusively on model output (i.e. maps) without providing readers with any means to critically examine modelled relationships and that MAXENT's logistic output was frequently (54% of articles) and incorrectly interpreted as occurrence probability. 5. We conclude with a series of recommendations foremost that researchers analyse data in a presence–absence framework whenever possible, because fewer assumptions are required and inferences can be made about clearly defined parameters such as occurrence probability.

Methods in Ecology and Evolution

Neighborhood and habitat effects on vital rates: expansion of the Barred Owl in the Oregon Coast Ranges

In this paper, we modify dynamic occupancy models developed for detection-nondetection data to allow for the dependence of local vital rates on neighborhood occupancy, where neighborhood is defined very flexibly. Such dependence of occupancy dynamics on the status of a relevant neighborhood is pervasive, yet frequently ignored. Our framework permits joint inference about the importance of neighborhood effects and habitat covariates in determining colonization and extinction rates. Our specific motivation is the recent expansion of the Barred Owl (Strix varia) in western Oregon, USA, over the period 1990-2010. Because the focal period was one of dramatic range expansion and local population increase, the use of models that incorporate regional occupancy (sources of colonists) as determinants of dynamic rate parameters is especially appropriate. We began our analysis of 21 years of Barred Owl presence/nondetection data in the Tyee Density Study Area (TDSA) by testing a suite of six models that varied only in the covariates included in the modeling of detection probability. We then tested whether models that used regional occupancy as a covariate for colonization and extinction outperformed models with constant or year-specific colonization or extinction rates. Finally we tested whether habitat covariates improved the AIC of our models, focusing on which habitat covariates performed best, and whether the signs of habitat effects are consistent with a priori hypotheses. We conclude that all covariates used to model detection probability lead to improved AIC, that regional occupancy influences colonization and extinction rates, and that habitat plays an important role in determining extinction and colonization rates. As occupancy increases from low levels toward equilibrium, colonization increases and extinction decreases, presumably because there are more and more dispersing juveniles. While both rates are affected, colonization increases more than extinction decreases. Colonization is higher and extinction is lower in survey polygons with more riparian forest. The effects of riparian forest on extinction rates are greater than on colonization rates. Model results have implications for management of the invading Barred Owl, both through habitat alteration and removal.

Oregon

Joint estimation of habitat dynamics and species interactions: Disturbance reduces co-occurrence of non-native predators with an endangered toad

1. Ecologists have long been interested in the processes that determine patterns of species occurrence and co-occurrence. Potential short-comings of many existing empirical approaches that address these questions include a reliance on patterns of occurrence at a single time point, failure to account properly for imperfect detection and treating the environment as a static variable. 2. We fit detection and non-detection data collected from repeat visits using a dynamic site occupancy model that simultaneously accounts for the temporal dynamics of a focal prey species, its predators and its habitat. Our objective was to determine how disturbance and species interactions affect the co-occurrence probabilities of an endangered toad and recently introduced non-native predators in stream breeding habitats. For this, we determined statistical support for alternative processes that could affect co-occurrence frequency in the system. 3. We collected occurrence data at stream segments in two watersheds where streams were largely ephemeral and one watershed dominated by perennial streams. Co-occurrence probabilities of toads with non-native predators were related to disturbance frequency, with low co-occurrence in the ephemeral watershed and high co-occurrence in the perennial watershed. This occurred because once predators were established at a site, they were rarely lost from the site except in cases when the site dried out. Once dry sites became suitable again, toads colonized them much more rapidly than predators, creating a period of predator-free space. 4. We attribute the dynamics to a storage effect, where toads persisting outside the stream environment during periods of drought rapidly colonized sites when they become suitable again. Our results support that even in highly connected stream networks, temporal disturbance can structure frequencies with which breeding amphibians encounter non-native predators. 5. Dynamic multi-state occupancy models are a powerful tool for rigorously examining hypotheses about inter-species and species–habitat interactions. In contrast to previous methods that infer dynamic processes based on static patterns in occupancy, the approach we took allows the dynamic processes that determine species–species and species–habitat interactions to be directly estimated.

Journal of Animal Ecology

Modeling habitat dynamics accounting for possible misclassification

Land cover data are widely used in ecology as land cover change is a major component of changes affecting ecological systems. Landscape change estimates are characterized by classification errors. Researchers have used error matrices to adjust estimates of areal extent, but estimation of land cover change is more difficult and more challenging, with error in classification being confused with change. We modeled land cover dynamics for a discrete set of habitat states. The approach accounts for state uncertainty to produce unbiased estimates of habitat transition probabilities using ground information to inform error rates. We consider the case when true and observed habitat states are available for the same geographic unit (pixel) and when true and observed states are obtained at one level of resolution, but transition probabilities estimated at a different level of resolution (aggregations of pixels). Simulation results showed a strong bias when estimating transition probabilities if misclassification was not accounted for. Scaling-up does not necessarily decrease the bias and can even increase it. Analyses of land cover data in the Southeast region of the USA showed that land change patterns appeared distorted if misclassification was not accounted for: rate of habitat turnover was artificially increased and habitat composition appeared more homogeneous. Not properly accounting for land cover misclassification can produce misleading inferences about habitat state and dynamics and also misleading predictions about species distributions based on habitat. Our models that explicitly account for state uncertainty should be useful in obtaining more accurate inferences about change from data that include errors.

Landscape Ecology

Likelihood analysis of species occurrence probability from presence-only data for modelling species distributions

1. Understanding the factors affecting species occurrence is a pre-eminent focus of applied ecological research. However, direct information about species occurrence is lacking for many species. Instead, researchers sometimes have to rely on so-called presence-only data (i.e. when no direct information about absences is available), which often results from opportunistic, unstructured sampling. MAXENT is a widely used software program designed to model and map species distribution using presence-only data. 2. We provide a critical review of MAXENT as applied to species distribution modelling and discuss how it can lead to inferential errors. A chief concern is that MAXENT produces a number of poorly defined indices that are not directly related to the actual parameter of interest – the probability of occurrence ( ψ ). This focus on an index was motivated by the belief that it is not possible to estimate ψ from presence-only data; however, we demonstrate that ψ is identifiable using conventional likelihood methods under the assumptions of random sampling and constant probability of species detection. 3. The model is implemented in a convenient r package which we use to apply the model to simulated data and data from the North American Breeding Bird Survey. We demonstrate that MAXENT produces extreme under-predictions when compared to estimates produced by logistic regression which uses the full (presence/absence) data set. We note that MAXENT predictions are extremely sensitive to specification of the background prevalence, which is not objectively estimated using the MAXENT method. 4. As with MAXENT, formal model-based inference requires a random sample of presence locations. Many presence-only data sets, such as those based on museum records and herbarium collections, may not satisfy this assumption. However, when sampling is random, we believe that inference should be based on formal methods that facilitate inference about interpretable ecological quantities instead of vaguely defined indices.

Methods in Ecology and Evolution

Studying biodiversity: is a new paradigm really needed?

Authors in this journal have recommended a new approach to the conduct of biodiversity science. This data-driven approach requires the organization of large amounts of ecological data, analysis of these data to discover complex patterns, and subsequent development of hypotheses corresponding to detected patterns. This proposed new approach has been contrasted with more-traditional knowledge-based approaches in which investigators deduce consequences of competing hypotheses to be confronted with actual data, providing a basis for discriminating among the hypotheses. We note that one approach is directed at hypothesis generation, whereas the other is also focused on discriminating among competing hypotheses. Here, we argue for the importance of using existing knowledge to the separate issues of (a) hypothesis selection and generation and (b) hypothesis discrimination and testing. In times of limited conservation funding, the relative efficiency of different approaches to learning should be an important consideration in decisions about how to study biodiversity.

BioScience

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

The U.S. Geological Survey Ecosystem Science Strategy, 2012-2022 - Advancing discovery and application through collaboration

Ecosystem science is critical to making informed decisions about natural resources that can sustain our Nation’s economic and environmental well-being. Resource managers and policy-makers are faced with countless decisions each year at local, state, tribal, territorial, and national levels on issues as diverse as renewable and non-renewable energy development, agriculture, forestry, water supply, and resource allocations at the urban-rural interface. The urgency for sound decision-making is increasing dramatically as the world is being transformed at an unprecedented pace and in uncertain directions. Environmental changes are associated with natural hazards, greenhouse gas emissions, and increasing demands for water, land, food, energy, mineral, and living resources. At risk is the Nation’s environmental capital, the goods and services provided by resilient ecosystems that are vital to the health and well-being of human societies. Ecosystem science—the study of systems of organisms interacting with their environment and the consequences of natural and human-induced change on these systems—is necessary to inform decision-makers as they develop policies to adapt to these changes. This Ecosystems Science Strategy is built on a framework that includes basic and applied science. It highlights the critical roles that USGS scientists and partners can play in building scientific understanding and providing timely information to decision-makers. The strategy underscores the connection between scientific discoveries and the application of new knowledge. The strategy integrates ecosystem science and decision-making, producing new scientific outcomes to assist resource managers and providing public benefits. The USGS is uniquely positioned to play an important role in ecosystem science. With its wide range of expertise, the agency can bring holistic, cross-scale, interdisciplinary capabilities to the design and conduct of monitoring, research, and modeling and to new technologies for data collection, management, and visualization. Collectively, these capabilities can be used to reveal ecological patterns and processes, explain how and why ecosystems change, and forecast change over different spatial and temporal scales. USGS science can provide managers with options and decision-support tools to use resources sustainably. The USGS has long-standing, collaborative relationships with the DOI and other partners in the natural sciences, in both conducting science and its application. The USGS engages these partners in cooperative investigations that otherwise would lack the necessary support or be too expensive for a single bureau to conduct. The heart of this strategy is a framework and vision for USGS ecosystems science that focuses on five long-term goals, which are seen as interconnected and reinforcing components: • Improve understanding of ecosystem structure, function, and processes. The focus for this goal is an understanding of how ecosystems work, including the dynamics of species, their populations, interactions, and genetics, and how they change across spatial and temporal scales. • Advance understanding of how drivers influence ecosystem change. The challenges here are explaining the drivers of ecosystem change, their spatio-temporal patterns, their uncertainties and interactions, and their influence on ecosystem processes and dynamics. • Improve understanding of the services that ecosystems provide to society. Here the emphasis is on the measurement of environmental capital and ecosystem services, and the identification of sources and patterns of change in space and time. • Develop tools, technologies, and capacities to inform decision-making about ecosystems. This includes developing new technologies and approaches for conducting applications-oriented ecosystem science. A principal challenge will be how to quantify uncertainty and incorporate it in decision analysis. • Apply science to enhance strategies for management, conservation, and restoration of ecosystems. These challenges include development of novel approaches to monitoring, assessment, and restoration of ecosystems; new methods to address species of concern and communities at risk; and innovations in decision analysis and support to address imminent ecosystem changes or those that are underway. Closely integrated with the five goals are four strategic approaches that provide the path forward for the USGS Ecosystems Mission Area. These approaches cross-cut all of the goals and are seen as essential to the implementation of this strategy: • Assess information needs for ecosystem science through enhanced partnerships. Work with the DOI and other agencies and institutions to identify, design, and implement priority decision-driven ecological research. • Promote the use of interdisciplinary ecosystem science. Design and conduct interdisciplinary process-oriented research in ecosystem science. • Enhance modeling and forecasting. Build models to forecast ecosystem change, assess future management scenarios, and reduce uncertainties through an adaptive learning process. • Support decision-making. Use quantitative approaches to assess the vulnerabilities of ecosystems, habitats, and species, and evaluate strategies for adaptation, restoration, and sustainable management. Following the strategic approaches are a set of proposed actions that represent a sampling of specific activities that align with this strategy and that address the Nation’s most pressing environmental needs. The strategy emphasizes coordination of activities across the USGS mission areas pursuant to these goals. Ecosystem science is inherently interdisciplinary and requires a broad perspective that incorporates the biological and physical sciences, climate science, information technology, and scientific capacity in mission areas across the Bureau. With its emphasis on coordination, this strategy can provide a critical underpinning for integrated science efforts with scientists from multiple mission areas of the USGS working together. Of course, the USGS will continue to conduct both discipline-specific and interdisciplinary investigations, and both will continue to be vital parts of the ecosystem science portfolio. Finally, the strategy stresses the importance of coordination with other Federal agencies and organizations in the natural resources community. The USGS collaborates with resource agencies in the DOI and other organizations throughout the world to meet societal needs for species and ecosystem management. Working with these agencies and organizations, the USGS will play a key role over the next decade in advancing the scientific foundation for sustaining the natural resources that diverse, productive, resilient ecosystems provide.

Open-File Report

Structured decision making as a proactive approach to dealing with sea level rise in Florida

Sea level rise (SLR) projections along the coast of Florida present an enormous challenge for management and conservation over the long term. Decision makers need to recognize and adopt strategies to adapt to the potentially detrimental effects of SLR. Structured decision making (SDM) provides a rigorous framework for the management of natural resources. The aim of SDM is to identify decisions that are optimal with respect to management objectives and knowledge of the system. Most applications of SDM have assumed that the managed systems are governed by stationary processes. However, in the context of SLR it may be necessary to acknowledge that the processes underlying managed systems may be non-stationary, such that systems will be continuously changing. Therefore, SLR brings some unique considerations to the application of decision theory for natural resource management. In particular, SLR is expected to affect each of the components of SDM. For instance, management objectives may have to be reconsidered more frequently than under more stable conditions. The set of potential actions may also have to be adapted over time as conditions change. Models have to account for the non-stationarity of the modeled system processes. Each of the important sources of uncertainty in decision processes is expected to be exacerbated by SLR. We illustrate our ideas about adaptation of natural resource management to SLR by modeling a non-stationary system using a numerical example. We provide additional examples of an SDM approach for managing species that may be affected by SLR, with a focus on the endangered Florida manatee.

Florida

Spatial patch occupancy patterns of the Lower Keys marsh rabbit

Reliable estimates of presence or absence of a species can provide substantial information on management questions related to distribution and habitat use but should incorporate the probability of detection to reduce bias. We surveyed for the endangered Lower Keys marsh rabbit ( Sylvilagus palustris hefneri ) in habitat patches on 5 Florida Key islands, USA, to estimate occupancy and detection probabilities. We derived detection probabilities using spatial replication of plots and evaluated hypotheses that patch location (coastal or interior) and patch size influence occupancy and detection. Results demonstrate that detection probability, given rabbits were present, was <0.5 and suggest that naïve estimates (i.e., estimates without consideration of imperfect detection) of patch occupancy are negatively biased. We found that patch size and location influenced probability of occupancy but not detection. Our findings will be used by Refuge managers to evaluate population trends of Lower Keys marsh rabbits from historical data and to guide management decisions for species recovery. The sampling and analytical methods we used may be useful for researchers and managers of other endangered lagomorphs and cryptic or fossorial animals occupying diverse habitats.

Florida

An adaptive-management framework for optimal control of hiking near golden eagle nests in Denali National Park

Unintended effects of recreational activities in protected areas are of growing concern. We used an adaptive-management framework to develop guidelines for optimally managing hiking activities to maintain desired levels of territory occupancy and reproductive success of Golden Eagles (Aquila chrysaetos) in Denali National Park (Alaska, U.S.A.). The management decision was to restrict human access (hikers) to particular nesting territories to reduce disturbance. The management objective was to minimize restrictions on hikers while maintaining reproductive performance of eagles above some specified level. We based our decision analysis on predictive models of site occupancy of eagles developed using a combination of expert opinion and data collected from 93 eagle territories over 20 years. The best predictive model showed that restricting human access to eagle territories had little effect on occupancy dynamics. However, when considering important sources of uncertainty in the models, including environmental stochasticity, imperfect detection of hares on which eagles prey, and model uncertainty, restricting access of territories to hikers improved eagle reproduction substantially. An adaptive management framework such as ours may help reduce uncertainty of the effects of hiking activities on Golden Eagles

Alaska

Multispecies modeling for adaptive management of horseshoe crabs and red knots in the Delaware Bay

Adaptive management requires that predictive models be explicit and transparent to improve decisions by comparing management actions, directing further research and monitoring, and facilitating learning. The rufa subspecies of red knots ( Calidris canutus rufa ), which has recently exhibited steep population declines, relies on horseshoe crab ( Limulus polyphemus ) eggs as their primary food source during stopover in Delaware Bay during spring migration. We present a model with two different parameterizations for use in the adaptive management of horseshoe crab harvests in the Delaware Bay that links red knot mass gain, annual survival, and fecundity to horseshoe crab dynamics. The models reflect prevailing hypotheses regarding ecological links between these two species. When reported crab harvest from 1998 to 2008 was applied, projections corresponded to the observed red knot population abundances depending on strengths of the demographic relationship between these species. We compared different simulated horseshoe crab harvest strategies to evaluate whether, given this model, horseshoe crab harvest management can affect red knot conservation and found that restricting harvest can benefit red knot populations. Our model is the first to explicitly and quantitatively link these two species and will be used within an adaptive management framework to manage the Delaware Bay system and learn more about the specific nature of the linkage between the two species.

Delaware, New Jersey

Science, conservation, and camera traps

Biologists commonly perceive camera traps as a new tool that enables them to enter the hitherto secret world of wild animals. Camera traps are being used in a wide range of studies dealing with animal ecology, behavior, and conservation. Our intention in this volume is not to simply present the various uses of camera traps, but to focus on their use in the conduct of science and conservation. In this chapter, we provide an overview of these two broad classes of endeavor and sketch the manner in which camera traps are likely to be able to contribute to them. Our main point here is that neither photographs of individual animals, nor detection history data, nor parameter estimates generated from detection histories are the ultimate objective of a camera trap study directed at either science or management. Instead, the ultimate objectives are best viewed as either gaining an understanding of how ecological systems work (science) or trying to make wise decisions that move systems from less desirable to more desirable states (conservation, management). Therefore, we briefly describe here basic approaches to science and management, emphasizing the role of field data and associated analyses in these processes. We provide examples of ways in which camera trap data can inform science and management.

Book chapter

Estimating tiger abundance from camera trap data: Field surveys and analytical issues

Automated photography of tigers Panthera tigris for purely illustrative purposes was pioneered by British forester Fred Champion (1927, 1933) in India in the early part of the Twentieth Century. However, it was McDougal (1977) in Nepal who first used camera traps, equipped with single-lens reflex cameras activated by pressure pads, to identify individual tigers and study their social and predatory behaviors. These attempts involved a small number of expensive, cumbersome camera traps, and were not, in any formal sense, directed at “sampling” tiger populations.

Book chapter

Estimation of demographic parameters in a tiger population from long-term camera trap data

Chapter 7 (Karanth et al.) illustrated the use of camera trapping in combination with closed population capture–recapture (CR) models to estimate densities of tigers Panthera tigris. Such estimates can be very useful for investigating variation across space for a particular species (e.g., Karanth et al. 2004) or variation among species at a specific location. In addition, estimates of density continued at the same site(s) over multiple years are very useful for understanding and managing populations of large carnivores. Such multi-year studies can yield estimates of rates of change in abundance. Additionally, because the fates of marked individuals are tracked through time, biologists can delve deeper into factors driving changes in abundance such as rates of survival, recruitment and movement (Williams et al. 2002). Fortunately, modern CR approaches permit the modeling of populations that change between sampling occasions as a result of births, deaths, immigration and emigration (Pollock et al. 1990; Nichols 1992). Some of these early “open population” models focused on estimation of survival rates and, to a lesser extent, abundance, but more recent models permit estimation of recruitment and movement rates as well.

Book chapter