James Nichols, Ph.D.
Dr. Jim Nichols conducts research on animal population dynamics and management
Recent Accomplishments
Education
- B.S. Wake Forest University, Biology, 1971
- M.S. Louisiana State University, Wildlife Management, 1973
- Ph.D. Michigan State University, Wildlife Ecology, 1976
Professional Studies/Experience
- Adaptive management and assessment of habitat changes on migratory birds
- Development of models of mallard population dynamics for adaptive harvest management
- Development of methods to estimate parameters associated with animal population dynamics
- Statistical methods for species richness estimation
- Technical Assistance -Tiger Monitoring and Population Research
- Development of methods for estimating patch occupancy and patch-dynamic parameters from detection-nondetection survey data
- Development of methods to estimate species richness and community-dynamic parameters from species list data
Mentorship/Outreach
Professional societies/affiliations/committees/editorial boardsScientific/Oral Presentations, Abstracts
Honors, awards, recognition, elected offices
- 2005 - U.S. Presidential Rank Award (Meritorious Senior Professional)
- 2004 - U.S. Geological Survey Meritorious Service Award
- 2004 - IFAS Scholar Award, University of Florida
- 1998 - Promoted to Senior Scientist, U.S. Geological Survey
- 1991 - The George W. Snedecor Award of the American Statistical Association
- 1991 - The Wildlife Society's Wildlife Publication Award for Monograph
- 1984 - Southeastern Section of the Wildlife Society, Outstanding Publication Award
Scientific/Oral Presentations, Abstracts
Science and Products
Filter Total Items: 417
Joint estimation of habitat dynamics and species interactions: Disturbance reduces co-occurrence of non-native predators with an endangered toad 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...
Authors
David A.W. Miller, Cheryl S. Brehme, James E. Hines, James D. Nichols, Robert N. Fisher
Neighborhood and habitat effects on vital rates: expansion of the Barred Owl in the Oregon Coast Ranges 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...
Authors
Charles B. Yackulic, Janice Reid, Raymond Davis, James E. Hines, James D. Nichols, Eric Forsman
Modeling habitat dynamics accounting for possible misclassification 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...
Authors
Sophie Veran, Kevin J. Kleiner, Remi Choquet, Jaime Collazo, James D. Nichols
Evidence, models, conservation programs and limits to management Evidence, models, conservation programs and limits to management
Walsh et al. (2012) emphasized the importance of obtaining evidence to assess the effects of management actions on state variables relevant to objectives of conservation programs. They focused on malleefowl Leipoa ocellata, ground-dwelling Australian megapodes listed as vulnerable. They noted that although fox Vulpes vulpes baiting is the main management action used in malleefowl...
Authors
J.D. Nichols
Likelihood analysis of species occurrence probability from presence-only data for modelling species distributions 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...
Authors
J. Andrew Royle, Richard B. Chandler, Charles Yackulic, James D. Nichols
Studying biodiversity: is a new paradigm really needed? 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...
Authors
James D. Nichols, Evan G. Cooch, Jonathan M. Nichols, John R. Sauer
The U.S. Geological Survey Ecosystem Science Strategy, 2012-2022 - Advancing discovery and application through collaboration 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...
Authors
Byron K. Williams, G. Lynn Wingard, Gary Brewer, James E. Cloern, Guy R. Gelfenbaum, Robert B. Jacobson, Jeffrey L. Kershner, Anthony D. McGuire, James D. Nichols, Carl D. Shapiro, Charles van Riper, Robin P. White
Density estimation in tiger populations: combining information for strong inference 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...
Authors
Arjun M. Gopalaswamy, J. Andrew Royle, Mohan Delampady, James D. Nichols, K. Ullas Karanth, David W. Macdonald
On valuing patches: Estimating contributions to metapopulation growth with reverse-time capture-recapture modelling On valuing patches: Estimating contributions to metapopulation growth with reverse-time capture-recapture modelling
Metapopulation ecology has historically been rich in theory, yet analytical approaches for inferring demographic relationships among local populations have been few. We show how reverse-time multi-state capture–recapture models can be used to estimate the importance of local recruitment and interpopulation dispersal to metapopulation growth. We use ‘contribution metrics’ to infer...
Authors
J.S. Sanderlin, P.M. Waser, J.E. Hines, J.D. Nichols
Spatial patch occupancy patterns of the Lower Keys marsh rabbit 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...
Authors
Mitchell J. Eaton, Phillip T. Hughes, James D. Nichols, Anne Morkill, Chad Anderson
Augmenting superpopulation capture-recapture models with population assignment data Augmenting superpopulation capture-recapture models with population assignment data
Ecologists applying capture-recapture models to animal populations sometimes have access to additional information about individuals' populations of origin (e.g., information about genetics, stable isotopes, etc.). Tests that assign an individual's genotype to its most likely source population are increasingly used. Here we show how to augment a superpopulation capture-recapture model...
Authors
Zhi Wen, Kenneth Pollock, James Nichols, Peter Waser
Structured decision making as a proactive approach to dealing with sea level rise in Florida 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...
Authors
J. Martin, P.L. Fackler, James D. Nichols, B. C. Lubow, Mitchell J. Eaton, Michael C. Runge, Bradley Stith, Catherine A. Langtimm
Science and Products
Filter Total Items: 417
Joint estimation of habitat dynamics and species interactions: Disturbance reduces co-occurrence of non-native predators with an endangered toad 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...
Authors
David A.W. Miller, Cheryl S. Brehme, James E. Hines, James D. Nichols, Robert N. Fisher
Neighborhood and habitat effects on vital rates: expansion of the Barred Owl in the Oregon Coast Ranges 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...
Authors
Charles B. Yackulic, Janice Reid, Raymond Davis, James E. Hines, James D. Nichols, Eric Forsman
Modeling habitat dynamics accounting for possible misclassification 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...
Authors
Sophie Veran, Kevin J. Kleiner, Remi Choquet, Jaime Collazo, James D. Nichols
Evidence, models, conservation programs and limits to management Evidence, models, conservation programs and limits to management
Walsh et al. (2012) emphasized the importance of obtaining evidence to assess the effects of management actions on state variables relevant to objectives of conservation programs. They focused on malleefowl Leipoa ocellata, ground-dwelling Australian megapodes listed as vulnerable. They noted that although fox Vulpes vulpes baiting is the main management action used in malleefowl...
Authors
J.D. Nichols
Likelihood analysis of species occurrence probability from presence-only data for modelling species distributions 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...
Authors
J. Andrew Royle, Richard B. Chandler, Charles Yackulic, James D. Nichols
Studying biodiversity: is a new paradigm really needed? 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...
Authors
James D. Nichols, Evan G. Cooch, Jonathan M. Nichols, John R. Sauer
The U.S. Geological Survey Ecosystem Science Strategy, 2012-2022 - Advancing discovery and application through collaboration 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...
Authors
Byron K. Williams, G. Lynn Wingard, Gary Brewer, James E. Cloern, Guy R. Gelfenbaum, Robert B. Jacobson, Jeffrey L. Kershner, Anthony D. McGuire, James D. Nichols, Carl D. Shapiro, Charles van Riper, Robin P. White
Density estimation in tiger populations: combining information for strong inference 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...
Authors
Arjun M. Gopalaswamy, J. Andrew Royle, Mohan Delampady, James D. Nichols, K. Ullas Karanth, David W. Macdonald
On valuing patches: Estimating contributions to metapopulation growth with reverse-time capture-recapture modelling On valuing patches: Estimating contributions to metapopulation growth with reverse-time capture-recapture modelling
Metapopulation ecology has historically been rich in theory, yet analytical approaches for inferring demographic relationships among local populations have been few. We show how reverse-time multi-state capture–recapture models can be used to estimate the importance of local recruitment and interpopulation dispersal to metapopulation growth. We use ‘contribution metrics’ to infer...
Authors
J.S. Sanderlin, P.M. Waser, J.E. Hines, J.D. Nichols
Spatial patch occupancy patterns of the Lower Keys marsh rabbit 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...
Authors
Mitchell J. Eaton, Phillip T. Hughes, James D. Nichols, Anne Morkill, Chad Anderson
Augmenting superpopulation capture-recapture models with population assignment data Augmenting superpopulation capture-recapture models with population assignment data
Ecologists applying capture-recapture models to animal populations sometimes have access to additional information about individuals' populations of origin (e.g., information about genetics, stable isotopes, etc.). Tests that assign an individual's genotype to its most likely source population are increasingly used. Here we show how to augment a superpopulation capture-recapture model...
Authors
Zhi Wen, Kenneth Pollock, James Nichols, Peter Waser
Structured decision making as a proactive approach to dealing with sea level rise in Florida 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...
Authors
J. Martin, P.L. Fackler, James D. Nichols, B. C. Lubow, Mitchell J. Eaton, Michael C. Runge, Bradley Stith, Catherine A. Langtimm