Modeling species occurrence dynamics with multiple states and imperfect detection.

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.

[1]  James D. Nichols,et al.  Monitoring of biological diversity in space and time , 2001 .

[2]  R. Swihart,et al.  Absent or undetected? Effects of non-detection of species occurrence on wildlife-habitat models , 2004 .

[3]  Carl D. Shapiro,et al.  Adaptive management: The U.S. Department of the Interior technical guide , 2009 .

[4]  J. Andrew Royle,et al.  A GENERAL CLASS OF MULTINOMIAL MIXTURE MODELS FOR ANURAN CALLING SURVEY DATA , 2005 .

[5]  David R. Anderson,et al.  Breeding Dispersal In the California Spotted Owl , 2006 .

[6]  J. Dupuis.  Bayesian estimation of movement and survival probabilities from capture-recapture data , 1995 .

[7]  H. Pulliam,et al.  Sources, Sinks, and Population Regulation , 1988, The American Naturalist.

[8]  J. Nichols,et al.  Monitoring for conservation. , 2006, Trends in ecology & evolution.

[9]  H. Possingham,et al.  IMPROVING PRECISION AND REDUCING BIAS IN BIOLOGICAL SURVEYS: ESTIMATING FALSE‐NEGATIVE ERROR RATES , 2003 .

[10]  J. D. Lebreton,et al.  Multistate recapture models: Modelling incomplete individual histories , 2002 .

[11]  M. Seamans,et al.  HABITAT SELECTION IN A CHANGING ENVIRONMENT: THE RELATIONSHIP BETWEEN HABITAT ALTERATION AND SPOTTED OWL TERRITORY OCCUPANCY AND BREEDING DISPERSAL , 2007 .

[12]  J. Nichols,et al.  ESTIMATING SITE OCCUPANCY, COLONIZATION, AND LOCAL EXTINCTION WHEN A SPECIES IS DETECTED IMPERFECTLY , 2003 .

[13]  M. Seamans,et al.  Spotted owl demography in the central Sierra Nevada , 2001 .

[14]  Darryl I. MacKenzie,et al.  Flexible hierarchical mark-recapture modeling for open populations using WinBUGS , 2009, Environmental and Ecological Statistics.

[15]  James T. Peterson,et al.  Occupancy Estimation and Modeling Darryl I. MacKenzie James D. Nichols J. Andrew Royle Kenneth H. Pollock Larissa L. Bailey James E. Hines , 2006 .

[16]  J. Andrew Royle.  Modeling Abundance Index Data from Anuran Calling Surveys , 2004 .

[17]  Linda A. Weir,et al.  North American Amphibian Monitoring Program (NAAMP) , 2005 .

[18]  P. Holgate,et al.  Matrix Population Models. , 1990 .

[19]  J. Andrew Royle,et al.  A Bayesian state-space formulation of dynamic occupancy models. , 2007, Ecology.

[20]  David R. Anderson,et al.  CLIMATE, HABITAT QUALITY, AND FITNESS IN NORTHERN SPOTTED OWL POPULATIONS IN NORTHWESTERN CALIFORNIA , 2000 .

[21]  Atte Moilanen,et al.  Implications of empirical data quality to metapopulation model parameter estimation and application , 2002 .

[22]  Julien Martin,et al.  Perturbation analysis for patch occupancy dynamics. , 2009, Ecology.

[23]  GARY C. WHITE,et al.  Multistate Survival Models and Their Extensions in Program MARK , 2006 .

[24]  J. Andrew Royle,et al.  Estimating species richness and accumulation by modeling species occurrence and detectability. , 2006, Ecology.

[25]  M. Conroy,et al.  Analysis and Management of Animal Populations , 2002 .

[26]  Michael G. Anderson,et al.  Ecology and Management of Breeding Waterfowl , 1992 .

[27]  James D. Nichols,et al.  Population dynamics of breeding waterfowl , 1992 .

[28]  J. Nichols,et al.  Occupancy estimation and modeling with multiple states and state uncertainty. , 2007, Ecology.

[29]  M. Seamans,et al.  Sources of variability in spotted owl population growth rate: testing predictions using long-term mark–recapture data , 2007, Oecologia.

[30]  P H Harvey,et al.  THE NATAL AND BREEDING DISPERSAL OF BIRDS , 1982 .

[31]  J. Nichols,et al.  The Role of Local Populations within a Landscape Context: Defining and Classifying Sources and Sinks , 2006, The American Naturalist.