Estimating occupancy dynamics for large-scale monitoring networks: Amphibian breeding occupancy across protected areas in the northeast United States

Ecology and Evolution

Volumn 5, Issue 21, 2015, Pages 4735-4746

  Miller, David A W ^a   Grant, Evan H Campbell ^b  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b PATUXENT WILDLIFE RESEARCH CENTER   (United States)

Author keywords

Ambystoma maculatum; Hierarchical models; Luthobates sylvaticus; Occupancy; Population trend

Indexed keywords

EID: 84946477453     PISSN: None     EISSN: 20457758     Source Type: Journal    
DOI: 10.1002/ece3.1679     Document Type: Article

References (45)

1. Adams, M. J., D. A. W. Miller, E. Muths, P. S. Corn, E. H. C. Grant, L. L. Bailey, et al. 2013. Trends in Amphibian Occupancy in the United States (ed HYH Chen). PLoS One 8:e64347.
2. Berven, K. 1990. Factors affecting population fluctuations in larval and adult stages of the wood frog (Rana sylvatica). Ecology 71:1599-1608.
3. Bolker, B. M., M. E. Brooks, C. J. Clark, S. W. Geange, J. R. Poulsen, M. H. H. Stevens, et al. 2009. Generalized linear mixed models: a practical guide for ecology and evolution. Trends Ecol. Evol. 24:127-135.
4. Brooks, R. T. 2004. Weather-related effects on woodland vernal pool hydrology and hydroperiod. Wetlands 24:104-114.
5. Cam, E., W. A. Link, E. G. Cooch, J.-Y. Monnat, and E. Danchin. 2002. Individual covariation in life-history traits: seeing the trees despite the forest. Am. Nat. 159:96-105.
6. Chelgren, N. D., M. J. Adams, L. L. Bailey, and R. B. Bury. 2011. Using multilevel spatial models to understand salamander site occupancy patterns after wildfire. Ecology 92:408-421.
7. Colburn, E. A. 2004. Vernal pools: natural history and conservation. McDonald & Woodward Pub Co., Blacksburg, Virginia.
8. Cubaynes, S., C. Doutrelant, A. Grégoire, P. Perret, B. Faivre, and O. Gimenez. 2012. Testing hypotheses in evolutionary ecology with imperfect detection: capture-recapture structural equation modeling. Ecology 93:248-255.
9. Denwood, M. J. 2008. Runjags: run Bayesian MCMC models in the BUGS syntax from within R. R package version 9.
10. Dorazio, R. M., and J. A. Royle. 2005. Estimating Size and Composition of Biological Communities by Modeling the Occurrence of Species. J. Am. Stat. Assoc. 100:389-398.
11. Dorazio, R. M., J. A. Royle, B. Söderström, and A. Glimskär. 2006. Estimating species richness and accumulation by modeling species occurrence and detectability. Ecology 87:842-854.
12. Ford, J. H., M. V. Bravington, and J. Robbins. 2012. Incorporating individual variability into mark-recapture models. Methods Ecol. Evol. 3:1047-1054.
13. Gelman, A., and J. Hill. 2006. Data analysis using regression and multilevel/hierarchical models. Cambridge Univ. Press, Cambridge, Massachusetts.
14. Gibbs, J., K. Whiteleather, and F. Schueler. 2005. Changes in frog and toad populations over 30 years in New York State. Ecol. Appl. 15:1148-1157.
15. Gimenez, O., T. Anker-Nilssen, and V. Grosbois. 2012. Exploring causal pathways in demographic parameter variation: path analysis of mark-recapture data. Methods Ecol. Evol. 3:427-432.
16. Grant, E. H. C., E. F. Zipkin, J. D. Nichols, and J. P. Campbell. 2013. A strategy for monitoring and managing declines in an amphibian community. Conserv. Biol., 27:1245-1253.
17. Hooten, M. B., and N. T. Hobbs. 2015. A guide to Bayesian model selection for ecologists. Ecol. Monogr., 85:3-28. 140521113529001.
18. Johnson, D. S., P. B. Conn, M. B. Hooten, J. C. Ray, and B. A. Pond. 2013. Spatial occupancy models for large data sets. Ecology 94:801-808.
19. Kéry, M., and J. Royle. 2008. Hierarchical Bayes estimation of species richness and occupancy in spatially replicated surveys. J. Appl. Ecol. 45:589-598.
20. Kéry, M., and M. Schaub. 2012. Bayesian population analysis using WinBUGS: a hierarchical perspective. Academic Press, San Diego.
21. King, R., S. P. Brooks, B. J. T. Morgan, and T. Coulson. 2006. Factors influencing soay sheep survival: a Bayesian analysis. Biometrics 62:211-220.
22. King, R., B. J. T. Morgan, O. Gimenez, and S. P. Brooks. 2010. Bayesian analysis for population ecology. CRC Press, Boca Raton.
23. Lannoo, M. J. 2005. Amphibian declines: the conservation status of United States species. University of California Press, Berkeley.
24. MacKenzie, D., J. Nichols, G. Lachman, S. Droege, J. A. Royle, and C. Langtimm. 2002. Estimating site occupancy rates when detection probabilities are less than one. Ecology 83:2248-2255.
25. MacKenzie, D., J. Nichols, and J. Hines. 2003. Estimating site occupancy, colonization, and local extinction when a species is detected imperfectly. Ecology 84:2200-2207.
26. MacKenzie, D. I., J. D. Nichols, J. A. Royle, K. H. Pollock, L. L. Bailey, and J. E. Hines. 2006. Occupancy estimation and modeling: inferring patterns and dynamics of species occurrence. Academic Press, New York.
27. McClintock, B. T., J. D. Nichols, L. L. Bailey, D. I. MacKenzie, W. L. Kendall, and A. B. Franklin. 2010. Seeking a second opinion: uncertainty in disease ecology. Ecol. Lett. 13:659-674.
28. Miller, D. A. W., B. L. Talley, K. R. Lips, and E. H. Campbell Grant. 2012. Estimating patterns and drivers of infection prevalence and intensity when detection is imperfect and sampling error occurs. Methods Ecol. Evol. 3:850-859.
29. Mordecai, R. S., B. J. Mattsson, C. J. Tzilkowski, and R. J. Cooper. 2011. Addressing challenges when studying mobile or episodic species: hierarchical Bayes estimation of occupancy and use. J. Appl. Ecol. 48:56-66.
30. Nichols, J., L. Bailey, A. F. O'Connell, N. W. Talancy, E. H. C. Grant, A. T. Gilbert, et al. 2008. Multi-scale occupancy estimation and modelling using multiple detection methods. J. Appl. Ecol. 45:1321-1329.
31. Pechmann, J. H. K., D. E. Scott, R. D. Semlitsch, J. Cadwell, L. Vitt, and J. Gibbons. 1991. Declining amphibian populations: the problem of separating human impacts from natural fluctuations. Science 253:892-895.
32. Petranka, J. W., E. M. Harp, C. T. Holbrook, and J. A. Hamel. 2007. Long-term persistence of amphibian populations in a restored wetland complex. Biol. Conserv. 138:371-380.
33. Plummer, M. 2003. JAGS: a program for analysis of Bayesian graphical models using Gibbs sampling. in K. Hornik, F. Leisch and A. Zeileis, eds. Proceedings of the 3rd International Workshop on Distributed Statistical Computing. Vienna, Austria.
34. R Core Team. 2012. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
35. Royle, J. A., and R. M. Dorazio. 2008. Hierarchical modeling and inference in ecology: the analysis of data from populations, metapopulations and communities. Academic Press, New York.
36. Royle, J. A., and M. Kéry. 2007. A Bayesian state-space formulation of dynamic occupancy models. Ecology 88:1813-1823.
37. Rubbo, M. J., and J. M. Kiesecker. 2005. Amphibian Breeding Distribution in an Urbanized Landscape. Conserv. Biol. 19:504-511.
38. Schwarz, C. 2002. Real and quasi-experiments in capture-recapture studies. J. Appl. Stat. 29:459-473.
39. Stuart, S., J. Chanson, N. Cox, B. Young, A. Rodrigues, D. Fischman, et al. 2004. Status and Trends of Amphibian Declines and Extinctions Worldwide. Science 306:1783-1786.
40. Trenham, P., W. Koenig, M. Mossman, S. Stark, and L. Jagger. 2003. Regional dynamics of wetland-breeding frogs and toads: turnover and synchrony. Ecol. Appl. 13:1522-1532.
41. Van Meter, R., L. L. Bailey, E. H. C. Grant, B. County, M. Estuarine, and E. Sciences. 2008. Methods for estimating the amount of vernal pool habitat in the northeastern United States. Wetlands 28:585-593.
42. Wake, D. 1991. Declining amphibian populations. Science 253:860.
43. Williams, B. K., J. D. Nichols, and M. J. Conroy. 2002. Analysis and management of animal populations: modeling, estimation, and decision making. Academic Press, New York.
44. Zipkin, E. F., A. DeWan, and J. Andrew Royle. 2009. Impacts of forest fragmentation on species richness: a hierarchical approach to community modelling. J. Appl. Ecol. 46:815-822.
45. Zipkin, E. F., E. H. C. Grant, and W. F. Fagan. 2012. Evaluating the predictive abilities of community occupancy models using AUC while accounting for imperfect detection. Ecol. Appl. 22:1962-1972.