Estimating occupancy dynamics for large-scale monitoring networks

Amphibian breeding occupancy across protected areas in the northeast United States

David Andrew Miller, Evan H.Campbell Grant

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

Regional monitoring strategies frequently employ a nested sampling design where a finite set of study areas from throughout a region are selected and intensive sampling occurs within a subset of sites within the individual study areas. This sampling protocol naturally lends itself to a hierarchical analysis to account for dependence among subsamples. Implementing such an analysis using a classic likelihood framework is computationally challenging when accounting for detection errors in species occurrence models. Bayesian methods offer an alternative approach for fitting models that readily allows for spatial structure to be incorporated. We demonstrate a general approach for estimating occupancy when data come from a nested sampling design. We analyzed data from a regional monitoring program of wood frogs (Lithobates sylvaticus) and spotted salamanders (Ambystoma maculatum) in vernal pools using static and dynamic occupancy models. We analyzed observations from 2004 to 2013 that were collected within 14 protected areas located throughout the northeast United States. We use the data set to estimate trends in occupancy at both the regional and individual protected area levels. We show that occupancy at the regional level was relatively stable for both species. However, substantial variation occurred among study areas, with some populations declining and some increasing for both species. In addition, When the hierarchical study design is not accounted for, one would conclude stronger support for latitudinal gradient in trends than when using our approach that accounts for the nested design. In contrast to the model that does not account for nesting, the nested model did not include an effect of latitude in the 95% credible interval. These results shed light on the range-level population status of these pond-breeding amphibians, and our approach provides a framework that can be used to examine drivers of local and regional occurrence dynamics.

Original languageEnglish (US)
Pages (from-to)4735-4746
Number of pages12
JournalEcology and Evolution
Volume5
Issue number21
DOIs
StatePublished - Jan 1 2015

Fingerprint

amphibian
amphibians
protected area
conservation areas
breeding
monitoring
sampling
vernal pools
Ambystoma
Bayesian theory
ephemeral pool
salamanders and newts
dynamic models
species occurrence
latitudinal gradient
frog
experimental design
pond
monitoring network
Rana sylvatica

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Ecology
  • Nature and Landscape Conservation

Cite this

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abstract = "Regional monitoring strategies frequently employ a nested sampling design where a finite set of study areas from throughout a region are selected and intensive sampling occurs within a subset of sites within the individual study areas. This sampling protocol naturally lends itself to a hierarchical analysis to account for dependence among subsamples. Implementing such an analysis using a classic likelihood framework is computationally challenging when accounting for detection errors in species occurrence models. Bayesian methods offer an alternative approach for fitting models that readily allows for spatial structure to be incorporated. We demonstrate a general approach for estimating occupancy when data come from a nested sampling design. We analyzed data from a regional monitoring program of wood frogs (Lithobates sylvaticus) and spotted salamanders (Ambystoma maculatum) in vernal pools using static and dynamic occupancy models. We analyzed observations from 2004 to 2013 that were collected within 14 protected areas located throughout the northeast United States. We use the data set to estimate trends in occupancy at both the regional and individual protected area levels. We show that occupancy at the regional level was relatively stable for both species. However, substantial variation occurred among study areas, with some populations declining and some increasing for both species. In addition, When the hierarchical study design is not accounted for, one would conclude stronger support for latitudinal gradient in trends than when using our approach that accounts for the nested design. In contrast to the model that does not account for nesting, the nested model did not include an effect of latitude in the 95{\%} credible interval. These results shed light on the range-level population status of these pond-breeding amphibians, and our approach provides a framework that can be used to examine drivers of local and regional occurrence dynamics.",
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Estimating occupancy dynamics for large-scale monitoring networks : Amphibian breeding occupancy across protected areas in the northeast United States. / Miller, David Andrew; Grant, Evan H.Campbell.

In: Ecology and Evolution, Vol. 5, No. 21, 01.01.2015, p. 4735-4746.

Research output: Contribution to journalArticle

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