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DiRenzo GV, Miller DAW, Hossack BR, Sigafus BH, Howell PE, Muths E, Grant EHC. Accommodating the role of site memory in dynamic species distribution models. Ecology 2021; 102:e03315. [PMID: 33630306 DOI: 10.1002/ecy.3315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/16/2020] [Accepted: 12/06/2020] [Indexed: 11/09/2022]
Abstract
First-order dynamic occupancy models (FODOMs) are a class of state-space model in which the true state (occurrence) is observed imperfectly. An important assumption of FODOMs is that site dynamics only depend on the current state and that variations in dynamic processes are adequately captured with covariates or random effects. However, it is often difficult to understand and/or measure the covariates that generate ecological data, which are typically spatiotemporally correlated. Consequently, the non-independent error structure of correlated data causes underestimation of parameter uncertainty and poor ecological inference. Here, we extend the FODOM framework with a second-order Markov process to accommodate site memory when covariates are not available. Our modeling framework can be used to make reliable inference about site occupancy, colonization, extinction, turnover, and detection probabilities. We present a series of simulations to illustrate the data requirements and model performance. We then applied our modeling framework to 13 yr of data from an amphibian community in southern Arizona, USA. In this analysis, we found residual temporal autocorrelation of population processes for most species, even after accounting for long-term drought dynamics. Our approach represents a valuable advance in obtaining inference on population dynamics, especially as they relate to metapopulations.
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Affiliation(s)
- Graziella V DiRenzo
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, 16802, USA.,U.S. Geological Survey, Patuxent Wildlife Research Center, 1 Migratory Way, Turners Falls, Massachusetts, 01376, USA
| | - David A W Miller
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Blake R Hossack
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Missoula, Montana, 59812, USA.,Wildlife Biology Program, W.A. Franke College of Forestry and Conservation, University of Montana, Missoula, Montana, 59812, USA
| | - Brent H Sigafus
- U.S. Geological Survey, Southwest Biological Science Center, 520 N. Park Avenue, Tucson, Arizona, 85719, USA
| | - Paige E Howell
- U.S. Geological Survey, Patuxent Wildlife Research Center, 12311 Beech Forest Road, Laurel, Maryland, 20708, USA
| | - Erin Muths
- U.S. Geological Survey, 2150 Centre Avenue Building C, Fort Collins, Colorado, 80526, USA
| | - Evan H C Grant
- U.S. Geological Survey, Patuxent Wildlife Research Center, 1 Migratory Way, Turners Falls, Massachusetts, 01376, USA
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DiRenzo GV, Che-Castaldo C, Rugenski A, Brenes R, Whiles MR, Pringle CM, Kilham SS, Lips KR. Disassembly of a tadpole community by a multi-host fungal pathogen with limited evidence of recovery. Ecol Appl 2017; 27:309-320. [PMID: 28052493 DOI: 10.1002/eap.1443] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/28/2016] [Accepted: 08/24/2016] [Indexed: 06/06/2023]
Abstract
Emerging infectious diseases can cause host community disassembly, but the mechanisms driving the order of species declines and extirpations following a disease outbreak are unclear. We documented the community disassembly of a Neotropical tadpole community during a chytridiomycosis outbreak, triggered by the generalist fungal pathogen, Batrachochytrium dendrobatidis (Bd). Within the first 11 months of Bd arrival, tadpole density and occupancy rapidly declined. Species rarity, in terms of tadpole occupancy and adult relative abundance, did not predict the odds of tadpole occupancy declines. But species losses were taxonomically selective, with glassfrogs (Family: Centrolenidae) disappearing the fastest and tree frogs (Family: Hylidae) and dart-poison frogs (Family: Dendrobatidae) remaining the longest. We detected biotic homogenization of tadpole communities, with post-decline communities resembling one another more strongly than pre-decline communities. The entire tadpole community was extirpated within 22 months following Bd arrival, and we found limited signs of recovery within 10 years post-outbreak. Because of imperfect species detection inherent to sampling species-rich tropical communities and the difficulty of devising a single study design protocol to sample physically complex tropical habitats, we used simulations to provide recommendations for future surveys to adequately sample diverse Neotropical communities. Our unique data set on tadpole community composition before and after Bd arrival is a valuable baseline for assessing amphibian recovery. Our results are of direct relevance to conservation managers and community ecologists interested in understanding the timing, magnitude, and consequences of disease outbreaks as emerging infectious diseases spread globally.
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Affiliation(s)
- Graziella V DiRenzo
- Department of Biology, University of Maryland, College Park, Maryland, 20744, USA
| | | | - Amanda Rugenski
- School of Life Sciences, Arizona State University, Tempe, Arizona, 85281, USA
| | - Roberto Brenes
- Department of Biology, Carroll University, Waukesha, Wisconsin, 53186, USA
| | - Matt R Whiles
- Department of Zoology and Center for Ecology, Southern Illinois University, Carbondale, Illinois, 62901, USA
| | | | - Susan S Kilham
- Department of Biodiversity, Earth and Environmental Science, Drexel University, Philadelphia, Pennsylvania, 19104, USA
| | - Karen R Lips
- Department of Biology, University of Maryland, College Park, Maryland, 20744, USA
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