Journal ArticleDOI
Using multispecies occupancy models to improve the characterization and understanding of metacommunity structure
TLDR
A framework that integrates multispecies occupancy models with the current EMS framework, detection error-corrected EMS (DECEMS), which will lead to more accurate descriptions of metacommunity structure and to a greater understanding of the mechanisms by which different structures arise.Abstract:
Two of the most prominent frameworks to develop in ecology over the past decade are metacommunity ecology, which seeks to characterize multispecies distributions across space, and occupancy modeling, which corrects for imperfect detection in an effort to better understand species occurrence patterns. Although their goals are complementary, metacommunity theory and statistical occupancy modeling methods have developed independently. For instance, the elements of metacommunity structure (EMS) framework uses species occurrence data to classify metacommunity structure and link it to underlying environmental gradients. While the efficacy of this approach relies on the quality of the data, few studies have considered how imperfect detection, which is widespread in ecological surveys and the major focus of occupancy modeling, affects the outcome. We introduce a framework that integrates multispecies occupancy models with the current EMS framework, detection error-corrected EMS (DECEMS). This method offers two distinct advantages. First, DECEMS reduces bias in characterizing metacommunity structure by using repeated surveys and occupancy models to disentangle species-specific occupancy and detection probabilities, ultimately bringing metacommunity structure classification into a more probabilistic framework. Second, occupancy modeling allows estimation of species-specific responses to environmental covariates, which will increase our ability to link species-level effects to metacommunity-wide patterns. After reviewing the EMS framework, we introduce a simple multispecies occupancy model and show how DECEMS can work in practice, highlighting that detection error often causes EMS to assign incorrect structures. To emphasize the broader applicability of this approach, we further illustrate that DECEMS can reduce the rate of structure misclassification by more than 20% in some cases, even proving useful when detection error rates are quite low (-10%). Integrating occupancy models and the EMS framework will lead to more accurate descriptions of metacommunity structure and to a greater understanding of the mechanisms by which different structures arise.read more
Citations
More filters
Journal ArticleDOI
Modelling of species distributions, range dynamics and communities under imperfect detection: advances, challenges and opportunities
TL;DR: Modelling advances in imperfect detection of species distributions are summarized, evidence about effects of imperfect detection and the difficulties of working with it are discussed, and the current outlook for future research and application of these methods are concluded.
Journal ArticleDOI
The macroecology of infectious diseases: a new perspective on global-scale drivers of pathogen distributions and impacts
Patrick R. Stephens,Sonia Altizer,Katherine F. Smith,A. Alonso Aguirre,James H. Brown,Sarah A. Budischak,James E. Byers,Tad A. Dallas,T. Jonathan Davies,John M. Drake,Vanessa O. Ezenwa,Maxwell J. Farrell,John L. Gittleman,Barbara A. Han,Shan Huang,Rebecca A. Hutchinson,Pieter T. J. Johnson,Charles L. Nunn,David W. Onstad,Andrew W. Park,Gonzalo M. Vazquez-Prokopec,John Paul Schmidt,Robert Poulin +22 more
TL;DR: How the perspectives and tools of macroecology, a field that investigates patterns and processes at broad spatial, temporal and taxonomic scales, are expanding scientific understanding of global infectious disease ecology is considered.
Journal ArticleDOI
Model selection and assessment for multi-species occupancy models
TL;DR: Several different contemporary Bayesian hierarchical approaches for checking and validating multi-species occupancy models are examined and applied to a freshwater aquatic study system in Colorado, USA, to better understand the diversity and distributions of plains fishes.
Journal ArticleDOI
Predicting cryptic links in host-parasite networks.
TL;DR: This work develops an algorithm to predict missing links in networks based on conditional probability estimation and associated, node-level features, and validates this algorithm on simulated data, and then applies it to a desert small mammal host-parasite network.
Journal ArticleDOI
A two-species occupancy model accommodating simultaneous spatial and interspecific dependence.
Christopher T. Rota,Christopher K. Wikle,Roland Kays,Tavis Forrester,William J. McShea,Arielle W. Parsons,Joshua J. Millspaugh +6 more
TL;DR: A two-species occupancy model that accommodates both interspecific and spatial dependence is proposed and a point-referenced multivariate hierarchical spatial model is used to account for both spatial and interspecific dependence.
References
More filters
Journal ArticleDOI
The metacommunity concept: a framework for multi-scale community ecology
Mathew A. Leibold,Marcel Holyoak,Nicolas Mouquet,Nicolas Mouquet,Priyanga Amarasekare,Jonathan M. Chase,Martha F. Hoopes,Robert D. Holt,Jonathan B. Shurin,Richard Law,David Tilman,Michel Loreau,Andrew Gonzalez +12 more
TL;DR: This framework is used to discuss why the metacommunity concept is useful in modifying existing ecological thinking and illustrate this with a number of both theoretical and empirical examples.
Journal ArticleDOI
Estimating site occupancy rates when detection probabilities are less than one
Darryl I. MacKenzie,James D. Nichols,Gideon B. Lachman,Sam Droege,J. Andrew Royle,Catherine A. Langtimm +5 more
TL;DR: In this paper, a model and likelihood-based method for estimating site occupancy rates when detection probabilities are 0.3 was proposed for American toads (Bufo americanus) and spring peepers (Pseudacris crucifer).
Journal ArticleDOI
The Individualistic Concept of the Plant Association
TL;DR: The units of vegetation, which form the subject of our discussions this week, were just as easily visible to primitive man as they are to us today as discussed by the authors. But they were neglected by scientists, whose thoughts were turned in different directions, but they were recognized by -the laity.
Journal ArticleDOI
Null model analysis of species co-occurrence patterns
TL;DR: The analysis of presence-absence matrices with null model randomization tests has been a major source of controversy in community ecology for over two decades as mentioned in this paper, and the performance of nine null model algorithms and four co-occurrence indices with respect to Type I and Type II errors has been systematically compared.