Journal article
Rarefaction and extrapolation with beta diversity under a framework of Hill numbers: The iNEXT.beta3D standardization
Ecological Monographs, Vol.93(4), pp.1-32
2023
Abstract
Based on sampling data, we propose a rigorous standardization method to measure and compare beta diversity across datasets. Here beta diversity, which quantifies the extent of among-assemblage differentiation, relies on Whittaker's original multiplicative decomposition scheme, but we use Hill numbers for any diversity order q ≥ 0. Richness-based beta diversity (q = 0) quantifies the extent of species identity shift, whereas abundance-based (q > 0) beta diversity also quantifies the extent of difference among assemblages in species abundance. We adopt and define the assumptions of a statistical sampling-model as the foundation for our approach, treating sampling data as a representative sample taken from an assemblage. The approach makes a clear distinction between the theoretical assemblage level (unknown properties/parameters of the assemblage) and the sampling data level (empirical/observed statistics computed from data). At the assemblage level, beta diversity for N assemblages reflects the interacting effect of the species abundance distribution and spatial/temporal aggregation of individuals in the assemblage. At the data level, observed beta (= gamma/alpha) diversity depends not only on among-assemblage differentiation but also on sampling effort/completeness, which in turn induces dependence of beta on alpha and gamma diversity. How to remove the dependence of richness-based beta diversity on its gamma component (species pool) has been intensely debated. Our approach is to standardize gamma and alpha based on sample coverage (an objective measure of sample completeness). For a single assemblage, the iNEXT method was developed, through interpolation (rarefaction) and extrapolation with Hill numbers, to standardize samples by sampling effort/completeness. Here we adapt the iNEXT standardization to alpha and gamma diversity, i.e., alpha and gamma diversity are both assessed at the same level of sample coverage, to formulate standardized, coverage-based beta diversity. This extension of iNEXT to beta diversity required the development of novel concepts and theories, including a formal proof and empirical demonstration that the resulting standardized beta diversity removes the dependence of beta diversity on both gamma and alpha values, and thus reflects the pure among-assemblage differentiation. The proposed standardization is illustrated with spatial, temporal and spatio-temporal datasets, while the freeware iNEXT.beta3D facilitates all computations and graphics.
Details
- Title
- Rarefaction and extrapolation with beta diversity under a framework of Hill numbers: The iNEXT.beta3D standardization
- Authors
- Anne Lien Ju Chao (Corresponding Author) - National Tsing Hua UniversitySimon Thorn (Author) - Czech Academy of SciencesChun-Huo Chiu (Author) - National Taiwan UniversityFaye Moyes (Author) - University of St AndrewsKai-Hsiang Hu (Author) - National Tsing Hua UniversityRobin Chazdon (Author) - University of the Sunshine Coast, Queensland, Tropical Forests & People Research CentreJessie Wu (Author) - National Tsing Hua UniversityLuiz Fernando S. Magnago (Author) - Universidade Federal do Sul da BahiaMaria Dornelas (Author) - University of St AndrewsDavid Zelený (Author) - National Taiwan UniversityRobert K Colwell (Author) - University of ConnecticutAnne E. Magurran (Author) - University of St Andrews
- Publication details
- Ecological Monographs, Vol.93(4), pp.1-32
- Publisher
- John Wiley & Sons, Inc.
- DOI
- 10.1002/ecm.1588
- ISSN
- 1557-7015
- Grant note
- NERC-MOST 108-2923-M-007-003 and NE/T004487/1 / Natural Environment Research Council RPG-2019-402 / Leverhulme Trust NSF DEB0424767, NSF DEB-0639393 and NSF DEB-1147429 / US National Science Foundation RC-2018-021 / Leverhulme Trust 307984/2022-2 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
- Organisation Unit
- University of the Sunshine Coast, Queensland; Tropical Forests & People Research Centre; Forest Research Institute
- Language
- English
- Record Identifier
- 99743097302621
- Output Type
- Journal article
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