Article A Generalized Framework for Analyzing Taxonomic, Phylogenetic, and Functional Community Structure Based on Presence–Absence Data János Podani 1,2,*, Sandrine Pavoine 3 and Carlo Ricotta 4 1 Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös University, H-1117 Budapest, Hungary 2 MTA-ELTE-MTM Ecology Research Group, Eötvös University, H-1117 Budapest, Hungary 3 Centre d'Ecologie et des Sciences de la Conservation (CESCO), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, 75005 Paris, France ;
[email protected] 4 Department of Environmental Biology, University of Rome ‘La Sapienza’, 00185 Rome, Italy;
[email protected] * Correspondence:
[email protected] Received: 17 October 2018; Accepted: 6 November 2018; Published: 12 November 2018 Abstract: Community structure as summarized by presence–absence data is often evaluated via diversity measures by incorporating taxonomic, phylogenetic and functional information on the constituting species. Most commonly, various dissimilarity coefficients are used to express these aspects simultaneously such that the results are not comparable due to the lack of common conceptual basis behind index definitions. A new framework is needed which allows such comparisons, thus facilitating evaluation of the importance of the three sources of extra information in relation to conventional species-based representations. We define taxonomic, phylogenetic and functional beta diversity of species assemblages based on the generalized Jaccard dissimilarity index. This coefficient does not give equal weight to species, because traditional site dissimilarities are lowered by taking into account the taxonomic, phylogenetic or functional similarity of differential species in one site to the species in the other. These, together with the traditional, taxon- (species-) based beta diversity are decomposed into two additive fractions, one due to taxonomic, phylogenetic or functional excess and the other to replacement.