betapart: an R package for the study of beta diversity

TLDR

Beta diversity, the variation in species composition among sites, arises from species replacement (turnover) and species loss (nestedness). The authors present betapart, an R package that computes total dissimilarity (Sørensen or Jaccard) and its turnover and nestedness components. betapart enables spatial and temporal beta‑diversity analyses by providing multiple‑site and pairwise dissimilarity measures that account for compositional heterogeneity and multivariate structure, and by computing turnover and nestedness components over time. Example analyses show that separating turnover and nestedness components clarifies the mechanisms driving biodiversity patterns. Summary 1.

Abstract

Summary 1. Beta diversity, that is, the variation in species composition among sites, can be the result of species replacement between sites (turnover) and species loss from site to site (nestedness). 2. We present betapart , an R package for computing total dissimilarity as Sørensen or Jaccard indices, as well as their respective turnover and nestedness components. 3. betapart allows the assessment of spatial patterns of beta diversity using multiple‐site dissimilarity measures accounting for compositional heterogeneity across several sites or pairwise measures providing distance matrices accounting for the multivariate structure of dissimilarity. 4. betapart also allows computing patterns of temporal difference in assemblage composition, and its turnover and nestedness components. 5. Several example analyses are shown, using the data included in the package, to illustrate the relevance of separating the turnover and nestedness components of beta diversity to infer different mechanisms behind biodiversity patterns.