Using coverage-based rarefaction to infer non-random species distributions

Abstract

1. Biodiversity is non-randomly distributed in space and understanding how spatial structure of species diversity responds to ecological, biogeographic and anthropogenic drivers is one of the major quests of modern ecology. However, metrics of community differentiation such as Whittaker's beta-diversity fail to unambiguously capture species turnover when they are compared across assemblages with changing species pool sizes, species abundance distributions and numbers of individuals. This is due to an effect of changing sample completeness.2. Here, we propose a method that combines the benefits of individual-based and coverage based rarefaction to standardize beta-diversity estimates by sample completeness at the gamma-scale. We test the performance of our metric, ߚ , using simulations of spatially explicit communities that change both species pool size and intraspecific spatial aggregation. Additionally, we re-analyse the "Gentry" plot dataset to investigate patterns of tree beta-diversity along a latitudinal gradient. 2 3. We find that our metric, ߚ , captures changes in intraspecific aggregation independent of changes in the species pool size, while Whittaker's beta-diversity and standardized estimates based on the number of individuals respond to species pool size as well as spatial aggregation. Our coverage-based estimates of beta-diversity do not exhibit a latitudinal pattern in the empirical tree dataset. 4. Our simulations show that coverage-based standardization of beta-diversity offers a powerful tool for the unraveling of spatial and compositional biodiversity change. Potential applications of the approach range from a better description of basic biogeographic diversity patterns to the consolidation of local and regional diversity trends in the current biodiversity crisis.

Geographical homogenization but little net change in the local richness of Canadian butterflies

“…In a similar vein, variation in sampling effort can also affect measurements of beta diversity, because communities with different completeness may show spurious differentiation owing to imperfect detection (i.e., proportion of unseen species in each community) even if there is no true dissimilarity (Engel et al., 2021). As such, traditional beta diversity metrics (such as Sørensen’s or Jaccard’s) can underestimate true similarity between plots (see Chao et al., 2005); this is especially problematic in incidence‐based metrics that are sensitive to the occurrence of rare species (Beck et al., 2013).…”

“…In a similar vein, variation in sampling effort can also affect measurements of beta diversity, because communities with different completeness may show spurious differentiation owing to imperfect detection (i.e., proportion of unseen species in each community) even if there is no true dissimilarity (Engel et al, 2021).…”

A conceptual guide to measuring species diversity

“…Using a range of Hill diversities, including richness, may help ecologists refine hypotheses and models of biodiversity response to scale and global change, which local richness alone can, famously, fail to illustrate clearly (Chase and Knight 2013, Cardinale et al 2018). When coverage and Hill diversity are used together, they should enable ecologists to separate patterns in relative abundances from patterns in total abundance, address artefacts of sampling completeness at different scales (Kraft et al 2011, Engel et al 2020), and develop richer hypotheses about patterns in species abundances over space and time (McGill et al 2007).…”

Universal drivers of cheese microbiomes

“… 39 PRJNA476316 180 82,455 81,258 75,293 DNA Yes NA NA 38.2 Serrano, Cerrado, Araxa, Colonial, Curd, CampodasVertentes, Serro, Canastra, Cerrado, Caipira, CampodasVertentes, Cerrado, Caipira, Butter, Marajo, Curd, Cow Brazil Yes Engel et al. 40 PRJNA499132 43 278,760 278,576 233,882 DNA No NA NA 33.1 Brie, Cheddar, Jarlsburg, Gruyere Cow Canada Yes Chao et al. 41 PRJNA523139 97 24,883 24,056 24,003 DNA Yes 5.2 NA 13.6 Camembert; Reblochon Cow France Yes McMurdie et al.…”