Dos and don'ts when inferring assembly rules from diversity patterns

Abstract

Aim: More than ever, ecologists seek to understand how species are distributed and have assembled into communities using the "filtering framework". This framework is based on the hypothesis that local assemblages result from a series of abiotic and biotic filters applied to regional species pools and that these filters leave predictable signals in observed diversity patterns. In theory, statistical comparisons of expected and observed patterns enable data-driven tests of assembly processes. However, so far this framework has fallen short in delivering generalizable conclusions, challenging whether (and how) diversity patterns can be used to characterize and understand underlying assembly processes better.Methods: By synthesizing the previously raised critiques and suggested solutions in a comprehensive way, we identify 10 pitfalls that can lead to flawed interpretations of α-diversity patterns, summarize solutions developed to circumvent these pitfalls and provide general guidelines. Results:We find that most issues arise from an overly simplistic view of potential processes that influence diversity patterns, which is often motivated by practical constraints on study design, focal scale and methodology. We outline solutions for each pitfall, such as methods spanning over spatial, environmental or phylogenetic scales, and suggest guidelines for best scientific practices in community ecology.

The contribution of the edaphic factor as a driver of recent plant diversification in a Mediterranean biodiversity hotspot

“…We relied on the RPE metric to identify centres of recent in situ diversification (neoendemism, low RPE) of Iberian plant species and their environmental correlates. It could be argued that low RPE values may also be the result of phylogenetic clustering due to habitat filtering based on phylogenetically conserved traits adapted to particular environmental conditions (Gerhold et al., 2015; Münkemüller et al., 2020; Webb et al., 2002) or coexistence of close relatives with conserved niches but small performance differences (Mayfield & Levine, 2010). However, we assume that the identified environmental factors are related to recent diversification for several reasons.…”

Unravelling the small‐island effect through phylogenetic community ecology

“…These different situations have been interpreted as being indicative of different community assembly processes (e.g. habitat filtering resulting in clustered patterns; see Münkemüller et al, 2020, for a review).…”

A dimmer shade of pale: revealing the faint signature of local assembly processes on the structure of strongly filtered plant communities

“…Independence Co-occurrence Convergence Divergence Convergence Divergence Convergence Divergence Seed mass 4 0 3 0 3 1 Leaf thickness 4 1 4 2 1 1 Vegetative height 0 0 5 0 4 1 LDMC 1 1 3 1 3 3 92 mechanisms in structuring plant communities has been relatively successful at relatively large spatial and/or environmental scales (Götzenberger et al 2012, HilleRisLambers et al 2012. However, the picture is more imprecise when examining community assembly at very large spatial scales (Münkemüller et al 2020) or, on the contrary, when the focus is set on the local communities of a unique type of vegetation (Götzenberger et al 2012). Our study shows that by using a hierarchical combination of increasingly complex null models, it is possible to unravel the faint signal of processes affecting local community assembly after the sieving action of the strong primary abiotic filters that sort out the regional species pool (Keddy 1992, Pärtel et al 2011.…”