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

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 alpha-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. Among key future challenges are the integration of mechanistic modelling and multi-trophic interactions. Main conclusions Our conclusion is that the filtering framework still holds promise, but only if researchers successfully navigate major pitfalls, foster the integration of mechanistic modelling and multi-trophic interactions and directly account for uncertainty in their conclusions.