Concepts and applications in functional diversity

1. The use of functional diversity analyses in ecology has grown exponentially over the past two decades, broadening our understanding of biological diversity and its change across space and time. Virtually all ecological sub-disciplines recognise the critical value of looking at species and communities from a functional perspective, and this has led to a proliferation of methods for estimating contrasting dimensions of functional diversity.

2. Differences between these methods and their development generated terminological inconsistencies and confusion about the selection of the most appropriate approach for addressing any particular ecological question, hampering the potential for comparative studies, simulation exercises and meta-analyses.

3. Two general mathematical frameworks for estimating functional diversity are prevailing: those based on dissimilarity matrices (e.g. Rao entropy, functional dendrograms) and those relying on multidimensional spaces, constructed as either convex hulls or probabilistic hypervolumes.

4. We review these frameworks, discuss their strengths and weaknesses and provide an overview of the main R packages performing these calculations. In parallel, we propose a way for organising functional diversity metrics in a unified scheme to quantify the richness, divergence and regularity of species or individuals under each framework. This overview offers a roadmap for confidently approaching functional diversity analyses both theoretically and practically.