Decoupling phylogenetic and functional diversity toreveal hidden signals in community assembly

Abstract

Functional traits and phylogeny offer different, and often complementary, information about ecological dif-ferences between species, an essential step to uncover biodiversity assembly mechanisms and their feedbacks toecosystem functions. However, traits and phylogeny areoftenrelatedduetounderlying trait evolution. Conse-quently, when combined, their shared information can be overemphasized, hindering their complementarity. It istherefore desirable to decouple their unique and overlapping contributions.2.We propose a conceptual and mathematical framework that produces a set of meaningful measures of ecolog-ical differences between species.3.We test the properties of these measures and the validity of the approach with extensive simulated data toshow (i) the information provided by decoupling traits from phylogeny and vice versa, and (ii) that decouplingtrait and phylogenetic information can uncover otherwise hidden signals underlying species coexistence and turn-over. The application of the approachis further illustrated using a large dataset of Central European meadowsas a case study.4.Decoupling traits and phylogeny particularly reveals the importance of differentiation between phylogeneti-cally related species, which can be essential to understand species replacements along environmental gradientsand the combined action of environmental filtering and limiting similarity within communities.5.Decoupling traits and phylogeny provides an avenue for connecting macro-evolutionary and local factorsaffecting coexistence and for understanding how complex species differences affect multiple ecosystem functions.We present an R function called ‘decouple’, which allows a simple and wide application of the framework.