PT  - JOURNAL ARTICLE
AU  - Pedro Cardoso
AU  - Thomas Guillerme
AU  - Stefano Mammola
AU  - Thomas J. Matthews
AU  - Francois Rigal
AU  - Caio Graco-Roza
AU  - Gunilla Stahls
AU  - Jose Carlos Carvalho
TI  - Calculating functional diversity metrics using neighbor-joining trees
AID  - 10.1101/2022.11.27.518065
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.11.27.518065
4099  - http://biorxiv.org/content/early/2022/11/27/2022.11.27.518065.short
4100  - http://biorxiv.org/content/early/2022/11/27/2022.11.27.518065.full
AB  - The study of functional diversity (FD) provides ways to understand phenomena as complex as community assembly or the dynamics of biodiversity change under multiple pressures. Different frameworks are used to quantify FD, either based on dissimilarity matrices (e.g., Rao entropy, functional dendrograms) or multidimensional spaces (e.g. convex hulls, kernel-density hypervolumes). While the first does not enable the measurement of FD within a richness/divergence/regularity framework, or results in the distortion of the functional space, the latter does not allow for comparisons with phylogenetic diversity (PD) measures and can be extremely sensitive to outliers.We propose the use of neighbor-joining trees (NJ) to represent and quantify functional diversity in a way that combines the strengths of current FD frameworks without many of their weaknesses. Our proposal is also uniquely suited for studies that compare FD with PD, as both share the use of trees (NJ or others) and the same mathematical principles.We test the ability of this novel framework to represent the initial functional distances between species with minimal functional space distortion and sensitivity to outliers. The results using NJ are compared with conventional functional dendrograms, convex hulls, and kernel-density hypervolumes using both simulated and empirical datasets.Using NJ we demonstrate that it is possible to combine much of the flexibility provided by multidimensional spaces with the simplicity of tree-based representations. Moreover, the method is directly comparable with PD measures, and enables quantification of the richness, divergence and regularity of the functional space.Competing Interest StatementThe authors have declared no competing interest.