Quantifying Phylogenetic Beta Diversity: Distinguishing between ‘True’ Turnover of Lineages and Phylogenetic Diversity Gradients

David Mouillot,Camille Albouy,Fabien Leprieur,David R. Bellwood,Peter F. Cowman,Julien De Bortoli

doi:10.1371/journal.pone.0042760

Abstract

The evolutionary dissimilarity between communities (phylogenetic beta diversity PBD) has been increasingly explored by ecologists and biogeographers to assess the relative roles of ecological and evolutionary processes in structuring natural communities. Among PBD measures, the PhyloSor and UniFrac indices have been widely used to assess the level of turnover of lineages over geographical and environmental gradients. However, these indices can be considered as ‘broad-sense’ measures of phylogenetic turnover as they incorporate different aspects of differences in evolutionary history between communities that may be attributable to phylogenetic diversity gradients. In the present study, we extend an additive partitioning framework proposed for compositional beta diversity to PBD. Specifically, we decomposed the PhyloSor and UniFrac indices into two separate components accounting for ‘true’ phylogenetic turnover and phylogenetic diversity gradients, respectively. We illustrated the relevance of this framework using simple theoretical and archetypal examples, as well as an empirical study based on coral reef fish communities. Overall, our results suggest that using PhyloSor and UniFrac may greatly over-estimate the level of spatial turnover of lineages if the two compared communities show contrasting levels of phylogenetic diversity. We therefore recommend that future studies use the ‘true’ phylogenetic turnover component of these indices when the studied communities encompass a large phylogenetic diversity gradient.

Highlights

Phylogenies are increasingly used (i) to understand the origins and histories of species within a community, (ii) to assess the relative roles of environmental sorting, competitive exclusion and evolutionary and biogeographical processes in shaping community structure [1,2,3] (iii) to predict the level of ecosystem functioning [4] and the delivery of services [5], and (iv) to guide conservation prioritization [6,7]
The UniFrac index is expressed as the total branch length unique to each community relative to the total branch length linking all species in both communities and measures the proportion of evolutionary history unique to each community [12]
The present study participates to this emerging field of research called ‘‘ecophylogenetics’’ [48]

Summary

Introduction

Phylogenies are increasingly used (i) to understand the origins and histories of species within a community (i.e. alpha diversity), (ii) to assess the relative roles of environmental sorting, competitive exclusion and evolutionary and biogeographical processes in shaping community structure [1,2,3] (iii) to predict the level of ecosystem functioning [4] and the delivery of services [5], and (iv) to guide conservation prioritization [6,7] These arguments have recently been extended to phylogenetic beta diversity (PBD hereafter) that measures the phylogenetic dissimilarity among communities [8,9,10]. The UniFrac index is expressed as the total branch length unique to each community relative to the total branch length linking all species in both communities and measures the proportion of evolutionary history unique to each community [12]

Objectives

Conclusion