Influence of tree shape and evolutionary time‐scale on phylogenetic diversity metrics

Abstract

During the last decades, describing, analysing and understanding the phylogenetic structure of species assemblages has been a central theme in both community ecology and macro-ecology. Among the wide variety of phylogenetic structure metrics, three have been predominant in the literature: Faith's phylogenetic diversity (PD), which represents the sum of the branch lengths of the phylogenetic tree linking all species of a particular assemblage, the mean pairwise distance between all species in an assemblage (MPD) and the pairwise distance between the closest relatives in an assemblage (MNTD). Comparisons between studies using one or several of these metrics are difficult because there has been no comprehensive evaluation of the phylogenetic properties each metric captures. In particular it is unknown how PD relates to MDP and MNTD. Consequently, it is possible that apparently opposing patterns in different studies might simply reflect differences in metric properties. Here, we aim to fill this gap by comparing these metrics using simulations and empirical data. We first used simulation experiments to test the influence of community structure and size on the mismatch between metrics whilst varying the shape and size of the phylogenetic tree of the species pool. Second we investigated the mismatch between metrics for two empirical datasets (gut microbes and global carnivoran assemblages). We show that MNTD and PD provide similar information on phylogenetic structure, and respond similarly to variation in species richness and assemblage structure. However, MPD demonstrate a very different behaviour, and is highly sensitive to deep branching structure. We suggest that by combining complementary metrics that are sensitive to processes operating at different phylogenetic depths (i.e. MPD and MNTD or PD) we can obtain a better understanding of assemblage structure.

Habitat filtering not dispersal limitation shapes oceanic island floras: species assembly of the Galápagos archipelago

“…), and the greater sensitivity of SES.PD to more terminal structure makes it better suited for exploring assembly processes working at finer temporal and spatial scales (Mazel et al . ). To examine the importance of speciation in driving archipelago phylogenetic structure, we recalculated each metric excluding species that were endemic to the Galápagos (156 species considered here) under the assumption that endemic species are more likely to be the products of in situ speciation.…”

Agricultural land‐use history causes persistent loss of plant phylogenetic diversity

“…We standardized phylogenetic diversity in this way for three reasons: (1) to explore changes in phylogenetic diversity that were independent of species richness, (2) to produce a metric with the same units as phylogenetic diversity (millions of years) for ease of interpretation, and (3) because it had a nearly 1:1 relationship ( r > 0.999, N = 108, P < 0.001) with the standardized effect size calculation used in other studies (Mazel et al. ). We determined expected phylogenetic diversity using the “pdmoments” function in the PhyloMeasures package (Tsirogiannis and Sandel ).…”

“…We also calculated MNTD effect size because it is commonly used in other studies; however, we only include it in the supplemental materials because it was strongly correlated with standardized phylogenetic diversity (Mazel et al. ).…”

Plant species richness across the Himalaya driven by evolutionary history and current climate

“…We used PDI as a measure of phylogenetic richness. Because NRI measures phylogenetic relatedness across the whole phylogeny under question (i.e., based on mean pairwise distance) whereas PDI is a tip-weighted phylogenetic index (Mazel et al 2016) and mean family age does not account for age variation among genera within a family, our main analyses were based on NRI. The mean family age of each assemblage was calculated as the sum of family ages of all species in the assemblage divided by the number of species in the assemblage.…”