2.3. Phylogenetic diversity dimensions and metrics

We applied the framework of Tucker et al. (2017) and selected three leading metrics describing three phylogenetic diversity dimensions: richness, divergence, and regularity (Table 1). Faith's PD (Faith, 1992) describes the amount of evolutionary history across species (sum of branch lengths) and is a leading measure of phylogenetic richness. Mean phylogenetic distance between each pair of species (MPD; Webb et al., 2002) is a leading measure of phylogenetic divergence. Variation of pairwise phylogenetic distances between each pair of species (VPD; Clarke & Warwick, 2001) is a leading measure of phylogenetic regularity (lower variation indicates higher regularity). We also identified species richness in each plot.

According to Vellend et al. (2011), one can distinguish two qualitatively different types of phylogenetic diversity indices. Faith's PD, MPD, and VPD are type II metrics which are calculated using a subset phylogeny of a focal subset of species (e.g., a vegetation plot). Type I indices are based on the whole species pool phylogeny; each species has its distinctness score calculated. These scores are then used to calculate a phylogenetic diversity measure of a plot (for example, summed evolutionary distinctiveness; Redding & Mooers, 2006). However, type I indices are highly correlated with Faith's PD (Vellend et al., 2011), suggesting they are closely related to the phylogenetic richness dimension, and so we did not consider them. We calculated indices using functions (pd and mpd) from the picante package (Kembel et al., 2010). To compute VPD, we modified the mpd function to calculate the variation of pairwise phylogenetic distances (not the mean as in the original function). All metrics were abundance weighted by percentage cover. To calculate abundance‐weighted Faith's PD (Barker, 2002), we used the R function of Swenson (2014).