2) Phylogenetic diversity
To ensure that the species names matched the Angiosperm Phylogeny Group
III (APG III, 2009), the Plant List
(http://www.theplantlist.org/)
database was used to proof read the 351 species names in the plots. Then
we generated a phylogenetic tree with branch length for the 337 species
using the online program Phylomatic 3
(http://phylodiversity.net/phylomatic/)
(Appendix S2), based on the phylogeny of Zanne (2014) which was
generated using sequence data of seven gene regions available in
GenBank, as well as fossil data. To represent different components
(richness, evenness and divergence) of phylogenetic diversity, we
calculated three indices as follows. Phylogenetic species variability
(PSV) quantifies how phylogenetic relatedness decreases the variance of
a hypothetical trait shared by all species in a community, and is used
here as a metric for divergence (Helmus et al. 2007; Potter &
Woodall 2014). Phylogenetic species richness (PSR) is calculated as the
number of species in a community multiplied by the community’s PSV.
Phylogenetic species evenness (PSE), on the other hand, is the metric of
PSV modified to incorporate relative species abundances (Helmus et
al. 2007). All phylogenetic diversity indices are calculated using the
R package “picante” (Kembel et al. 2010).