We followed the classic approach to intertaxonomic diversity analysis by comparing patterns of species richness and phylotype richness of plants and bacteria, respectively, along the gradient. We also quantified the phylogenetic diversity of every sampled community by calculating the sum of the branch length in a phylogeny that connects all species in a community and the root (Faith, 1992b). Phylogenetic diversity is more inclusive than a simple count of species or types, in that it quantifies the evolutionary history of a group of taxa (Vane-Wright et al., 1991). Conservation biologists are interested in preserving phylogenetic diversity, as this is fundamental to maximizing evolutionary options for the future (Faith, 1994; Myers and Knoll, 2001; Sechrest et al., 2002; Forest et al., 2007). Phylogenetic diversity is also believed to correspond to “feature diversity,” meaning the number of evolutionarily derived traits within a biological community (Faith, 1992b).

In addition to measuring phylogenetic diversity, we quantified community phylogenetic structure along the gradient by using two commonly used metrics: a mean pairwise distance metric sensitive to phylogeny-wide patterns [net relatedness index (NRI)] and a nearest-taxon-based measure sensitive to patterns at the “tips” of the phylogeny [nearest taxon index (NTI)] (Webb et al., 2002). The degree of phylogenetic relatedness quantified by these metrics provides insight into drivers of community assembly. Assuming phylogenetic niche conservatism, phylogenetic clustering within a local assemblage is considered consistent with the hypothesis that selective filters (e.g., environmental conditions) cause local assemblages to comprise closely related taxa (Webb et al., 2002). Phylogenetic overdispersion, on the other hand, can be explained by two possible biotic interactions: competition (Webb et al., 2002) or facilitation (Lortie, 2007; Valiente-Banuet and Verdu, 2007). In the case of competition, more closely related species are hypothesized to compete more strongly with one another. This results in competitive exclusion, which leads to a community of distantly related species. In the case of facilitation, facilitator species are hypothesized to create microhabitats that permit distantly related species adapted to different environments to persist within a local assemblage.

In addition to considering patterns in the diversity and phylogenetic structure within communities along the elevation gradient (alphadiversity), we investigated how community composition changes across a landscape (beta-diversity). Ecologists have long recognized that beta-diversity is important for understanding the biodiversity of montane ecosystems (Jaccard, 1912; Whittaker, 1960; Harte et al., 1999; Brehm et al., 2003; Mena and Vazequez-Dominguez, 2005). We examined beta-diversity in terms of compositional similarity, defined as the fraction of taxa shared between two samples (Sørensen index), and phylogenetic