analyses have used a nomenclatural approach by focusing on species identities. However, the increasing availability of molecular phylogenies has renewed interest in using phylogenetic approaches to study the forces that influence patterns of biodiversity and biogeography [e.g., Chave et al. (2007)]. Because many species traits are generally conserved during the evolution of a lineage, one would expect a positive relationship between a measure of the phylogenetic relatedness of two species and a measure of their overall ecological similarity (phylogenetic niche conservatism) (Harvey and Pagel, 1991). As a result, analysis of the degree of phylogenetic relatedness of taxa found within and across communities should provide insight into the ecological and evolutionary processes that organize these communities.
Here, in an effort to assess the generality of elevational diversity patterns and the forces that structure these patterns, we quantified both plant and soil bacterial diversity patterns along an elevational gradient in the Colorado Rocky Mountains. A parsimonious hypothesis is that if the forces structuring biodiversity across the gradient are the same for bacteria and plants, then the resulting taxon and phylogenetic biogeographic patterns will be similar for both groups. Alternatively, if ecological and evolutionary processes along elevational gradients differ between the two groups (e.g., the taxa differ in their dispersal ability, response to environmental heterogeneity, interspecific interactions, or speciation rates), then we would expect them to be characterized by distinct patterns of diversity. To test these hypotheses, we adopted a multifaceted approach that examines diversity in the context of both ecological and evolutionary patterns. Therefore, in addition to the established convention of quantifying patterns of taxon richness and taxon turnover along the gradient [e.g., Whittaker (1960, 1967)], we examined several biodiversity measures that incorporate information about the phylogenetic structure, phylogenetic diversity, and phylogenetic turnover of plant and bacterial communities.
While the sampling methods and taxonomy used to quantify plant diversity are well established and standardized, microbial surveys vary greatly in their approach to characterizing diversity (Eisen, 2007). We determined the bacterial community composition of our soil samples by analyzing a PCR-amplified region of 16S ribosomal DNA, the most commonly used indicator of microbial biodiversity. Because bacteria are overwhelmingly diverse in soils, we chose PCR primers that narrowed our focal group to the phylum Acidobacteria. This subgroup of bacteria is diverse and ubiquitous in soils (Janssen, 2006) and thought to play an important role in biogeochemical cycling (Eichorst et al., 2007).