the angiosperm phylogenic tree topology was constructed by using the widely accepted supertree approach (Webb and Donoghue, 2005), and branch lengths were assigned based on estimates of the minimum age of internal nodes (see Materials and Methods). Comparative analyses using molecular approaches alone for both plants and microbes would improve our confidence in such phylogenetic comparisons. Such approaches will be facilitated in the future by increased accessibility to molecular data.
Microorganisms (especially prokaryotes) are very diverse in soils (Torsvik et al., 1990; Janssen, 2006). On par with most microbial diversity studies, it is likely that we sampled the most abundant taxa in each soil core along the elevational gradient. Sampling effort (i.e., the proportion of a community that is sampled) is known to significantly influence taxonomic biodiversity patterns (Plotkin et al., 2002; Woodcock et al., 2006; Green and Plotkin, 2007; Morlon et al., 2008). To our knowledge the influence of sampling effort on phylogenetic biodiversity patterns has not been explored. For example, estimators are available to predict the taxon richness (Hughes et al., 2001) and taxon similarity (Chao et al.,