sampling dates with the aim of sampling each community at the same relative phenological time point. Any individuals that could not be identified to species or differentiated from known species were excluded from the analysis. This affected between 10% and 15% of the possible species at each site. We used version R20031202 of Phylomatic to construct a tree topology consisting of all of the angiosperms identified in all our quadrats, based on the Angiosperm Phylogeny Group (APG) II backbone (Angiosperm Phylogeny Group II, 2003; Webb and Donoghue, 2005) and used results from recent plant cladistics studies to resolve polytomies (Worberg et al., 2007; Winkworth et al., 2008). The final tree we used for our analyses was almost completely resolved to the family level. We assigned branch lengths to the tree by using the Phylocom module BLADJ to constrain the internal nodes with available age estimates (Wikstrom et al., 2001) and interpolated the other nodes for which direct age estimates are not available.
We define the term community as all phylotypes originating from a single soil core (bacteria) or species identified in a single quadrat (plants). Taxon richness within each community was quantified as the total number of species or phylotypes within that community. Phylogenetic diversity within each community was quantified as the minimum total branch length connecting all species within the community to the root of the phylogenetic tree (Faith, 1992b). Phylogenetic diversity was calculated by using the pd module within Phylocom-3.40 (by C. O. Webb, D. D. Ackerly, and S. W. Kemble; available at http://phylodiversity.net/phylocom/). We used a rarefaction sampling approach to account for the unequal sample sizes of each microbial community (number of clones) by calculating the mean of the taxon richness and phylogenetic diversity of 1,000 randomized subsamples of each community. Each community was subsampled by the number of clones in the smallest library (75 clones).
Using the classical NRI and NTI (Webb, 2000; Webb et al., 2002), we measured the extent to which co-occurring species in a community are phylogenetically related compared with what is expected by chance. With both indices, the phylogenetic structure of the observed community was compared to a null expectation obtained by randomly sampling the pool of all of the species identified in the study 1,000 times, while constraining both the number of taxa in the community and species occurrence across