FIG. 4.
Examples of phylogenetic trees depicting patterns of relationships that would result in the four possible results from the two tests of differentiation discussed in this paper. The open and solid squares represent different communities, and the trees are drawn with branch lengths proportional to the amounts of sequence evolution. Clear differentiation is evident if both FST and P tests are significant. By contrast, insignificance for both tests implies that the samples from two communities are drawn from the same pool of sequences. A significant FST test coupled with an insignificant P test implies that the tree contains several clades of closely related bacteria that are unique to one community or the other but that these clades are interspersed throughout the phylogenetic tree of all samples. Finally, a significant P test coupled with an insignificant FST test might reflect the existence of highly divergent lineages within each community (such that the within-community diversity approaches the total diversity) but indicate that there is significant covariation between community and phylogeny.