A unified theory of biodiversity and biogeography should be founded upon a synthetic framework relevant to all domains of life. The extraordinary abundance and diversity of Bacteria and Archaea on Earth suggest that microorganisms will play a prominent role in the advancement of such a biodiversity theory. Although the empirical data needed to inform and test biodiversity theory is accruing at a rapid pace, our understanding of microbial biodiversity is substantially lacking in comparison to that of plants and animals. Exploring the microbial world is challenged by the narrow window through which its overwhelming diversity is observed, and understanding how microbial communities assemble is challenged by the difficulty, for microbes, to test ecological hypotheses in the field. To help overcome these issues, we develop theory, investigating the effect of sampling on observed biodiversity patterns, and analyzing phylogenetic structure to infer ecological processes. We focus on one of the most widely studied biogeography patterns in ecology: the decay of community similarity with distance. We propose an approach for incorporating evolutionary history in distance-decay analyses and apply this approach to examine an elevational diversity gradient for plants and microbes.

Results/Conclusions Our results suggest that the distance-decay relationship should be robust to sampling only the most abundant species in a community, but sensitive to the grain at which communities are sampled, and that the compositional and phylogenetic structure of micro- and macroorganism communities along elevational gradients are fundamentally different. We discuss these results in the context of advancing biodiversity theory.