Phylogenetic scale matters: Assessment of bacterial community structure at broad phylogenetic scales obscures fine-scale patterns of clustering and overdispersion
Phylogenetic community ecology hinges on the concept of niche conservatism, where organisms that are more closely related are, on average, functionally more similar than expected by chance. As microbial ecologists collect even more sequence data from their field sites, there has been a shift in focus from natural history-based identification of different communities to teasing out the ecological processes driving microbial community structure. The incorporation of phylogeny into microbial community analyses has opened the door to assessing the potential influence of habitat filtering and competition on microbial community structure. Numerous studies use phylogenetic patterns of microbes to infer ecological processes shaping community structure. However, in many cases, the default phylogenetic resolution of these analyses is often far too broad for valid interpretation. The primary objective of our study was to understand the influence of phylogenetic scale and tree topology on degree of overdispersion of microbial taxa. Phylogenies were estimated using Practical Alignment using SATé and TrAnsitivity (PASTA; Mirarab et al 2014) on bacterial OTUs, defined and clustered at 97% sequence similarity. We employed nodesig, NRI, and NTI in the program Phylocom (v. 4.2; Webb et al 2002) to assess the degree of overdispersion and/or clustering through phylogenetic tree space.
We found an asymptotically positive relationship between phylogenetic scale and both NRI and NTI values. At broad phylogenetic scales, such as the domain and phylum levels, we find overwhelming evidence of phylogenetic clustering. In contrast, at finer scales, approximately corresponding to the order, family and genus levels, overdispersion is the prevailing phylogenetic pattern. Not surprisingly, if niche conservatism holds to some extent, we expect competition to be most influential at fine phylogenetic scales, where as clustering patterns might be expected at larger scales. Tree topology influenced phylogenetic structural changes at broader scales, likely due to more unresolved nodes at the broader phylum levels of the bacterial phylogeny. Our results highlight the importance of phylogenetic scale when identifying patterns of microbial community structure.