Limited codiversification of the gut microbiota with humans

Gut bacteria exhibit striking variation across different human populations, but the evolutionary forces that have shaped this diversity are less well understood. Recent work has argued that many species of gut bacteria have codiversified with modern humans, based on the phylogenetic correlations between human and microbial genomes. Here we reanalyze these data and show that the correlations between human and microbial phylogenies are often substantially weaker than between unlinked human chromosomes, and that similar correlations can arise through geographic structure alone. These results suggest that traditional codiversification has been limited in recent human history, and highlight alternative strategies for quantifying the extent of human-microbe coevolution.