Data from: Stability and phylogenetic correlation in gut microbiota: lessons from ants and apes

Correlation between gut microbiota and host phylogeny could reflect codiversification over shared evolutionary history, or a selective environment that is more similar in related hosts. These alternatives imply substantial differences in the relationship between host and symbiont, but can they be distinguished based on patterns in the community data themselves? Here, we explore patterns of phylogenetic correlation in the distribution of gut bacteria among species of turtle ants (genus Cephalotes), which host a dense gut microbial community. We use 16S rRNA pyrosequencing from 25 Cephalotes species to show that their gut community is remarkably stable, from the colony to the genus level. Despite this overall similarity, the existing differences among species’ microbiota significantly correlate with host phylogeny. We introduce a novel analytical technique to test whether these phylogenetic correlations are derived from recent bacterial evolution, as would be expected in the case of codiversification, or from broader shifts more likely to reflect environmental filters imposed by factors like diet or habitat. We also test this technique on a published dataset of ape microbiota, confirming earlier results while revealing previously undescribed patterns of phylogenetic correlation. Our results indicate a high degree of partner fidelity in the Cephalotes microbiota, suggesting that vertical transmission of the entire community could play an important role in the evolution and maintenance of the association. As additional comparative microbiota data become available, the techniques presented here can be used to explore trends in the evolution of host-associated microbial communities.