Cospeciation and genome evolution in the diverse yet conserved turtle ant gut microbiome

Turtle ants, of the genus Cephalotes, host a diverse community of symbiotic bacteria within their digestive systems. The members of the core community span 9 orders, with additional diversity at lower taxonomical levels. While our understanding of how these bacteria may be benefiting the ant has grown, the evolutionary histories of these symbionts is not well understood. Here, we present work focusing on how these symbionts have evolved to become core members of the Cephalotes gut community. Using a genomic approach made possible by the successful isolation and culturing of many core symbionts as well as metagenomic binning, we have inferred the phylogenetic relationships between the symbionts and their closest relatives. We show that the degree of congruence between symbiont phylogeny and Cephalotes host phylogeny differs between different symbionts, reflecting a disparity in transmission fidelity among symbionts living within the same community, despite a single hypothesized mode of transmission. With an ancestral state reconstruction approach, we show that reductions in symbiont genome size have commonly occurred since entering the turtle ant microbiome some 40+ million years ago. Changes in genome content have been impacted by a combination of gene loss and horizontal gene transfer, shaping several likely nutritive functions of these gut bacteria. These results begin to illustrate the diverse evolutionary histories of this conserved gut microbiome, leading to questions about how this symbiotic relationship has affected the biology of both host and symbionts.