TITLE: “Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history”
ABSTRACT: Despite the importance of gut commensal microbiota to human health, there is little knowledge about their evolutionary histories, including their demographic histories and distributions of fitness effects (DFE) of mutations. Here, we infer the demographic histories and DFEs for amino-acid changing mutations of 27 of the most prevalent and abundant commensal gut microbial species in North Americans over timescales exceeding human generations. We find reductions in genetic variation in North American versus African rural microbiomes. Additionally, some species in North American microbiomes display contractions in population size and others expansions, potentially occurring at several key historical moments in human history. DFEs across species vary from highly to mildly deleterious, with accessory genes experiencing more drift compared to core genes. Within genera, DFEs tend to be more congruent, reflective of underlying phylogenetic relationships. Together, these findings suggest that gut microbes have distinct evolutionary histories, possibly reflecting their unique roles.
