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Inference of demography and selection from human gut commensal microbiota

Nandita Garud, UCLA
Tuesday October 8, 12-1pm
Zoom Link:听
In Person: 550 Sherbrooke, Room 189

Abstract:听Despite the importance of gut commensal microbiota to human health, there is little knowledge about their evolutionary histories, including their population demographic histories, their distributions of fitness effects (DFE) of new mutations, or targets of adaptation. Here, we infer the demographic histories, DFEs and selective sweeps from ~30 of the most highly prevalent and abundant commensal gut microbial species in North Americans over timescales exceeding human generations using a collection of lineages inferred from a panel of healthy hosts. We find some species in North American microbiomes display contractions in population size and others expansions, potentially occurring at several key historical moments in human history such as the agriculture revolution. DFEs across species vary from highly to mildly deleterious, with DFEs tending to be more congruent within genera versus between, reflective of underlying phylogenetic relationships. Finally, we discover pervasive selective sweeps across human gut microbiomes, including at key genesinvolved in the metabolism of maltodextrin, a synthetic starch that has recently become a widespread component of Western diets. In sum, we demonstrate that critical selective and demographic events over the course of human history have had a significant impact on genetic variation in the human gut microbiome.