Dynamics of bacterial recombination in the human gut microbiome

Horizontal gene transfer is a ubiquitous force in microbial evolution. Previous studies have shown that the human gut is a hot spot for gene transfer between species. However, the more subtle exchange of DNA within species, better known as "recombination," is less well characterized in this ecosystem. Rates of recombination are often inferred using parametric approaches that leverage simple null models from population genetics. These models often omit key factors like natural selection and population structure, which can alter signatures of recombination among contemporary DNA sequences. In this talk, we will show how the broad range of timescales within the human gut microbiota provides new opportunities to measure individual recombination events directly, leveraging nonparametric approaches that require minimal population genetic assumptions. These methods enable quantitative comparisons of recombination across a range of phylogenetically diverse species, which highlight general regions of "phase space" that could benefit from future theoretical exploration.