title: Gene flow in microbial communities could explain unexpected patterns of synonymous variation in theEscherichia colicore genome.
abstract: Researchers contest the importance of gene flow in bacterial core genomes, as traditionalists view microbes as predominantly clonal, asexually reproducing organisms. Contrary to the traditional perspective,Escherichia colicore genes vary greatly in their levels of synonymous genetic diversity. This observation indicates that the relative importance of evolutionary forces such as mutation, selection, and recombination varies from gene to gene. In this paper, I highlight why the synonymous diversity observation is broadly relevant to researchers interested in the evolutionary dynamics of microbial populations and communities. I explain how a model of evolution called the coalescent relates neutral diversity (i.e. mutations with negligible fitness effects) to mutation rates, evolutionary time, and a parameter called effective population size. I then describe the possible ways in which mutation, selection, and recombination can explain observed patterns of synonymous diversity inE. coli.Finally, I describe a model forE. coligenome evolution in which different loci are subject to varying levels of gene flow among co-occurring microbes and viruses in the environment. Researchers can falsify the gene flow hypothesis by sequencing genes and strains isolated from stable microbiomes or by carrying out evolution experiments that trace gene genealogies in real-time.
authors.affiliation: Department of Integrative Biology, Michigan State University, East Lansing, MI, USA; Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA; BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA.
authors.forename: Rohan
authors.initials: R
authors.lastname: Maddamsetti
keywords: Escherichia coli; experimental evolution; gene flow; genetic diversity; genome evolution; microbiome; molecular evolution; population genomics