ECOLOGY AND EVOLUTION OF BACTERIAL POPULATIONS IN THE WILD

Populations are fundamental units that form the basis of our understanding of evolution, ecology, and systematics. They are typically thought of as groups of organisms that share a gene pool in which adaptive mutations can spread leading to a common ecological niche. Yet for bacteria and archaea, widespread and frequent horizontal gene transfer has confounded efforts to apply a population framework. Using marine vibrios as a model, we show that in spite of high gene turnover, it is possible to define genotypic clusters, which represent ecologically cohesive populations. These display many hallmarks of animal and plant populations, including speciation, shared gene pools, and social interactions. We generalize these insights by showing that clusters in gene-flow networks correspond to previously defined ecologically differentiated populations among diverse bacteria and archaea. We propose a reverse ecology approach where gene-flow clusters serve as hypotheses of population structure allowing for rapid ordering of microbial diversity into ecologically differentiated populations and allows for interpretation of gene frequencies within populations in light of environmental selection.