Adaptive diversification events that underly the diversity of the living world have been studied by an experimental evolution strategy initiated by Richard Lenski in 1988. Twelve populations founded from a common ancestor of Escherichia coli are propagated independently since more than 55,000 generations by daily transfer in a glucose-limited minimal medium. A diversification event emerged after 6500 generations of evolution in only one of the twelve populations, called Ara-2, resulting in two lineages of differentiated cells, called S and L, that coexist ever since owing to negative frequency-dependent interactions. Two properties make this polymorphism original and important: its length as the longest one ever observed in evolution experiments, and its uniqueness as it occurred only once in the twelve populations founded from the same ancestor. The aim of this work was to identify the mechanisms of the long-term coexistence of the S and L lineages, together with the genetic bases of their emergence. The maintenance of the polymorphism is characterized by a strong dynamic of the ecological relationships between S and L, with with L seeming to encroach over time on the niche of S, which reacts to avoid extinction. The emergence of the S lineage is due to the succession of three mutations, necessary and sufficient to establish its phenotypes. All three mutations affect genes encoding global transcriptional regulators, with two of them being involved in the regulation of central metabolism. For one of them, the evolved allele alters the DNA binding ability of the evolved protein. Although this polymorphism is unique, the same three genes are targets of natural selection in most other populations of the evolution experiment. For two of them, only the substituted allele of the Ara-2 population results in the phenotypes of the S lineage. Thus, the uniqueness of this diversification event is linked to a succession of precise mutational events that affect the global regulatory network in the cell. Those gradual modifications lead thus to the emergence of the longest polymorphism ever identified during evolution experiments in the laboratory.
