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The accumulation of adaptive mutations is essential for survival in novelenvironments. However, in clonal populations with a high mutational supply, thepower of natural selection is expected to be limited. This is due to clonalinterference - the competition of clones carrying different beneficialmutations - which leads to the loss of many small effect mutations and fixationof large effect ones. If interference is abundant, then mechanisms forhorizontal transfer of genes, which allow the immediate combination ofbeneficial alleles in a single background, are expected to evolve. However, therelevance of interference in natural complex environments, such as the gut, ispoorly known. To address this issue, we studied the invasion of beneficialmutations responsible for Escherichia coli's adaptation to the mouse gut anddemonstrate the pervasiveness of clonal interference. The observed dynamics ofchange in frequency of beneficial mutations are consistent with soft sweeps,where a similar adaptive mutation arises repeatedly on different haplotypeswithout reaching fixation. The genetic basis of the adaptive mutations revealeda striking parallelism in independently evolving populations. This was mainlycharacterized by the insertion of transposable elements in both coding andregulatory regions of a few genes. Interestingly in most populations, weobserved a complete phenotypic sweep without loss of genetic variation. Theintense clonal interference during adaptation to the gut environment, heredemonstrated, may be important for our understanding of the levels of straindiversity of E. coli inhabiting the human gut microbiota and of itsrecombination rate.

The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps