  The accumulation of adaptive mutations is essential for survival in novel
environments. However, in clonal populations with a high mutational supply, the
power of natural selection is expected to be limited. This is due to clonal
interference - the competition of clones carrying different beneficial
mutations - which leads to the loss of many small effect mutations and fixation
of large effect ones. If interference is abundant, then mechanisms for
horizontal transfer of genes, which allow the immediate combination of
beneficial alleles in a single background, are expected to evolve. However, the
relevance of interference in natural complex environments, such as the gut, is
poorly known. To address this issue, we studied the invasion of beneficial
mutations responsible for Escherichia coli's adaptation to the mouse gut and
demonstrate the pervasiveness of clonal interference. The observed dynamics of
change in frequency of beneficial mutations are consistent with soft sweeps,
where a similar adaptive mutation arises repeatedly on different haplotypes
without reaching fixation. The genetic basis of the adaptive mutations revealed
a striking parallelism in independently evolving populations. This was mainly
characterized by the insertion of transposable elements in both coding and
regulatory regions of a few genes. Interestingly in most populations, we
observed a complete phenotypic sweep without loss of genetic variation. The
intense clonal interference during adaptation to the gut environment, here
demonstrated, may be important for our understanding of the levels of strain
diversity of E. coli inhabiting the human gut microbiota and of its
recombination rate.
