Data from: Adaptation, clonal interference, and frequency-dependent interactions in a long-term evolution experiment with Escherichia coli

Twelve replicate populations of Escherichia coli have been evolving in the
laboratory for >25 years and 60,000 generations. We analyzed
bacteria from whole-population samples frozen every 500 generations
through 20,000 generations for one well-studied population, called Ara−1.
By tracking 42 known mutations in these samples, we reconstructed the
history of this population’s genotypic evolution over this period. The
evolutionary dynamics of Ara−1 show strong evidence of selective sweeps as
well as clonal interference between competing lineages bearing different
beneficial mutations. In some cases, sets of several mutations approached
fixation simultaneously, often conveying no information about their order
of origination; we present several possible explanations for the existence
of these mutational cohorts. Against a backdrop of rapid selective sweeps
both earlier and later, two genetically diverged clades coexisted for
>6000 generations before one went extinct. In that time, many
additional mutations arose in the clade that eventually prevailed. We show
that the clades evolved a frequency-dependent interaction, which prevented
the immediate competitive exclusion of either clade, but which collapsed
as beneficial mutations accumulated in the clade that prevailed. Clonal
interference and frequency dependence can occur even in the simplest
microbial populations. Furthermore, frequency dependence may generate
dynamics that extend the period of coexistence that would otherwise be
sustained by clonal interference alone.