Data from: Diverse phenotypic and genetic responses to short-term selection in evolving Escherichia coli populations

Beneficial mutations fuel adaptation by altering phenotypes that enhance
the fit of organisms to their environment. However, the phenotypic effects
of mutations often depend on ecological context, making the distribution
of effects across multiple environments essential to understanding the
true nature of beneficial mutations. Studies that address both the genetic
basis and ecological consequences of adaptive mutations remain rare. Here,
we characterize the direct and pleiotropic fitness effects of a collection
of 21 first-step beneficial mutants derived from naïve and adapted
genotypes used in a long-term experimental evolution of Escherichia coli.
Whole-genome sequencing was able to identify the majority of beneficial
mutations. In contrast to previous studies, we find diverse fitness
effects of mutations selected in a simple environment and few cases of
genetic parallelism. The pleiotropic effects of these mutations were
predominantly positive but some mutants were highly antagonistic in
alternative environments. Further, the fitness effects of mutations
derived from the adapted genotypes were dramatically reduced in nearly all
environments. These findings suggest that many beneficial variants are
accessible from a single point on the fitness landscape, and the fixation
of alternative beneficial mutations may have dramatic consequences for
niche breadth reduction via metabolic erosion.