Data from: Selection bias in mutation accumulation

Mutation accumulation (MA) experiments, in which de
novo mutations are sampled and subsequently characterized, are an
essential tool in understanding the processes underlying evolution. In
microbial populations, MA protocols typically involve a period of
population growth between severe bottlenecks, such that a single
individual can form a visible colony. While it has long been appreciated
that the action of positive selection during this growth phase cannot be
eliminated, it is typically assumed to be negligible. Here, we quantify
the effect of both positive and negative selection in MA studies,
demonstrating that selective effects can substantially bias the
distribution of fitness effects (DFE) and mutation rates estimated from
typical MA protocols in microbes. We then present a simple correction for
this bias which applies to both beneficial and deleterious mutations, and
can be used to correct the observed DFE in multiple environments. We use
simulated MA experiments to illustrate the extent to which the MA-inferred
DFE differs from the underlying true DFE, and demonstrate that the
proposed correction accurately reconstructs the true DFE over a wide range
of scenarios; we also provide an example of these corrections applied to
experimental data. These results highlight that positive selection during
microbial MA experiments is in fact not negligible, but can be corrected
to gain a more accurate understanding of fundamental evolutionary
parameters.