Predicting the evolution of bacterial populations with an epistatic selection-mutation model

A general model, based on evolutionary first-order principles, is proposed and applied to the experimentally observed evolution of Escherichia coli in the long-term evolution experiment. It incorporates two recently noticed phenomena related to mutations: (i) the fact that the marginal improvement from a beneficial mutation declines with increasing fitness or diminishing returns epistasis and (ii) for some hypermutator variants, the mutation rate for the bacterial DNA undergoes a sudden increase by at least one order of magnitude. The model can simultaneously predict the experimental mean fitness trajectory, as well as other observables, such as the variance trajectory and the mean substitution trajectory, all through the 50,000 bacterial generations presently available.