The Dynamics of Genetic Draft in Rapidly Adapting Populations

Abstract: The accumulation of beneficial mutations on many competing genetic backgrounds in rapidly adapting populations has a striking impact on evolutionary dynamics. This effect, known as clonal interference, causes erratic fluctuations in the frequencies of observed mutations, randomizes the fixation times of successful mutations, and leaves distinct signatures on patterns of genetic variation. Here, we show how this form of `genetic draft' affects the forward-time dynamics of site frequencies in rapidly adapting asexual populations. We calculate the probability that mutations at individual sites shift in frequency over a characteristic timescale, extending Gillespie's original model of draft to the case where many strongly selected beneficial mutations segregate simultaneously. We then derive the sojourn time of mutant alleles, the expected fixation time of successful mutants, and the site frequency spectrum of beneficial and neutral mutations. We show how this form of draft affects inferences in the McDonald-Kreitman test, and how it relates to recent observations that some aspects of genetic diversity are described by the Bolthausen-Sznitman coalescent in the limit of very rapid adaptation. Finally, we describe how our method can be extended to model evolution on fitness landscapes that include some forms of epistasis, such as landscapes that are partitioned into two or more incompatible evolutionary trajectories.