Correlations between mutations under recurrent genetic hitchhiking

Sweeping beneficial mutations can dramatically perturb the variation at neighboring sites in the genome ("genetic hitchhiking"). While the effects of isolated selective sweeps have been studied in detail, the cumulative effect of recurrent hitchhiking remains poorly characterized in long recombining genomes. Previous theoretical work has focused on predicting the patterns of genetic diversity at a single neutral site, which can be hard to distinguish from the effects of other population genetic processes. Since sites that hitchhike together share similar frequency dynamics until they are unlinked by recombination, the correlation between sites contains richer information about the evolutionary forces at play. Yet, incorporating strong selection and recombination into the conventional framework of coalescent theory has been a long-standing challenge. Here, we will describe a forward-in-time approach that stratifies the dynamics of variants by their present-day frequencies, which provides new opportunities to predict the multi-site effects of recurrent hitchhiking.