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Selective sweeps are typically associated with a local reduction of geneticdiversity around the adaptive site. However, selective sweeps can also quicklycarry neutral mutations to observable population frequencies if they ariseearly in a sweep and hitchhike with the adaptive allele. We show that theinterplay between mutation and exponential amplification through hitchhikingresults in a characteristic frequency spectrum of the resulting novel haplotypevariation that depends only on the ratio of the mutation rate and the selectioncoefficient of the sweep. Based on this result, we develop an estimator for theselection coefficient driving a sweep. Since this estimator utilizes the novelvariation arising from mutations during a sweep, it does not rely onpreexisting variation and can also be applied to loci that lack recombination.Compared with standard approaches that infer selection coefficients from thesize of dips in genetic diversity around the adaptive site, our estimatorrequires much shorter sequences but sampled at high population depth in orderto capture low-frequency variants; given such data, it consistently outperformsstandard approaches. We investigate analytically and numerically how theaccuracy of our estimator is affected by the decay of the sweep pattern overtime as a consequence of random genetic drift and discuss potential effects ofrecombination, soft sweeps, and demography. As an example for its use, we applyour estimator to deep sequencing data from HIV populations.

Estimating the Strength of Selective Sweeps from Deep Population Diversity Data