Recent genome sequencing studies with large sample sizes in humans have discovered a vast quantity of low-frequency variants, providing an important source of information to analyze how selection is acting on human genetic variation. In order to estimate the strength of natural selection acting on low-frequency variants, we have developed a likelihood-based method that uses the lengths of pairwise identity-by-state between haplotypes carrying low-frequency variants. We show that in some non-equilibrium populations (such as those that have had recent population expansions) it is possible to distinguish between positive or negative selection acting on a set of variants. With our new framework, one can infer a fixed selection intensity acting on a set of variants at a particular frequency, or a distribution of selection coefficients for standing variants and new mutations. We apply our method to the UK10K phased haplotype dataset of 3,781 individuals and find a similar proportion of neutral, moderately deleterious, and deleterious variants compared to previous estimates made using the site frequency spectrum. We discuss several interpretations for this result, including that selective constraints have remained constant over time.

Haplotype-based inference of the distribution of fitness effects