We performed several steps to filter the genome for high-quality neutral sites, which were based on a previously described ascertainment scheme30 (Supplementary Information 1.10). After filtering, positions in the genome were annotated for how strongly affected they were by selection at linked sites using the background selection coefficient, McVicker’s B statistic60. We used all sites annotated with a B value for performing general analyses. However, when performing demographic inferences, we limited our analyses to regions of the genome within the top 1% of the genome-wide distribution of B (B ≥ 0.994). These sites correspond to regions of the genome inferred to be under the weakest amount of background selection (that is, under the weakest effects of selection at linked sites). Sites in the genome were also polarized to ancestral and derived states using ancestral annotations called with high-confidence from the GRCh37 e71 ancestral sequence. After keeping only polymorphic bi-allelic sites, we had 20,324,704 sites, of which 191,631 had B ≥ 0.994. We also identified 91,177 fourfold degenerate synonymous sites (irrespective of B) that were polymorphic (bi-allelic) and had high-confidence ancestral and derived states.
