We examined selective sweeps by identifying genes with high ratios of divergence (human-specific lineage substitutions relative to chimp and macaque) compared with polymorphism within humans, which are predicted to increase between-species divergence and decrease within-population diversity. We identified genes in which the ratio of nonsynonymous to synonymous divergence was high relative to the ratio of non-synonymous to synonymous SNVs (25). We also identified genes with either a high or low ratio of π in AAs relative to π in EAs and genes with diversity estimates in the bottom 20th percentile in which at least one SNV had an FST ≥ 0.3. In total, 114 genes met one or more of these criteria (table S4). About 25% of these genes have been implicated as targets of positive selection (26). The 114 candidate selection genes were significantly enriched (false discovery rate ≤ 5%) for five KEGG pathways, including olfactory transduction and metabolic pathways (table S5).
