Natural selection can affect levels of DNA variation across genes in multiple ways: strongly deleterious mutations will be rapidly eliminated by natural selection, weakly deleterious mutations can segregate in populations but rarely become fixed, and selection at nearby sites (both purifying and adaptive) can reduce genetic variation through background selection35 and the hitchhiking effect36. The effect of these different forces on genetic variation can be disentangled by examining patterns of diversity and divergence within and around known functional elements. The low coverage data enables, for the first time, genome wide analysis of such patterns in multiple populations. Fig. 5a (top) shows the pattern of diversity relative to genic regions measured by aggregating estimates of heterozygosity around protein coding genes. Within genes, exons harbor the least diversity (about 50% of that of introns) and 5′ and 3′ UTRs harbor slightly less diversity than immediate flanking regions and introns. However, this variation in diversity is fully explained by the level of divergence (Fig. 5a lower) consistent with the common part of the allele frequency spectrum being dominated by effectively neutral variants, and weakly deleterious variants contributing only to the rare end of the frequency spectrum.
