One signal of recent positive selection is an unusually long haplotype around the selected marker, but it is difficult to fine-map the selected variant within such long haplotypes on the basis of population genetic data alone. Large CNVs, by virtue of their potential functional impact, may make a useful first screen for deconstructing such signals. Accordingly, we have surveyed our CNVs for signs of recent positive selection using population differentiation9 and two previously described approaches40,41 relying on haplotype structure (integrated haplotype score: iHS, and cross-population extended haplotype homozygosity: XP-EHH). Several of the CNVs exhibited iHS in the top 1% of the genomic distribution: 7 in CEU, 1 in CHB+JPT, 18 in YRI, all of which seem to represent population-specific signals. The most impressive signal is around CNVR8151.1 in YRI: a standardized iHS of 3.39, in the top 700 out of 2.26 million markers (top 0.03% of the genome). This deletion lies between the APOL2 and APOL4 genes involved in pathogen immunity and previously reported to have been under positive selection in primates42. The top XP-EHH signal is CNVR3685.1, a deletion
