Human populations examined for evidence of selection, and host genes associated with HIV-1 found to be under potential selection. (A) Map showing locations of five human populations in sub-Saharan Africa that are part of the Human Genome Diversity Panel  and for which pairwise population genomic comparisons were conducted to identify regions potentially under selection. The Biaka are a Western Pygmy group in the Central African Republic that historically resided in a region where the strains of SIV that gave rise to HIV-1 are endemic in non-human primates. The Mbuti are an Eastern Pygmy group in the Democratic Republic of Congo. The Mbuti historically have resided where SIV strains that gave rise to HIV-1 are not present, as have the other non-Pygmy African populations listed. (B) Host genes associated with HIV-1 (HGAHs) under potential selection were revealed by genomic comparisons of each pair of African populations. The genomic locations of HGAHs were compared to regions of the genome identified using SNPs as potentially under selection  (regions of low heterozygosity within and/or high variance of F
between populations). HGAHs potentially under selection are indicated by the different lines or arrows connecting each pair of populations, with the type of selection indicated by the key. “New” selection in one or both populations indicates selection after the divergence of the two populations. “Old” selection is selection that occurred prior to the divergence of the two populations. There was evidence for selection in the Biaka for CUL5, PARD3B, TRIM5, and TSG101.