Evolution of haplotypes encompassing the GIP locus. (A) Plots of the extent of haplotype homozygosity in the 1.0-Mb region surrounding rs2291725 in CEU, ASN, and YRI as assessed by Haplotter (Voight et al. 2006). These plots are divided into two parts. The upper portion shows haplotypes with the ancestral GIP^103T allele in blue, and the lower portion shows haplotypes with the derived GIP^103C allele in red. Adjacent haplotypes with the same color carry identical genotypes spanning the region between a select SNP and rs2291725. (B) Plots of the breakdown of EHH over the distance between rs2291725 and neighboring SNPs at increasing distances. EHH decays much slower at the derived allele (red) compared with the ancestral allele (blue) in ASN and CEU. The position of rs2291725 at the center of the plots is indicated by a vertical dotted line. (C) Evolution of haplotypes within a 70-kb core haploblock in the three HapMap II populations. A total of 13 haplotypes was found in the core region from rs196241 to rs2291726 (37 SNPs at chr 17, 44325258–44394253). The frequencies of these haplotypes (GIP-A∼M) in YRI, CEU, and ASN are shown in the lower left panel. There are 12 haplotypes in YRI, whereas CEU and ASN are represented by five and four haplotypes, respectively. GIP-A is the only haplotype containing the derived GIP^103C allele and is indicated by a dotted box. An unrooted tree analysis of these haplotypes showed that the GIP-A haplotype diverged from others early in human evolution (GeneBee). The frequency of each haplotype in a select population is indicated by the size of the pie at the tip of each branch.