The Finnish Caucasian and Plains Indian haplotype block structure and extended LD patterns across GABRG1 and GABRA2 were similar to that found in the HapMap European American and Asian populations and in a recent study of 13 SNPs covering the region between GABRG1 intron 7 and GABRA2 intron 3 (Ittiwut et al, 2007). It has been shown that LD between distant markers is due to the presence of extended haplotype superblocks in individuals with ancient chromosomes which have escaped historic recombination (Buzas et al, 2004). When we looked at extended haplotypes with frequencies ≥ 0.05, we found three long-distance haplotypes that were common to both populations with total frequencies that were lower in the Plains Indians (0.31) than in the Finns: (0.57). The Plains Indians experienced a bottleneck in the recent genetic past therefore lower frequencies of ancestral haplotypes might be expected. The ancient superblock structure has been partially disrupted by recombination in the region between GABRG1 and GABRA2, and also in the Caucasian GABRG1 intron 2.
