Consistent long-range linkage disequilibrium generated by admixture in a Bantu-Semitic hybrid population

Both the optimal marker density for genome scans in case-control association studies and the appropriate study design for the testing of candidate genes depend on the genomic pattern of linkage disequilibrium (LD). In this study, we provide the first conclusive demonstration that the diverse demographic histories of human populations have produced dramatic differences in genomewide patterns of LD. Using a panel of 66 markers spanning the X chromosome, we show that, in the Lemba, a Bantu-Semitic hybrid population, markers less than or equal to similar to 21 cM apart have a significantly greater tendency to show LD than do unlinked markers. In three populations with less evidence of admixture, however, excess LD disappears >2 cM. Moreover, analysis of Bantu and Ashkenazi populations as putative parental populations of the Lemba shows a significant relationship between allele-frequency differentials and the LD observed in the Lemba, which demonstrates that much of the excess LD is due to admixture. Our results suggest that demographic history has such a profound effect on LD that it will not be possible to predict patterns a priori but that it will be necessary to empirically evaluate the patterns in all populations of interest.