Estimating African American admixture proportions by use of population-specific alleles

We analyzed the European genetic contribution to 10 populations of African descent in the United States (Maywood, Illinois; Detroit; New York; Philade lphia; Pittsburgh; Baltimore; Charleston, South Carolina; New Orleans; and Houston) and in Jamaica, using nine autosomal DNA markers. These markers ei ther are population-specific or show frequency differences >45 % between th e parental populations and are thus especially informative for admixture. E uropean genetic ancestry ranged from 6.8% (Jamaica) to 22.5% (New Orleans). The unique utility of these markers is reflected in the low variance assoc iated with these admixture estimates (SEM 1.3%-2.7%). We also estimated the male and female European contribution to African Americans, on the basis o f informative mtDNA (haplogroups H and L) and Y Alu polymorphic markers. Re sults indicate a sex-biased gene flow from Europeans, the male contribution being substantially greater than the female contribution. mtDNA haplogroup s analysis shows no evidence of a significant maternal Amerindian contribut ion to any of the 10 populations. We detected significant nonrandom associa tion between two markers located 22 cM apart (FY-null and AT3), most likely due to admixture linkage disequilibrium created in the interbreeding off t he two parental populations. The strength of this association and the subst antial genetic distance between FY and AT3 emphasize the importance of admi red populations as a useful resource for mapping traits with different prev alence in two parental populations.