In order to further evaluate how consistently different subsets markers can estimate individual admixture we examined the correlation of ancestry assignments. Using the 128 In4 results as the standard we compared the estimated contribution of one of the ancestral parental populations contributing to each of three different admixed populations. These include West African contribution in AFA, European contribution in PRA, and Amerindian contribution in MAM and MXN. The latter two groups (MAM and MXN) were combined since the admixture proportions are similar. Marker sets chosen for their optimum ability to discriminate between four ancestral populations (In4 sets), and two ancestral populations (In2 sets) were examined (Fig. 2). The correlation values (r2) for West African contribution in AFA are high, ranging between 0.988 for 96 In4 to 0.835 for 24 In4, suggesting that small number of markers are sufficient to identify West African contribution. Similar results in AFA were also observed using the marker sets selected specifically to distinguish European and West African (e.g. 0.976 for 48 In2 European/West African). As anticipated, the markers chosen for European/Amerindian differences did not accurately distinguish European/African admixture.
