The large variation amongst the Mestizo examined in the mean Native American ancestry and in individual admixture proportions, and the regionally differentiated Native American ancestry, testify to the marked genetic heterogeneity of Latin American populations. These observations have a number of implications for the application of admixture mapping in the region. The large variation in mean Native American ancestry between populations implies that the power of admixture mapping will vary considerably in studies targeting different geographic areas[14]. The differentiated Native Ancestry of Mestizos will affect the informativeness of admixture maps across populations and could result in an increase of false positives when admixture mapping is attempted populations other than the one from which informative markers were selected. Ideally, admixture maps should therefore be developed for each Mestizo population studied. An alternative would be to select markers for mapping based on their lack of differentiation across Native American populations. Our results also show that mean African ancestry in Mestizo populations is typically low (<10%). This reduces the potential complexity of an extensive three way admixture and confirms that admixture mapping in
