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 these populations should be feasible within the two-population admixture framework usually considered[24],[42]. Mapping in Mestizos should thus be practical with marker maps that mainly distinguish Native from European ancestry (or Native from non-Native ancestry), possibly supplemented by the exclusion of outlier individuals showing a marked increase in African ancestry. It is likely, however, that areas where historically there has been substantial African immigration (e.g. circum-Caribbean areas) will show higher levels of African admixture and represent additional challenges for admixture mapping. Finally, individual admixture estimates can vary markedly in certain Mestizo populations, particularly in large urban agglomerations such as Mexico City (Figure 4). These populations could be particularly useful for evaluating the effect of ancestry on phenotype, an important initial step prior to admixture mapping of genes influencing such phenotypic variation.
