Admixture analyses generally face the difficulty of not knowing with certainty the specific ancestral populations that were involved in the admixture, particularly since such ancestral populations might not be available for study or they could have undergone extensive genetic drift. Admixture estimates are therefore usually obtained by pooling data from related putative ancestral population samples, as a way to approximate a “mean” ancestral gene pool. All previous reports of admixture in Latin American populations have therefore pooled population data from African, European and Native American samples into “continental” samples; as done for the analyses discussed above. However, since there is a high level of population structure amongst ancestral Native American populations [23] it is conceivable that the Native component of Mestizos could be genetically differentiated across different geographic regions. We investigated whether it is possible to detect such an underlying genetic differentiation amongst Mestizos through an admixture analysis allowing for a structured ancestral Native American population sample (see Methods). The results from this analysis are not strictly ancestry proportions reflecting an underlying admixture between multiple Native populations. This is particularly
