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 so because the proportions obtained are influenced by the variable degree of genetic relatedness amongst the various Native groups examined. Rather, these proportions reflect the relative genetic similarity of the Native American component in the Mestizo to the Native groups considered in the analyses. Figure 5 shows such a partitioning of the Native American ancestry in Mestizos when admixture is estimated with data from Native Americans subdivided based on linguistic grounds; using the classification of Ruhlen[40] (the corresponding values and errors of these estimates are presented in Table S4). Generally, the native component in the Mestizo shows greatest genetic similarity to Native populations from the linguistic stock which is most widespread in the region where the Mestizo population sampled is located (Figure 1): Central/Northern Amerind in Mexico City and Oriente; Chibchan-Paezan in CVCR, Medellin and Peque; Andean in Pasto, Salta, Catamarca and Quetalmahue. RGS shows no strong similarity to Natives from any linguistic stock but is the Mestizo population with
