nantly European (with generally low levels of African ancestry). Similar results were found in Colombians and Ecuadorians, whereas Dominicans and Puerto Ricans showed the greatest variation in the African ancestry (Fig. 8.1). Interestingly, at K = 7, we were able to capture signals of continental substructure such as a Southwest to Northeast gradient in Europe and a Native American component that is absent in the two Amazonian indigenous populations (Karitiana and Surui) but that substantially contributes to all other studied Latino populations. We also note that several of the individuals from the Maya and Quechua Native American samples (and to a lesser extent Nahua and Pima) from the Human Genome Diversity Panel (CEPH-HGDP) show moderate levels of European admixture, consistent with previous studies of these populations (Jakobsson et al., 2008). Interestingly, this is not the case for the Aymara and Quechua samples genotyped by Mao et al. (2007).
We also undertook principal component analysis (PCA) of the autosomal genotype data from Hispanic/Latino and putative ancestral populations using the smartpca program from the software package eigenstrat (Fig. 8.2A) (Patterson et al., 2006a). The first two principal components of the PCA strongly support the notion that the three ancestral populations contributing to the Hispanic/Latino genomic diversity correspond exactly to Native American, European, and African ancestry. The Hispanic/Latino populations showed different profiles of ancestry, as exemplified by the fitting of ellipses to the covariance matrix of each population’s first two PCs (Fig. 8.2C). Subsequent PCs showed substructure within Africa, Native