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tries are in agreement with FRAPPE and STRUCTURE results in which Ecuadorians have the highest Native American proportions, followed by Colombians (showing greater European contribution), and with Puerto Ricans and Dominicans showing the highest African ancestry—specially Dominicans, who show very low contribution from Native Americans (Fig. 8.1). We also used the PCA-based methods of Bryc et al. (2010) to infer ancestry at each locus for the samples genotyped on the Affymetrix 500K, which included more than 100 Mexican samples genotyped by the POPRES project (Nelson et al., 2008) and diverse Native American populations genotyped by Mao et al. (2007). The local admixture tracks for each individual are in large agreement with the genome-wide average ancestry proportions (Fig. 8.3, Middle).

To investigate the genetic relationships among admixed Hispanic/Latino populations and putative ancestral groups, we compared patterns of population divergence among the inferred segments of European, African, and Native American ancestry and corresponding putative source populations using Wright’s FST measure. Specifically, we used LAMP to reconstruct for each individual in our dataset, segments of European, African, and Native American ancestry across both the maximal SNP dataset for all of the admixed and putative source population individuals (i.e., either the 610K Illumina for Puerto Rican, Ecuadorian, Columbian, and Dominican or 500k for Mexicans from Guadalajara) as well as ~70k SNPs common to both platforms. To calculate FST at a given SNP for a given pair of populations, we included only individuals with unambiguous ancestry assignment (i.e., individuals with two European-, two Native American–, or two African-origin chromosomes). One potential confounder for this analysis is that sample sizes differ substantially among subpopulations within major continental regions (e.g., in the Native American set, we have sample sizes that range from n = 7 for Colombian indigenous Americans in HGDP to n = 29 for Nahua from Mexico in the Mao et al. dataset). To minimize the potential bias of differences in sample size, we randomly selected n = 7 individuals from all potential subpopulations and recomputed Wright’s FST. As seen in Table 8.1, we found that consistent with historical records, our results show that African segments of the Hispanic/Latino populations are more closely related to the Bantu-speaking populations of West Africa than other populations. Specifically, we found that the Colombians and Ecuadorians are most closely related to the Kenyan Bantu populations, whereas the Puerto Ricans and Dominicans are closest to the Yoruba from Nigeria. Likewise, European segments show the lowest FST values when compared with Southwest European populations (individuals from Spain and Portugal), as well as French and Italian individuals. Native American segments of the Hispanic/Latino individuals show the least genetic differentiation with Mesoamerican (e.g., Maya and Nahua),

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