African; but, in contrast, 20 of 27 Puerto Rican individuals had mitochondrial haplotypes of Native American origin, suggesting a strong female Native American and male European and African sex bias contribution. Overall, in all of the Hispanic/Latino populations that we analyzed, we found evidence of greater European ancestry on the Y chromosome and higher Native American ancestry on the mtDNA and X chromosome consistent with previous findings (Dipierri et al., 1998; Green et al., 2000; Sans et al., 2002; Carvajal-Carmona et al., 2003; González-Andrade et al., 2007; Marrero et al., 2007; Mendizabal et al., 2008).
Our work has important implications for understanding the population genetic history of Latin America as well as ancestry of U.S.-based Hispanic/Latino populations. As has been previously documented, we found large variation in the proportions of European, African, and Native American ancestry among Mexicans, Puerto Ricans, Dominicans, Ecuadorians, and Colombians, but also within each of these groups. These trends are a consequence of variation in rates of migration from ancestral European and African source populations as well as population density Native Americans in pre-Columbian times (Sans, 2000). We found that Dominicans and Puerto Ricans in our study showed the highest levels of African ancestry, consistent with historical records. European settlers to island nations in the Caribbean basin largely displaced Native American populations by the early to mid-16th century and concurrently imported large African slave populations for large-scale colonial agricultural production (largely of sugar). In contrast, Colombia has wider geographic differences ranging from Caribbean coasts to Andean valleys and mountains, which could explain the enrichment of African ancestry in some individuals and not in others, likely representing the differences in origin within Colombia. Finally, Mexico and Ecuador are two continental countries that had high densities of Native Americans during pre-Columbian times; as expected, the individuals from these two countries show the highest degree of Native American ancestry. Our findings clearly show that the involuntary migration of Africans through the slave trade appears to have left a clear trace in Hispanic/Latino populations proximal to these routes.
From the FST analysis, we found that the high-density genotype data that we have collected is quite informative regarding the personal genetic ancestry of admixed Hispanic/Latino individuals. Specifically, we found that individuals differ dramatically within and among populations and that we can reliably identify subpopulations within major geographic regions (i.e., Europe, Africa, and the Americas) that exhibit lower pairwise