FST (and, therefore, higher genetic similarity) to the inferred European, African, and Native American segments for the 212 individuals studied. We found, for example, that Nahua showed the lowest FST in Mexicans, consistent with the observation that the Nahua are one of the largest Native American populations in this region and are likely to have contributed to the genomes of admixed individuals in Mexico (as opposed, for instance, to the Mexican Pima who fall outside the Mesoamerican cultural region and show considerably higher levels of differentiation). We also found that the lowest FST for the African regions of the Dominican and Puerto Rican genomes are with the Yoruba, a Bantu-speaking West African population that has been shown to be genetically similar to the African segments of African Americans sampled in the United States (Bryc et al., 2010). Although we have limited Native American populations and Hispanic/Latino sample sizes and, thus, the differences in FST with different subcontinental populations suggest that there exists a reasonably strong signal of which present-day populations are most closely related to the ancestral populations that contributed ancestry to each of the Hispanic/Latino populations.
When comparing inferred continental ancestry of the X and Y chromosomes and mitochondrial vs. the autosomal genome, we observed an enrichment of European Y-chromosome vs. autosomal genetic material, and a greater percentage of both Native American and African ancestry on the X-chromosomes and mtDNA compared with the autosomes for the Hispanic/Latino individuals in this study. This suggests a predominance of European males and Native American/African females in the ancestral genetic pool of Latinos, consistent with previous studies. A particularly interesting observation from our work on sex-biased admixture is that the pattern exists not only within populations but among Hispanic/Latino populations as well. In all populations studied, there is an enrichment of Native American ancestry both on the X chromosome and mtDNA compared with the autosomes. This would suggest a greater female Native American contribution to the genome of Latinos. A different result was obtained in relation to African ancestry. We found a smaller difference between mean African ancestry on the X chromosome and the autosomes, compared with the difference in Native American ancestry. Furthermore, unlike in Native American ancestry, we found an overwhelming representation of Native American mtDNA haplogroups in Puerto Ricans, even though non-European ancestry on the autosomes was largely African.
It is important to note that this observation does not necessarily undermine the model of sex-biased admixture among European male and African females in the founding of Hispanic/Latino populations, especially when one considers the predominance of European Y chromosomes in all groups studied. However, it suggests that admixture between Euro-