Native American in origin (i.e., Mexicans and Ecuadorians). Furthermore, greater Native American ancestry on the X chromosome in Puerto Ricans did not necessarily imply greater Amerindian ancestry on the autosomes. This finding is similar to those observed by analyzing fine-scale genome pattern of population structure and admixture among African Americans, West Africans, and Europeans (Lind et al., 2007).
Finally, we used SNP and microsatellite genotyping to identify the canonical Y chromosome and mtDNA haplotypes for each of the Hispanic/Latino individuals that we genotyped. Details of the loci and classifications are found in Tables S1 and S2 (available online at www.pnas.org/cgi/content/full/0914618107/DCSupplemental). We found an excess of European Y chromosome haplotypes and a higher proportion of Native American and African mtDNA haplotypes, consistent with previous studies (Fig. 8.6). In addition, we found several non-European Y chromosomal haplotypes with most likely origins from North Africa and the Middle East. We observed that African-derived haplotypes were the predominant origin of mtDNA in Dominicans (17 of 27 individuals), matching the greater African vs. Native American origins of this population on the autosomes and X chromosomes. However, in Puerto Ricans we did not find evidence of a high African female contribution. The predominant Y chromosomal origins in the Puerto Ricans sampled were European and