Mitochondrial DNA Analysis Reveals Substantial Native American Ancestry in Puerto Rico

1 Abstract To estimate the maternal contribution of Native Americans to the human gene pool of Puerto Ricans—a population of mixed African, Eu- ropean, and Amerindian ancestry—the mtDNAs of two sample sets were screened for restriction fragment length polymorphisms (RFLPs) defining the four major Native American haplogroups. The sample set collected from people who claimed to have a maternal ancestor with Native American phys- iognomic traits had a statistically significant higher frequency of Native American mtDNAs (69.6%) than did the unbiased sample set (52.6%). This higher frequency suggests that, despite the fact that the native Taino culture has been extinct for centuries, the Taino contribution to the current popula- tion is considerable and some of the Taino physiognomic traits are still pres- ent. Native American haplogroup frequency analysis shows a highly struc- tured distribution, suggesting that the contribution of Native Americans foreign to Puerto Rico is minimal. Haplogroups A and C cover 56.0% and 35.6% of the Native American mtDNAs, respectively. No haplogroup D mtDNAs were found. Most of the linguistic, biological, and cultural evidence suggests that the Ceramic culture of the Tainos originated in or close to the Yanomama territory in the Amazon. However, the absence of haplogroup A in the Yanomami suggests that the Yanomami are not the only Taino ances- tors.