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The indigenous Mazahua and Otomi have inhabited the same localities in Estado de Mexico since pre-Columbian times. Their languages, Mazahua and Otomi, belong to the Otomanguean linguistic family, and, while they share cultural traditions and a regional history that suggest close genetic relationships and common ancestry, the historical records concerning their origin are confusing. To understand the biological relationships between Mazahua and Otomi we analyzed the mitochondrial DNA (mtDNA) genetic variation. We identified the mtDNA haplogroups by restriction fragment length polymorphism typing and sequenced the hypervariable region I of the mtDNA control region in 141 Mazahua and 100 Otomi. These results showed that Otomi exhibit a higher frequency of haplogroup A than B, whereas Mazahua exhibit the opposite pattern. The most frequent subhaplogroups are A2, B2 and C1, in order of their frequency, among the Otomi EM. Meanwhile the subhaplogroups B2, D1, and A2, in that order, are most common among the Mazahua 1. The most frequent haplotypes (Ht) of haplogroups A and B are Ht2 (A) and Ht58 (B2g1) in the Mazahua 1 and Ht8 (A2), Ht22 (A2ao1) and Ht53 (B2c2b) in Otomi EM.

The genetic differences between the Mazahua and Otomi EM suggest a distant shared ancestry and a moderate degree of maternal admixture that has not obscured the difference of their mitochondrial DNA patterns. These unexpected results suggest the Mazahua and Otomi probably descend from the same group but separated very early and admixed with other Mesoamerican populations before their arrival in Central Mexico. The historical evidence of conflicting relations between the Mazahua and Otomi and the almost nonexistence of marriage between them could be responsible for maintaining only a moderate degree of maternal admixture.