Demographic History of Indigenous Populations in Mexico Explored Through Whole Mitogenome Analysis

Mitochondrial DNA plays a key role in understanding the demographic history of human populations. Particularly in the Americas, nine widespread Native American specific mitochondrial lineages have been identified. Here we performed the whole mitogenome sequencing of 572 Indigenous individuals from 60 populations spanning the Mexican territory. To minimize the effects of European and African admixture, we focused on individuals with at least 90% Native American ancestry, estimated by ADMIXTURE. We identified all the five major Native American haplogroups clades, with A2 being the most prevalent (53.9%), followed by B2 (24.0%), C1 (17.6%), D1 (4.3%), and D4h3a (0.2%). We also identified 82 different subhaplogroup widespread across the country, revealing shared mtDNA haplogroups in populations from distant regions. Moreover, mitochondrial DNA variation in the Mexican Native populations is not structured by geography or linguistic affiliation, suggesting complex gene flow across regions. Demographic reconstructions based on whole mitogenomes showed an exponential increase the maternal Ne around 10 kya in all tested regions. All these findings suggest a mitochondrial genetic persistence through Mexico and possibly the Americas.