Maternal lineage diversity based on mitochondrial DNA in a population sample from Mexico City

The founding mitochondrial lineages of the Native American population (haplogroups A, B, C, and D) originated in East Asia and reached the American continent via the Bering Strait approximately 15,000 to 18,000 years ago. Subsequent events, including European colonization and the transatlantic slave trade, substantially reshaped the maternal genetic landscape across the Americas.

Sequences at positions 16,024-372, including hypervariable regions I and II of the mtDNA control region, were analyzed in saliva samples from 280 unrelated individuals (97 males and 183 females) residing across sixteen boroughs of Mexico City.

The haplotype diversity was estimated at 99.85%, with a discrimination capacity of 88.2%, a random match probability of 0.0051, and a nucleotide diversity of 1.19%. Native American haplogroups collectively accounted for 89.66% of the sample. Haplogroups of Western Eurasian origin represented 8.2%, while those of African origin comprised 2.141%.

The predominance of Native American haplogroups underscores the persistence of pre-Columbian maternal lineages in the region. In contrast, the minor presence of Western Eurasian and African haplogroups indicates that, within Mexico City, the demographic impact of colonization and subsequent admixture on maternal lineages was comparatively limited. These findings highlight how regional genetic patterns can reflect broad continental historical processes while preserving strong Indigenous maternal continuity. Finally, the diversity parameters support the utility of mtDNA analysis for human identification, particularly in complex forensic contexts.