The presence of Native Americans, Europeans, and Africans has led to the development
of a multi-ethnic, admixed population in Chile. This study aimed to contribute to the
characterization of the uniparental genetic structure of three Chilean regions.
Newborns from seven hospitals in Independencia, Providencia, Santiago, Curicó,
Cauquenes, Valdívia, and Puerto Montt communes, belonging to the Chilean regions of
Santiago, Maule, and Los Lagos, were studied. The presence of Native American
mitochondrial DNA (mtDNA) haplogroups and two markers present in the non-recombinant
region of the Y chromosome, DYS199 and DYS287, indicative of Native American and
African ancestry, respectively, was determined. A high Native American matrilineal
contribution and a low Native American and African patrilineal contributions were
found in all three studied regions. As previously found in Chilean admixed
populations, the Native American matrilineal contribution was lower in Santiago than
in the other studied regions. However, there was an unexpectedly higher contribution
of Native American ancestry in one of the studied communes in Santiago, probably due
to the high rate of immigration from other regions of the country. The population
genetic sub-structure we detected in Santiago using few uniparental markers requires
further confirmation, owing to possible stratification for autosomal and X-chromosome
markers.