Genetic Diversity and Differentiation in Urban and Indigenous Populations of Mexico: Patterns of Mitochondrial DNA and Y-Chromosome Lineages

Abstract

Aside from the admixture between indigenous people and people from overseas, populations in Mexico changed drastically after the Spanish conquest of the sixteenth century, forming an intricate history that has been underutilized in understanding the genetic population structure of Mexicans. To infer historical processes of isolation, dispersal, and assimilation, we examined the phylogeography of mitochondrial (mt) DNA and Y-chromosome lineages in 3,026 individuals from 10 urban and nine indigenous populations by identifying single nucleotide polymorphisms. A geographic array with a predominance of Amerindian lineages was observed for mtDNA, with northern indigenous populations being divergent from the central and southern indigenous populations; urban populations showed low differentiation with isolation by distance. Y-chromosome variation distinguished urban and indigenous populations through the Amerindian haplogroup Q frequency. The MtDNA and the Y-chromosome together primarily distinguished urban and indigenous populations, with different geographic arrays for both. Gene flow across geographical distance and between the urban and indigenous realms appears to have altered the pre-Hispanic phylogeography in central and southern Mexico, mainly by displacement of women, while maintaining the indigenous isolation in the north, southeast, and Zapotec regions. Most Amerindian mtDNA diversity currently occurs in urban populations and appears to be reduced among indigenous people.

Acknowledgements

We are much indebted to all the people from the state capitals and the indigenous communities who generously participated in this research, as well as to the personnel at the authoring institutions who gave technical, legal, and/or administrative support. We also appreciate the constructive criticism of two anonymous reviewers, and thank F. Bulmer, A. Hoholik, A. M. Waller, and two editors from Taylor & Francis for their assistance in the English edition.

Funding

This work was funded by the agreement 23496-381-18-III-09 between Instituto de Investigaciones Antropológicas, UNAM, and Instituto Nacional de Medicina Genómica, as well as by project PAPIIT-UNAM IN400913. The authors declare no conflict of interest or financial benefits from this work, which is entirely academic.

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Funding

This work was funded by the agreement 23496-381-18-III-09 between Instituto de Investigaciones Antropológicas, UNAM, and Instituto Nacional de Medicina Genómica, as well as by project PAPIIT-UNAM IN400913. The authors declare no conflict of interest or financial benefits from this work, which is entirely academic.