The genetics of Mexico recapitulates Native American substructure and affects biomedical traits

TLDR

Mexico’s rich cultural and ethnic diversity is mirrored by largely uncharacterized fine‑scale genome‑wide variation. The authors examined genomic variation in over 1,000 individuals from 20 indigenous and 11 mestizo populations across Mexico. They uncovered pronounced genetic stratification among indigenous groups—some as differentiated as Europeans from East Asians—whose pre‑Columbian substructure is reflected in mestizo ancestry and is significantly associated with lung function, highlighting the need to account for fine‑scale ancestry in medical and population genetic studies.

Abstract

Mexico harbors great cultural and ethnic diversity, yet fine-scale patterns of human genome-wide variation from this region remain largely uncharacterized. We studied genomic variation within Mexico from over 1000 individuals representing 20 indigenous and 11 mestizo populations. We found striking genetic stratification among indigenous populations within Mexico at varying degrees of geographic isolation. Some groups were as differentiated as Europeans are from East Asians. Pre-Columbian genetic substructure is recapitulated in the indigenous ancestry of admixed mestizo individuals across the country. Furthermore, two independently phenotyped cohorts of Mexicans and Mexican Americans showed a significant association between subcontinental ancestry and lung function. Thus, accounting for fine-scale ancestry patterns is critical for medical and population genetic studies within Mexico, in Mexican-descent populations, and likely in many other populations worldwide.