Mexican Population Genetics

In the fifteenth century, prior to the Conquest of Mexico, Mexican territory was inhabited by many different Native groups located mainly in Mesoamerica, but also in Northern Mexico, inhabited by nomadic or semi-nomadic peoples. The Mexican population of today is the result of complex and ongoing admixture processes that began with the Conquest of Mexican territory by the Spaniards in 1521. The admixture process occurred mainly between Native Americans and Europeans, although there was a smaller contribution of the African population introduced by slave traders during the colonial period. Currently, there are 68 acknowledged Native American languages in Mexico. Native populations not only contributed very importantly to the admixture process of the Mexican population, but currently up to 21% of Mexicans identify themselves as members of one of the acknowledged Indigenous groups of Mexico. Moreover, according to a recent survey, approximately 7% of the Mexican population, that is over 7 million Mexicans, speak a Native language.

From the introduction to a new open access study of Mexican population genetics.

The sample size is small, but carefully chosen and rich:

Whole genomes of a total of 15 Mexican individuals were sequenced, including 12 NAs from six distinct ethnic groups (Tarahumara and Tepehuano from the North; Nahua, Totonaca, Zapoteca from the South; and Maya from the South-East) and a trio of Mexican Mestizos (mother, father, and offspring). NA participants were selected considering ancestry, linguistic group, geographic location, and representation of three of the main genetic clusters previously described in the NA Map of Mexico: Northern, Southern, and Mayan, as described by Moreno-Estrada et al. Estimated NA ancestry using genome-wide data was over 98% in all indigenous participants, except for both Tepehuanos who were selected for having the highest NA ancestry (91%) among those available for whole-genome sequencing (WGS).

The study reveals pre-Columbian population structure and effective population sizes.