Abstract
The genetic makeup of Indigenous populations inhabiting Mexico has been strongly influenced by geography and demographic history. Here, we perform a genome-wide analysis of 716 newly genotyped individuals from 60 of the 68 recognized ethnic groups in Mexico. We show that the genetic structure of these populations is strongly influenced by geography, and our demographic reconstructions suggest a decline in the population size of all tested populations in the last 15–30 generations. We find evidence that Aridoamerican and Mesoamerican populations diverged roughly 4–9.9 ka, around the time when sedentary farming started in Mesoamerica. Comparisons with ancient genomes indicate that the Upward Sun River 1 (USR1) individual is an outgroup to Mexican/South American Indigenous populations, whereas Anzick-1 was more closely related to Mesoamerican/South American populations than to those from Aridoamerica, showing an even more complex history of divergence than recognized so far.
Highlights
The genetic makeup of Indigenous populations inhabiting Mexico has been strongly influenced by geography and demographic history
These data show that the genetic structure observed in present-day Indigenous Mexican populations reflects complex demographic, cultural, and geographic events, and suggests that there may have been an overlap in the timing of these events, such as the spread of farming and cultural diversification in the differentiation of Aridoamerican/Mesoamerican populations
The influence of the geographic location in the differentiation of Mexican Indigenous populations was observed in the Principal component analysis (PCA), which defined three clusters coincident with the North, Center/ South, and Southeast regions of the Mexican territory, indicating that the geographic distribution influences the genetic structure in Indigenous populations (Fig. 1b, c)
Summary
The genetic makeup of Indigenous populations inhabiting Mexico has been strongly influenced by geography and demographic history. The 68 recognized ethnic groups in Mexico are clustered into 11 linguistic families[7], with unique customs and cultures These populations can be divided into two main geographic/cultural areas: Mesoamerica and Aridoamerica. We perform a population genetics study by genotyping at the genome-wide level 716 individuals from 60 of the 68 recognized ethnic groups in Mexico belonging to the Metabolic Analysis in an Indigenous Sample (MAIS) cohort[9,10,11], which were merged with previously published data sets, yielding a total of 1086 Native Americans from Mexico, representing all linguistic families except Kickapoo (Algonquian language family) (Fig. 1a and Supplementary Table 1). We find that the genetic structure of Mexican indigenous populations is influenced by geography and geographic barriers, historical events, such as the establishment of sedentary agriculture in Mesoamerica, or European contact. Comparisons with ancient genomes from America show that populations from Aridoamerica and some from Mesoamerica may carry an additional ancestry from an unknown population related to the SNA/ANC-A branch that split above the Anzik-1 individual
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