The genomic landscape of Mexican Indigenous populations brings insights into the peopling of the Americas

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.

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MRI-based neuroimaging
All data analyses in this work were done following the standard pipelines available for each software.
The whole genotype data from the 716 Indigenous individuals from MAIS cohort is available under restricted access to protect the privacy of the participants and in alignment with the Institutional Review Board approval and the individual informed consents forms. Access can be obtained through a data-access agreement.
No statistical methods were used to predetermine sample sizes. Sample size in this study was limited by the aviability of samples from each ethnic group included here.
Genome wide genotyping was done for all samples in this work. The following paragraph explaining the exclusion procceses is included in the methods subsections "Samples and data handling": "To perform our estimations, we generated several datasets merging our genotype data with those previously published for several world-wide populations and modern and ancient Native American individuals as follows. For data generated using only an SNV array, we performed the data handling and quality control procedures in Plink V 1.9(ref.62). Each dataset was processed individually, including per marker and per sample examinations. We removed SNVs with genotyping rates < 98% and those with a minor allele frequency of 1%, and then removed mitochondrial and sex chromosome SNVs. Finally, we excluded individuals with missing rates > 3% and with discordant gender information." Due the nature of our population genetics study, there is no need for replication because we did not perform any experimental procedure.
Samples were grouped based on the ethnic group who each participant report. In other cases were grouped based on their geographic location (North, Northwest, Center, South and Southeast).
No blinding techniques were implemented because they are not necesary for population genetics studies.