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

Humberto García-Ortiz, Francisco Barajas-Olmos, Cecilia Contreras-Cubas, Miguel Ángel Cid-Soto, Emilio J. Córdova, Federico Centeno-Cruz, Elvia Mendoza-Caamal, Isabel Cicerón-Arellano, Marlen Flores-Huacuja, Paulina Baca, Deborah A. Bolnick, Meradeth Snow, Silvia Esperanza Flores-Martínez, Rocio Ortiz-Lopez, Austin W. Reynolds, Antonio Blanchet, Mirna Morales-Marín, Rafael Velázquez-Cruz, Aleksandar David Kostic, Carlos Galaviz-HernándezAlejandra Guadalupe García-Zapién, José Concepción Jiménez-López, Guadalupe León-Reyes, Eva Gabriela Salas-Bautista, Blanca Patricia Lazalde-Ramos, Juan Luis Jiménez-Ruíz, Guadalupe Salas-Martínez, Jazmín Ramos-Madrigal, Elaheh Mirzaeicheshmeh, Yolanda Saldaña-Alvarez, María del Carmen Abrahantes-Pérez, Francisco Loeza-Becerra, Raúl Mojica-Espinosa, Federico Sánchez-Quinto, Héctor Rangel-Villalobos, Martha Sosa-Macías, José Sánchez-Corona, Augusto Rojas-Martinez, Angélica Martínez-Hernández, Lorena Orozco

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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.

Original languageEnglish
Article number5942
JournalNature Communications
Volume12
Issue number1
DOIs
StatePublished - Dec 1 2021

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