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-Hernández, Alejandra 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 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 and Lorena Orozco ()
Additional contact information
Humberto García-Ortiz: Instituto Nacional de Medicina Genómica, Tlalpan
Francisco Barajas-Olmos: Instituto Nacional de Medicina Genómica, Tlalpan
Cecilia Contreras-Cubas: Instituto Nacional de Medicina Genómica, Tlalpan
Miguel Ángel Cid-Soto: Instituto Nacional de Medicina Genómica, Tlalpan
Emilio J. Córdova: Instituto Nacional de Medicina Genómica, Tlalpan
Federico Centeno-Cruz: Instituto Nacional de Medicina Genómica, Tlalpan
Elvia Mendoza-Caamal: Instituto Nacional de Medicina Genómica, Tlalpan
Isabel Cicerón-Arellano: Instituto Nacional de Medicina Genómica, Tlalpan
Marlen Flores-Huacuja: Instituto Nacional de Medicina Genómica, Tlalpan
Paulina Baca: Instituto Nacional de Medicina Genómica, Tlalpan
Deborah A. Bolnick: University of Connecticut
Meradeth Snow: University of Montana
Silvia Esperanza Flores-Martínez: Instituto Mexicano del Seguro Social (IMSS)
Rocio Ortiz-Lopez: Escuela de Medicina y Ciencias de la Salud. Universidad Autonoma de Nuevo Leon, Centro de Investigacion y Desarrollo en Ciencias de la Salud
Austin W. Reynolds: Baylor University
Antonio Blanchet: Instituto Nacional de Medicina Genómica, Tlalpan
Mirna Morales-Marín: Instituto Nacional de Medicina Genómica, Tlalpan
Rafael Velázquez-Cruz: Instituto Nacional de Medicina Genómica, Tlalpan
Aleksandar David Kostic: Joslin Diabetes Center
Carlos Galaviz-Hernández: Instituto Politécnico Nacional, CIIDIR-Durango
Alejandra Guadalupe García-Zapién: Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara
José Concepción Jiménez-López: Museo Nacional de Antropología
Guadalupe León-Reyes: Instituto Nacional de Medicina Genómica, Tlalpan
Eva Gabriela Salas-Bautista: Museo Nacional de Antropología
Blanca Patricia Lazalde-Ramos: Universidad Autónoma de Zacatecas
Juan Luis Jiménez-Ruíz: Instituto Nacional de Medicina Genómica, Tlalpan
Guadalupe Salas-Martínez: Instituto Nacional de Medicina Genómica, Tlalpan
Jazmín Ramos-Madrigal: The University of Copenhagen
Elaheh Mirzaeicheshmeh: Instituto Nacional de Medicina Genómica, Tlalpan
Yolanda Saldaña-Alvarez: Instituto Nacional de Medicina Genómica, Tlalpan
María Carmen Abrahantes-Pérez: Instituto Nacional de Medicina Genómica, Tlalpan
Francisco Loeza-Becerra: Universidad Michoacana de San Nicolás de Hidalgo
Raúl Mojica-Espinosa: Instituto Nacional de Medicina Genómica, Tlalpan
Federico Sánchez-Quinto: Instituto Nacional de Medicina Genómica, Tlalpan
Héctor Rangel-Villalobos: Universidad de Guadalajara Ocotlán
Martha Sosa-Macías: Instituto Politécnico Nacional, CIIDIR-Durango
José Sánchez-Corona: Instituto Mexicano del Seguro Social (IMSS)
Augusto Rojas-Martinez: Escuela de Medicina y Ciencias de la Salud. Universidad Autonoma de Nuevo Leon, Centro de Investigacion y Desarrollo en Ciencias de la Salud
Angélica Martínez-Hernández: Instituto Nacional de Medicina Genómica, Tlalpan
Lorena Orozco: Instituto Nacional de Medicina Genómica, Tlalpan

Nature Communications, 2021, vol. 12, issue 1, 1-12

Abstract: 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.

Date: 2021
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DOI: 10.1038/s41467-021-26188-w

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