Demographic history and biologically relevant genetic variation of Native Mexicans inferred from whole-genome sequencing

Sandra Romero-Hidalgo, Adrián Ochoa-Leyva, Alejandro Garcíarrubio, Victor Acuña-Alonzo, Erika Antúnez-Argüelles, Martha Balcazar-Quintero, Rodrigo Barquera-Lozano, Alessandra Carnevale, Fernanda Cornejo-Granados, Juan Carlos Fernández-López, Rodrigo García-Herrera, Humberto García-Ortíz, Ángeles Granados-Silvestre, Julio Granados, Fernando Guerrero-Romero, Enrique Hernández-Lemus, Paola León-Mimila, Gastón Macín-Pérez, Angélica Martínez-Hernández, Marta Menjivar, Enrique Morett, Lorena Orozco, Guadalupe Ortíz-López, Fernando Pérez-Villatoro, Javier Rivera-Morales, Fernando Riveros-McKay, Marisela Villalobos-Comparán, Hugo Villamil-Ramírez, Teresa Villarreal-Molina, Samuel Canizales-Quinteros () and Xavier Soberón ()
Additional contact information
Sandra Romero-Hidalgo: Instituto Nacional de Medicina Genómica (INMEGEN)
Adrián Ochoa-Leyva: Instituto Nacional de Medicina Genómica (INMEGEN)
Alejandro Garcíarrubio: Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM)
Victor Acuña-Alonzo: Escuela Nacional de Antropología e Historia
Erika Antúnez-Argüelles: Instituto Nacional de Medicina Genómica (INMEGEN)
Martha Balcazar-Quintero: Universidad Iberoamericana
Rodrigo Barquera-Lozano: Escuela Nacional de Antropología e Historia
Alessandra Carnevale: Instituto Nacional de Medicina Genómica (INMEGEN)
Fernanda Cornejo-Granados: Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM)
Juan Carlos Fernández-López: Instituto Nacional de Medicina Genómica (INMEGEN)
Rodrigo García-Herrera: Instituto Nacional de Medicina Genómica (INMEGEN)
Humberto García-Ortíz: Instituto Nacional de Medicina Genómica (INMEGEN)
Ángeles Granados-Silvestre: UNAM
Julio Granados: Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán
Fernando Guerrero-Romero: Instituto Mexicano del Seguro Social
Enrique Hernández-Lemus: Instituto Nacional de Medicina Genómica (INMEGEN)
Paola León-Mimila: Instituto Nacional de Medicina Genómica (INMEGEN)
Gastón Macín-Pérez: Escuela Nacional de Antropología e Historia
Angélica Martínez-Hernández: Instituto Nacional de Medicina Genómica (INMEGEN)
Marta Menjivar: Instituto Nacional de Medicina Genómica (INMEGEN)
Enrique Morett: Instituto Nacional de Medicina Genómica (INMEGEN)
Lorena Orozco: Instituto Nacional de Medicina Genómica (INMEGEN)
Guadalupe Ortíz-López: Hospital Juárez de México
Fernando Pérez-Villatoro: Instituto Nacional de Medicina Genómica (INMEGEN)
Javier Rivera-Morales: Escuela Nacional de Antropología e Historia
Fernando Riveros-McKay: Instituto Nacional de Medicina Genómica (INMEGEN)
Marisela Villalobos-Comparán: Instituto Nacional de Medicina Genómica (INMEGEN)
Hugo Villamil-Ramírez: Instituto Nacional de Medicina Genómica (INMEGEN)
Teresa Villarreal-Molina: Instituto Nacional de Medicina Genómica (INMEGEN)
Samuel Canizales-Quinteros: Instituto Nacional de Medicina Genómica (INMEGEN)
Xavier Soberón: Instituto Nacional de Medicina Genómica (INMEGEN)

Nature Communications, 2017, vol. 8, issue 1, 1-8

Abstract: Abstract Understanding the genetic structure of Native American populations is important to clarify their diversity, demographic history, and to identify genetic factors relevant for biomedical traits. Here, we show a demographic history reconstruction from 12 Native American whole genomes belonging to six distinct ethnic groups representing the three main described genetic clusters of Mexico (Northern, Southern, and Maya). Effective population size estimates of all Native American groups remained below 2,000 individuals for up to 10,000 years ago. The proportion of missense variants predicted as damaging is higher for undescribed (~ 30%) than for previously reported variants (~ 15%). Several variants previously associated with biological traits are highly frequent in the Native American genomes. These findings suggest that the demographic and adaptive processes that occurred in these groups shaped their genetic architecture and could have implications in biological processes of the Native Americans and Mestizos of today.

Date: 2017
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DOI: 10.1038/s41467-017-01194-z

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