The evolutionary history and unique genetic diversity of Indigenous Americans

, owing to the limited availability of genomic data. Here we present data on 128 high-coverage Indigenous American genomes and show they harbour extensive and previously uncharacterized genetic diversity, reflecting at least three dispersals into South America, followed by regional differentiation and long-term continuity. We identified widespread natural selection signals in genes associated with immunity, metabolism, reproduction and development, which were shaped by adaptation to diverse environmental conditions. Notably, several genomic regions exhibit a remarkable allele sharing with Australasian populations, probably originating from an ancient admixture event and partly maintained by selection for more than 10,000 years. We also detected distinct contributions from archaic humans with adaptive introgression affecting key biological functions. The limited overlap between the regions of Australasian affinity and archaic ancestry indicates independent evolutionary origins of these signals. These findings challenge simplified models of continental settlements and show a more dynamic and complex evolutionary history for the Indigenous peoples in America.

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Publication Details

Journal
Nature
Published
2026-04-22
DOI
https://doi.org/10.1038/s41586-026-10406-w
Primary Topic
Forensic and Genetic Research
Type
article
Field-Weighted Citation Impact
0.00

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article

The evolutionary history and unique genetic diversity of Indigenous Americans

Renan Barbosa Lemes, Graciela Bailliet, Julio Lara‐Riegos, Antonia Walter et al.
Nature
Forensic and Genetic Research
article

The evolutionary history and unique genetic diversity of Indigenous Americans

Renan Barbosa Lemes, Graciela Bailliet, Julio Lara‐Riegos, Antonia Walter, David Comas, Emilia Vásquez-Domínguez, Rodrigo Barquera, Ricardo Fujita, Hemanoel Passarelli‐Araujo, María Cátira Bortolini, João Farias Guerreiro, Tábita Hünemeier, José Geraldo Mill, Cláudio M. Bravi, Ana M. Tito-Álvarez, Susana Revollo, Marcos Araújo Castro e Silva, Carlos Eduardo G. Amorim, Virgínia Ramallo, María Laura Parolín, Kelly Nunes, Chiara Barbieri, Diana Iraíz Hernández-Zaragoza, Oana del Castillo-Chávez, Lilian Kimura, José R. Sandoval, MA Ribeiro, María Ermila Moo-Mezeta, Camilo Zurita, Fabrício R. Santos, Ricardo Serrano-Osuna, Trija Nag Chowdhury, Putira Sacuena, Daniela Macías-Herrera, Julio César Torres-Romero, Abraham Aguilar-Campos
article en

Abstract

, owing to the limited availability of genomic data. Here we present data on 128 high-coverage Indigenous American genomes and show they harbour extensive and previously uncharacterized genetic diversity, reflecting at least three dispersals into South America, followed by regional differentiation and long-term continuity. We identified widespread natural selection signals in genes associated with immunity, metabolism, reproduction and development, which were shaped by adaptation to diverse environmental conditions. Notably, several genomic regions exhibit a remarkable allele sharing with Australasian populations, probably originating from an ancient admixture event and partly maintained by selection for more than 10,000 years. We also detected distinct contributions from archaic humans with adaptive introgression affecting key biological functions. The limited overlap between the regions of Australasian affinity and archaic ancestry indicates independent evolutionary origins of these signals. These findings challenge simplified models of continental settlements and show a more dynamic and complex evolutionary history for the Indigenous peoples in America.

NatureVol. 653(8113)
Universidade Federal de Minas Gerais (BR), Universidad Mayor de San Andrés (BO), Universidade Federal do Rio Grande do Sul (BR), Mexican Social Security Institute (MX), Universitat Pompeu Fabra (ES), University of Cagliari (IT), Universidade de São Paulo (BR), University of Zurich (CH), Universidad de San Martín de Porres (PE), Autonomous University of Yucatán (MX), Universidad de Las Américas (EC), Zürcher Fachhochschule (CH), Max Planck Institute for Evolutionary Anthropology (DE), Hospital General De Zona (MX), Institut de Biologia Evolutiva (ES), Centro Científico Tecnológico Patagónico (AR), National Institute of Anthropology and History (MX), Instituto Multidisciplinario de Biología Celular (AR), Escuela Nacional de Antropología e Historia, Universidade Federal do Espírito Santo (BR), Arizona State University (US), Universidade Federal do Pará (BR)
National Science Foundation, European Commission, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, Fundação de Amparo à Pesquisa do Estado de São Paulo, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Conselho Nacional de Desenvolvimento Científico e Tecnológico, Universität Zürich, Agencia Estatal de Investigación, National Institute of General Medical Sciences
Life in Land
Openalex Percentile: Top 22%
Forensic and Genetic Research
DOIOpen Access PDFOpenAlex
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