An international research team has sequenced the largest genomic dataset yet assembled for Indigenous peoples of the Americas, generating 199 genomes from individuals spanning North America to Patagonia. Led by the Institute of Evolutionary Biology together with the University of São Paulo, the study includes 128 genomes that had never been published before and offers new insight into Indigenous genetic diversity, population history, and adaptation.
The project, part of the Indigenous American Genomic Diversity Project, produced 128 high-coverage whole genomes from eight Latin American countries: Argentina, Bolivia, Brazil, Colombia, Ecuador, Mexico, Paraguay, and Peru. These data represent 45 populations and 28 linguistic families. When high-quality genomes from existing databases were added, the total rose to 199 contemporary Indigenous individuals from 53 populations and 31 linguistic families. Ancient DNA was also incorporated to help reconstruct deeper historical and evolutionary patterns.
The sequencing effort identified more than one million genetic variants not previously observed in other populations. This highlights the extent of Indigenous genomic diversity that has remained underrepresented in global reference data. Because the Americas include environments ranging from the Amazon rainforest to the Andes, the study also detected signs of natural selection linked to immune response, metabolism, growth, and fertility.
The findings, published recently in Nature, expand understanding of Indigenous population history as well. Most current Indigenous peoples in the Americas descend from a migration that occurred about 15,000 years ago via Beringia. The study supports a second migration wave around 9,000 years ago and, for the first time, identifies a third wave approximately 1,300 years ago, when Indigenous populations moved from Mesoamerica into South America and the Caribbean. The genetic footprint of this later movement was found in present-day South American populations and in ancient Caribbean individuals.
The research also confirms the strong genetic bottleneck caused by European colonization, which reduced Indigenous genetic diversity to a fraction of its original level. Even so, some regions show genetic continuity lasting more than 9,000 years. In addition, the study found that around 2% of the genome in some Indigenous peoples shows affinity with populations in Australasia, suggesting an ancient, unsampled Asian population called Ypykuéra. It also confirmed that 1% to 3% of the genome comes from archaic hominids such as Neanderthals and Denisovans, with variants that may have contributed to adaptation in the Americas.
Publication details: Castro e Silva, M.A., Nunes, K., Ribeiro, M.R. et al. The evolutionary history and unique genetic diversity of Indigenous Americans. Nature (2026). https://doi.org/10.1038/s41586-026-10406-w
The project, part of the Indigenous American Genomic Diversity Project, produced 128 high-coverage whole genomes from eight Latin American countries: Argentina, Bolivia, Brazil, Colombia, Ecuador, Mexico, Paraguay, and Peru. These data represent 45 populations and 28 linguistic families. When high-quality genomes from existing databases were added, the total rose to 199 contemporary Indigenous individuals from 53 populations and 31 linguistic families. Ancient DNA was also incorporated to help reconstruct deeper historical and evolutionary patterns.
The sequencing effort identified more than one million genetic variants not previously observed in other populations. This highlights the extent of Indigenous genomic diversity that has remained underrepresented in global reference data. Because the Americas include environments ranging from the Amazon rainforest to the Andes, the study also detected signs of natural selection linked to immune response, metabolism, growth, and fertility.
The findings, published recently in Nature, expand understanding of Indigenous population history as well. Most current Indigenous peoples in the Americas descend from a migration that occurred about 15,000 years ago via Beringia. The study supports a second migration wave around 9,000 years ago and, for the first time, identifies a third wave approximately 1,300 years ago, when Indigenous populations moved from Mesoamerica into South America and the Caribbean. The genetic footprint of this later movement was found in present-day South American populations and in ancient Caribbean individuals.
The research also confirms the strong genetic bottleneck caused by European colonization, which reduced Indigenous genetic diversity to a fraction of its original level. Even so, some regions show genetic continuity lasting more than 9,000 years. In addition, the study found that around 2% of the genome in some Indigenous peoples shows affinity with populations in Australasia, suggesting an ancient, unsampled Asian population called Ypykuéra. It also confirmed that 1% to 3% of the genome comes from archaic hominids such as Neanderthals and Denisovans, with variants that may have contributed to adaptation in the Americas.
Publication details: Castro e Silva, M.A., Nunes, K., Ribeiro, M.R. et al. The evolutionary history and unique genetic diversity of Indigenous Americans. Nature (2026). https://doi.org/10.1038/s41586-026-10406-w