A groundbreaking international study has compiled the largest and most comprehensive genomic dataset of Indigenous American populations to date. Published in the journal Nature, the research sequenced 128 high-coverage whole genomes from individuals across eight Latin American countries, shedding new light on the complex evolutionary history, unique genetic diversity, and health implications for Indigenous peoples. The study reveals over a million previously unknown genetic variants and uncovers a hidden third wave of migration into South America.
The research, part of the Indigenous American Genomic Diversity Project, combined newly sequenced genomes with existing databases to analyze a total of 199 contemporary Indigenous individuals from 53 populations, alongside ancient DNA data. This unprecedented effort aims to address the historical underrepresentation of Indigenous American populations in genomic research, which has left significant gaps in understanding human diversity and evolution.
Geographic distribution of the indigenous American individuals included in the study. Each point represents a sampling location and its size is proportional to the number of individuals in that population. (Hemanoel Passareli-Araujo/Nature)
A Million New Variants and Ancient Migrations
One of the most striking findings is the discovery of over a million genetic variants not previously observed in other global populations. These variants highlight the unique genetic diversity of Indigenous Americans, shaped by their adaptation to diverse environments, from the Amazon rainforest to the high-altitude Andes. Researchers identified genetic signatures of natural selection related to immune response, metabolism, and growth, demonstrating how these populations adapted to distinct ecological pressures.
Beyond genetic diversity, the study provides a clearer picture of the migration patterns that populated the Americas. While it is widely accepted that most Indigenous Americans descend from a migration via Beringia around 15,000 years ago, followed by a second wave 9,000 years ago, this new research has identified evidence of a third wave. Occurring roughly 1,300 years ago, this migration involved the movement of Indigenous populations from Mesoamerica into South America and the Caribbean, leaving a genetic footprint still visible today.
- Genetic studies link indigenous peoples in the Amazon and Australasia
- Did Paleoamericans Reach South America First?
Three major dispersals shaped the genetic diversity of the indigenous peoples of South America. (IMAGE) From left to right, each panel represents one of these dispersals. The right panel shows the third dispersal (<1,300 years), associated with Mesoamerican populations, which contributed extensively to South America and the Caribbean. These populations mixed with groups from the first dispersal (including contributions from Population Y) and, in the Andes and the Southern Cone, primarily with populations from the second dispersal, maintaining genetic continuity for up to 9,000 years in these regions. (Marcos Araújo Castro e Silva/Nature)
The Australasian Connection and Archaic Ancestry
The genomic data also revealed fascinating ancestral connections. The study confirms that around 2% of the genome in some South American Indigenous populations shows genetic affinity with populations in Australasia, including Australia and New Guinea. This connection, known as the Ypykuéra (Y-lineage), suggests ancient intermixing with an unsampled Asian population over 10,000 years ago.
Furthermore, the research confirms that between 1% and 3% of the Indigenous American genome comes from archaic hominids like Neanderthals and Denisovans. Importantly, these ancient relatives contributed genetic variants that proved crucial for adapting to the diverse environments of the American continent.
- Denisovan DNA Gift Lives On In Modern Indigenous Americans
- How DNA Analysis Ended Scientific Disputes in the Case of the Kennewick Man
Overcoming the Bottleneck of Colonization
The study also starkly illustrates the profound "bottleneck" effect caused by European colonization, which decimated Indigenous populations by up to 90%. Despite this catastrophic loss of genetic diversity, the researchers observed remarkable genetic continuity spanning more than 9,000 years in certain regions, demonstrating the resilience of these populations.
"Current genetic diversity is only a fraction of the original," explained Tábita Hünemeier, principal investigator at the Institute of Evolutionary Biology. "Even so, we can see genetic continuity spanning more than 9,000 years in some regions."
The inclusion of Indigenous populations in genomic research is not just about understanding the past; it has vital implications for the future. By identifying previously unknown genetic variants with medical relevance, this dataset creates opportunities to improve biomedical research, disease prevention, and drug design for Indigenous communities and the global population alike.
Top image: Representation of Indigenous Americans. Source: AI Generated
By Gary Manners
References
Amorim, C.E.G., et al. 2026. Largest genomic dataset of Indigenous Americans to date sheds light on history, diversity and health. ASU News. Available at: https://news.asu.edu/20260422-science-and-technology-new-research-tracing-genomic-threads-indigenous-ancestry
Castro e Silva, M.A., et al. 2026. The evolutionary history and unique genetic diversity of Indigenous Americans. Nature. Available at: https://www.nature.com/articles/s41586-026-10406-w
Hünemeier, T., et al. 2026. Unraveling the genomic roots of Indigenous peoples. EurekAlert!. Available at: https://www.eurekalert.org/news-releases/1124930
Nature Research Briefing. 2026. Genomic roots of Indigenous Americans uncovered. Nature. Available at: https://www.nature.com/articles/d41586-026-01173-9
