Largest genomic dataset of Indigenous Americans to date sheds light on history, diversity and health
Three major dispersals shaped the genetic diversity of the Indigenous peoples of South America, starting more than 9,000 years ago (as seen above left), with the last migration (as seen above right) at approximately 1,300 years ago. Image courtesy of Marcos Araújo Castro e Silva
The story of Indigenous peoples in the Americas is woven through their DNA, and scientists are beginning to trace its threads in new ways.
In a new study published today in Nature, an international team led by the Institute of Evolutionary Biology, with partners at the University of São Paulo and Arizona State University, analyzed genomes from Indigenous populations spanning North America to Patagonia. The result is the largest dataset of its kind, helping researchers trace the genetic threads of ancestry across the Americas.
The research, part of the Indigenous American Genomic Diversity Project, includes 128 newly sequenced, high-coverage whole genomes from eight Latin American countries — Argentina, Bolivia, Brazil, Colombia, Ecuador, Mexico, Paraguay and Peru — representing 45 populations and 28 linguistic families.
The team combined these with high-quality genomes from preexisting databases, taking the total to 199 contemporary Indigenous individuals from 53 populations and 31 linguistic families. Ancient DNA data was also incorporated, allowing researchers to explore deeper questions about populations and evolution.
“Our findings provide the most comprehensive view of Indigenous American genomic diversity and evolutionary history to date,” said study co-author Carlos Eduardo G. Amorim, an anthropological geneticist and assistant professor in ASU's School of Human Evolution and Social Change.
“Genetic information from Indigenous American populations is essential because these groups have been historically underrepresented in genomic research, leaving major gaps in our understanding of human diversity, evolution and health. Because of that, substantial genetic variation in humans remains undocumented, among which are variants with biomedical relevance to these communities and humanity more broadly,” Amorim said.
The study identified more than 1 million genetic variants not previously documented in other populations, highlighting the unique diversity of Indigenous genomes. From the Amazon rainforest to the high-altitude Andes, the varied environments of the Americas have shaped how populations adapt. The team identified genetic signatures of natural selection tied to immune response, metabolism, growth and fertility.
“These results demonstrate the need to better represent these populations in genomics. From drug design to disease prevention, understanding human genomic diversity benefits both Indigenous communities and the global population," said Tábita Hünemeier, principal investigator at the Institute of Evolutionary Biology and leader of the study.
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Proportions of genetic ancestry inferred from the DNA analyzed in the study. The average ancestry of each population is represented on a map of the Americas.
Image courtesy of Marcos Araújo Castro e Silva
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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.
Image courtesy of Hemanoel Passareli-Araujo
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A researcher meets with members of the Mapuche community in Argentine Patagonia. Collaboration with communities was an integral part of the study.
Photo by Carlos Eduardo Guerra Amorim
For Amorim, this diversity is important to highlight and goes beyond the DNA.
“It is important to emphasize that Indigenous populations are not a single, homogeneous group. There is substantial cultural and biological diversity across these communities," said Amorim, who is also core faculty in ASU's Center for Evolution and Medicine and a research scientist with ASU's Institute of Human Origins. "While some of our findings are discussed at a continental scale, we recognize that these populations differ in many aspects of their history, culture and biology, and should not be treated as a single unit.”
Nearly a decade of research and collaboration went into the study, involving researchers from across the Global South and Latin America, as well as ongoing partnerships with Indigenous communities.
Partnership with the Indigenous communities was an integral and important part of the study.
“The research was conducted in accordance with the ethical standards of each participating country. Informed consent was obtained from every participant, primarily in written form but also orally when needed, and in some cases, at the community or tribal level. We returned the results to participating communities in accessible formats, including tailored presentations and written materials with visuals, such as booklets. The feedback from the communities was very positive,” Amorim said.
Beyond genetic diversity, the study also sheds light on migration patterns across the Americas.
The migration of Asian populations into the Americas via Beringia marked the last major chapter of human continental movement. With few exceptions, primarily among Arctic groups, most Indigenous peoples in the Americas trace their ancestry to a migration that occurred about 15,000 years ago. After entering North America, these early populations rapidly expanded across the continent. Around 9,000 years ago, a second wave of migration partially replaced earlier groups.
Now, for the first time, researchers have identified evidence of a third wave, occurring roughly 1,300 years ago, when Indigenous populations moved from Mesoamerica into South America and the Caribbean. Its genetic signature appears in present-day South American populations and in ancient Caribbean remains.
The research also confirms the profound “bottleneck” effect caused by European colonization.
“Current genetic diversity is only a fraction of the original, as colonization decimated Indigenous populations by 90%. Even so, we can see genetic continuity spanning more than 9,000 years in some regions,” Hünemeier said.
The study also reveals new insights into the genetic ancestry of some Indigenous Americans, revealing that around 2% of the genome shows genetic affinity with populations in Australasia, including those in Australia, New Guinea and the Andaman Islands. This connection, present in South American individuals dating back more than 10,000 years and in very similar proportions, suggests the influence of an ancient, unsampled Asian population, known as Ypykuéra (Y-lineage), which intermixed with the ancestors of these populations.
The study also confirms that between 1% and 3% of the genome comes from archaic hominids, such as Neanderthals and Denisovans, a proportion similar to that seen in other regions, although there is a distinctive pattern. Importantly, these hominids contributed genetic variants that proved key to adaptation to the American continent, as evidenced by signs of natural selection found in the genome.
Beyond uncovering the past, the study also lays a foundation for future research.
“From a bioanthropological perspective, it will allow us to refine models of population history in the Americas, better understand how genetic diversity is structured across regions, and investigate how our ancestors have adapted to different environmental pressures,” Amorim said.
“The dataset also creates opportunities to improve biomedical research by making it more representative of global diversity," he said. "This can help identify genetic variants that are currently missing from reference datasets, many with medical relevance, and thus improve our understanding of disease risk and treatment response across these populations.”
This article was adapted from a press release from the Institute of Evolutionary Biology, a joint center of the Spanish National Research Council and Pompeu Fabra University.
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