Indigenous DNA Reveals a Ghost Lineage With No Fossils

Hidden inside the DNA of living Indigenous people in the Americas is a signal from a population that, as far as anyone can tell, has never left a single bone, tool, or fossil behind.

A Project Built With Indigenous Communities

The findings come from the Indigenous American Genomic Diversity Project, an international effort led by researchers at Spain’s Institute of Evolutionary Biology and Pompeu Fabra University, including first author Marcos Araújo Castro e Silva and Tábita Hünemeier, who heads the institute’s Human Population Genomics Lab. The team sequenced 128 new genomes from people living in Argentina, Bolivia, Brazil, Colombia, Ecuador, Mexico, Paraguay, and Peru, then combined them with 71 previously published Indigenous genomes for a combined dataset covering 45 populations and 28 language families. Until now, only two Amazonian Indigenous populations had been genetically characterized, and because of their isolation, Castro e Silva noted, they weren’t very representative. Hünemeier said the team worked with Indigenous communities throughout to develop the study and integrate its findings into their own histories. The results were published April 22 in the journal Nature.

Three Waves Into South America

The analysis found South America was settled in at least three separate waves, one of them previously unknown. The earliest wave reached the continent more than 9,000 years ago. A second, genetically distinct lineage, shared today by the Quechua of Peru, spread through Central America and into South America around 9,000 years ago. The newly identified third dispersal likely arrived at least 1,300 years ago from groups related to Mesoamerica. That timing roughly overlaps with the decline of major Mesoamerican centers like Teotihuacan between AD 650 and 750, but Hünemeier told Live Science the genetic data doesn’t point to a single event. Instead, it suggests a more gradual, complex process involving increasing connectivity and gene flow between Mesoamerica, the Caribbean, and South America over time.

The Ghost in the Genome

The most striking result came from something researchers weren’t expecting to find at all. The genomes carried traces of an ancient Asian population, a ghost lineage that contributed genes to both Indigenous Americans and early Australasians, the ancient peoples of a region covering present-day Australia, New Zealand, and the Pacific Islands. The team named this signal Ypykuéra, meaning ancestor in the Tupi language of Brazil. It appears at low but consistent levels in Indigenous people across the Americas and has been present for more than 10,000 years. What makes it a ghost is the physical record: no fossil evidence of the Ypykuéra population has ever been found anywhere. Hünemeier said the findings reinforce the idea that the peopling of the Americas was more dynamic and complex than previously thought, involving contributions from ancestral populations not yet represented in the archaeological or fossil record.

Genes Shaped by a New Continent

The genomes also revealed how natural selection shaped the people who settled what the researchers call the final frontier of human migration. Genes tied to immune function, energy metabolism, fertility, fetal growth, and malaria protection persisted at high levels in Indigenous populations, reflecting adaptation to demanding new environments like the Amazon rainforest and the high Andes. Some of these genes are also found in modern Australasian populations, suggesting several ancient Ypykuéra traits were positively selected to help Indigenous Americans thrive in unfamiliar landscapes. Overall, the project found Indigenous Americans are less genetically diverse than other continental human groups, but still more diverse than previously understood.

A Fraction of What Once Existed

Hünemeier stressed that today’s genetic diversity represents only a fraction of the original, since European colonization decimated Indigenous populations by roughly 90 percent. The combined effects of population collapse, fragmentation, and isolation, along with epidemics, enslavement, and warfare, created severe evolutionary bottlenecks. Even so, the study observed genetic continuity of more than 9,000 years in some regions. Carlos Eduardo Amorim, an anthropologist at Arizona State University and study co-author, said genetic information from Indigenous American populations is essential because these groups have historically been underrepresented in genomic research, leaving major gaps in the understanding of human diversity, evolution, and health.

Sources

This report draws on original coverage by Live Science of the peer-reviewed study by Araújo Castro e Silva, Hünemeier, and colleagues, published in Nature (2026).