A sweeping new genetic study reconstructed more than 6,000 years of human history in southern South America. It reveals at least three major population dispersals into the continent and uncovers previously hidden links to Oceania. Drawing on 128 high-quality genomes from 45 Indigenous populations alongside ancient DNA, the research identifies an early peopling possibly dating back 15,000 years or more. It also finds later movements that reshaped the region’s genetic and cultural landscape. One previously unrecognized wave appears to have originated with Mesoamerican-related groups at least 1,300 years ago, leaving a genetic footprint from Mesoamerica to the Caribbean and into southern South America, and pointing to extensive migrations as a key driver of cultural diversity in the Southern Cone, according to Folha de S.Paulo.
The research team analyzed the genetic material of 52 Indigenous individuals from the Pampas, northwestern Patagonia, the Paraná Delta, and eastern Uruguay. The fossil remains date from 6,000 to 150 years ago. Their results show that the Middle Holocene Pampas held at least three genetically distinct ancestries, contradicting earlier assumptions of a single, continuous profile in the region. The data suggest limited contact with groups from southern Patagonia during this time. The work further identified over a million previously unknown genetic variants in Indigenous genomes from the Americas, underscoring how much of global human diversity has remained underrepresented in genetic research.
Kinship to Oceania
Across all the studied regions, genetically distinct groups appear to have spread and intermingled over millennia. Cultural changes were repeatedly influenced by migration and admixture. Large-scale migratory movements in the mid- and late Holocene left a lasting imprint on the genetic makeup and cultural expressions of populations across the Southern Cone.
While separated by vast distances and time, certain populations in the Americas retain hallmarks of ancestry related to modern-day Oceania. Researchers report the persistence of the so-called Ypykuéra signal—an ancient Asian “ghost lineage” with similarities to genome regions found in Australasian groups—present in ancient Brazilian genomes and in some Indigenous peoples for over 10,000 years.
This suggests contact with an unknown, ancient Asian population long before European arrival. Together with evidence for multiple waves of movement into South America, including the Mesoamerican-related dispersal roughly 1,300 years ago, these patterns point to greater mobility and genetic complexity than previous archaeological models alone had indicated.
Catastrophic losses
The study’s historical arc also extends into the upheavals that followed European contact. Researchers describe profound changes to the cultural diversity of present-day South American nations as European institutions and systems supplanted or replaced many Indigenous ones. This transformation coincided with massive displacement and catastrophic demographic losses among Indigenous communities.
Across the Americas, Indigenous peoples experienced a drastic population decline—estimated between 40% and 90%—driven by epidemics introduced from Europe and Africa, enslavement, and conquest. These forces created evolutionary bottlenecks that still shape genetic diversity today. The genetic record captured in both ancient remains and living descendants reflects deep-time migrations and regional interconnections, as well as the severe disruptions of the colonial era, which continue to constrain the range of Indigenous genetic variation.
“European colonization was accompanied by a massive displacement of the Indigenous population, whose genetic diversity is still greatly reduced today,” said Prof. Dr. Cosimo Posth.