Ancient DNA shows Andean farming spread through culture, not conquest

Somewhere around 800 years ago, a group of maize farmers began arriving in Argentina's Uspallata Valley. They were not invaders. They carried no weapons that left archaeological traces, and the locals did not flee. Instead, the newcomers were buried alongside long-established residents in shared cemetery sites. But their bones told a different story from those of their neighbors - childhood nutritional stress etched into their skeletons, tuberculosis DNA preserved in their remains, and isotopic chemical signatures showing they had migrated from somewhere else in the broader region.

Who were these people, and why did they leave their homes?

A study published in Nature, led by the Microbial Paleogenomics Unit at Institut Pasteur in Paris, pieces together the answer using ancient DNA from 46 individuals, stable isotope analysis of bones and teeth, archaeological records, and paleoclimate data. The result is a 2,000-year reconstruction of one valley's population history that speaks to a much larger and more fundamental question in human history: how did farming spread across South America?

Local people adopted crops, not the other way around

The debate over agricultural expansion has occupied archaeologists for decades. When farming shows up in a new region, two very different scenarios could explain it. Farmers could have physically moved into the area and displaced or absorbed local populations. Or existing hunter-gatherer communities could have learned to cultivate crops through sustained contact with their agricultural neighbors - adopting the technology without being replaced by its practitioners.

Material culture alone often cannot distinguish between these scenarios with confidence, since pottery styles, tool kits, and agricultural techniques can spread through trade and imitation as easily as through population movement. The Uspallata Valley, located at the southern margin of Andean farming spread where agriculture arrived much later than in the major domestication centers of the continent, offered an ideal natural experiment to disentangle these possibilities.

The genetic data delivered a definitive verdict. Researchers found strong genetic continuity between hunter-gatherers living in the valley around 2,200 years ago and the farming populations that followed more than a millennium later. The DNA of the farmers was essentially the same as the DNA of the earlier foragers. Local people adopted crops and agricultural techniques through cultural transmission without being demographically replaced by incoming farming populations.

Co-first author Pierre Luisi, a researcher at CONICET in Argentina who began this work as a postdoc at Institut Pasteur, emphasized a further implication. The study documents a genetic component with very deep divergence that persists in modern populations of the region. Its continued presence directly contradicts historical narratives that claimed indigenous descendants had gone extinct following the establishment and growth of the Argentine nation-state.

Flexible farming, not rigid dependence

Carbon and nitrogen isotopes preserved in archaeological bones and teeth revealed what these ancient people ate averaged over their lifetimes. The picture was not one of steady, progressive agricultural intensification moving in a single direction. Instead, maize consumption fluctuated substantially over the centuries, consistent with flexible, opportunistic farming in which agriculture supplemented rather than replaced traditional foraging and hunting strategies.

But at one major cemetery site called Potrero Las Colonias, dating to roughly 800-600 years ago, the dietary pattern changed sharply and dramatically. Most individuals buried there showed exceptionally high maize dependence - among the highest values documented anywhere in the southern Andes. Their strontium isotope signatures, which reflect the geological characteristics of the area where a person grew up, indicated they were not local to the Uspallata Valley. These were migrants who had come from elsewhere.

A shrinking community under compound pressures

The migrant group's genomic profile told a troubling story. They were genetically close to local populations - part of the same broad metapopulation distributed across the region - but their genomes showed clear signatures of sustained demographic decline over multiple generations. This was not a thriving, expanding community colonizing new territory. It was a population that had been shrinking under persistent and compounding stress for a long time before arriving in the valley.

Multiple independent lines of evidence converged on what was producing that stress. Paleoclimate records from the broader region document a period of prolonged climatic instability coinciding with the migrants' arrival and demographic decline. Skeletal markers in the migrants showed evidence of childhood nutritional deprivation - markers that form during critical developmental windows and persist into adulthood. And ancient pathogen DNA analysis revealed the presence of Mycobacterium tuberculosis at the site, carrying a strain that fell within a lineage known from pre-contact South America.

The detection of tuberculosis this far south was unexpected. Previous ancient TB findings in the Americas had been documented only in Peru and Colombia, considerably farther north. Finding it in western Argentina expands the known geographic range of pre-Columbian tuberculosis and raises new questions about how the disease circulated across the continent, what ecological conditions sustained its transmission, and whether it contributed to the demographic pressures on the migrant community.

Women held the kinship network together

Genomic kinship analysis added a remarkable dimension to the story of these migrants. Many of the individuals buried at Potrero Las Colonias were closely related to each other, but they were not all buried at the same time. The pattern was consistent with sustained, multigenerational movement into the Uspallata Valley over the course of decades - not a single mass migration event but repeated, coordinated relocations over a long period.

A large kinship network structured primarily through maternal links connected the migrant individuals across burial layers. A single mitochondrial DNA lineage dominated across the group, meaning most migrants shared a common maternal ancestor. This pattern suggests that women played a central organizing role in maintaining family continuity and coordinating the mobility of extended family groups during a period of severe environmental and health pressures.

Co-first author Ramiro Barberena, an archaeologist at CONICET, offered a plain assessment: no farming community abandons its fields and homes casually. The evidence was most consistent with people moving under overwhelming pressure - force majeure in the original legal sense - relying on family bonds and kinship networks to navigate overlapping crises of climate instability, food insecurity, and infectious disease.

Peaceful coexistence in a stressed landscape

Despite the pressures driving the migration, the archaeological record showed no evidence of violence between local and incoming populations. Migrants and long-term residents were occasionally buried within the same mortuary contexts, sharing cemetery space in a way that implies social integration rather than conflict. Whatever tensions may have existed between a declining migrant community and an established local population sharing the same valley during a period of environmental stress, those tensions did not escalate into armed conflict that left physical traces in the skeletal or material record.

What the bones cannot tell us

The study's considerable strength lies in its integration of multiple independent data sources - genetics, stable isotopes, archaeology, paleoclimate reconstruction, and pathogen genomics - into a coherent narrative. But each source has inherent limitations. Ancient DNA preservation is uneven and influenced by burial conditions, and 46 individuals across 2,000 years represent a sampling of the population rather than its entirety. Stable isotope signatures capture long-term dietary averages but miss short-term fluctuations and seasonal variation. The tuberculosis detection, while scientifically significant, comes from a single site and cannot establish the disease's prevalence in the broader region.

The study also cannot fully explain why the migrant farming community was declining demographically. Climate instability, nutritional stress, and infectious disease likely interacted and reinforced each other in a downward spiral, but the relative contribution of each factor and the precise causal chain remains uncertain. Whether similar dynamics of crisis-driven, kinship-organized migration played out in other southern Andean valleys during this period is unknown - this is one exceptionally detailed case study, not a demonstrated continental pattern.

The research was conducted in close collaboration with Huarpe Indigenous communities, whose ancestors are among the people studied. Three community members - Claudia Herrera, Graciela Coz, and Matias Candito - co-authored the article. Regular meetings with the research team shaped the questions asked, how evidence was interpreted, and how results would be communicated publicly. A Spanish translation with accessible explanations accompanies the publication to facilitate local access to the findings.