A new interdisciplinary study published in Nature traces more than 2,000 years of population history in Argentina’s Uspallata Valley (UV), a key southern edge of ancient Andean farming. The research offers new insight into how agriculture reshaped societies and how people coped with long periods of hardship. By combining ancient human and pathogen DNA with isotopic data, archaeology, and paleoclimate records-and working closely with Huarpe Indigenous communities-the team shows how local hunter-gatherers adopted farming, how later maize-based societies faced sustained stress, and how strong family connections may have helped people endure instability.
One long-standing question is whether agriculture spread mainly through migrating farmers or through local groups adopting crops and techniques. Archaeological evidence alone often cannot clearly separate these possibilities, since both can produce similar material remains. The Uspallata Valley provides a rare opportunity to explore this question because farming arrived there later than in other parts of South America.
Researchers led by the Microbial Paleogenomics Unit (MPU) at Institut Pasteur analyzed genome-wide ancient DNA from 46 individuals, spanning early hunter-gatherers to later farming populations. The results show strong genetic continuity between hunter-gatherers (~2,200 years ago) and people living more than 1,000 years later as maize farming-and other crops-spread. This suggests that farming was largely adopted by local populations rather than introduced by large incoming groups.
Deep Genetic Roots and Indigenous Continuity
The findings also fill an important gap in understanding the genetic history of southern Andean populations. “Beyond the local story of Uspallata, we are also filling a gap in South American human genetic diversity by documenting a genetic component that was previously only suggested by analysing present-day populations, and that now proves to have a very deep divergence and current persistence in the region,” explains Pierre Luisi, co-first author of the study, researcher in CONICET, Argentina, who started this work as postdoc in the MPU at Institut Pasteur, France.
“The persistence of this ancestral genetic component in populations today has important implications, since it argues against narratives claiming the extinction of indigenous descendants in the region since the establishment and growth of the Argentine state-nation.”
Diet, Mobility, and a Shift to Intensive Maize Farming
To understand daily life, researchers analyzed stable isotopes preserved in bones and teeth. Carbon and nitrogen isotopes reveal long-term diet, while strontium isotopes indicate where a person lived and whether they moved during their lifetime.
The data show that maize consumption changed over time, pointing to flexible farming practices rather than a steady shift toward full agricultural dependence. However, between ~800 and 600 years ago, a different pattern emerged at a major burial site called Potrero Las Colonias. Many individuals there relied heavily on maize-among the highest levels recorded in the southern Andes-and showed non-local strontium signatures, indicating they had moved into the area. Who were these migrants, and where did they come from?
Migration, Decline, and Signs of Stress
Further genetic and isotopic evidence suggests these migrants came from nearby regions rather than distant populations. They were closely related to local groups and part of the same broader population network. Even so, genomic data reveal that this group experienced a sharp and long-term population decline, indicating ongoing stress across generations.
Multiple lines of evidence point to a complex crisis. Paleoclimate records show extended periods of environmental instability that coincide with the population decline. At the individual level (individual’s lives), skeletal remains show signs of childhood malnutrition and disease. Ancient DNA also revealed tuberculosis at the site, belonging to a lineage known from pre-contact South America. Its presence this far south, beyond previously documented areas in Peru and Colombia, raises new questions about how the disease spread and persisted.
“Detecting tuberculosis this far south in a pre-contact context is striking,” says Nicolás Rascovan, head of the Microbial Paleogenomics Unit at Institut Pasteur. “It expands the geographic frame for understanding how tuberculosis circulated in the past and highlights the value of integrating pathogen genomics into broader reconstructions of human history.”
Family Networks Helped Communities Survive
Genetic analysis of family relationships adds another important layer. Many of the migrants were closely related but were buried at different times, suggesting ongoing, multi-generational movement into the valley. These kinship networks were largely organized through maternal lines, with one mitochondrial lineage dominating, pointing to a key role for women in maintaining family continuity and coordinating movement.
There is no evidence of violent conflict, and locals and newcomers were sometimes buried together, suggesting peaceful coexistence.
Together, the findings indicate that migration based on family ties served as a survival strategy during overlapping pressures-environmental instability, food shortages and disease. “No farming community abandons fields and homes lightly,” says archaeologist and co-first author Ramiro Barberena, a researcher at CONICET. “Our results are most consistent with people moving under force majeure, relying on family networks to navigate crisis.”
Barberena adds: “Understanding how these transitions unfolded and what they meant for demography, economy, and health helps us better grasp the pathways that shaped today’s societies-and to think about risks and challenges of climate change and demographic pressures.”
Working With Indigenous Communities
The study also emphasizes the importance of collaboration with Indigenous communities. Members of the Huarpe community were involved throughout the research process, contributing to interpretation and narrative framing. Three community members co-authored the study (Claudia Herrera, Graciela Coz and Matías Candito). Ongoing discussions helped address permissions, uncertainties, and how findings would be shared. A Spanish-language version with accessible explanations was also produced to support local engagement.
“Archaeology and paleogenomics are not neutral when they involve the ancestors of living people,” says Rascovan. “Working with communities changes how we do science: it shapes the questions we ask, how we interpret evidence, and how we communicate what we can-and cannot-conclude.”
Rethinking How Agriculture Shaped Human History
More broadly, the research shows that the transition to agriculture, one of the most transformative changes in human history, did not follow a single path. Instead, it unfolded differently depending on local environments and social dynamics. By combining genetic, archaeological, environmental, and pathogen data, the study reveals how ancient communities dealt with overlapping challenges such as climate instability, food stress, and disease.
These long-term insights into how people adapted and survived, especially through cooperation and family networks, offer valuable perspective for understanding resilience in the face of modern climate and health challenges.
