A new interdisciplinary study published in Nature reconstructs over 2,000 years of population history in Argentina's Uspallata Valley (UV), a southern frontier of Andean farming spread in ancient times, with broader lessons on how agriculture shaped societies and how communities endured crises. By combining ancient human and pathogen genomics with isotopic analyses, archaeology and paleoclimate records–and working in close collaboration with Huarpe Indigenous communities–, the research reveals how local hunter-gatherers adopted agriculture, how more recent intensive maize farmers experienced prolonged stress, and how kinship-based mobility may have helped communities persist through instability.
A central question in studies of farming's spread is whether agriculture expanded mainly as farmers moved into new regions, or as local hunter-gatherers adopted crops and techniques through cultural transmission. Archaeology by itself often cannot distinguish the two with confidence, since both can leave comparable traces in material culture. The Uspallata Valley, at the southern margin of Andean farming spread, offers a key setting to disentangle these scenarios, because agriculture arrived in this region much later than in major domestication centres across South America.
This work, led by the Microbial Paleogenomics Unit (MPU) at Institut Pasteur, generated genome-wide ancient DNA data from 46 individuals spanning the earlier hunter-gatherer period to later farming populations. The results reveal strong genetic continuity between hunter-gatherers (~2,200 years ago) living in the region before farming was adopted and those living more than a millennium later as maize farming–and other crops– expanded.
The study also helps unravel long-term population history in the southern Andes. "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."
To reconstruct how people lived, the team combined genetics with chemical signals preserved in bones and teeth, called stable isotopes. Carbon and nitrogen isotopes reveal an average of the foods eaten over a lifetime, while strontium isotopes reflect the area where a person lived, and can thus indicate whether individuals moved during life. These analyses show that maize consumption fluctuated in UV over time, consistent with flexible farming rather than a progressive transition into strong farming dependence. But between ~800 and 600 years ago, the record shows a different story at one major cemetery site called Potrero Las Colonias: most individuals show an exceptionally high maize reliance–among the highest documented for the southern Andes and non-local strontium signatures, indicating that they were migrants. Who were these non-local farmers and where were they coming from?
Isotopic and genetic data indicated that these migrations occurred within a constrained geographic range rather than across distant, previously unrelated areas. Migrants were genetically close to local groups and belonged to the same metapopulation. Yet genomic analyses show that this migrant group experienced strong and sustained demographic decline, suggesting a shrinking population under persistent stress over many generations.
Multiple lines of evidence indicate that these farmers faced a multidimensional crisis. At a larger temporal scale, paleoclimate records point to prolonged climatic instability, coinciding with the demographic decline. At shorter temporal scales (individual's lives), skeletons show markers consistent with nutritional stress during childhood and infection. Indeed, ancient DNA revealed the presence of tuberculosis in the site, with the detected strain falling within a lineage known from pre-contact South America. Its presence far south of previously documented contexts in Peru and Colombia raises new questions about routes of spread and the ecological conditions that sustained this infectious disease. "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."
Genomic kinship analyses add another key layer: many of the migrants were closely related but not buried at the same time–consistent with sustained, concerted and transgenerational movement into UV over decades. A large kinship network is structured mainly through maternal links and a single mitochondrial lineage dominated across migrants, suggesting an important role of women by maintaining family continuity and organizing mobility. Importantly, there is no evidence of violence, and locals and migrants were occasionally buried within shared mortuary contexts, pointing to peaceful coexistence between groups in the region.
Together, these findings suggest that kinship-based migration and strong family bonds functioned as resilience strategies during a period of concurring pressures–environmental instability, food insecurity and disease. "No farming community abandons fields and homes lightly," says the 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."
The study also highlights the ethical and integrative value of the research, which was done in close interaction with indigenous communities. Huarpe community members were actively involved throughout the project, contributed to interpretation and narrative framing, and three of them co-authored the article (Claudia Herrera, Graciela Coz and Matías Candito). Regular meetings with the research team allowed discussing permissions, uncertainties and how results would be communicated. A Spanish translation with non-specialist explanations accompanies the study to facilitate local access.
"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."
More broadly, the study highlights that one of the most transformative processes in human history–the adoption of agriculture–did not unfold in a single, universal way, but followed diverse paths shaped by local environments and social networks. By combining genetics, isotopes, archaeology, climate records and pathogen evidence, this work shows how past communities coped with overlapping pressures of environmental instability, food stress and disease. Understanding how people navigated crisis in the past–including the role of family ties and cooperation networks–offers a deep-time and wider perspective that can inform how we think about resilience in the face of today's climate and health challenges.
