Local agricultural transition, crisis and migration in the Southern Andes

The transition to agriculture was a transformative process in human history with demographic and social consequences that varied widely. However, its dynamics in South America remain understudied. The Uspallata Valley (UV), located within the southern frontier of Andean agriculture, provides a singular setting to explore how farming societies emerged and evolved. Here, we show that agriculture in UV was initially adopted by local hunter-gatherers, as evidenced by genetic continuity between pre-farming and farming populations inferred from 46 newly sequenced ancient human genomes. These groups carried a distinct genetic component within the American diversity, suggesting a unique population history. Following agricultural intensification, we identify the arrival of migrants from nearby regions into UV between ~810–700 cal years BP, shortly predating the Inka arrival. Genomic, isotopic, and kinship analyses indicate that these migrants had intensive maize diets and moved in family groups, likely organized around matrilineal ties. They show multiple signs of stress, including nutritional deficiencies and tuberculosis, confirmed by bacterial genome sequencing, and experienced a long-term demographic decline. We suggest that social organization and mobility were forms of resilience in response to intersecting stressors—subsistence dependency and specialization, environmental instability, and disease—within a broader socio-ecological crisis.