A recent study of ancient human genomes tracks an 8,000-year history of a previously unknown genetic lineage in the central Southern Cone of South America. The research reconstructs how early populations migrated, settled, and mixed across present-day Argentina and Paraguay over the last ten millennia. The findings, published in Nature, resolve long-standing questions regarding the genetic history of indigenous populations in this region.
The study examines the genetic ancestry of the indigenous peoples who lived in the central Southern Cone, a geographically diverse territory. It stretches from the Andes mountains in the west to eastern river plains and southern grasslands. Archaeological evidence points to human habitation in this area stretching back to the late Pleistocene, around 14,000 years ago. Current models of how humans peopled South America rely heavily on genetic data from the central Andes, Amazonia, and Patagonia. The central area covering present-day Argentina has historically lacked robust ancient DNA sampling.
This absence of data leaves open questions about how early populations moved through the varied environments of the Southern Cone during the Holocene epoch. Researchers want to know whether the groups settling the coastal Pampas, the dry valleys of the northwest, and the central hills were part of continuous, isolated populations or if they frequently migrated. An ancestry lineage represents a continuous line of descent from a specific group of ancestors. Tracking these lineages helps scientists reconstruct ancient migrations and map changing community structures.
The investigation was led by Javier Maravall-López, a researcher affiliated with Harvard University, with joint supervision by David Reich of Harvard University and Rodrigo Nores of the Universidad Nacional de Córdoba. The team gathered 344 bone and tooth samples from 310 ancient individuals discovered across various archaeological sites in the region. They successfully extracted and sequenced genome-wide data for 238 individuals who lived between 150 and 10,000 years ago.
To read the ancient genetic codes, the researchers used a targeted nucleic-acid enrichment technique. They screened the samples for more than one million single-nucleotide polymorphisms. A single-nucleotide polymorphism is a variation at a single position in a DNA sequence, acting like a specific genetic marker that scientists can use to compare how closely related different individuals are.
The team combined their new sequences with existing genetic data from 588 ancient indigenous Americans and modern native groups. They applied statistical models to measure the shared genetic drift between populations. Shared drift indicates how much genetic history two groups have in common before their lineages split. The researchers also looked at segments of DNA called runs of homozygosity. These are identical stretches of genetic code inherited from both parents, and calculating their length provides evidence of historical community sizes and the rate of mating between close relatives.
The oldest sequenced individual in the study lived in the Pampas region approximately 10,000 years ago. The genetic markers from this individual suggest an early separation from the populations that eventually settled the central Andes and eastern Brazil. This early resident shared the most genetic affinity with individuals who lived in the Southern Cone thousands of years later. This provides evidence that a distinct genetic profile had begun taking shape in the region by 10,000 years ago.
The analysis also revealed a deep, previously unsampled lineage native to central Argentina. The earliest representative of this central Argentina lineage is an individual dating back 8,500 years. This specific ancestry persisted for thousands of years as the primary genetic fingerprint of the region with very little disruption from outside migration. The communities carrying this ancestry appear to have lived in relative geographical isolation for millennia.
While the central Argentina lineage was highly stable in its core territory, it gradually contributed to other populations through three distinct periods of genetic mixing. By about 3,300 years ago, individuals belonging to the central Argentina lineage began mixing with groups living in the Pampas grasslands. Over the subsequent centuries, this central ancestry grew in prominence and became the dominant genetic component in the Pampas region by the last millennium.
Another line of gene flow extended into the Gran Chaco, a lowland plains region in the north. Ancient individuals from this area show a mixture of the central Argentina lineage and ancestry related to tropical and subtropical forest populations. In the Paraná River zone, the study detected genetic signatures linked with Brazilian groups in an individual from 400 years ago. This aligns with archaeological records of the Guaraní people expanding their territory into the river basin area.
The study provides insights into historical social structures. In the northwest region of Argentina, the genetic patterns from about 1,000 years ago indicate a high rate of close-kin unions. This kinship model matches practices found in the central Andes during the same period, where communities favored marriages within their own specific socio-political units. These internal marriages allowed communities to maintain control over local resources and foster internal cooperation, suggesting that northwest Argentina groups adopted structural systems similar to their Andean neighbors.
A primary challenge of the study is the sparse sampling from the deepest time periods. Finding well-preserved skeletal remains from the Early Holocene and Middle Holocene is difficult, which limits the resolution of the early timelines. The Pampas, Gran Chaco, and Pantanal regions also have smaller sample sizes compared to the central plains and hills, making it harder to track the exact timing of migration events in those specific ecological zones.
The lack of samples from the Pampas between 6,800 and 3,300 years ago leaves a gap in understanding exactly when and how the central Argentina lineage first moved into the grasslands. More densely sampled time series from these specific missing periods would enable a richer characterization of the population flow. Obtaining additional high-quality ancient genomes from the Gran Chaco and Pantanal could clarify the complex historical interactions between the forest-dwelling populations and those on the southern plains.
The paper, “Eight millennia of continuity of a previously unknown lineage in Argentina,” was authored by Javier Maravall-López, Josefina M. B. Motti, Nicolás Pastor, María Pía Tavella, Mariana Fabra, Pilar Babot, Mariano Bonomo, Silvia E. Cornero, Guillermo N. Lamenza, Diego Catriel Leon, Paula C. Miranda de Zela, Gustavo G. Politis, Sofía C. Angeletti, G. Roxana Cattáneo, Mariana Dantas, Hilton Drube, Lucia G. Gonzalez Baroni, Salomón Hocsman, Andrés D. Izeta, Reinaldo A. Moralejo, Verónica Aldazabal, Diego M. Basso, Cristina Bayón, María Guillermina Couso, Ulises D’ Andrea, Paula Del Río, Germán G. Figueroa, Romina Frontini, Mariela Edith Gonzalez, Andrés G. Laguens, Jorge G. Martínez, Pablo G. Messineo, Beatriz Nores, Daniel E. Olivera, Gisela M. Sario, Analía Sbattella, Clara Scabuzzo, Aldana M. Tavarone, Rodrigo Vecchi, Kim Callan, Ella Caughran, Oscar Estrada, Trudi Frost, Lora Iliev, Aisling Kearns, Jack Kellogg, Kim-Louise Krettek, Ann Marie Lawson, Matthew Mah, Nihal Manjila, Adam Micco, Iris Patterson, Lijun Qiu, Xavier Roca-Rada, Gregory Soos, Peter A. Webb, J. Noah Workman, Nadin Rohland, Nick Patterson, Iosif Lazaridis, Lars Fehren-Schmitz, Cosimo Posth, Bastien Llamas, Swapan Mallick, Darío A. Demarchi, Graciela S. Cabana, David Reich, and Rodrigo Nores.