The Genetic History of the Southern Cone - Human genetic diversity across languages and cultures

Explore the genomic diversity and population history in the Southern Cone

After their initial migration from Beringia, the first settlers of the Americas journeyed southward until they reached the Southern Cone. Although this timeline is widely accepted, archaeological evidence points to surprisingly early dates for the earliest human remains in this area. Recent ancient DNA studies reveal a complex population structure that challenges our current understanding of early migration patterns. Could the Southern Cone represent more than just the final chapter in the peopling of the Americas? How does this history connect to the indigenous heritage of the region?

Possible demographic and cultural trajectories influencing the history of the Southern Cone. From Arango-Isaza et al. 2023a

The history of South America was portrayed as genetically homogeneous and shaped primarily by a single founding bottleneck followed by isolation and post-contact population collapse. This narrative was largely based on uniparental markers and genome-wide SNP arrays, both limited in their ability to capture fine-scale structure and unbiased estimates of genetic diversity. The southern regions of South America preserve some of the earliest archaeological evidence of human presence in the Americas (Dillehay et al. 2015), yet their population history remains incompletely understood, as few studies have been searching for their genetic roots (De la Fuente et al. 2018, Nakatsuka et al. 2020). South American genetic diversity is structured around several deep ancestry blocks, broadly corresponding to the Southern Cone, the Central Andes, and Amazonia, but historically the genetic focus has been more on the contrast between the last two.

In the Southern Cone, the Mapuche are a key indigenous group, living mainly in southern Chile and parts of Argentina. Archaeological evidence shows population continuity from the early centuries CE to the groups met by Europeans in the 16th century. Central Chile was conquered by the Inca in the 15th century and then by the Spanish from 1541. Further south, a conflict with the ruling forces impacted indigenous peoples. By 1641, a frontier was set, with the region of Araucanía south of it remaining mostly independent until Chilean and Argentinean conquest in the 1860s–1880s.

Mapuche art in display at the Chilean Museum of Pre-Columbian Art

Recent genomic and palaeogenomic research challenges this simplified view by combining whole-genome sequencing, dense regional sampling, and ancient DNA from Patagonia and southern Chile. These approaches raise new questions: How diverse were Indigenous populations of the Southern Cone prior to European contact? To what extent did regional populations interact with each other and with the rest of the continent? How do present-day Indigenous ancestries relate to ancient populations, subsistence strategies, and linguistic histories?

Genome-wide analyses of present-day Indigenous populations reveal that different Mapuche populations (Pehuenche, Lafkenche, and Huilliche) show a shared Southern Cone origin, with diversification from far southern populations during the Middle Holocene and limited evidence for later large-scale migration from the north. At the same time, signals of gene flow between the Central and Southern Andes suggest demographic interactions that may have accompanied the spread of cultural traits, including crops and linguistic influences from Quechua words into Mapudungun (the traditional language of the Mapuche). Genetics contributes to the debate on when the contact with the Central Andes have occurred, suggesting that it might pre-date the (relatively recent) contact with the Inca.

Whole-genome sequencing from Central-Southern Chile further reveals levels of nucleotide diversity comparable to those observed in many Eurasian populations, alongside the discovery of over one million previously undocumented variants. In addition, analyses identify a subtle pulse of ancestry from an ancient source affecting this region, undetectable using SNP arrays alone. These findings imply large and sustained effective population sizes prior to European contact and demonstrate that earlier assessments of low diversity in the Southern Cone were strongly shaped by data limitations rather than biological reality.

It is interesting to note how Mapudungun, a language isolate, is not spoken by an isolated group: genetic data describes a numerically large and connected population. The complex demography of the continent can be anchored to the formation of material culture (like ceramic) and immaterial culture (like languages). Demographic structure may predate cultural and linguistic divergence in a region. In South America, key archaeological events align with sedentarization 6 to 4 kya, coinciding with early ceramic cultures, while language families formed more recently. Southern Cone languages belong to small families like Chonan, nearly extinct, or isolated ones like Mapudungun, making their deep origins unclear. Other language families may have existed and vanished without trace. Thus, genetic or archaeological events could relate to earlier families now absent from today’s linguistic landscape.

Ancient DNA adds a crucial temporal dimension to this picture. Palaeogenomic analyses of individuals from the Chonos Archipelago, spanning approximately 1,500 years, identify a distinct Indigenous ancestry associated with maritime hunter-gatherers of northwestern Patagonian channels. This Chonos-related ancestry forms part of a broader late-Holocene Patagonian genetic landscape, most closely related to present-day Kawésqar populations, while also revealing internal north–south structure and points of contact with populations from Chiloé and southern Mapuche groups. These results provide direct genetic evidence for population continuity, regional interaction, and the transmission of maritime knowledge among Patagonian peoples.

Together, these studies show that the population history of the Southern Cone is characterized by deep regional structure, high genomic diversity, and long-term interaction rather than isolation. They underscore the importance of integrating whole-genome data, ancient DNA, archaeology, linguistics, and community-engaged research (Arango-Isaza et al. 2023b) to reconstruct the complex histories of Indigenous populations and to better connect present-day ancestries with the earliest chapters of human settlement in the Americas.

El joven Lautaro, Pedro Subercaseaux – Wikimedia commons