Genomic insights into the origin and diversification of late maritime hunter-gatherers from the Chilean Patagonia

Significance Recent genomic studies of ancient and modern humans from the Americas have given a comprehensive view of the peopling of the continent. However, regional characterization of ancient and modern individuals is lacking, being key to unveiling fine-scale differences within the continent. We present genome-wide analyses of ancient and modern individuals from South America from Western Patagonia. We found a strong affinity between modern and ancient individuals from the region, providing evidence of continuity in the region for the last ∼1,000 years and regional genetic structure within Southern South America. In particular, the analysis of these ancient genomes helps address questions related to the maritime tradition in the region and its diversification posterior to the split from terrestrial hunter-gatherers. Patagonia was the last region of the Americas reached by humans who entered the continent from Siberia ∼15,000–20,000 y ago. Despite recent genomic approaches to reconstruct the continental evolutionary history, regional characterization of ancient and modern genomes remains understudied. Exploring the genomic diversity within Patagonia is not just a valuable strategy to gain a better understanding of the history and diversification of human populations in the southernmost tip of the Americas, but it would also improve the representation of Native American diversity in global databases of human variation. Here, we present genome data from four modern populations from Central Southern Chile and Patagonia (n = 61) and four ancient maritime individuals from Patagonia (∼1,000 y old). Both the modern and ancient individuals studied in this work have a greater genetic affinity with other modern Native Americans than to any non-American population, showing within South America a clear structure between major geographical regions. Native Patagonian Kawéskar and Yámana showed the highest genetic affinity with the ancient individuals, indicating genetic continuity in the region during the past 1,000 y before present, together with an important agreement between the ethnic affiliation and historical distribution of both groups. Lastly, the ancient maritime individuals were genetically equidistant to a ∼200-y-old terrestrial hunter-gatherer from Tierra del Fuego, which supports a model with an initial separation of a common ancestral group to both maritime populations from a terrestrial population, with a later diversification of the maritime groups.

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