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Paleogenomic data are commonly used to test archaeological questions, but paleogenomics best informs ancient population histories when applied using a biocultural approach that contextualizes genomic analyses within a socio-historic framework. In this study, we focus on hunter-gatherer populations from southern Patagonia and Tierra del Fuego (Fuego-Patagonia) who have inhabited the region for more than 10,500 years. These groups practiced subsistence strategies that relied on either marine or terrestrial resources, or a mix of both. Some prior studies suggest that Marine and Terrestrial groups descended from the same ancestral group, while others indicate they had distinct ancestries. Here, we examined genome-wide data from 40 newly sequenced and 30 previously reported ancient Fuegian-Patagonians spanning 6,800 years, as well as sociocultural evidence from archaeological, ethnohistorical, and linguistic sources. Previous analyses of the newly sequenced individuals suggested that Marine and Terrestrial groups had distinct ancestries that diverged ~14,000 years ago. To further elucidate the genetic relationships among Terrestrial, Marine, and Mixed Economy groups, we examined population substructure using PCA, ADMIXTURE, tests of genetic distances, and f-statistics. We found that some Marine and Mixed Economy individuals from the Middle Holocene shared ancestry with Late Holocene Terrestrial groups, while Terrestrial and Marine groups from the Late Holocene showed distinct ancestries and limited admixture until Historic times. We contextualized these paleogenomic results with evidence from sociocultural sources, adding further nuance and justiܪcation to our conclusions. This study highlights the complexities of local population histories and demonstrates the importance of including sociocultural data in paleogenomic studies. 

Historically, hunter-gatherers living east and west of the Andean foothills of southern South America (Fuego-Patagonia) practiced different subsistence strategies. To the east, the wide open and relatively dry pampas presented a climate ideal for Terrestrial hunter-gatherers who depended on terrestrial animals (e.g., Lama guanicoe). In contrast, Marine hunter-gatherers who lived on islands in the western archipelago, a colder and wetter environment, mainly subsisted on marine resources (e.g., seals and shellfish). Archaeological evidence dates Terrestrial hunter-gatherers’ presence in Fuego-Patagonia to at least ~10,500 BP, whereas Marine hunter-gatherers’ presence dates to ~6,500 BP and is associated with highly specialized tools that have only been observed in the archaeological record after this time. Genetic analyses of some ancient Fuegian-Patagonians have supported the hypothesis that Marine hunter-gatherers migrated into the region after Terrestrial hunter-gatherers, around 6,500 BP (7,500 calBP), while analyses of other individuals suggest that Marine hunter-gatherers descended from the earlier Terrestrial hunter-gatherer groups. Here, we test these hypotheses by analyzing newly collected genome-wide data from n=46 ancient Chilean Fuegian-Patagonian individuals belonging to Marine, Terrestrial, and Mixed-economy archaeological sites dating to 6,895–304 calBP. We explored basic population structure among these hunter-gatherer groups using PCA and ADMIXTURE. We calculated π, pairwise-FST, and f-statistics, and developed demographic simulations to further examine genetic relationships among the groups. The results of this study shed light on local demographic patterns of ancient southern South American groups, which in turn provides more insight into broader population histories of South America. This study was funded by FONDECYT (Chile), National Geographic Society, National Science Foundation, and Wenner-Gren Foundation. C. M. Balentine is supported by an NSF Graduate Research Fellowship.