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Abstract ObjectivesThis study aims to characterize the genetic histories of ancient hunter‐gatherer groups in Fuego‐Patagonia (Chile) with distinct Marine, Terrestrial, and Mixed Economy subsistence strategies. Mitochondrial (mtDNA) and Y‐chromosome data were generated to test three hypotheses. H₀: All individuals were drawn from the same panmictic population; H₁: Terrestrial groups first populated the region and gave rise to highly specialized Marine groups by ~7,500 cal BP; or H₂: Marine and Terrestrial groups represent distinct ancestral lineages who migrated independently into the region. MethodsAncient DNA was extracted from the teeth of 50 Fuegian‐Patagonian individuals dating from 6,895 cal BP to after European arrival, and analyzed alongside other individuals from previous studies. Individuals were assigned to Marine, Terrestrial, and Mixed Economy groups based on archeological context and stable isotope diet inferences, and mtDNA (HVR1/2) and Y‐chromosome variation was analyzed. ResultsEndogenous aDNA was obtained from 49/50 (98%) individuals. Haplotype diversities, F_STcomparisons, and exact tests of population differentiation showed that Marine groups were significantly different from Terrestrial groups based on mtDNA (p < 0.05). No statistically significant differences were found between Terrestrial and Mixed Economy groups. Demographic simulations support models in which Marine groups diverged from the others by ~14,000 cal BP. Y‐chromosome results showed similar patterns but were not statistically significant due to small sample sizes and allelic dropout. DiscussionThese results support the hypothesis that Marine and Terrestrial economic groups represent distinct ancestral lineages who diverged during the time populations were expanding in the Americas, and may represent independent migrations into Fuego‐Patagonia. 

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.