Present-day Admixed Genomes Reveal Prehistoric Adaptation to Cold, Maritime Diet, and Local Pathogens in Patagonia

Patagonia represents the final frontier of the human out-of-Africa expansion, where humans have lived for at least 13,500 years, yet the genetic adaptations of its indigenous populations remain understudied. We analyzed genome-wide data from 71 present-day individuals across 7 Patagonian locations. Our analyses reveal widespread European admixture initiating approximately 10 to 12 generations ago, followed by region-specific demographic trajectories. We identified a profound north-south genetic differentiation. Populations from the Chiloé Archipelago and Argentinean Patagonia share ancestry with the Mapuche, whereas individuals from Tierra del Fuego exhibit a unique, deeply rooted genetic component shared with ancient Fueguian groups. To identify prehistoric local adaptations, we performed selection scans on masked Native American genomic segments. We detected robust selection signals predating European contact in genes associated with height and skeletal development (SUPT3H, CADM1, RUNX2), lipid metabolism (MSMO1, LYPLA1, SORT1/PSCR1/CELSR2), and energy homeostasis (ZNF202). Furthermore, we observed a significant enrichment of Native American ancestry within the Major Histocompatibility Complex on chromosome 6. In conclusion, our findings indicate that the current admixed populations in Patagonia exhibit signals of local adaptation that likely originated in their ancient indigenous ancestors. These groups accumulated critical morphological, metabolic, and immunological adaptations to their extreme environment and local pathogens, traits that remained highly beneficial even after European admixture.