Present-day admixed genomes reveal prehistoric adaptation to cold, maritime diet, and local pathogens in Patagonia

Patagonia, the last region settled by humans after the out-of-Africa migration, provides a unique case for studying genetic adaptations to extreme environments. Despite archaeological evidence of human occupation for at least 13,500 years, the genetic history of Indigenous Patagonians remains understudied. Here, we analyze genome-wide data from individuals with high Native American ancestry to investigate their genetic structure, admixture history, and response to environmental pressures through selection. Our results reveal widespread European admixture, which in Chilean Patagonia started 5 generations earlier than in the capital of the colony, suggesting prolonged European contact relative to lower latitudes. We identified a strong north-south genomic differentiation, where common ancestry with Mapuche people is observed in northern Patagonia while Tierra del Fuego shows a unique component of genetic variation. We found selection signals predating European contact, possibly shaped during the settlement of native ancestors in Patagonia. These signals support adaptation to extreme cold and maritime diet, including genomic regions associated with height (SUPT3H, CADM1, RUNX2), lipid metabolism (MSMO1, SORT1/PSCR2, CELSR2), and energy homeostasis (ZNF202). Furthermore, enrichment of Native American ancestry was observed in the MHC complex, likely representing the genetic footprint of past selection events driven by adaptation to endemic pathogens that were still beneficial after admixture with Europeans. These findings provide novel insights into the genetic legacy of Patagonian populations, demonstrating how natural selection has shaped their resilience to environmental challenges and the dynamics of demographic changes over time.