Reconstructing the Deep History of South America

The early diversification of Native Central and South Americans remains poorly understood because of a paucity of ancient DNA. We report genome-wide data from 41 individuals forming four parallel time transects from Belize, Brazil, Peru, and the Southern Cone, of which 35 are more than 3,000 years old. The primary ancestral population of Central and South Americans radiated rapidly followed by a high degree of continuity in multiple regions for up to 8,000 years, in stark contrast to Eurasia and Africa where there were multiple waves of replacement. Our data are consistent with a simple model of deriving almost entirely from one of those two lineages. We document two previously unknown streams of gene flow from North to South America that brought ancestry distinctive from the type predominant today: one contributing to peoples of Peru and Chile by 4,500 years ago, and one contributed to ~10,000 year old individuals from Lapa do Santo in Brazil. Finally, we contradict the hypothesis that the “Paleoamerican” skeletal morphology that has been inferred for skeletons including those at Lapa do Santo derives from a separate spread from Asia to the Americas; instead, their deep sources are the same as that of other Native Americans.