Eight millennia of continuity of a previously unknown lineage in Argentina

The central Southern Cone of South America was one of the last regions of the globe to be peopled, yet remains underrepresented in ancient DNA. We generated new genome-wide data from 238 ancient individuals spanning ten millennia. The oldest, from the Pampas region and dating to 10000 years before present (BP), had distinct genetic affinity with Middle Holocene Southern Cone individuals, showing that differentiation from the Central Andes and Central East Brazil had begun by this time. Individuals dating to 4600-150BP primarily descended from a hitherto-unsampled deep lineage whose earliest representative is an individual dating to around 8500BP. This Central Argentina lineage co-existed with two other lineages during the Mid-Holocene, and within Central Argentina, this ancestry persisted for thousands of years with no evidence of interregional migration. Central Argentina ancestry was involved in three distinct gene flows: it mixed into the Pampas by 3300BP and became the main component there after 800BP; with Central Andes ancestry in Northwest Argentina; and with Tropical and Subtropical Forest ancestry in the Gran Chaco. In Northwest Argentina, there was an increased rate of close kin unions by 1000BP, paralleling the pattern in the Central Andes. In the Paraná River region, a 400BP individual with a Guaraní archaeological association clusters with Brazilian groups, consistent with Guaraní presence by this time.