SummaryWe report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ∼9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions.

The discovery of human remains from the Lauricocha cave in the Central Andean highlands in the 1960’s provided the first direct evidence for human presence in the high altitude Andes. The skeletons found at this site were ascribed to the Early to Middle Holocene and represented the oldest known population of Western South America, and thus were used in several studies addressing the early population history of the continent. However, later excavations at Lauricocha led to doubts regarding the antiquity of the site. Here, we provide new dating, craniometric, and genetic evidence for this iconic site. We obtained new radiocarbon dates, generated complete mitochondrial genomes and nuclear SNP data from five individuals, and re-analyzed the human remains of Lauricocha to revise the initial morphological and craniometric analysis conducted in the 1960’s. We show that Lauricocha was indeed occupied in the Early to Middle Holocene but the temporal spread of dates we obtained from the human remains show that they do not qualify as a single contemporaneous population. However, the genetic results from five of the individuals fall within the spectrum of genetic diversity observed in pre-Columbian and modern Native Central American populations.

The analysis of animal bones recovered from preceramic period deposits at Uchcumachay Cave and other sites in the Puna of Junín has documented the development of an economy involving primary camelid utilization beginning around 5,500 B.C. and culminating with the appearance of domestic forms between 2,500 and 1,750 B.C. A model that can be used to explain this process in both the Puna of Junín and the Central Andes has been presented.

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Basis of the exchange between north peruvian and south ecuatorian societies: a transitional zone between 1500 B.C. and 600 A.C. Abstract This paper is a collaborative effort by researchers working in Ecuador and Peru, to explore the relationship between two clearly differenciated cultural areas (North and Central Andes) on the basis of a definition and study of the prehistory transitional zone located between Río Jubones in Southern Ecuador and Río Olmos in Northern Peru between 1500 B.C. and 600 A.C.