Genetic studies have consistently indicated a single common origin of Native American groups from Central and South America1,2,3,4. However, some morphological studies have suggested a more complex picture, whereby the northeast Asian affinities of present-day Native Americans contrast with a distinctive morphology seen in some of the earliest American skeletons, which share traits with present-day Australasians (indigenous groups in Australia, Melanesia, and island Southeast Asia)5,6,7,8. Here we analyse genome-wide data to show that some Amazonian Native Americans descend partly from a Native American founding population that carried ancestry more closely related to indigenous Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans. This signature is not present to the same extent, or at all, in present-day Northern and Central Americans or in a ∼12,600-year-old Clovis-associated genome, suggesting a more diverse set of founding populations of the Americas than previously accepted.
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We are grateful to the Native American volunteers who contributed the DNA samples used to generate the new data reported in this study and to the Fundação Nacional do Índio (FUNAI, Brazil) for logistical support in sample collection. We thank W. Klitz and C. Winkler for sharing samples for whole-genome sequencing. We thank L. Fehren-Schmitz, Q. Fu, G. Hellenthal, A. Kim, I. Lazaridis, M. Lipson, I. Mathieson, D. Meltzer, P. Moorjani and J. Pickrell for comments and A. Tandon for technical assistance. We thank T. Ferraz and R. Bisso-Machado for assistance with DNA extraction for the genotyping of Brazilian samples. We performed whole-genome sequencing as part of the Simons Genome Diversity Project. Genotyping of the Brazilian samples was performed at the Children’s Hospital of Philadelphia and we particularly thank C. Hou for her support in this. M.C.B., T.H., M.L.P.-E. and F.M.S. were supported by Conselho Nacional do Desenvolvimento Científico e Tecnológico and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brazil). P.S. was supported by the Wenner-Gren foundation and the Swedish Research Council (VR grant 2014-453). D.R. was supported by US National Science Foundation HOMINID grant BCS-1032255, US National Institutes of Health grant GM100233, Simons Foundation Grant 280376 and the Howard Hughes Medical Institute.
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Extended data tables
This file contains Supplementary Text and Data 1-6, Supplementary Tables and additional references.