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.