Studies of Native South American genetic diversity have helped to shed light on the peopling and differentiation of the continent, but available data are sparse for the major ecogeographic domains. These include the Pacific Coast, a potential early migration route; the Andes, home to the most expansive complex societies and to one of the most widely spoken indigenous language families of the continent (Quechua); and Amazonia, with its understudied population structure and rich cultural diversity. Here, we explore the genetic structure of 176 individuals from these three domains, genotyped with the Affymetrix Human Origins array. We infer multiple sources of ancestry within the Native American ancestry component; one with clear predominance on the Coast and in the Andes, and at least two distinct substrates in neighboring Amazonia, including a previously undetected ancestry characteristic of northern Ecuador and Colombia. Amazonian populations are also involved in recent gene-flow with each other and across ecogeographic domains, which does not accord with the traditional view of small, isolated groups. Long-distance genetic connections between speakers of the same language family suggest that indigenous languages here were spread not by cultural contact alone. Finally, Native American populations admixed with post-Columbian European and African sources at different times, with few cases of prolonged isolation. With our results we emphasize the importance of including understudied regions of the continent in high-resolution genetic studies, and we illustrate the potential of SNP chip arrays for informative regional-scale analysis.
Bibliographical noteFunding Information:
Samples were collected during anthropological fieldwork expeditions by R.B. and C.Z. (Ecuador, 2007), L.A. (Colombia, 2012), C.B., R.F., J.R.S., and O.A. (Peru, 1998, 2007, 2009, 2014, 2015), and A.A.C. and R.S.O. (Mexico, 2016). The sampling collection and the project were approved by the Ethics Committee of the University of San Martín de Porres, Lima (Comité Institucional de Ética en Investigación de la Universidad de San Martín de Porres— Clínica Cada Mujer, Ofício No. 579-2015-CIEI-USMP-CCM, 12/05/2015), the ethics committee of the Universidad del Valle in Cali, Colombia (Acta No. 021-010), the Ethics Commission of the University of Leipzig Medical Faculty (232/16-ek), the Ethics Committee of the University of Jena (Ethik-Kommission des Universit€atsklinikums Jena, Bearbeitungs-Nr. 4840-06/16), the Research Council for Science and Technology (Consejo Nacional de Ciencia y Tecnología—CONACyT, grant # 69856; Instituto Nacional de Ciencias Médicas y de la Nutrición Salvador Zubirán Ref.: 1518), and the National Commission for Scientific Research of the Mexican Institute for Social Security (IMSS; CNIC Salud 2013-01-201471). All methods were performed in compliance with the rules of the Declaration of Helsinki. The samples analyzed in this study represent only a small fraction of the population living in the target regions of Mexico, Peru, Colombia and Ecuador, and so is only partially representative of the complex demographic history of these regions and of their inhabitants’ ancestors.
We thank all the study participants and fieldwork assistants from Colombia, Ecuador, Mexico, and Peru for making this study possible. The study was supported by a Wenner-Gren postdoctoral grant (Gr. 9395) to C.B., by the University Research Priority Program of Evolution in Action of the University of Zurich to C.B. and K.K.S., and by MEXT Kakenhi 18H05080 to K.K.S. L.F.S. was supported by a U.S. National Science Foundation grant (NSF: A15-0187-001). L.A. was supported by a graduate grant from COLCIENCIAS. We thank David Reich and collaborators for providing a formatted data set of published data used for population comparisons, Adrian Pearce for historical contextualization of European and African admixture in Peru, Vladimir Bajić, Hiba Babiker, Cosimo Posth, and Thiseas Christos Lamnidis for computational analysis assistance.
© 2019 The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
- Native American population genetics
- South American prehistory
- human migration
- runs of homozygosity