Genomic insights into the origin and diversification of late maritime hunter-gatherers from the Chilean Patagonia

Patagonia was the last region of the Americas reached by humans who entered the continent from Siberia ∼15,000–20,000 y ago. Despite recent genomic approaches to reconstruct the continental evolutionary history, regional characterization of ancient and modern genomes remains understudied. Exploring the genomic diversity within Patagonia is not just a valuable strategy to gain a better understanding of the history and diversification of human populations in the southernmost tip of the Americas, but it would also improve the representation of Native American diversity in global databases of human variation. Here, we present genome data from four modern populations from Central Southern Chile and Patagonia (n = 61) and four ancient maritime individuals from Patagonia (∼1,000 y old). Both the modern and ancient individuals studied in this work have a greater genetic affinity with other modern Native Americans than to any non-American population, showing within South America a clear structure between major geographical regions. Native Patagonian Kawéskar and Yámana showed the highest genetic affinity with the ancient individuals, indicating genetic continuity in the region during the past 1,000 y before present, together with an important agreement between the ethnic affiliation and historical distribution of both groups. Lastly, the ancient maritime individuals were genetically equidistant to a ∼200-y-old terrestrial hunter-gatherer from Tierra del Fuego, which supports a model with an initial separation of a common ancestral group to both maritime populations from a terrestrial population, with a later diversification of the maritime groups. © 2018 National Academy of Sciences. All Rights Reserved.

aHuman Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago 8380453, Chile; bCentre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark; cInternational Laboratory for Human Genome Research, National Autonomous University of Mexico, Juriquilla 76230, Santiago de Querétaro, Mexico; dCenter for Computational, Evolutionary and Human Genomics, Stanford University, Stanford, CA 94305; eArc Bio, LLC, Menlo Park, CA 94025; fDepartment of Genetics, Stanford University, Stanford, CA 94305; gInstitute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland; hCentro de Estudios del Hombre Austral, Instituto de la Patagonia, Universidad de Magallanes, Punta Arenas 6213029, Chile; iNational Laboratory of Genomics for Biodiversity, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, 36821 Guanajuato, Mexico; jInterdisciplinary Centre of Marine and Environmental Research, University of Porto, Novo Edificio do Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal; kDepartment of Medicine, University of California, San Francisco, CA 94131; lDepartment of Bioengineering and Therapeutic Science, University of California, San Francisco, CA 94158; mDepartment of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; nDepartment of Zoology, University of Cambridge, Cambridge CB2 1TN, United Kingdom; and oWellcome Genome Campus, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom ACKNOWLEDGMENTS. We thank the contribution of the “Instituto de la Patagonia” and Stanford Sequencing Center. We thank Consuelo Quinto for helpful comments on earlier versions of this manuscript. This work was supported by Comisión Nacional de Investigación Científica y Tecnológica Grant USA2013-0015 and Fondo Nacional de Ciencia y Tecnología Grants 1140544 and 1170726. M.C.Á.-A.’s laboratory is supported by Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica–Universidad Nacional Autónoma de México Grant IA206817. A.-S.M. and D.C.D. were supported by Swiss National Science Foundation Grant PZ00P3_154717 and European Research Council Starting Grant 679330. A.M.-E. was supported by International Center for Genetic Engineering and Biotechnology Grant CRP/ MEX15-04_EC. Sequencing of modern DNA was partially funded by Fund of Scientific and Technological Equipment (FONDEQUIP) Grant EQM140157.