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Sci Adv. 2016 Apr 1;2(4):e1501385. doi: 10.1126/sciadv.1501385. eCollection 2016 Apr.

Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas.

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Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia.
Department of Anthropology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.; Howard Hughes Medical Institute, Boston, MA 20815, USA.
Department of Archaeology and History, La Trobe University, Melbourne, Victoria 3086, Australia.
School of Mathematical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia.
Museo de Sitio Huaca Pucllana, Miraflores, Lima 18, Peru.
Departamento de Humanidades, Pontificia Universidad Católica del Perú, Lima 32, Peru.
Departamento de Humanidades, Pontificia Universidad Católica del Perú, Lima 32, Peru.; Centro de Investigaciones Arqueológicas del Museo de Sitio de Ancón, Lima 38, Peru.
Instituto Nacional de Antropología e Historia, Ciudad de Mexico, Mexico City 6500, Mexico.
Unidad de Arqueología y Museos, Ministerio de Culturas y Turismo de Bolivia, La Paz 3165, Bolivia.
Universidad de Magallanes, Punta Arenas 6210427, Chile.
Peabody Museum of Archaeology and Ethnology at Harvard University, Boston, MA 02138, USA.
Instituto de Investigaciones de Alta Montaña, Universidad Católica de Salta, Salta 4400, Argentina.; Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz 2290, Cdad. Autónoma de Buenos Aires, Argentina.
National Geographic Society, Washington, DC 20036, USA.
Instituto de Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano-Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina.
Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile.
School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia.


The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.


Ancient DNA; Beringia; Native America; colonization

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