title: Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas.
abstract: 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.
authors.affiliation: Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia.
authors.forename: Bastien
authors.identifier: 0000-0002-5550-9176
authors.initials: B
authors.lastname: Llamas
authors.affiliation: Department of Anthropology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Lars
authors.identifier: 0000-0001-5510-1114
authors.initials: L
authors.lastname: Fehren-Schmitz
authors.affiliation: Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia.
authors.forename: Guido
authors.initials: G
authors.lastname: Valverde
authors.affiliation: Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia.
authors.forename: Julien
authors.identifier: 0000-0001-9350-7369
authors.initials: J
authors.lastname: Soubrier
authors.affiliation: 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.
authors.forename: Swapan
authors.identifier: 0000-0002-4531-4439
authors.initials: S
authors.lastname: Mallick
authors.affiliation: 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.
authors.forename: Nadin
authors.initials: N
authors.lastname: Rohland
authors.affiliation: 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.
authors.forename: Susanne
authors.initials: S
authors.lastname: Nordenfelt
authors.affiliation: Department of Archaeology and History, La Trobe University, Melbourne, Victoria 3086, Australia.
authors.forename: Cristina
authors.identifier: 0000-0003-4948-2226
authors.initials: C
authors.lastname: Valdiosera
authors.affiliation: Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia.
authors.forename: Stephen M
authors.identifier: 0000-0002-0202-9654
authors.initials: SM
authors.lastname: Richards
authors.affiliation: School of Mathematical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia.
authors.forename: Adam
authors.initials: A
authors.lastname: Rohrlach
authors.affiliation: Museo de Sitio Huaca Pucllana, Miraflores, Lima 18, Peru.
authors.forename: Maria Inés Barreto
authors.initials: MI
authors.lastname: Romero
authors.affiliation: Museo de Sitio Huaca Pucllana, Miraflores, Lima 18, Peru.
authors.forename: Isabel Flores
authors.initials: IF
authors.lastname: Espinoza
authors.affiliation: Departamento de Humanidades, Pontificia Universidad Católica del Perú, Lima 32, Peru.
authors.forename: Elsa Tomasto
authors.identifier: 0000-0002-5326-8102
authors.initials: ET
authors.lastname: Cagigao
authors.affiliation: Departamento de Humanidades, Pontificia Universidad Católica del Perú, Lima 32, Peru.; Centro de Investigaciones Arqueológicas del Museo de Sitio de Ancón, Lima 38, Peru.
authors.forename: Lucía Watson
authors.initials: LW
authors.lastname: Jiménez
authors.affiliation: Departamento de Humanidades, Pontificia Universidad Católica del Perú, Lima 32, Peru.
authors.forename: Krzysztof
authors.identifier: 0000-0002-1523-1624
authors.initials: K
authors.lastname: Makowski
authors.affiliation: Instituto Nacional de Antropología e Historia, Ciudad de Mexico, Mexico City 6500, Mexico.
authors.forename: Ilán Santiago Leboreiro
authors.initials: IS
authors.lastname: Reyna
authors.affiliation: Instituto Nacional de Antropología e Historia, Ciudad de Mexico, Mexico City 6500, Mexico.
authors.forename: Josefina Mansilla
authors.initials: JM
authors.lastname: Lory
authors.affiliation: Unidad de Arqueología y Museos, Ministerio de Culturas y Turismo de Bolivia, La Paz 3165, Bolivia.
authors.forename: Julio Alejandro Ballivián
authors.identifier: 0000-0002-0432-530X
authors.initials: JA
authors.lastname: Torrez
authors.affiliation: Universidad de Magallanes, Punta Arenas 6210427, Chile.
authors.forename: Mario A
authors.initials: MA
authors.lastname: Rivera
authors.affiliation: Peabody Museum of Archaeology and Ethnology at Harvard University, Boston, MA 02138, USA.
authors.forename: Richard L
authors.initials: RL
authors.lastname: Burger
authors.affiliation: 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.
authors.forename: Maria Constanza
authors.initials: MC
authors.lastname: Ceruti
authors.affiliation: National Geographic Society, Washington, DC 20036, USA.
authors.forename: Johan
authors.identifier: 0000-0002-1142-0479
authors.initials: J
authors.lastname: Reinhard
authors.affiliation: National Geographic Society, Washington, DC 20036, USA.
authors.forename: R Spencer
authors.identifier: 0000-0002-8171-1204
authors.initials: RS
authors.lastname: Wells
authors.affiliation: 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.
authors.forename: Gustavo
authors.identifier: 0000-0003-4161-9873
authors.initials: G
authors.lastname: Politis
authors.affiliation: Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile.
authors.forename: Calogero M
authors.initials: CM
authors.lastname: Santoro
authors.affiliation: Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile.
authors.forename: Vivien G
authors.initials: VG
authors.lastname: Standen
authors.affiliation: Department of Archaeology and History, La Trobe University, Melbourne, Victoria 3086, Australia.
authors.forename: Colin
authors.identifier: 0000-0001-5901-8780
authors.initials: C
authors.lastname: Smith
authors.affiliation: 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.
authors.forename: David
authors.initials: D
authors.lastname: Reich
authors.affiliation: School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia.
authors.forename: Simon Y W
authors.identifier: 0000-0002-0361-2307
authors.initials: SY
authors.lastname: Ho
authors.affiliation: Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia.
authors.forename: Alan
authors.initials: A
authors.lastname: Cooper
authors.affiliation: Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia.
authors.forename: Wolfgang
authors.identifier: 0000-0003-2475-2007
authors.initials: W
authors.lastname: Haak
mesh_terms: D000569:Americas; D001106:Archaeology; D001499:Bayes Theorem; D002677:Chile; D000072441:DNA, Ancient; D004272:DNA, Mitochondrial / Q000235:genetics*; D004641:Emigration and Immigration; D014644:Genetic Variation; D005828:Genetics, Population; D054629:Genome, Mitochondrial / Q000235:genetics; D006239:Haplotypes / Q000235:genetics; D006801:Humans; D007198:Indians, North American / Q000235:genetics; D010802:Phylogeny; D013020:South America
chemical_list: D000072441:DNA, Ancient; D004272:DNA, Mitochondrial
keywords: Ancient DNA; Beringia; Native America; colonization