Cited by 290

The DOI matches its Crossref record; 15 of the 15 references it cites were found in a registry or an index.

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

Llamas, Bastien, Fehren-Schmitz, Lars, Valverde, Guido, Soubrier, Julien, Mallick, Swapan, Rohland, Nadin, Nordenfelt, Susanne, Valdiosera, Cristina, Richards, Stephen M., Rohrlach, Adam, Romero, Maria Inés Barreto, Espinoza, Isabel Flores, Cagigao, Elsa Tomasto, Jiménez, Lucía Watson, Makowski, Krzysztof, Reyna, Ilán Santiago Leboreiro, Lory, Josefina Mansilla, Torrez, Julio Alejandro Ballivián, Rivera, Mario A., Burger, Richard L., Ceruti, Maria Constanza, Reinhard, Johan, Wells, R. Spencer, Politis, Gustavo, Santoro, Calogero M., Standen, Vivien G., Smith, Colin, Reich, David, Ho, Simon Y. W., Cooper, Alan, Haak, Wolfgang·2016·Science Advances

Abstract

Native American population history is reexamined using a large data set of pre-Columbian mitochondrial genomes.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1126/sciadv.1501385

Cites

15 of 15 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 69

  1. 10.1126/science.1153569 · DOI · Paper page
  2. J. H. Greenberg, C. G. Turner II, S. L. Zegura, L. Campbell, J. A. Fox, W. S. Laughlin, E. J. E. Szathmary, K. M. Weiss, E. Woolford, The settlement of the Americas: A comparison of the linguistic, dental, and genetic evidence. Curr. Anthropol. 27, 477–497 (1986). · DOI
  3. 10.1016/j.epsl.2014.06.026 · DOI
  4. C. A. S. Mandryk, H. Josenhans, D. W. Fedje, R. W. Mathewes, Late quaternary paleoenvironments of Northwestern North America: Implications for inland versus coastal migration routes. Quat. Sci. Rev. 20, 301–314 (2001). · DOI
  5. 10.1016/j.quascirev.2013.06.001 · DOI
  6. T. G. Arnold, Radiocarbon dates from the ice-free corridor. Radiocarbon 44, 437–454 (2002). · DOI
  7. M. Livi-Bacci, The depopulation of Hispanic America after the conquest. Popul. Dev. Rev. 32, 199–232 (2006). · DOI
  8. V. Battaglia, V. Grugni, U. A. Perego, N. Angerhofer, J. E. Gomez-Palmieri, S. R. Woodward, A. Achilli, N. Myres, A. Torroni, O. Semino, The first peopling of South America: New evidence from Y-chromosome haplogroup Q. PLOS One 8, e71390 (2013). · DOI
  9. 10.1371/journal.pone.0000829 · DOI
  10. C. J. Mulligan, A. Kitchen, M. M. Miyamoto, Updated three-stage model for the peopling of the Americas. PLOS One 3, e3199 (2008). · DOI
  11. K. B. Schroeder, T. G. Schurr, J. C. Long, N. A. Rosenberg, M. H. Crawford, L. A. Tarskaia, L. P. Osipova, S. I. Zhadanov, D. G. Smith, A private allele ubiquitous in the Americas. Biol. Lett. 3, 218–223 (2007). · DOI
  12. S. Wang, C. M. Lewis Jr, M. Jakobsson, S. Ramachandran, N. Ray, G. Bedoya, W. Rojas, M. V. Parra, J. A. Molina, C. Gallo, G. Mazzotti, G. Poletti, K. Hill, A. M. Hurtado, D. Labuda, W. Klitz, R. Barrantes, M. C. Bortolini, F. M. Salzano, M. L. Petzl-Erler, L. T. Tsuneto, E. Llop, F. Rothhammer, L. Excoffier, M. W. Feldman, N. A. Rosenberg, A. Ruiz-Linares, Genetic variation and population structure in Native Americans. PLOS Genet. 3, e185 (2007). · DOI
  13. U. A. Perego, N. Angerhofer, M. Pala, A. Olivieri, H. Lancioni, B. H. Kashani, V. Carossa, J. E. Ekins, A. Gómez-Carballa, G. Huber, B. Zimmermann, D. Corach, N. Babudri, F. Panara, N. M. Myres, W. Parson, O. Semino, A. Salas, S. R. Woodward, A. Achilli, A. Torroni, The initial peopling of the Americas: A growing number of founding mitochondrial genomes from Beringia. Genome Res. 20, 1174–1179 (2010). · DOI
  14. 10.1038/nature11258 · DOI · Paper page
  15. U. A. Perego, A. Achilli, N. Angerhofer, M. Accetturo, M. Pala, A. Olivieri, B. H. Kashani, K. H. Ritchie, R. Scozzari, Q.-P. Kong, N. M. Myres, A. Salas, O. Semino, H.-J. Bandelt, S. R. Woodward, A. Torroni, Distinctive Paleo-Indian migration routes from Beringia marked by two rare mtDNA haplogroups. Curr. Biol. 19, 1–8 (2009). · DOI · Paper page
  16. 10.1038/nature14895 · DOI · Paper page
  17. M. Bodner, U. A. Perego, G. Huber, L. Fendt, A. W. Röck, B. Zimmermann, A. Olivieri, A. Gómez-Carballa, H. Lancioni, N. Angerhofer, M. C. Bobillo, D. Corach, S. R. Woodward, A. Salas, A. Achilli, A. Torroni, H.-J. Bandelt, W. Parson, Rapid coastal spread of first Americans: Novel insights from South America’s Southern Cone mitochondrial genomes. Genome Res. 22, 811–820 (2012). · DOI
  18. S. Y. W. Ho, R. Lanfear, L. Bromham, M. J. Phillips, J. Soubrier, A. G. Rodrigo, A. Cooper, Time-dependent rates of molecular evolution. Mol. Ecol. 20, 3087–3101 (2011). · DOI
  19. S. Y. W. Ho, P. Endicott, The crucial role of calibration in molecular date estimates for the peopling of the Americas. Am. J. Hum. Genet. 83, 142–146 (2008). · DOI
  20. 10.1038/ncomms2656 · DOI
  21. 10.1111/mec.12953 · DOI
  22. N. J. R. Fagundes, R. Kanitz, R. Eckert, A. C. S. Valls, M. R. Bogo, F. M. Salzano, D. G. Smith, W. A. Silva Jr, M. A. Zago, A. K. Ribeiro-dos-Santos, S. E. B. Santos, M. L. Petzl-Erler, S. L. Bonatto, Mitochondrial population genomics supports a single pre-Clovis origin with a coastal route for the peopling of the Americas. Am. J. Hum. Genet. 82, 583–592 (2008). · DOI · Paper page
  23. A. Achilli, U. A. Perego, C. M. Bravi, M. D. Coble, Q.-P. Kong, S. R. Woodward, A. Salas, A. Torroni, H.-J. Bandelt, The phylogeny of the four pan-American mtDNA haplogroups: Implications for evolutionary and disease studies. PLOS One 3, e1764 (2008). · DOI
  24. N. J. R. Fagundes, R. Kanitz, S. L. Bonatto, Reply to Ho and Endicott. Am. J. Hum. Genet. 83, 146–147 (2008). · DOI
  25. D. H. O’Rourke, J. A. Raff, The human genetic history of the Americas: The final frontier. Curr. Biol. 20, R202–R207 (2010). · DOI
  26. 10.1126/science.1250768 · DOI
  27. E. J. Dixon, Late Pleistocene colonization of North America from Northeast Asia: New insights from large-scale paleogeographic reconstructions. Quat. Int. 285, 57–67 (2013). · DOI
  28. T. G. Schurr, S. T. Sherry, Mitochondrial DNA and Y chromosome diversity and the peopling of the Americas: Evolutionary and demographic evidence. Am. J. Hum. Biol. 16, 420–439 (2004). · DOI
  29. 10.1126/science.1156533 · DOI · Paper page
  30. D. H. O’Rourke, M. G. Hayes, S. W. Carlyle, Spatial and temporal stability of mtDNA haplogroup frequencies in Native North America. Hum. Biol. 72, 15–34 (2000).
  31. D. A. Bolnick, D. G. Smith, Unexpected patterns of mitochondrial DNA variation among Native Americans from the Southeastern United States. Am. J. Phys. Anthropol. 122, 336–354 (2003). · DOI
  32. B. D. O’Fallon, L. Fehren-Schmitz, Native Americans experienced a strong population bottleneck coincident with European contact. Proc. Natl. Acad. Sci. U.S.A. 108, 20444–20448 (2011). · DOI
  33. C. N. K. Anderson, U. Ramakrishnan, Y. L. Chan, E. A. Hadly, Serial SimCoal: A population genetics model for data from multiple populations and points in time. Bioinformatics 21, 1733–1734 (2004). · DOI
  34. M. Escabias, A. M. Aguilera, M. J. Valderrama, Principal component estimation of functional logistic regression: Discussion of two different approaches. J. Nonparametr. Stat. 16, 365–384 (2004). · DOI
  35. I. Camminatie, A. Lucadamo, Estimating multinomial logit model with multicollinear data. Asian J. Math. Stat. 3, 93–101 (2010). · DOI
  36. 10.1371/journal.pone.0127141 · DOI
  37. M. Meyer, M. Kircher, Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 2010, 1–10 (2010). · DOI
  38. 10.1093/molbev/mss075 · DOI
  39. J. Heled, A. J. Drummond, Bayesian inference of population size history from multiple loci. BMC Evol. Biol. 8, 289 (2008). · DOI
  40. M. A. Beaumont in Simulation Genetics and Human Prehistory S. Matsumura P. Forster C. Renfrew Eds. (McDonald Institute for Archaeological Research Cambridge 2008) pp. 135–154.
  41. 10.1186/1756-0500-5-337 · DOI
  42. 10.1016/j.ajhg.2012.03.002 · DOI
  43. 10.1007/978-1-61779-516-9_23 · DOI · Paper page
  44. J. E. L. Templeton, M. Brotherton, B. Llamas, J. Soubrier, W. Haak, A. Cooper, J. J. Austin, DNA capture and next-generation sequencing can recover whole mitochondrial genomes from highly degraded samples for human identification. Invest. Genet. 4, 26 (2013). · DOI
  45. S. Kumar, C. Bellis, M. Zlojutro, P. E. Melton, J. Blangero, J. E. Curran, Large scale mitochondrial sequencing in Mexican Americans suggests a reappraisal of Native American origins. BMC Evol. Biol. 11, 293 (2011). · DOI
  46. 10.1093/molbev/mss020 · DOI · Paper page
  47. M. Molak, E. D. Lorenzen, B. Shapiro, S. Y. W. Ho, Phylogenetic estimation of timescales using ancient DNA: The effects of temporal sampling scheme and uncertainty in sample ages. Mol. Biol. Evol. 30, 253–262 (2013). · DOI
  48. M. Molak, M. A. Suchard, S. Y. W. Ho, D. W. Beilman, B. Shapiro, Empirical calibrated radiocarbon sampler: A tool for incorporating radiocarbon-date and calibration error into Bayesian phylogenetic analyses of ancient DNA. Mol. Ecol. Resour. 15, 81–86 (2015). · DOI
  49. S. Y. W. Ho, R. Lanfear, M. J. Phillips, I. Barnes, J. A. Thomas, S.-O. Kolokotronis, B. Shapiro, Bayesian estimation of substitution rates from ancient DNA sequences with low information content. Syst. Biol. 60, 366–375 (2011). · DOI
  50. S. Duchêne, D. Duchêne, E. C. Holmes, S. Y. W. Ho, The performance of the date-randomization test in phylogenetic analyses of time-structured virus data. Mol. Biol. Evol. 32, 1895–1906 (2015). · DOI
  51. W. A. Gould, M. Raynolds, D. A. Walker, Vegetation, plant biomass, and net primary productivity patterns in the Canadian Arctic. J. Geophys. Res. 108, 1–14 (2003). · DOI
  52. H. Lieth R. H. Whittaker Eds. Primary Productivity of the Biosphere (Springer-Verlag Berlin 1975). · DOI
  53. C. Smith Late Stone Age Hunters of the British Isles (Routledge New York 1992). · DOI
  54. P. Rowley-Conwy, R. Layton, Foraging and farming as niche construction: Stable and unstable adaptations. Philos. Trans. R. Soc. Lond. B Biol. Sci. 366, 849–862 (2011). · DOI · Paper page
  55. H. Schutkowski Human Ecology: Biocultural Adaptations in Human Communities (Springer-Verlag Berlin 2006).
  56. R. Frankham, Effective population size/adult population size ratios in wildlife: A review. Genet. Res. 89, 491–503 (2007). · DOI
  57. F. P. Palstra, D. J. Fraser, Effective/census population size ratio estimation: A compendium and appraisal. Ecol. Evol. 2, 2357–2365 (2012). · DOI
  58. M. Ingman, H. Kaessmann, S. Pääbo, U. Gyllensten, Mitochondrial genome variation and the origin of modern humans. Nature 408, 708–713 (2000). · DOI
  59. E. B. Starikovskaya, R. I. Sukernik, O. A. Derbeneva, N. V. Volodko, E. Ruiz-Pesini, A. Torroni, M. D. Brown, M. T. Lott, S. H. Hosseini, K. Huoponen, D. C. Wallace, Mitochondrial DNA diversity in indigenous populations of the southern extent of Siberia, and the origins of Native American haplogroups. Ann. Hum. Genet. 69, 67–89 (2005). · DOI
  60. R. S. Just, T. M. Diegoli, J. L. Saunier, J. A. Irwin, T. J. Parsons, Complete mitochondrial genome sequences for 265 African American and U.S. “Hispanic” individuals. Forensic Sci. Int. Genet. 2, e45–e48 (2008). · DOI
  61. M. Derenko, B. Malyarchuk, T. Grzybowski, G. Denisova, I. Dambueva, M. Perkova, C. Dorzhu, F. Luzina, H. K. Lee, T. Vanecek, R. Villems, I. Zakharov, Phylogeographic analysis of mitochondrial DNA in northern Asian populations. Am. J. Hum. Genet. 81, 1025–1041 (2007). · DOI
  62. M. Ingman, U. Gyllensten, Rate variation between mitochondrial domains and adaptive evolution in humans. Hum. Mol. Genet. 16, 2281–2287 (2007). · DOI
  63. N. V. Volodko, E. B. Starikovskaya, I. O. Mazunin, N. P. Eltsov, P. V. Naidenko, D. C. Wallace, R. I. Sukernik, Mitochondrial genome diversity in arctic Siberians, with particular reference to the evolutionary history of Beringia and Pleistocenic peopling of the Americas. Am. J. Hum. Genet. 82, 1084–1100 (2008). · DOI
  64. A. Hartmann, M. Thieme, L. K. Nanduri, T. Stempfl, C. Moehle, T. Kivisild, P. J. Oefner, Validation of microarray-based resequencing of 93 worldwide mitochondrial genomes. Hum. Mutat. 30, 115–122 (2009). · DOI
  65. 10.1371/journal.pone.0015214 · DOI
  66. S. Cardoso, M. A. Alfonso-Sánchez, L. Valverde, D. Sánchez, M. T. Zarrabeitia, A. Odriozola, B. Martínez-Jarreta, M. M. de Pancorbo, Genetic uniqueness of the Waorani tribe from the Ecuadorian Amazon. Heredity 108, 609–615 (2012). · DOI
  67. M. Derenko, B. Malyarchuk, G. Denisova, M. Perkova, U. Rogalla, T. Grzybowski, E. Khusnutdinova, I. Dambueva, I. Zakharov, Complete mitochondrial DNA analysis of eastern Eurasian haplogroups rarely found in populations of northern Asia and eastern Europe. PLOS One 7, e32179 (2012). · DOI
  68. M. de Saint Pierre, C. M. Bravi, J. M. B. Motti, N. Fuku, M. Tanaka, E. Llop, S. L. Bonatto, M. Moraga, An alternative model for the early peopling of southern South America revealed by analyses of three mitochondrial DNA haplogroups. PLOS One 7, e43486 (2012). · DOI
  69. A. Achilli, U. A. Perego, H. Lancioni, A. Olivieri, F. Gandini, B. H. Kashani, V. Battaglia, V. Grugni, N. Angerhofer, M. P. Rogers, R. J. Herrera, S. R. Woodward, D. Labuda, D. G. Smith, J. S. Cybulski, O. Semino, R. S. Malhi, A. Torroni, Reconciling migration models to the Americas with the variation of North American native mitogenomes. Proc. Natl. Acad. Sci. U.S.A. 110, 14308–14313 (2013). · DOI

Cited by

Sorted by citations

Metadata

Authors
Llamas, B., Fehren-Schmitz, L., Valverde, G., Soubrier, J., Mallick, S., Rohland, N., Nordenfelt, S., Valdiosera, C., Richards, S. M., Rohrlach, A., Romero, M. I. B., Espinoza, I. F., Cagigao, E. T., Jiménez, L. W., Makowski, K., Reyna, I. S. L., Lory, J. M., Torrez, J. A. B., Rivera, M. A., Burger, R. L., Ceruti, M. C., Reinhard, J., Wells, R. S., Politis, G., Santoro, C. M., Standen, V. G., Smith, C., Reich, D., Ho, S. Y. W., Cooper, A., & Haak, W.
Affiliations
  • 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.
  • 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.
  • 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.
  • 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.
Venue
Science Advances
Published
2016-04
Volume
2
Issue
4
ISSN
2375-2548
Cited by
290
References
15
Language
en
Funders
Australian Research Council (ID0EPPCM6714)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review