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

Science Advances

Volumn 2, Issue 4, 2016, Pages

  Llamas, Bastien ^a   Fehren Schmitz, Lars ^b   Valverde, Guido ^a   Soubrier, Julien ^a   Mallick, Swapan ^c,d,e   Rohland, Nadin ^c,d,e   Nordenfelt, Susanne ^c,d,e   Valdiosera, Cristina ^f   Richards, Stephen M ^a   Rohrlach, Adam ^a   Romero, Maria Inés Barreto ^g   Espinoza, Isabel Flores ^g   Cagigao, Elsa Tomasto ^h   Jiménez, Lucía Watson ^h,i   Makowski, Krzysztof ^h   Reyna, Ilán Santiago Leboreiro ^j   Lory, Josefina Mansilla ^j   Torrez, Julio Alejandro Ballivián ^k   Rivera, Mario A ^l   Burger, Richard L ^m   Ceruti, Maria Constanza ^n,o   Reinhard, Johan ^p   Wells, R Spencer ^p,t   Politis, Gustavo ^q   Santoro, Calogero M ^r   Standen, Vivien G ^r   Smith, Colin ^f   Reich, David ^c,d,e   Ho, Simon Y W ^s   Cooper, Alan ^a   Haak, Wolfgang ^a,u   more..

^a UNIVERSITY OF ADELAIDE   (Australia)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

^d BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^e HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^f LA TROBE UNIVERSITY   (Australia)

^g Museo de Sitio Huaca Pucllana   (Peru)

^h PONTIFICIA UNIVERSIDAD CATÓLICA DEL PERÚ   (Peru)

ⁱ Centro de Investigaciones Arqueológicas del Museo de Sitio de Ancón   (Peru)

^j INSTITUTO NACIONAL DE ANTROPOLOGÍA E HISTORIA   (Mexico)

^k Unidad de Arqueología y Museos   (Bolivia)

^l UNIVERSIDAD DE MAGALLANES   (Chile)

^m HARVARD UNIVERSITY   (United States)

ⁿ Universidad Catolica de Salta   (Argentina)

^o Facultad de Ciencias Naturales e Instituto M Lillo   (Argentina)

^p NATIONAL GEOGRAPHIC SOCIETY   (United States)

^q UNIVERSIDAD NACIONAL DEL CENTRO DE LA PROVINCIA DE BUENOS AIRES   (Argentina)

^r UNIVERSIDAD DE TARAPACÁ   (Chile)

^s UNIVERSITY OF SYDNEY   (Australia)

^t UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^u MAX PLANCK INSTITUTE FOR THE SCIENCE OF HUMAN HISTORY   (Germany)

more..

Author keywords

[No Author keywords available]

Indexed keywords

CALIBRATION; STATISTICAL TESTS;

CALIBRATION POINTS; COALESCENT ANALYSIS; EXTINCTION RATES; GENETIC DIVERSITY; MITOCHONDRIAL DNA; MULTIPLE LOGISTIC REGRESSION; NATIVE AMERICANS; PRINCIPAL COMPONENTS;

POPULATION STATISTICS;

ANCIENT DNA; MITOCHONDRIAL DNA;

AMERICAN INDIAN; ARCHEOLOGY; BAYES THEOREM; CHILE; GENETIC VARIATION; GENETICS; HAPLOTYPE; HUMAN; MIGRATION; MITOCHONDRIAL GENOME; PHYLOGENY; POPULATION GENETICS; SOUTH AMERICA; WESTERN HEMISPHERE;

AMERICAS; ARCHAEOLOGY; BAYES THEOREM; CHILE; DNA, ANCIENT; DNA, MITOCHONDRIAL; EMIGRATION AND IMMIGRATION; GENETIC VARIATION; GENETICS, POPULATION; GENOME, MITOCHONDRIAL; HAPLOTYPES; HUMANS; INDIANS, NORTH AMERICAN; PHYLOGENY; SOUTH AMERICA;

EID: 84973892872     PISSN: None     EISSN: 23752548     Source Type: Journal    
DOI: 10.1126/sciadv.1501385     Document Type: Article

References (86)

1. T. Goebel, M. R. Waters, D. H. O'Rourke, The late Pleistocene dispersal of modern humans in the Americas. Science 319, 1497-1502 (2008
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
3. M. A. Taylor, I. L. Hendy, D. K. Pak, Deglacial ocean warming and marine margin retreat of the Cordilleran Ice Sheet in the North Pacific Ocean. Earth Planet. Sci. Lett. 403, 89-98 (2014
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
5. E. J. Gowan, An assessment of the minimum timing of ice free conditions of the western Laurentide Ice Sheet. Quat. Sci. Rev. 75, 100-113 (2013
6. T. G. Arnold, Radiocarbon dates from the ice-free corridor. Radiocarbon 44, 437-454 (2002
7. M. Livi-Bacci, The depopulation of Hispanic America after the conquest. Popul. Dev. Rev. 32, 199-232 (2006
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
9. E. Tamm, T. Kivisild, M. Reidla, M. Metspalu, D. G. Smith, C. J. Mulligan, C. M. Bravi, O. Rickards, C. Martinez-Labarga, E. K. Khusnutdinova, S. A. Fedorova, M. V. Golubenko, V. A. Stepanov, M. A. Gubina, S. I. Zhadanov, L. P. Ossipova, L. Damba, M. I. Voevoda, J. E. Dipierri, R. Villems, R. S. Malhi, Beringian standstill and spread of Native American founders. PLOS One 2, e829 (2007
10. C. J. Mulligan, A. Kitchen, M. M. Miyamoto, Updated three-stage model for the peopling of the Americas. PLOS One 3, e3199 (2008
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
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
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
14. D. Reich, N. Patterson, D. Campbell, A. Tandon, S. Mazieres, N. Ray, M. V. Parra, W. Rojas, C. Duque, N. Mesa, L. F. García, O. Triana, S. Blair, A. Maestre, J. C. Dib, C. M. Bravi, G. Bailliet, D. Corach, T. Hünemeier, M. Cátira Bortolini, F. M. Salzano, M. L. Petzl-Erler, V. Acuña-Alonzo, C. Aguilar-Salinas, S. Canizales-Quinteros, T. Tusié-Luna, L. Riba, M. Rodríguez-Cruz, M. Lopez-Alarcón, R. Coral-Vazquez, T. Canto-Cetina, I. Silva-Zolezzi, J. C. Fernandez-Lopez, A. V. Contreras, G. Jimenez-Sanchez, M. J. Gómez-Vázquez, J. Molina, Á. Carracedo, A. Salas, C. Gallo, G. Poletti, D. B. Witonsky, G. Alkorta-Aranburu, R. I. Sukernik, L. Osipova, S. A. Fedorova, R. Vasquez, M. Villena, C. Moreau, R. Barrantes, D. Pauls, L. Excoffier, G. Bedoya, F. Rothhammer, J.-M. Dugoujon, G. Larrouy, W. Klitz, D. Labuda, J. Kidd, K. Kidd, A. Di Rienzo, N. B. Freimer, A. L. Price, A. Ruiz-Linares, Reconstructing Native American population history. Nature 488, 370-374 (2012
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
16. P. Skoglund, S. Mallick, M. C. Bortolini, N. Chennagiri, T. Hünemeier, M. L. Petzl-Erler, F. M. Salzano, N. Patterson, D. Reich, Genetic evidence for two founding populations of the Americas. Nature 525, 104-108 (2015
17. M. Raghavan, M. Steinrücken, K. Harris, S. Schiffels, S. Rasmussen, M. DeGiorgio, A. Albrechtsen, C. Valdiosera, M. C. Ávila-Arcos, A.-S. Malaspinas, A. Eriksson, I. Moltke, M. Metspalu, J. R. Homburger, J. Wall, O. E. Cornejo, J. V. Moreno-Mayar, T. S. Korneliussen, T. Pierre, M. Rasmussen, P. F. Campos, P. de Barros Damgaard, M. E. Allentoft, J. Lindo, E. Metspalu, R. Rodríguez-Varela, J. Mansilla, C. Henrickson, A. Seguin-Orlando, H. Malmström, T. Stafford Jr., S. S. Shringarpure, A. Moreno-Estrada, M. Karmin, K. Tambets, A. Bergström, Y. Xue, V. Warmuth, A. D. Friend, J. Singarayer, P. Valdes, F. Balloux, I. Leboreiro, J. L. Vera, H. Rangel-Villalobos, D. Pettener, D. Luiselli, L. G. Davis, E. Heyer, C. P. E. Zollikofer, M. S. P. de León, C. I. Smith, V. Grimes, K.-A. Pike, M. Deal, B. T. Fuller, B. Arriaza, V. Standen, M. F. Luz, F. Ricaut, N. Guidon, L. Osipova, M. I. Voevoda, O. L. Posukh, O. Balanovsky, M. Lavryashina, Y. Bogunov, E. Khusnutdinova, M. Gubina, E. Balanovska, S. Fedorova, S. Litvinov, B. Malyarchuk, M. Derenko, M. J. Mosher, D. Archer, J. Cybulski, B. Petzelt, J. Mitchell, R. Worl, P. J. Norman, P. Parham, B. M. Kemp, T. Kivisild, C. Tyler-Smith, M. S. Sandhu, M. Crawford, R. Villems, D. G. Smith, M. R. Waters, T. Goebel, J. R. Johnson, R. S. Malhi, M. Jakobsson, D. J. Meltzer, A. Manica, R. Durbin, C. D. Bustamante, Y. S. Song, R. Nielsen, E. Willerslev, Genomic evidence for the Pleistocene and recent population history of Native Americans. Science 349, aab3884 (2015
18. 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 Americas Southern Cone mitochondrial genomes. Genome Res. 22, 811-820 (2012
19. 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
20. 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
21. Q. Fu, A. Mittnik, P. L. F. Johnson, K. Bos, M. Lari, R. Bollongino, C. Sun, L. Giemsch, R. Schmitz, J. Burger, A. M. Ronchitelli, F. Martini, R. G. Cremonesi, J. Svoboda, P. Bauer, D. Caramelli, S. Castellano, D. Reich, S. Pääbo, J. Krause, A revised timescale for human evolution based on ancient mitochondrial genomes. Curr. Biol. 23, 553-559 (2013
22. P. Brotherton, W. Haak, J. Templeton, G. Brandt, J. Soubrier, C. J. Adler, S. M. Richards, C. Der Sarkissian, R. Ganslmeier, S. Friederich, V. Dresely, M. van Oven, R. Kenyon, M. B. Van der Hoek, J. Korlach, K. Luong, S. Y. W. Ho, L. Quintana-Murci, D. M. Behar, H. Meller, K. W. Alt, A. Cooper, S. Adhikarla, A. K. G. Prasad, R. Pitchappan, A. V. Santhakumari, E. Balanovska, O. Balanovsky, J. Bertranpetit, D. Comas, B. Martínez-Cruz, M. Melé, A. C. Clarke, E. A. Matisoo-Smith, M. C. Dulik, J. B. Gaieski, A. C. Owings, T. G. Schurr, M. G. Vilar, A. Hobbs, H. Soodyall, A. Javed, L. Parida, D. E. Platt, A. K. Royyuru, L. Jin, S. Li, M. E. Kaplan, N. C. Merchant, R. J. Mitchell, C. Renfrew, D. R. Lacerda, F. R. Santos, D. F. S. Hernanz, R. S. Wells, P. Swamikrishnan, C. Tyler-Smith, P. P. Vieira, J. S. Ziegle; for The Genographic Consortium, Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans. Nat. Commun. 4, 1764 (2013
23. S. Y. W. Ho, S. Duchêne, Molecular-clock methods for estimating evolutionary rates and timescales. Mol. Ecol. 23, 5947-5965 (2014
24. M. van Oven, M. Kayser, Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum. Mutat. 30, E386-E394 (2009
25. 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
26. 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).
27. N. J. R. Fagundes, R. Kanitz, S. L. Bonatto, Reply to Ho and Endicott. Am. J. Hum. Genet. 83, 146-147 (2008
28. D. H. O'Rourke, J. A. Raff, The human genetic history of the Americas: The final frontier. Curr. Biol. 20, R202-R207 (2010
29. J. F. Hoffecker, S. A. Elias, D. H. O'Rourke, Out of Beringia. Science 343, 979-980 (2014
30. 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
31. 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
32. T. D. Dillehay, C. Ramírez, M. Pino, M. B. Collins, J. Rossen, J. D. Pino-Navarro, Monte Verde: Seaweed, food, medicine, and the peopling of South America. Science 320, 784-786 (2008
33. 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
34. 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
35. 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
36. 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
37. 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
38. I. Camminatie, A. Lucadamo, Estimating multinomial logit model with multicollinear data. Asian J. Math. Stat. 3, 93-101 (2010
39. L. Fehren-Schmitz, B. Llamas, S. Lindauer, E. Tomasto-Cagigao, S. Kuzminsky, N. Rohland, F. R. Santos, P. Kaulicke, G. Valverde, S. M. Richards, S. Nordenfelt, V. Seidenberg, S. Mallick, A. Cooper, D. Reich, W. Haak, A re-Appraisal of the early Andean human remains from Lauricocha in Peru. PLOS One 10, e0127141 (2015
40. G. G. Politis, M. A. Gutiérrez, C. Scabuzzo, Eds., Estado actual de las investigaciones en el sitio arqueológico Arroyo Seco 2 (partido de Tres Arroyos, provincia de Buenos Aires, Argentina), Serie monográfica (INCUAPA, Olavarría, 2014
41. W. Haak, I. Lazaridis, N. Patterson, N. Rohland, S. Mallick, B. Llamas, G. Brandt, S. Nordenfelt, E. Harney, K. Stewardson, Q. Fu, A. Mittnik, E. Bánffy, C. Economou, M. Francken, S. Friederich, R. G. Pena, F. Hallgren, V. Khartanovich, A. Khokhlov, M. Kunst, P. Kuznetsov, H. Meller, O. Mochalov, V. Moiseyev, N. Nicklisch, S. L. Pichler, R. Risch, M. A. R. Guerra, C. Roth, A. Szécsényi-Nagy, J. Wahl, M. Meyer, J. Krause, D. Brown, D. Anthony, A. Cooper, K. W. Alt, D. Reich, Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207-211 (2015
42. M. Meyer, M. Kircher, Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 2010, 1-10 (2010
43. A. J. Drummond, M. A. Suchard, D. Xie, A. Rambaut, Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969-1973 (2012
44. J. Heled, A. J. Drummond, Bayesian inference of population size history from multiple loci. BMC Evol. Biol. 8, 289 (2008
45. M. Rasmussen, S. L. Anzick, M. R. Waters, P. Skoglund, M. DeGiorgio, T. W. Stafford Jr., S. Rasmussen, I. Moltke, A. Albrechtsen, S. M. Doyle, G. D. Poznik, V. Gudmundsdottir, R. Yadav, A.-S. Malaspinas, S. S. White V, M. E. Allentoft, O. E. Cornejo, K. Tambets, A. Eriksson, P. D. Heintzman, M. Karmin, T. S. Korneliussen, D. J. Meltzer, T. L. Pierre, J. Stenderup, L. Saag, V. M. Warmuth, M. C. Lopes, R. S. Malhi, S. Brunak, T. Sicheritz-Ponten, I. Barnes, M. Collins, L. Orlando, F. Balloux, A. Manica, R. Gupta, M. Metspalu, C. D. Bustamante, M. Jakobsson, R. Nielsen, E. Willerslev, The genome of a late Pleistocene human from a Clovis burial site in western Montana. Nature 506, 225-229 (2014
46. 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.
47. R Development Core Team, R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, Vienna, 2010
48. S. Lindgreen, AdapterRemoval: Easy cleaning of next-generation sequencing reads. BMC Res. Notes 5, 337 (2012
49. D. M. Behar, M. van Oven, S. Rosset, M. Metspalu, E.-L. Loogväli, N. M. Silva, T. Kivisild, A. Torroni, R. Villems, A "Copernican" reassessment of the human mitochondrial DNA tree from its root. Am. J. Hum. Genet. 90, 675-684 (2012
50. H. Li, R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009
51. M. Schubert, A. Ginolhac, S. Lindgreen, J. F. Thompson, K. A. Al-Rasheid, E. Willerslev, A. Krogh, L. Orlando, Improving ancient DNA read mapping against modern reference genomes. BMC Genomics 13, 178 (2012
52. M. Kircher, Analysis of high-Throughput ancient DNA sequencing data. Methods Mol. Biol. 840, 197-228 (2012
53. A. Ginolhac, M. Rasmussen, M. T. P. Gilbert, E. Willerslev, L. Orlando, mapDamage: Testing for damage patterns in ancient DNA sequences. Bioinformatics 27, 2153-2155 (2011
54. 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
55. J. Dabney, M. Knapp, I. Glocke, M.-T. Gansauge, A. Weihmann, B. Nickel, C. Valdiosera, N. García, S. Pääbo, J.-L. Arsuaga, M. Meyer, Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl. Acad. Sci. U.S.A. 110, 15758-15763 (2013
56. N. Rohland, E. Harney, S. Mallick, S. Nordenfelt, D. Reich, Partial uracil-DNA-glycosylase treatment for screening of ancient DNA. Philos. Trans. R. Soc. Lond. B Biol. Sci. 370, 20130624 (2014
57. Q. Fu, M. Meyer, X. Gao, U. Stenzel, H. A. Burbano, J. Kelso, S. Pääbo, DNA analysis of an early modern human from Tianyuan Cave, China. Proc. Natl. Acad. Sci. U.S.A. 110, 2223-2227 (2013
58. M. Meyer, Q. Fu, A. Aximu-Petri, I. Glocke, B. Nickel, J.-L. Arsuaga, I. Martínez, A. Gracia, J. M. B. de Castro, E. Carbonell, S. Pääbo, A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature 505, 403-406 (2014
59. A. R. Quinlan, I. M. Hall, BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010
60. H. Jonsson, A. Ginolhac, M. Schubert, P. L. F. Johnson, L. Orlando, mapDamage2.0: Fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682-1684 (2013
61. 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
62. R. Lanfear, B. Calcott, S. Y. W. Ho, S. Guindon, Partitionfinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol. Biol. Evol. 29, 1695-1701 (2012
63. 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
64. 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
65. A. J. Drummond, S. Y. W. Ho, M. J. Phillips, A. Rambaut, Relaxed phylogenetics and dating with confidence. PLOS Biol. 4, e88 (2006
66. 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
67. 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
68. 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
69. H. Lieth, R. H. Whittaker, Eds., Primary Productivity of the Biosphere (Springer-Verlag, Berlin, 1975
70. C. Smith, Late Stone Age Hunters of the British Isles (Routledge, New York, 1992
71. 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
72. H. Schutkowski, Human Ecology: Biocultural Adaptations in Human Communities (Springer-Verlag, Berlin, 2006
73. R. Frankham, Effective population size/adult population size ratios in wildlife: A review. Genet. Res. 89, 491-503 (2007
74. F. P. Palstra, D. J. Fraser, Effective/census population size ratio estimation: A compendium and appraisal. Ecol. Evol. 2, 2357-2365 (2012
75. M. Ingman, H. Kaessmann, S. Pääbo, U. Gyllensten, Mitochondrial genome variation and the origin of modern humans. Nature 408, 708-713 (2000
76. 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
77. 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
78. 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
79. M. Ingman, U. Gyllensten, Rate variation between mitochondrial domains and adaptive evolution in humans. Hum. Mol. Genet. 16, 2281-2287 (2007
80. 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
81. 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
82. M. Derenko, B. Malyarchuk, T. Grzybowski, G. Denisova, U. Rogalla, M. Perkova, I. Dambueva, I. Zakharov, Origin and post-glacial dispersal of mitochondrial DNA haplogroups C and D in northern Asia. PLOS One 5, e15214 (2010
83. 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
84. 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
85. 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
86. 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