Ancient DNA perspectives on American colonization and population history

American Journal of Physical Anthropology

Volumn 146, Issue 4, 2011, Pages 503-514

  Raff, Jennifer A ^a,b   Bolnick, Deborah A ^c   Tackney, Justin ^a   O'Rourke, Dennis H ^a  

^a UNIVERSITY OF UTAH   (United States)

^b NORTHWESTERN UNIVERSITY   (United States)

^c UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

Americas; ancient DNA; genetics

Indexed keywords

DNA; MITOCHONDRIAL DNA;

AMERICAN INDIAN; ANCIENT DNA ANALYSIS; ARCHEOLOGY; DNA DETERMINATION; EARLY MODERN PERIOD; EVOLUTION; GENE FREQUENCY; GENE SEQUENCE; GENETIC VARIABILITY; HAPLOTYPE; HISTORICAL PERIOD; HISTORY; HUMAN; MOLECULAR CLONING; MOLECULAR GENETICS; PALEOANTHROPOLOGY; PHYLOGENY; POPULATION DISPERSAL; POPULATION GENETICS; POPULATION HISTORY; REVIEW; UNITED STATES;

AMERICAN NATIVE CONTINENTAL ANCESTRY GROUP; AMERICAS; ANALYSIS OF VARIANCE; DNA, MITOCHONDRIAL; EMIGRATION AND IMMIGRATION; HAPLOTYPES; HISTORY, 21ST CENTURY; HISTORY, ANCIENT; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; PRINCIPAL COMPONENT ANALYSIS;

EID: 80855123486     PISSN: 00029483     EISSN: 10968644     Source Type: Journal    
DOI: 10.1002/ajpa.21594     Document Type: Review

References (71)

1. Bolnick DA, Smith DG,. 2007. Migration and social structure among the Hopewell: evidence from ancient DNA. Am Antiq 72: 627-644.
2. Cabana GS, Hunley K, Kaestle FA,. 2008. Population continuity or replacement? A novel computer simulation approach and its application to the Numic expansion (western Great Basin, USA). Am J Phys Anthropol 135: 438-447. (Pubitemid 351416117)
3. Carlyle SW, Parr RL, Hayes MG, O'Rourke DH,. 2000. The context of maternal lineages in the Greater Southwest. Am J Phys Anthropol 113: 85-101.
4. Carnese FR, Mendisco F, Keyser C, Dejean CB, Dugooujon J-M, Bravi CM, Ludes B, Crubézy E,. 2010. Paleogenetical study of pre-Columbian samples from Pampa Grande (Salta Argentina). Am J Phys Anthropol 141: 452-462.
5. Crawford MH, Rubicz RC, Zlojutro M,. 2010. Origins of Aleuts and the genetic structure of populations of the archipelago: molecular and archaeological perspectives. Hum Biol 82: 695-718.
6. Demarchi DA, Panzetta-Dutari GM, Colantonio SE, Marcellino AJ,. 2001. Absence of the 9-bp deletion of mitochondrial DNA in pre-Hispanic inhabitants of Argentina. Hum Biol 73: 575-582. (Pubitemid 32773768)
7. Endicott P, Ho SY,. 2008. A Bayesian evaluation of human mitochondrial substitution rates. Am J Hum Genet 82: 895-902.
8. Eshleman JA,. 2002. Mitochondrial DNA and prehistoric population movements in Western North America. Ph.D. dissertation, University of California, Davis.
9. Excoffier L, Lischer HEL,. 2010. Arlequin suite ver. 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10: 564-567.
10. Fagundes NJR, Kkanitz R, Eckert R, Valls ACS, Bogo MR, Salzano FM, Smith DG, Silva WA, Zago MA, Ribeiro-dos-Santos AK, Santos SEB, Petzl-Erler ML, Bonatto SL,. 2008. Mitochondrial population genomics supports a single Pre-Clovis origin with a coastal route for the peopling of the Americas. Am J Hum Gen 82: 583-592.
11. Fehren-Schmitz L, Reindel M, Cagigao ET, Hummel S, Herrmann B,. 2010. Pre-Columbian population dynamics in coastal southern Peru: a diachronic investigation of mtDNA patterns in the Palpa region by ancient DNA analysis. Am J Phys Anthropol 141: 208-221.
12. Fehren-Schmitz L, Warnberg O, Reindel M, Seidenberg V, Tomasto-Cagigao E, Isla-Cuadrado J, Hummel S, Herrmann B,. 2011. Diachronic investigations of mitochondrial and Y-chromosomal genetic markers in pre-Columbian Andean Highlanders from South Peru. Ann Hum Genet 75: 266-283.
13. Figueiro G, Sans M,. 2007. Primeros resultados del análisis de ADN mitochondrial del sitio Arroyo Seco 2. Provincia de Buenos Aires, Argentina. Rev Arg Antrop Biol 9: 78.
14. Garcia-Bour J, Perez-Perez A, Alvarez S, Fernandez A, Lopez-Parra AM, Arroyo-Pardo E, Turbõ Daniel,. 2004. Early population differentiation in extinct aborigines from Tierra del Fuego-Patagonia: ancient mtDNA sequences and Y-chromosome STR characterization. Am J Phys Anthropol 123: 361-370. (Pubitemid 38524548)
15. Gilbert MTP, Jenkins DL, Götherstrom A, Naveran N, Sanchez JJ, Hofreiter M, Thomsen PF, Binladen J, Higham TFG, Yohe II RM, Parr R, Cummings LS, Willerslev E,. 2008a. DNA from pre-Clovis human coprolites in Oregon. North America. Science 320: 786.
16. Gilbert MTP, Kivisild T, Gronnow B, Andersen PK, Metspalu E,., Axelsson E, Götherström A, Campos PF, Rasmussen M, Metspalu M, Higham TFG, Schwenninger J-L, Nathan R, De Hoog C-J, Koch A, Møller LN, Andreasen C, Meldgaard M, Villems R, Bendixen C, Willerslev E,. 2008b. Paleo-Eskimo mtDNA genome reveals matrilineal discontinuity in Greenland. Science 320: 1787-1789. (Pubitemid 351931295)
17. Goebel T, Waters MR, O'Rourke DH,. 2008. The Late Pleistocene dispersal of modern humans in the Americas. Science 319: 1497-1502. (Pubitemid 351398171)
18. González-José R, Bortolini MC, Santos FR, Bonatto SL,. 2008. The peopling of America: craniofacial shape variation on a continental scale and its interpretation from an interdisciplinary view. Am J Phys Anthropol 137: 175-187.
19. González-Oliver A, Márquez-Morfín L, Jiménez JC, Torre-Blanco A,. 2001. Founding Amerindian mitochondrial DNA lineages in ancient Maya from Xcaret. Quintana Roo. Am J Phys Anthropol 116: 230-235. (Pubitemid 33020941)
20. Halverson MS, Bolnick DA,. 2008. An ancient DNA test of a founder effect in Native American ABO blood group frequencies. Am J Phys Anthropol 137: 342-247.
21. Hayes MG,. 2002. Paleogenetic assessments of human migration and population replacement in North American arctic prehistory. Ph.D. Dissertation, Salt Lake City: University of Utah.
22. Hayes MG, Coltrain JB, O'Rourke DH,. 2003. Mitochondrial analyses of Dorset, Thule,Sadlermiut, and Aleut skeletal samples from the prehistoric North American Arctic. In:, Lynnerup N, Andreasen C, Berglund J, editors. Mummies in a new millennium: Proceedings of the 4th World Congress on Mummy Studies. Copenhagen: Danish Polar Center. p 125-128.
23. Hayes MG, Coltrain JB, O'Rourke DH,. 2005. Molecular archaeology of the Dorset, Thule, and Sadlermiut: ancestor-descendant relationships in eastern North American arctic prehistory. In:, Sutherland P, editor. Contributions to the Study of the Dorset Palaeo-Eskimos, Mercury Series, Archaeological Paper 167. Hull, Quebec: Canadian Museum of Civilization.
24. Henn BM, Gignoux CR, Feldman MW, Mountain JL,. 2008. Characterizing the time dependency of human mitochondrial DNA mutation rate estimates. Mol Biol Evol 26: 217-230.
25. Ho SY, Endicott P,. 2008. The crucial role of calibration in molecular date estimates for the peopling of the Americas. Am J Hum Genet 83: 142-146; author reply 146-147. (Pubitemid 351905733)
26. Kaestle FA,. 1998. Molecular evidence for prehistoric Native American population movement: the Numic expansion. Ph.D. dissertation, Department of Anthropology, University of California, Davis.
27. Kaestle PA, Horsburgh KA,. 2002. Ancient DNA in anthropology: methods, applications, and ethics. Yrbk Phys Anthropol 45: 92-130. (Pubitemid 36109384)
28. Kaestle F, Smith DG,. 2001. Ancient Native American DNA from western Nevada: implications for the Numic expansion hypothesis. Am J Phys Anthropol 115: 1-12.
29. Kemp BM, Reséndez A, Berrelleza JAR, Malhi RS, Smith DG,. 2005. An analysis of ancient Aztec mtDNA from Tlatelolco: pre-Columbian relations and the spread of Uto-Aztecan. In:, Reed DM, editor. Biomolecular archaeology: genetic approaches to the past. Occasional Paper No. 32. Southern Illinois University, Carbondale: Center for Archaeological Investigations. p 22-46.
30. Kemp BM, Malhi RS, McDonough J, Bolnick DA, Eshleman JA, Rickards O, Martinez-Labarga C, Johnson JR, Lorenz JG, Dixon J, Fifield TE, Heaton TH, Worl R, Smith DG,. 2007. Genetic analysis of Early Holocene skeletal remains from Alaska and its implications for the settlement of the Americas. Am J Phys Anthropol 132: 605-621. (Pubitemid 46474039)
31. Kemp BM, Schurr TG,. 2010. Ancient and modern genetic variation in the Americas. In:, Auerbach BM, editor. Human variation in the Americas. Center for Archaeological Investigations, Occasional Paper No. 38. Southern Illinois University Carbondale. pp. 12-50.
32. Kemp BM, Tung TA, Summar ML,. 2009. Genetic continuity after the collapse of the Wari empire: Mitochondrial DNA profiles from Wari and post-Wari populations in the ancient Andes. Am J Phys Anthropol 140: 80-91.
33. Lalueza C, Perez-Perez A, Prats E, Cornudella L, Turbon D,. 1997. Lack of founding Amerindian mitochondrial DNA lineages in extinct aborigines from Tierra de Fuego-Patagonia. Hum Mol Genet 6: 41-46. (Pubitemid 27033963)
34. Lalueza-Fox C, Calderõn FL, Calafell F, Morera B, Bertranpetit J,. 2001. MtDNA from extinct Tainos and the peopling of the Caribbean. Ann Hum Genet 65: 137-151. (Pubitemid 32452116)
35. Lalueza-Fox C, Gilbert MTP, Martínez-Fuentes AJ, Calafell F, Bertranpetit J,. 2003. Mitochondrial DNA from pre-Columbian Ciboneys from Cuba and the prehistoric colonization of the Caribbean. Am J Phys Anthropol 121: 97-108. (Pubitemid 36622384)
36. LeBlanc SA, Kreisman LSC, Kemp BM, Smiley FE, Carlyle SW, Dhody AN, Benjamin T,. 2007. Quids and aprons: ancient DNA from artifacts from the American southwest. J Field Archeol 32: 161-176.
37. Lewis CM, Buikstra JE, Stone AC,. 2007. Ancient DNA and genetic continuity in the South Central Andes. Latin Am Antiq 18: 145-160.
38. Luciani S, Fornaciari G, Rickards O, Labarga CM, Rollo F,. 2006. Molecular characterization of a pre-Columbian mummy and in situ coprolite. Am J Phys Anthropol 129: 620-629.
39. Malhi RS, Breece KE, Shook BAS, Kaestle FA, Chatters JC, Hackenberger S, Smith DG,. 2004. Patterns of mtDNA diversity in northwestern North America. Hum Biol 76: 33-54. (Pubitemid 38780638)
40. Malhi RS, Kemp BM, Eshleman JA, Cybulski J, Smith DG, Cousins S, Harry H,. 2007. Mitochondrial haplogroup M discovered in prehistoric North Americans. J Archeol Sci 34: 642-648. (Pubitemid 44914697)
41. Malhi RS, Cybulski JS, Tito RY, Johnson J, Harry H, Dan C,. 2010. Brief communication: Mitochondrial haplotype C4c confirmed as a founding genome in the Americas. Am J Phys Anthropol 141: 494-497.
42. Marchani EE, Rogers AR, O'Rourke DH,. 2007. The Thule migration: rejecting population histories using computer simulation. Am J Phys Anthropol 131: 281-284. (Pubitemid 47438662)
43. Merriwether DA, Reed DM, Ferrell RE,. 1997. Ancient and contemporary mitochondrial DNA variation in the Maya. In:, Whittington, SL, Reed DM, editors. Bones of the Maya: studies of ancient skeletons. Washington, DC: Smithsonian Institute Press. p 208-217.
44. Mills L,. 2003. Mitochondrial DNA analysis of the Ohio Hopewell of the Hopewell Mound Group. Ph.D. dissertation. The Ohio State University, Columbus.
45. Monsalve MV, Stone AC, Lewis CM, Rempel A, Richards M, Straathof D, Devine DV,. Molecular Analysis of the Kwäday Dän Ts'ínchi Ancient Remains Found in a Glacier in Canada. Am J Phys Anthropol 119: 288-291.
46. Moraga M, Santoro CM, Standen VG, Carvallo P, Rothhammer F,. 2005. Microevolution in prehistoric Andean populations: chronologic mtDNA variation in the desert valleys of northern Chile. Am J Phys Anthropol 127: 170-181. (Pubitemid 40664276)
47. Mulligan CJ, Kitchen A, Miyamoto MM,. 2008. Updated three-stage model for the peopling of the Americas. PLoS One. 3: e3199.
48. O'Rourke DH, Hayes MG, Carlyle SW,. 2000a. Ancient DNA studies in physical anthropology. Ann Rev Anthropol 29: 217-242.
49. O'Rourke DH, Hayes MG, Carlyle SW,. 2000b. Spatial and temporal stability of mtDNA haplogroup frequencies in native North America. Hum Biol 72: 15-34. (Pubitemid 30132300)
50. O'Rourke DH, Raff JA,. 2010. The human genetic history of the Americas: the final frontier. Curr Biol 20: R202-R207.
51. Parr RL, Carlyle SW, O'Rourke DH,. 1996. Ancient DNA analysis of Fremont Amerindians of the Great Salt Lake wetlands. Am J Phys Anthropol 99: 507-518. (Pubitemid 26106636)
52. Parr RL,. 1998. Molecular genetic analysis of the Great Salt Lake wetlands Fremont. Unpublished Ph.D. dissertation. Department of Anthropology, Salt Lake City: University of Utah.
53. Perego UA, Achilli A, Angerhofer N, Accetturo M, Pala M, Olivieri A, Kashani BH, Ritchie KH, Scozzari R, Kong Q-P, Myres NM, Salas A, Semino O, Bandelt H-J, Woodward SR, Torroni A,. 2009. Distinctive but concomitant Paleo-Indian migration routes from Beringia marked by two rare mtDNA haplogroups. Curr Biol 19: 1-8.
54. Perego UA, Angerhofer N, Pala M, Olivieri A, Lancioni H, Kashani BH, Carossa V, Ekins JE, Gõmez-Carballa A, Huber G, Zimmermann B, Corach D, Babudri N, Panara F, Myres NM, Parson W, Semino O, Salas A, Woodward SR, Achilli A, Torroni A,. 2010. The initial peopling of the Americas: a growing number of founding mitochondrial genomes from Beringia. Genome Res 20: 1174-1179.
55. Perez SI, Bernal V, Gonzalez PN, Sardi M, and, Politis GG,. 2009. Discrepancy between cranial and DNA data of early Americans: implications for American peopling. PLoS ONE 4 (5): e5746. doi:10.1371/journal.pone.0005746.
56. Raff JA,. 2008. An ancient DNA perspective on the prehistory of the Lower Illinois Valley. Ph.D. dissertation. Indiana University, Bloomington.
57. Raff JA, Tackney J, O'Rourke DH,. 2010. South from Alaska: a pilot aDNA study of genetic history on the Alaska Peninsula and the Eastern Aleutians. Hum Biol 82: 677-693.
58. Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A,., Moltke I, Metspalu M, Metspalu E, Kivisild T, Gupta R, Bertalan M, Nielsen K, Gilbert MTP, Wang Y, Raghavan M, Campos PF, Kamp HM, Wilson AS, Gledhill A, Tridico S, Bunce M, Lorenzen ED, Binladen J, Guo X, Zhao J, Zhang X, Zhang H, Li Z, Chen M, Orlando L, Kristiansen K, Bak M, Tommerup N, Bendixen C, Pierre TL, Grønnow B, Meldgaard M, Andreasen C, Fedorova SA, Osipova LP, Higham TFG, Ramsey CB, Hansen TVO, Nielsen FC, Crawford MH, Brunak S, Sicheritz- Pointén T, Villems R, Nielsen R, Krogh A, Wang J, Willerslev E,. 2010. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463: 757-762.
59. Rickards O, Martínez-Labarga C, Lum JK, De Stefano GF, Cann RL,. 1999. mtDNA history of the Cayapa Amerinds of Ecuador: detection of additional founding lineages for the Native American populations. Am J Hum Genet 65: 519-530. (Pubitemid 30463009)
60. Schroeder KB, Jakobsson M, Crawford MH, Schurr TG, Boca SM, Conrad DF, Tito RY, Osipova LP, Tarskaia LA, Zhadanov SI, Wall JD, Pritchard JK, Malhi RS, Smith DG, Rosenberg NA,. 2009. Haplotypic background of a private allele at high frequency in the Americas. Mol Biol Evol 26: 995-1016.
61. Shimada I, Shinoda K, Farnum J, Corruccini R, Watanabe H,. 2004. An integrated analysis of pre-Hispanic mortuary practices. Curr Anthropol 45: 369-390.
62. Shinoda K, Adachi N, Guillen S, Shimada I,. 2006. Mitochondrial DNA analysis of ancient Peruvian highlanders. Am J Phys Anthropol 131: 98-107. (Pubitemid 44267106)
63. Shook BAS, Smith DG,. 2008. Using ancient mtDNA to reconstruct the population history of northeastern North America. Am J Phys Anthropol 137: 14-29.
64. Smith S, Hayes MG, Cabana G, Huff C, Coltrain JB, O'Rourke DH,. 2009. Inferring population continuity versus replacement with aDNA: a cautionary tale from the Aleutian Islands. Hum Biol 81: 19-38.
65. Smith DG, Malhi RS, Eshleman JA, Kaestle FA, Kemp BM,. 2005. Mitochondrial DNA Haplogroups of Paleoamericans in North America. In:, Bonnichsen R, Lepper BT, Stanford D, Waters MR, editors. Paleoamerican origins: beyond Clovis. College Station, TX: Texas A&M University Press. p 243-254.
66. Snow MH, Durand KR, Smith DG,. 2010. Ancestral Puebloan mtDNA in context of the greater southwest. J Archeol Sci 37: 1635-1645.
67. Stone A, Stoneking M,. 1998. mtDNA analysis of a prehistoric Oneota population: implications for the peopling of the New World. Am J Hum Gen 62: 1153-1170. (Pubitemid 28199018)
68. Tamm E, Kivisild T, Reidla M, Metspalu M, Smith DG, Mulligan CJ, Bravis CM, Rickards O, Martinez-Labarga C, Khusnutdinova EK, Fedrova SA, Golubenko MV, Stepanov VA, Grubina MA, Zhadanov SI, Ossipova LP, Damba L, Voevoda MI, Dipierri JE, Villems R, Malhi RS,. 2007. Beringian standstill and spread of Native American founders. PLoS ONE 2: e829.
69. Van Oven M, Kayser M,. 2009. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30: E386-E394.
70. Wang S, Lewis CM, Jakobsson M, Ramachandran S, Ray N, Bedoya G, Rojas W, Parra MV, Molina JA, Gallo C, Mazzotti G, Poletti G, Hill K, Hurtado AM, Labuda D, Klitz W, Barrantes R, Bortolini MC, Salzano FM, Petzl-Erler ML, Tsuneto LT, Llop E, Rothhammer F, Excoffier L, Feldman MW, Rosenberg NA, Ruiz-Linares A,. 2007. Genetic variation and population structure in Native Americans. PLoS Genet 3: e185.
71. Yang NN, Mazières S, Bravi C, Ray N, Wang S, Burley M-W, Bedoya G, Rojas W, Parra MV, Molina JA, Gallo C, Poletti G, Hill K, Hurtado AM, Petzl-Erler ML, Tsuneto LT, Klintz W, Barrantes R, Llop E, Rothhammer F, Labuda D, Salzano FM, Bortolini M-C, Excoffier L, Dugoujon JM, Ruiz-Linares A,. 2010. Contrasting patterns of nuclear and mtDNA diversity in Native American populations. Ann Hum Genet 74: 525-538.