1932

Abstract

Studies of Native American genetic diversity and population history have been transformed over the last decade by important developments in anthropological genetics. During this time, researchers have adopted new DNA technologies and computational approaches for analyzing genomic data, and they have become increasingly sensitive to the views of research participants and communities. As new methods are applied to long-standing questions, and as more research is conducted in collaboration with indigenous communities, we are gaining new insights into the history and diversity of indigenous populations. This review discusses the recent methodological advances and genetic studies that have improved our understanding of Native American genomics and population histories. We synthesize current knowledge about Native American genomic variation and build a model of population history in the Americas. We also discuss the broader implications of this research for anthropology and related disciplines, and we highlight challenges and other considerations for future research.

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2016-10-21
2024-03-29
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Literature Cited

  1. 1000 Genomes Proj. Consort 2015. A global reference for human genetic variation. Nature 526:68–74 [Google Scholar]
  2. Achilli A, Perego UA, Lancioni H, Olivieri A, Gandini F. et al. 2013. Reconciling migration models to the Americas with the variation of North American native mitogenomes. PNAS 110:3514308–13 [Google Scholar]
  3. Alexander DH, Novembre J, Lange K. 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19:1655–64 [Google Scholar]
  4. Allentoft ME, Sikora M, Sjögren K-G, Rasmussen S, Rasmussen M. et al. 2015. Population genomics of Bronze Age Eurasia. Nature 522:167–72 [Google Scholar]
  5. Arbour L, Cook D. 2006. DNA on loan: issues to consider when carrying out genetic research with aboriginal families and communities. Community Genet. 9:153–60 [Google Scholar]
  6. Baca M, Doan K, Sobczyk M, Stankovic A, Weglenski P. 2012. Ancient DNA reveals kinship burial patterns of a pre-Columbian Andean community. BMC Genet. 13:30 [Google Scholar]
  7. Balestrery JE. 2010. The bureaucratic Iditarod: navigating the terrain of social policy and research in Alaska and beyond. J. Policy Pract. 9:2132–53 [Google Scholar]
  8. Ballard JW, Whitlock MC. 2004. The incomplete natural history of mitochondria. Mol. Ecol. 13:4729–44 [Google Scholar]
  9. Barbieri C, Heggarty P, Yao DY, Ferri G, De Fanti S. et al. 2014. Between Andes and Amazon: the genetic profile of the Arawak-speaking Yanesha. Am. J. Phys. Anthropol. 155:600–9 [Google Scholar]
  10. Bardill J. 2014. Native American DNA: ethical, legal, and social implications of an evolving concept. Annu. Rev. Anthropol. 43:155–66 [Google Scholar]
  11. Battaglia V, Grugni V, Perego UA, Angerhofer N, Gomez-Palmieri JE. et al. 2013. The first peopling of South America: new evidence from Y-chromosome haplogroup Q. PLOS ONE 8:8e71390 [Google Scholar]
  12. Beaulieu-Jones BR, O'Brien DM, Hopkins SE, Moore JH, Boyer BB, Gilbert-Diamond D. 2015. Sex, adiposity, and hypertension status modify the inverse effect of marine food intake on blood pressure in Alaska Native (Yup'ik) people. J. Nutr. 145:5931–38 [Google Scholar]
  13. Beaumont M. 2010. Approximate Bayesian computation in evolution and ecology. Annu. Rev. Ecol. Evol. Syst. 41:379–406 [Google Scholar]
  14. Benn Torres J, Vilar MG, Torres GA, Gaieski JB, Bharath Hernandez R. et al. 2015. Genetic diversity in the Lesser Antilles and its implications for the settlement of the Caribbean basin. PLOS ONE 10:10e0139192 [Google Scholar]
  15. Benn-Torres J, Bonilla C, Robbins CM, Waterman L, Moses TY. et al. 2008. Admixture and population stratification in African Caribbean populations. Ann. Hum. Genet. 72:90–98 [Google Scholar]
  16. Black TJ. 2011. Extraction of mitochondrial DNA from prehistoric dental calculus. MS Thesis, Cent. Wash. Univ., Ellensburg
  17. Bodner M, Perego UA, Huber G, Fendt L, Röck AW. et al. 2012. Rapid coastal spread of First Americans: novel insights from South America's Southern Cone mitochondrial genomes. Genome Res. 22:811–20 [Google Scholar]
  18. Bolnick DA, Bolnick DI, Smith DG. 2006. Asymmetric male and female genetic histories among Native Americans from Eastern North America. Mol. Biol. Evol. 23:112161–74 [Google Scholar]
  19. Bolnick DA, Bonine HM, Mata-Míguez J, Kemp BM, Snow MH, Leblanc SA. 2012. Nondestructive sampling of human skeletal remains yields ancient nuclear and mitochondrial DNA. Am. J. Phys. Anthropol. 147:293–300 [Google Scholar]
  20. Bolnick DA, Smith DG. 2003. Unexpected patterns of mitochondrial DNA variation among Native Americans from the southeastern United States. Am. J. Phys. Anthropol. 122:336–54 [Google Scholar]
  21. Briggs AW, Stenzel U, Meyer M, Krause J, Kircher M, Paabo S. 2010. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 38:e87 [Google Scholar]
  22. Bryc K, Velez C, Karafet T, Moreno-Estrada A, Reynolds A. et al. 2010. Colloquium paper: genome-wide patterns of population structure and admixture among Hispanic/Latino populations. PNAS 107:8954–61 [Google Scholar]
  23. Cabana GS, Lewis CM, Tito RY, Alan Covey R, Cáceres AM. et al. 2014. Population genetic structure of traditional populations in the Peruvian Central Andes and implications for South American population history. Hum. Biol. 86:147–65 [Google Scholar]
  24. Cann HM, de Toma C, Cazes L, Legrand MF, Morel V. et al. 2002. A human genome diversity cell line panel. Science 296:261–362 [Google Scholar]
  25. Carpenter ML, Buenrostro JD, Valdiosera C, Schroeder H, Allentoft ME. et al. 2013. Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries. Am. J. Hum. Genet. 93:852–64 [Google Scholar]
  26. Chatters JC, Kennett DJ, Asmerom Y, Kemp BM, Polyak V. et al. 2014. Late Pleistocene human skeleton and mtDNA link Paleoamericans and modern Native Americans. Science 344:750–54 [Google Scholar]
  27. Claw K, Garrison N. 2015. Bringing indigenous researchers to the forefront of genomics. SACNAS News Magazine. Jan. 15. http://sacnas.org/about/stories/sacnas-news/winter-2015-indigenous-genomics
  28. Cooper A, Poinar HN. 2000. Ancient DNA: Do it right or not at all. Science 289:111139 [Google Scholar]
  29. Cui Y, Lindo J, Hughes CE, Johnson JW, Hernandez AG. et al. 2013. Ancient DNA analysis of mid-Holocene individuals from the Northwest Coast of North America reveals different evolutionary paths for mitogenomes. PLOS ONE 8:7e66948 [Google Scholar]
  30. Dabney J, Knapp M, Glocke I, Gansauge M-T, Weihmann A. et al. 2013. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. PNAS 110:15758–63 [Google Scholar]
  31. Damgaard PB, Margaryan A, Schroeder H, Orlando L, Willerslev E, Allentoft ME. 2015. Improving access to endogenous DNA in ancient bones and teeth. Sci. Rep. 5:11184 [Google Scholar]
  32. de Saint Pierre M, Bravi CM, Motti JMB, Fuku N, Tanaka M. et al. 2012a. An alternative model for the early peopling of southern South America revealed by analyses of three mitochondrial DNA haplogroups. PLOS ONE 7:9e43486 [Google Scholar]
  33. de Saint Pierre M, Gandini F, Perego UA, Bodner M, Gómez-Carballa A. et al. 2012b. Arrival of Paleo-Indians to the Southern Cone of South America: new clues from mitogenomes. PLOS ONE 7:12e51311 [Google Scholar]
  34. Drummond AJ, Suchard MA, Xie D, Rambaut A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29:81969–73 [Google Scholar]
  35. Dulik MC, Owings AC, Gaieski JB, Vilar MG, Andre A. et al. 2012. Y-chromosome analysis reveals genetic divergence and new founding native lineages in Athapaskan- and Eskimoan-speaking populations. PNAS 109:228471–76 [Google Scholar]
  36. Fagundes N, Kanitz R, Eckert R. 2008. Mitochondrial population genomics supports a single pre-Clovis origin with a coastal route for the peopling of the Americas. Am. J. Hum. Genet. 82:583–92 [Google Scholar]
  37. Fehren-Schmitz L, Georges L. 2016. Ancient DNA reveals selection acting on genes associated with hypoxia response in pre-Columbian Peruvian Highlanders in the last 8500 years. Sci. Rep. 6:23485 [Google Scholar]
  38. Fehren-Schmitz L, Haak W, Machtle B, Masch F, Llamas B. et al. 2014. Climate change underlies global demographic, genetic, and cultural transitions in pre-Columbian southern Peru. PNAS 111:269443–48 [Google Scholar]
  39. Fehren-Schmitz L, Warnberg O, Reindel M, Seidenberg V, Tomasto-Cagigao E. et al. 2011. Diachronic investigations of mitochondrial and Y-chromosomal genetic markers in Pre-Columbian Andean Highlanders from South Peru. Ann. Hum. Genet. 75:266–83 [Google Scholar]
  40. Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368–76 [Google Scholar]
  41. Foll M, Shim H, Jensen JD. 2015. WFABC: a Wright-Fisher ABC-based approach for inferring effective population sizes and selection coefficients from time-sampled data. Mol. Ecol. Resour. 15:87–98 [Google Scholar]
  42. Gamba C, Hanghøj K, Gaunitz C, Alfarhan AH, Alquraishi SA. et al. 2015. Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing. Mol. Ecol. Resour. 16:459–69 [Google Scholar]
  43. Gansauge M-T, Meyer M. 2013. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat. Protoc. 8:4737–48 [Google Scholar]
  44. Gayà-Vidal M, Moral P, Saenz-Ruales N, Gerbault P, Tonasso L. et al. 2011. mtDNA and Y-chromosome diversity in Aymaras and Quechuas from Bolivia: different stories and special genetic traits of the Andean Altiplano populations. Am. J. Phys. Anthropol. 145:215–30 [Google Scholar]
  45. Gómez-Carballa A, Catelli L, Pardo-Seco J, Martinón-Torres F, Roewer L. et al. 2015. The complete mitogenome of a 500-year-old Inca child mummy. Sci. Rep. 5:16462 [Google Scholar]
  46. González-Martín A, Gorostiza A, Regalado-Liu L, Arroyo-Peña S, Tirado S. et al. 2015. Demographic history of indigenous populations in Mesoamerica based on mtDNA sequence data. PLOS ONE 10:8e0131791 [Google Scholar]
  47. Gorostiza A, Acunha-Alonzo V, Regalado-Liu L, Tirado S, Granados J. et al. 2012. Reconstructing the history of Mesoamerican populations through the study of the mitochondrial DNA control region. PLOS ONE 7:9e44666 [Google Scholar]
  48. Gravel S, Zakharia F, Moreno-Estrada A, Byrnes JK, Muzzio M. et al. 2013. Reconstructing Native American migrations from whole-genome and whole-exome data. PLOS Genet. 9:12e1004023 [Google Scholar]
  49. Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD. 2009. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLOS Genet. 5:10e1000695 [Google Scholar]
  50. Haak W, Lazaridis I, Patterson N, Rohland N, Mallick S. et al. 2015. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522:207–11 [Google Scholar]
  51. 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. Contributions to the Study of the Dorset Palaeo-Eskimos P Sutherland 11–32 Mercury Ser., Archaeol. Pap. 167 Hull, Quebec: Can. Mus. Civiliz. [Google Scholar]
  52. Hellenthal G, Busby GBJ, Band G, Wilson JF, Capelli C. et al. 2014. A genetic atlas of human admixture history. Science 343:747–51 [Google Scholar]
  53. Hoffecker JF, Elias SA, O'Rourke DH. 2014. Out of Beringia?. Science 343:979–80 [Google Scholar]
  54. Hoffecker JF, Elias SA, O'Rourke DH, Scott GR, Bigelow NH. 2016. Beringia and the global dispersal of modern humans. Evol. Anthropol. 25:64–78 [Google Scholar]
  55. Hofreiter M. 2012. Nondestructive DNA extraction from museum specimens. Ancient DNA: Methods and Protocols 840 B Shapiro, M Hofreiter 93–100 New York: Humana [Google Scholar]
  56. Hofreiter M. Goodchild H, Speller CF, Barlow A. , Paijmans JLA, et al. 2015. The future of ancient DNA: technical advances and conceptual shifts. BioEssays 37:3284–93 [Google Scholar]
  57. Homburger JR, Moreno-Estrada A, Gignoux CR, Nelson D, Sanchez E. et al. 2015. Genomic insights into the ancestry and demographic history of South America. PLOS Genet. 11:12e1005602 [Google Scholar]
  58. Hunley K, Healy M. 2011. The impact of founder effects, gene flow, and European admixture on Native American genetic diversity. Am. J. Phys. Anthropol. 146:530–38 [Google Scholar]
  59. Int. HapMap 3 Consort 2010. Integrating common and rare genetic variation in diverse human populations. Nature 467:52–58 [Google Scholar]
  60. Jakobsson M, Scholz SW, Scheet P, Gibbs JR, VanLiere JM. et al. 2008. Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451:998–1003 [Google Scholar]
  61. Jensen A. 2012. Culture and change: learning from the past through community archaeology on the North Slope. Polar Geogr. 35:3–4211–27 [Google Scholar]
  62. Jónsson H, Ginolhac A, Schubert M, Johnson PLF, Orlando L. 2013. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29:131682–84 [Google Scholar]
  63. Kemp B, Smith DG. 2010. Ancient DNA methodology: thoughts from Brian M. Kemp and David Glenn Smith of “Mitochondrial DNA of Protohistoric Remains of an Arikara Population from South Dakota.”. Hum. Biol. 2004:227–38 [Google Scholar]
  64. Kemp BM, González-Oliver A, Malhi RS, Monroe C, Schroeder KB. et al. 2010. Evaluating the Farming/Language Dispersal Hypothesis with Genetic Variation Exhibited by Populations in the Southwest and Mesoamerica. PNAS 107:156759–64 [Google Scholar]
  65. Kemp BM, Malhi RS, McDonough J, Bolnick DA, Eshleman JA. et al. 2007. Genetic analysis of Early Holocene skeletal remains from Alaska and its implications for the settlement of the Americas. Am. J. Phys. Anthropol. 132:605–21 [Google Scholar]
  66. Kemp BM, Schurr TG. 2010. Ancient and modern genetic variation in the Americas. Human Variation in the Americas: The Integration of Archaeology and Biological Anthropology BM Auerbach 12–50 Carbondale: South. Ill. Univ. [Google Scholar]
  67. Kitchen A, Miyamoto MM, Mulligan CJ. 2008. A three-stage colonization model for the peopling of the Americas. PLOS ONE 3:2e1596 [Google Scholar]
  68. Krause J, Briggs AW, Kircher M, Maricic T, Zwyns N. et al. 2010. A complete mtDNA genome of an early modern human from Kostenki, Russia. Curr. Biol. 20:231–36 [Google Scholar]
  69. Lachance J, Tishkoff SA. 2013. SNP ascertainment bias in population genetic analyses: why it is important, and how to correct it. BioEssays 35:780–86 [Google Scholar]
  70. LaFramboise T. 2009. Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances. Nucleic Acids Res. 37:134181–93 [Google Scholar]
  71. Li H, Durbin R. 2011. Inference of human population history from individual whole-genome sequences. Nature 475:493–96 [Google Scholar]
  72. Livi-Bacci M. 2006. The depopulation of Hispanic America after the conquest. Popul. Dev. Rev. 32:2199–232 [Google Scholar]
  73. Llamas B, Fehren-Schmitz L, Valverde G, Soubrier J, Rohland N. et al. 2016. Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas. Sci. Adv. 2:e1501385 [Google Scholar]
  74. Malaspinas AS. 2016. Methods to characterize selective sweeps using time serial samples: an ancient DNA perspective. Mol. Ecol. 25:124–41 [Google Scholar]
  75. Malhi RS, Bader AC. 2015. Engaging Native Americans in genomic research. Am. Anthropol. 117:4743–49 [Google Scholar]
  76. Malhi RS, Gonzalez-Oliver A, Schroeder KB, Kemp BM, Greenberg JA. et al. 2008. Distribution of Y chromosomes among native North Americans: a study of Athapaskan population history. Am. J. Phys. Anthropol. 137:412–24 [Google Scholar]
  77. Maples BK, Gravel S, Kenny EE, Bustamante CD. 2013. RFMix: a discriminative modeling approach for rapid and robust local-ancestry inference. Am. J. Hum. Genet. 93:2278–88 [Google Scholar]
  78. Mardis ER. 2013. Next-generation sequencing platforms. Annu. Rev. Anal. Chem. 6:287–303 [Google Scholar]
  79. Marshall C, Kaestle FA. 2013. Ancient DNA from Angel Mounds. Midcont. J. Archaeol. 38:2259–68 [Google Scholar]
  80. Mata-Míguez J, Overholtzer L, Rodríguez-Alegría E, Kemp BM, Bolnick DA. 2012. The genetic impact of Aztec imperialism: ancient mitochondrial DNA evidence from Xaltocan, Mexico. Am. J. Phys. Anthropol. 149:504–16 [Google Scholar]
  81. Mathieson I, McVean G. 2013. Estimating selection coefficients in spatially structured populations from time series data of allele frequencies. Genetics 193:973–84 [Google Scholar]
  82. Mathieson I, McVean G. 2014. Demography and the age of rare variants. PLOS Genet. 10:8e1004528 [Google Scholar]
  83. Mello MM, Wolf LE. 2010. The Havasupai Indian Tribe—lessons for research involving stored biologic samples. N. Engl. J. Med. 363:1–3 [Google Scholar]
  84. Mendisco F, Pemonge MH, Leblay E, Romon T, Richard G. et al. 2014. Where are the Caribs? Ancient DNA from ceramic period human remains in the Lesser Antilles. Phil. Trans. R. Soc B. 370:20130388 [Google Scholar]
  85. Miró-Herrans AT, Briggs-Cloud M, Sylestine A, Bolnick DA. 2016. Cultural and demographic influences on Native American mtDNA diversity in the southern United States. Am. J. Phys. Anthropol. S62:232 [Google Scholar]
  86. Misarti N, Finney BP, Jordan JW, Maschner HDG, Addison JA. et al. 2012. Early retreat of the Alaska Peninsula Glacier Complex and the implications for coastal migrations of First Americans. Quat. Sci. Rev. 48:1–6 [Google Scholar]
  87. Monroe C, Kemp BM, Smith DG. 2013. Exploring prehistory in the North American southwest with mitochondrial DNA diversity exhibited by Yumans and Athapaskans. Am. J. Phys. Anthropol. 150:618–31 [Google Scholar]
  88. Moreno-Estrada A, Gignoux CR, Fernandez-Lopez JC, Zakharia F, Sikora M. et al. 2014. The genetics of Mexico recapitulates Native American substructure and affects biomedical traits. Science 344:1280–85 [Google Scholar]
  89. Moreno-Estrada A, Gravel S, Zakharia F, McCauley JL, Byrnes JK. et al. 2013. Reconstructing the population genetic history of the Caribbean. PLOS Genet. 9:11e1003925 [Google Scholar]
  90. Mourier T, Ho SYW, Gilbert MTP, Willerslev E, Orlando L. 2012. Statistical guidelines for detecting past population shifts using ancient DNA. Mol. Biol. Evol. 29:92241–51 [Google Scholar]
  91. Navajo Nation Counc 2002. Approving a moratorium on genetic research studies conducted within the jurisdiction of the Navajo Nation until such time that a Navajo Nation human research code has been amended by the Navajo Nation Council. HSSCAP-20–02: Health and Social Services Committee of the Navajo Nation Council Window Rock, AZ: Navajo Nation Counc. [Google Scholar]
  92. O'Connor TD, Fu W, Mychaleckyj JC, Logsdon B, Auer P. et al. 2015. Rare variation facilitates inferences of fine-scale population structure in humans. Mol. Biol. Evol. 32:653–60 [Google Scholar]
  93. O'Fallon BD, Fehren-Schmitz L. 2011. Native Americans experienced a strong population bottleneck coincident with European contact. PNAS 108:5120444–48 [Google Scholar]
  94. O'Rourke DH, Raff JA. 2010. The human genetic history of the Americas: the final frontier. Curr. Biol. 20:4R202–7 [Google Scholar]
  95. Orlando L, Gilbert MTP, Willerslev E. 2015. Reconstructing ancient genomes and epigenomes. Nat. Rev. Genet. 16:June395–408 [Google Scholar]
  96. Ozga AT, Nieves-Colón MA, Honap TP, Sankaranarayanan K, Hofman CA. et al. 2016. Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus. Am. J. Phys. Anthropol. 160:220–28 [Google Scholar]
  97. Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N. et al. 2012. Ancient admixture in human history. Genetics 192:1065–93 [Google Scholar]
  98. Patterson N, Price AL, Reich D. 2006. Population structure and eigenanalysis. PLOS Genet. 2:12e190 [Google Scholar]
  99. Perego UA, Achilli A, Angerhofer N, Accetturo M, Pala M. et al. 2009. Distinctive Paleo-Indian migration routes from Beringia marked by two rare mtDNA haplogroups. Curr. Biol. 19:11–8 [Google Scholar]
  100. Perego UA, Angerhofer N, Pala M. 2010. The initial peopling of the Americas: a growing number of founding mitochondrial genomes from Beringia. Genome Res. 20:1174–79 [Google Scholar]
  101. Pickrell JK, Pritchard JK. 2012. Inference of population splits and mixtures from genome-wide allele frequency data. PLOS Genet. 8:11e1002967 [Google Scholar]
  102. Pickrell JK, Reich D. 2014. Toward a new history and geography of human genes informed by ancient DNA. Trends Genet. 30:9377–89 [Google Scholar]
  103. Pinhasi R, Fernandes D, Sirak K, Novak M, Connell S. et al. 2015. Optimal Ancient DNA yields from the inner ear part of the human petrous bone. PLOS ONE 10:6e0129102 [Google Scholar]
  104. Poinar HN, Kuch M, Sobolik KD, Barnes I, Stankiewicz AB. et al. 2001. Molecular analysis of dietary diversity for three archaic Native Americans. PNAS 98:84317–22 [Google Scholar]
  105. Raff J, 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. 82:677–93 [Google Scholar]
  106. Raff JA, Bolnick DA. 2014. Genetic roots of the first Americans. Nature 506:162–63 [Google Scholar]
  107. Raff JA, Bolnick DA. 2015. Does mitochondrial haplogroup X indicate ancient trans-Atlantic migration to the Americas? A critical re-evaluation. Paleoamerica 1:297–304 [Google Scholar]
  108. Raff JA, Bolnick DA, Tackney J, O'Rourke DH. 2011. Ancient DNA perspectives on American colonization and population history. Am. J. Phys. Anthropol. 146:503–14 [Google Scholar]
  109. Raff JA, Rzhetskaya M, Tackney J, Hayes MG. 2015. Mitochondrial diversity of Iñupiat people from the Alaskan North Slope provides evidence for the origins of the Paleo- and Neo-Eskimo peoples. Am. J. Phys. Anthropol. 157:603–14 [Google Scholar]
  110. Raghavan M, DeGiorgio M, Albrechtsen A, Moltke I, Skoglund P. et al. 2014a. The genetic prehistory of the New World Arctic. Science 345:1255832 [Google Scholar]
  111. Raghavan M, Skoglund P, Graf KE, Metspalu M, Albrechtsen A. et al. 2014b. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505:87–91 [Google Scholar]
  112. Raghavan M, Steinrucken M, Harris K, Schiffels S, Rasmussen S. et al. 2015. Genomic evidence for the Pleistocene and recent population history of Native Americans. Science 349:aab3884 [Google Scholar]
  113. Raj A, Stephens M, Pritchard JK. 2014. fastSTRUCTURE: variational inference of population structure in large SNP data sets. Genetics 197:573–89 [Google Scholar]
  114. Rasmussen M, Anzick SL, Waters MR, Skoglund P, DeGiorgio M. et al. 2014. The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature 506:225–29 [Google Scholar]
  115. Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A. et al. 2010. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463:757–62 [Google Scholar]
  116. Rasmussen M, Sikora M, Albrechtsen A, Korneliussen TS, Moreno-Mayar JV. et al. 2015. The ancestry and affiliations of Kennewick Man. Nature 523:455–58 [Google Scholar]
  117. Reardon J, TallBear K. 2012. Your DNA is our history. Curr. Anthropol. 53:S233–45 [Google Scholar]
  118. Reich D, Patterson N, Campbell D, Tandon A, Mazieres S. et al. 2012. Reconstructing Native American population history. Nature 488:370–74 [Google Scholar]
  119. Reynolds AW, Raff JA, Bolnick DA, Cook DC, Kaestle FA. 2015. Ancient DNA from the Schild site in Illinois: implications for the Mississippian transition in the Lower Illinois River Valley. Am. J. Phys. Anthropol. 156:434–48 [Google Scholar]
  120. Roewer L, Nothnagel M, Gusmão L, Gomes V, González M. et al. 2013. Continent-wide decoupling of Y-chromosomal genetic variation from language and geography in Native South Americans. PLOS Genet. 9:4e1003460 [Google Scholar]
  121. Rohland N, Harney E, Mallick S, Nordenfelt S, Reich D. 2015. Partial uracil-DNA-glycosylase treatment for screening of ancient DNA. Philos. Trans. R. Soc. B 370:20130624 [Google Scholar]
  122. Rohland N, Hofreiter M. 2007. Ancient DNA extraction from bones and teeth. Nat. Protoc. 2:1756–62 [Google Scholar]
  123. Rohland N, Reich D. 2012. Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture. Genome Res. 22:939–46 [Google Scholar]
  124. Rubicz R, Melton PE, Spitsyn V, Sun G, Deka R, Crawford MH. 2010. Genetic structure of native circumpolar populations based on autosomal, mitochondrial, and Y chromosome DNA markers. Am. J. Phys. Anthropol. 143:162–74 [Google Scholar]
  125. Schiffels S, Haak W, Paajanen P, Llamas B, Popescu E. et al. 2015. Iron Age and Anglo-Saxon genomes from East England reveal British migration history. Nat. Commun. 7:10408 [Google Scholar]
  126. Schraiber JG, Akey JM. 2015. Methods and models for unravelling human evolutionary history. Nat. Rev. Genet. 16:727–40 [Google Scholar]
  127. Schroeder KB, Schurr TG, Long JC, Rosenberg NA, Crawford MH. et al. 2007. A private allele ubiquitous in the Americas. Biol. Lett. 3:218–23 [Google Scholar]
  128. Sethuraman A, Hey J. 2016. IMa2p—parallel MCMC and inference of ancient demography under the isolation with migration (IM) model. Mol. Ecol. Resour. 16:1206–15 [Google Scholar]
  129. Shook BAS, Smith DG. 2008. Using ancient mtDNA to reconstruct the population history of northeastern North America. Am. J. Phys. Anthropol. 137:14–29 [Google Scholar]
  130. SIGMA Type 2 Diabetes Consort 2014. Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico. Nature 506:97–101 [Google Scholar]
  131. Skoglund P, Mallick S, Bortolini MC, Chennagiri N, Hünemeier T. et al. 2015. Genetic evidence for two founding populations of the Americas. Nature 523:104–8 [Google Scholar]
  132. Smith SE, Hayes MG, Cabana GS, Huff C, Coltrain JB, O'Rourke DH. 2009. Inferring population continuity versus replacement with aDNA: a cautionary tale from the Aleutian Islands. Hum. Biol. Int. Rec. Res. 81:4407–26 [Google Scholar]
  133. Snow M, Shafer H, Smith DG. 2011. The relationship of the Mimbres to other southwestern and Mexican populations. J. Archaeol. Sci. 38:113122–33 [Google Scholar]
  134. Söchtig J, Álvarez-Iglesias V, Mosquera-Miguel A, Gelabert-Besada M, Gómez-Carballa A, Salas A. 2015. Genomic insights on the ethno-history of the Maya and the “Ladinos” from Guatemala. BMC Genomics 16:131 [Google Scholar]
  135. Tackney JC, Potter BA, Raff J, Powers M, Watkins WS. et al. 2015. Two contemporaneous mitogenomes from terminal Pleistocene burials in eastern Beringia. PNAS 112:23201511903 [Google Scholar]
  136. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:3585–95 [Google Scholar]
  137. TallBear K. 2013. Native American DNA: Tribal Belonging and the False Promise of Genetic Science Minneapolis: Univ. Minn. Press
  138. Tamm E, Kivisild T, Reidla M, Metspalu M, Smith DG, Metspalu M, Smith DG. et al. 2007. Beringian standstill and spread of Native American founders. PLOS ONE 2:9e829 [Google Scholar]
  139. Torroni A, Schurr TG, Cabell MF, Brown MD, Neel JV. et al. 1993. Asian affinities and continental radiation of the four founding Native American mtDNAs. Am. J. Hum. Genet. 53:3563–90 [Google Scholar]
  140. Tsosie KS. 2015. The sovereign power of American Indian communities to engage or disengage in genetics research Presented at Am. Soc. Hum. Genet. Annu. Meet., Oct. 6–10, Baltimore, Md.
  141. Ubelaker DH. 2006. Population size: contact to nadir. Handbook of North American Indians: Environment, Origins, and Population D Stanford, BD Smith, DH Ubelaker, EJE Szathmary 694–701 Washington, DC: Smithson. Inst. Press [Google Scholar]
  142. Underhill PA, Kivisild T. 2007. Use of Y chromosome and mitochondrial DNA population structure in tracing human migrations. Annu. Rev. Genet. 41:539–64 [Google Scholar]
  143. Verdu P, Pemberton TJ, Laurent R, Kemp BM, Gonzalez-Oliver A. et al. 2014. Patterns of admixture and population structure in Native populations of Northwest North America. PLOS Genet. 10:8e1004530 [Google Scholar]
  144. Vilar MG, Melendez C, Sanders AB, Walia A, Gaieski JB. et al. 2014. Genetic diversity in Puerto Rico and its implications for the peopling of the Island and the West Indies. Am. J. Phys. Anthropol. 155:352–68 [Google Scholar]
  145. Vitti JJ, Grossman SR, Sabeti PC. 2013. Detecting natural selection in genomic data. Annu. Rev. Genet. 47:97–120 [Google Scholar]
  146. Voight BF, Kudaravalli S, Wen X, Pritchard JK. 2006. A map of recent positive selection in the human genome. PLOS Biol. 4:3e72 [Google Scholar]
  147. Volodko N, Starikovskaya E, Mazunin IO, Eltsov N, Naidenko PV. et al. 2008. 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. 82:1084–100 [Google Scholar]
  148. Wales N, Carøe C, Sandoval-Velasco M, Gamba C, Barnett R. et al. 2015. New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA. Biotechniques 59:368–71 [Google Scholar]
  149. Wang N, Zhou X, Tan FK, Foster MW, Arnett FC, Chakraborty R. 2004. Genetic signatures of pre-expansion bottleneck in the Choctaw population of Oklahoma. Am. J. Phys. Anthropol. 124:373–79 [Google Scholar]
  150. Wang S, Lewis CM, Jakobsson M, Ramachandran S, Ray N. et al. 2007. Genetic variation and population structure in Native Americans. PLOS Genet. 3:11e185 [Google Scholar]
  151. Wang S, Ray N, Rojas W, Parra MV, Bedoya G. et al. 2008. Geographic patterns of genome admixture in Latin American Mestizos. PLOS Genet. 4:3e1000037 [Google Scholar]
  152. Weir B, Cockerham CC. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38:61358–70 [Google Scholar]
  153. Yang DY, Eng B, Waye JS, Dudar JC, Saunders SR. 1998. Technical note: Improved DNA extraction from ancient bones using silica-based spin columns. Am. J. Phys. Anthropol. 105:539–43 [Google Scholar]
  154. Yang DY, Watt K. 2005. Contamination controls when preparing archaeological remains for ancient DNA analysis. J. Archaeol. Sci. 32:331–36 [Google Scholar]
  155. Yang NN, Mazières S, Bravi C, Ray N, Wang S. et al. 2010. Contrasting patterns of nuclear and mtDNA diversity in Native American populations. Ann. Hum. Genet. 74:6525–38 [Google Scholar]
  156. Zegura SL, Karafet TM, Zhivotovsky LA, Hammer MF. 2004. High-resolution SNPs and microsatellite haplotypes point to a single, recent entry of Native American Y chromosomes into the Americas. Mol. Biol. Evol. 21:1164–75 [Google Scholar]
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