1932

Abstract

The first decade of ancient genomics has revolutionized the study of human prehistory and evolution. We review new insights based on prehistoric modern human genomes, including greatly increased resolution of the timing and structure of the out-of-Africa expansion, the diversification of present-day non-African populations, and the earliest expansions of those populations into Eurasia and America. Prehistoric genomes now document population transformations on every inhabited continent—in particular the effect of agricultural expansions in Africa, Europe, and Oceania—and record a history of natural selection that shapes present-day phenotypic diversity. Despite these advances, much remains unknown, in particular about the genomic histories of Asia (the most populous continent) and Africa (the continent that contains the most genetic diversity). Ancient genomes from these and other regions, integrated with a growing understanding of the genomic basis of human phenotypic diversity, will be in focus during the next decade of research in the field.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-genom-083117-021749
2018-08-31
2024-04-13
Loading full text...

Full text loading...

/deliver/fulltext/genom/19/1/annurev-genom-083117-021749.html?itemId=/content/journals/10.1146/annurev-genom-083117-021749&mimeType=html&fmt=ahah

Literature Cited

  1. 1.  Allentoft ME, Sikora M, Sjogren K-G, Rasmussen S, Rasmussen M et al. 2015. Population genomics of Bronze Age Eurasia. Nature 522:167–72Documented movements of Bronze Age steppe populations in Europe and Asia.
    [Google Scholar]
  2. 2.  Arcaleni E 2006. Secular trend and regional differences in the stature of Italians, 1854–1980. Econ. Hum. Biol. 4:24–38
    [Google Scholar]
  3. 3.  Benazzi S, Douka K, Fornai C, Bauer CC, Kullmer O et al. 2011. Early dispersal of modern humans in Europe and implications for Neanderthal behaviour. Nature 479:525–28
    [Google Scholar]
  4. 4.  Berg JJ, Coop G 2014. A population genetic signal of polygenic adaptation. PLOS Genet 10:e1004412
    [Google Scholar]
  5. 5.  Berg JJ, Zhang X, Coop G 2017. Polygenic adaptation has impacted multiple anthropometric traits. bioRxiv 167551. https://doi.org/10.1101/167551
    [Crossref]
  6. 6.  Bersaglieri T, Sabeti PC, Patterson N, Vanderploeg T, Schaffner SF et al. 2004. Genetic signatures of strong recent positive selection at the lactase gene. Am. J. Hum. Genet. 74:1111–20
    [Google Scholar]
  7. 7.  Bollongino R, Nehlich O, Richards MP, Orschiedt J, Thomas MG et al. 2013. 2000 years of parallel societies in Stone Age central Europe. Science 342:479–81
    [Google Scholar]
  8. 8.  Bowler JM, Johnston H, Olley JM, Prescott JR, Roberts RG et al. 2003. New ages for human occupation and climatic change at Lake Mungo, Australia. Nature 421:837–40
    [Google Scholar]
  9. 9.  Bramanti B, Thomas M, Haak W, Unterlaender M, Jores P et al. 2009. Genetic discontinuity between local hunter-gatherers and central Europe's first farmers. Science 326:137–40
    [Google Scholar]
  10. 10.  Brandt G, Haak W, Adler CJ, Roth C, Szecsenyi-Nagy A et al. 2013. Ancient DNA reveals key stages in the formation of central European mitochondrial genetic diversity. Science 342:257–61
    [Google Scholar]
  11. 11.  Broushaki F, Thomas MG, Link V, López S, van Dorp L et al. 2016. Early Neolithic genomes from the eastern Fertile Crescent. Science 353:499Used shotgun genome sequences from the eastern Fertile Crescent to reveal a connection to South Asia.
    [Google Scholar]
  12. 12.  Burger J, Kirchner M, Bramanti B, Haak W, Thomas MG 2007. Absence of the lactase-persistence-associated allele in early Neolithic Europeans. PNAS 104:3736–41
    [Google Scholar]
  13. 13.  Cann RL, Stoneking M, Wilson AC 1987. Mitochondrial DNA and human evolution. Nature 325:31–36
    [Google Scholar]
  14. 14.  Cassidy LM, Martiniano R, Murphy EM, Teasdale MD, Mallory J et al. 2016. Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome. PNAS 113:368–73
    [Google Scholar]
  15. 15.  Clarkson C, Jacobs Z, Marwick B, Fullagar R, Wallis L et al. 2017. Human occupation of northern Australia by 65,000 years ago. Nature 547:306–10
    [Google Scholar]
  16. 16.  Dannemann M, Andrés AM, Kelso J 2016. Introgression of Neandertal- and Denisovan-like haplotypes contributes to adaptive variation in human Toll-like receptors. Am. J. Hum. Genet. 98:22–33
    [Google Scholar]
  17. 17.  Dannemann M, Kelso J 2017. The contribution of Neanderthals to phenotypic variation in modern humans. Am. J. Hum. Genet. 101:578–89
    [Google Scholar]
  18. 18.  DeGiorgio M, Jakobsson M, Rosenberg NA 2009. Explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa. PNAS 106:16057–62
    [Google Scholar]
  19. 19.  Enattah NS, Sahi T, Savilahti E, Terwilliger JD, Peltonen L, Jarvela I 2002. Identification of a variant associated with adult-type hypolactasia. Nat. Genet. 30:233–37
    [Google Scholar]
  20. 20.  Evershed RP, Payne S, Sherratt AG, Copley MS, Coolidge J et al. 2008. Earliest date for milk use in the Near East and southeastern Europe linked to cattle herding. Nature 455:528–31
    [Google Scholar]
  21. 21.  Fehren-Schmitz L, Jarman CL, Harkins KM, Kayser M, Popp BN, Skoglund P 2017. Genetic ancestry of Rapanui before and after European contact. Curr. Biol. 27:3209–15
    [Google Scholar]
  22. 22.  Flegontov P, Altinisik NE, Changmai P, Rohland N, Mallick S et al. 2017. Paleo-Eskimo genetic legacy across North America. bioRxiv 203018. https://doi.org/10.1101/203018
    [Crossref]
  23. 23.  Fregel R, Mendez FL, Bokbot Y, Martin-Socas D, Camalich-Massieu MD et al. 2017. Neolithization of North Africa involved the migration of people from both the Levant and Europe. bioRxiv 191569. https://doi.org/10.1101/191569
    [Crossref]
  24. 24.  Fu Q, Hajdinjak M, Moldovan O, Constantin S, Mallick S et al. 2015. An early modern human from Romania with a recent Neanderthal ancestor. Nature 524:216–19
    [Google Scholar]
  25. 25.  Fu Q, Li H, Moorjani P, Jay F, Slepchenko SM et al. 2014. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514:445–49
    [Google Scholar]
  26. 26.  Fu Q, Meyer M, Gao X, Stenzel U, Burbano HA et al. 2013. DNA analysis of an early modern human from Tianyuan Cave, China. PNAS 110:2223–27
    [Google Scholar]
  27. 27.  Fu Q, Mittnik A, Johnson Philip LF, Bos K, Lari M et al. 2013. A revised timescale for human evolution based on ancient mitochondrial genomes. Curr. Biol. 23:553–59
    [Google Scholar]
  28. 28.  Fu Q, Posth C, Hajdinjak M, Petr M, Mallick S et al. 2016. The genetic history of Ice Age Europe. Nature 534:200–5Described a genetic record of European Upper Paleolithic populations spanning more than 30,000 years.
    [Google Scholar]
  29. 29.  Gamba C, Jones ER, Teasdale MD, McLaughlin RL, González-Fortes G et al. 2014. Genome flux and stasis in a five millennium transect of European prehistory. Nat. Commun. 5:5257
    [Google Scholar]
  30. 30.  Gibbons A 2011. A new view of the birth of Homo sapiens. . Science 331:392–94
    [Google Scholar]
  31. 31.  Gilbert MTP, Jenkins DL, Gotherstrom A, Naveran N, Sanchez JJ et al. 2008. DNA from pre-Clovis human coprolites in Oregon, North America. Science 320:786–89
    [Google Scholar]
  32. 32.  González-Fortes G, Jones ER, Lightfoot E, Bonsall C, Lazar C et al. 2017. Paleogenomic evidence for multi-generational mixing between Neolithic farmers and Mesolithic hunter-gatherers in the lower Danube basin. Curr. Biol. 27:1801–10
    [Google Scholar]
  33. 33.  Grasgruber P, Cacek J, Kalina T, Sebera M 2014. The role of nutrition and genetics as key determinants of the positive height trend. Econ. Hum. Biol. 15:81–100
    [Google Scholar]
  34. 34.  Green RE, Krause J, Briggs AW, Maricic T, Stenzel U et al. 2010. A draft sequence of the Neandertal genome. Science 328:710–22
    [Google Scholar]
  35. 35.  Green RE, Krause J, Ptak SE, Briggs AW, Ronan MT et al. 2006. Analysis of one million base pairs of Neanderthal DNA. Nature 444:330–36
    [Google Scholar]
  36. 36.  Groucutt HS, Petraglia MD, Bailey G, Scerri EM, Parton A et al. 2015. Rethinking the dispersal of Homo sapiens out of Africa. Evol. Anthropol. 24:149–64
    [Google Scholar]
  37. 37.  Günther T, Malmström H, Svensson EM, Omrak A, Sánchez-Quinto F et al. 2018. Population genomics of Mesolithic Scandinavia: investigating early postglacial migration routes and high-latitude adaptation. PLOS Biol. 16e2003703
  38. 38.  Haak W, Lazaridis I, Patterson N, Rohland N, Mallick S et al. 2015. Massive migration from the steppe is a source for Indo-European languages in Europe. Nature 522:207–11Described the contribution of Eurasian steppe populations to present-day ancestry in Europe.
    [Google Scholar]
  39. 39.  Haber M, Doumet-Serhal C, Scheib C, Xue Y, Danecek P et al. 2017. Continuity and admixture in the last five millennia of Levantine history from ancient Canaanite and present-day Lebanese genome sequences. Am. J. Hum. Genet. 101:274–82
    [Google Scholar]
  40. 40.  Helgason A, Einarsson AW, Gumundsdottir VB, Sigursson A, Gunnarsdottir ED et al. 2015. The Y-chromosome point mutation rate in humans. Nat. Genet. 47:453–57
    [Google Scholar]
  41. 41.  Higham T, Compton T, Stringer C, Jacobi R, Shapiro B et al. 2011. The earliest evidence for anatomically modern humans in northwestern Europe. Nature 479:521–24
    [Google Scholar]
  42. 42.  Hofmanová Z, Kreutzer S, Hellenthal G, Sell C, Diekmann Y et al. 2016. Early farmers from across Europe directly descended from Neolithic Aegeans. PNAS 113:6886–91
    [Google Scholar]
  43. 43.  Huerta-Sánchez E, Jin X, Asan, Bianba Z, Peter BM et al. 2014. Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature 512:194–97
    [Google Scholar]
  44. 44.  Jablonski NG, Chaplin G 2017. The colours of humanity: the evolution of pigmentation in the human lineage. Philos. Trans. R. Soc. Lond. B 372:20160349
    [Google Scholar]
  45. 45.  Jeong C, Ozga AT, Witonsky DB, Malmström H, Edlund H et al. 2016. Long-term genetic stability and a high-altitude East Asian origin for the peoples of the high valleys of the Himalayan arc. PNAS 113:7485–90
    [Google Scholar]
  46. 46.  Jones ER, González-Fortes G, Connell S, Siska V, Eriksson A et al. 2015. Upper Palaeolithic genomes reveal deep roots of modern Eurasians. Nat. Commun. 6:8912Discovered a key ancestral Eurasian population in the Caucasus mountains.
    [Google Scholar]
  47. 47.  Jones ER, Zarina G, Moiseyev V, Lightfoot E, Nigst PR et al. 2017. The Neolithic transition in the Baltic was not driven by admixture with early European farmers. Curr. Biol. 27:576–82
    [Google Scholar]
  48. 48.  Kanzawa-Kiriyama H, Kryukov K, Jinam TA, Hosomichi K, Saso A et al. 2016. A partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan. J. Hum. Genet. 62:213–21
    [Google Scholar]
  49. 49.  Karmin M, Saag L, Vicente M, Sayres MAW, Järve M et al. 2015. A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome Res 25:459–66
    [Google Scholar]
  50. 50.  Keller A, Graefen A, Ball M, Matzas M, Boisguerin V et al. 2012. New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing. Nat. Commun. 3:698
    [Google Scholar]
  51. 51.  Kılınç Gülşah M, Omrak A, Özer F, Günther T, Büyükkarakaya Ali M et al. 2016. The demographic development of the first farmers in Anatolia. Curr. Biol. 26:2659–66
    [Google Scholar]
  52. 52.  Kong A, Frigge ML, Masson G, Besenbacher S, Sulem P et al. 2012. Rate of de novo mutations and the importance of father's age to disease risk. Nature 488:471–75
    [Google Scholar]
  53. 53.  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]
  54. 54.  Lao O, Lu TT, Nothnagel M, Junge O, Freitag-Wolf S et al. 2008. Correlation between genetic and geographic structure in Europe. Curr. Biol. 18:1241–48
    [Google Scholar]
  55. 55.  Lazaridis I, Mittnik A, Patterson N, Mallick S, Rohland N et al. 2017. Genetic origins of the Minoans and Mycenaeans. Nature 548:214–18
    [Google Scholar]
  56. 56.  Lazaridis I, Nadel D, Rollefson G, Merrett DC, Rohland N et al. 2016. Genomic insights into the origin of farming in the ancient Near East. Nature 536:419–24
    [Google Scholar]
  57. 57.  Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S et al. 2014. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513:409–13
    [Google Scholar]
  58. 58.  Li H, Durbin R 2011. Inference of human population history from individual whole-genome sequences. Nature 475:493–96
    [Google Scholar]
  59. 59.  Lindo J, Achilli A, Perego UA, Archer D, Valdiosera C et al. 2017. Ancient individuals from the North American Northwest Coast reveal 10,000 years of regional genetic continuity. PNAS 114:4093–98
    [Google Scholar]
  60. 60.  Lindo J, Huerta-Sánchez E, Nakagome S, Rasmussen M, Petzelt B et al. 2016. A time transect of exomes from a Native American population before and after European contact. Nat. Commun. 7:13175
    [Google Scholar]
  61. 61.  Lipson M, Reich D 2017. A working model of the deep relationships of diverse modern human genetic lineages outside of Africa. Mol. Biol. Evol. 34:889–902
    [Google Scholar]
  62. 62.  Lipson M, Szécsényi-Nagy A, Mallick S, Pósa A, Stégmár B et al. 2017. Parallel palaeogenomic transects reveal complex genetic history of early European farmers. Nature 551368–72
  63. 63.  Liu H, Prugnolle F, Manica A, Balloux F 2006. A geographically explicit genetic model of worldwide human-settlement history. Am. J. Hum. Genet. 79:230–37
    [Google Scholar]
  64. 64.  Liu W, Martinón-Torres M, Cai Y-J, Xing S, Tong H-W et al. 2015. The earliest unequivocally modern humans in southern China. Nature 526:696–99
    [Google Scholar]
  65. 65.  Llamas B, Fehren-Schmitz L, Valverde G, Soubrier J, Mallick S et al. 2016. Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas. Sci. Adv. 2:e1501385
    [Google Scholar]
  66. 66.  Llorente MG, Jones ER, Eriksson A, Siska V, Arthur KW et al. 2015. Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent. Science 350:820–22
    [Google Scholar]
  67. 67.  Malaspinas A-S, Westaway MC, Muller C, Sousa VC, Lao O et al. 2016. A genomic history of Aboriginal Australia. Nature 538:207–14
    [Google Scholar]
  68. 68.  Mallick S, Li H, Lipson M, Mathieson I, Gymrek M et al. 2016. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 538:201–6
    [Google Scholar]
  69. 69.  Manning K, Pelling R, Higham T, Schwenniger J-L, Fuller DQ 2011. 4500-year old domesticated pearl millet (Pennisetum glaucum) from the Tilemsi Valley, Mali: new insights into an alternative cereal domestication pathway. J. Archaeol. Sci. 38:312–22
    [Google Scholar]
  70. 70.  Martiniano R, Caffell A, Holst M, Hunter-Mann K, Montgomery J et al. 2016. Genomic signals of migration and continuity in Britain before the Anglo-Saxons. Nat. Commun. 7:10326
    [Google Scholar]
  71. 71.  Martiniano R, Cassidy LM, O'Maolduin R, McLaughlin R, Silva NM et al. 2017. The population genomics of archaeological transition in west Iberia: investigation of ancient substructure using imputation and haplotype-based methods. PLOS Genet 13:e1006852
    [Google Scholar]
  72. 72.  Mathieson I, Alpaslan-Roodenberg S, Posth C, Szécsényi-Nagy A, Rohland N et al. 2018. The genomic history of southeastern Europe. Nature 555197–203
  73. 73.  Mathieson I, Lazaridis I, Rohland N, Mallick S, Patterson N et al. 2015. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528:499–503Performed a genome-wide scan for selection over 10,000 years of European history.
    [Google Scholar]
  74. 74.  Meltzer DJ 2009. First Peoples in a New World: Colonizing Ice Age America Berkeley: Univ. Calif. Press
  75. 75.  Menozzi P, Piazza A, Cavalli-Sforza L 1978. Synthetic maps of human gene frequencies in Europeans. Science 201:786–92
    [Google Scholar]
  76. 76.  Meyer M, Arsuaga J-L, de Filippo C, Nagel S, Aximu-Petri A et al. 2016. Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins. Nature 531:504–7
    [Google Scholar]
  77. 77.  Meyer M, Kircher M, Gansauge M-T, Li H, Racimo F et al. 2012. A high-coverage genome sequence from an archaic Denisovan individual. Science 338:222–26
    [Google Scholar]
  78. 78.  Mittnik A, Wang C-C, Pfrengle S, Daubaras M, Zariņa G et al. 2018. The genetic prehistory of the Baltic Sea region. Nat. Commun. 9442
  79. 79.  Moorjani P, Sankararaman S, Fu Q, Przeworski M, Patterson N, Reich D 2016. A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years. PNAS 113:5652–57
    [Google Scholar]
  80. 80.  Moreno-Mayar JV, Rasmussen S, Seguin-Orlando A, Rasmussen M, Liang M et al. 2014. Genome-wide ancestry patterns in Rapanui suggest pre-European admixture with Native Americans. Curr. Biol. 24:2518–25
    [Google Scholar]
  81. 81.  Noonan JP, Coop G, Kudaravalli S, Smith D, Krause J et al. 2006. Sequencing and analysis of Neanderthal genomic DNA. Science 314:1113–18
    [Google Scholar]
  82. 82.  Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR et al. 2008. Genes mirror geography within Europe. Nature 456:98–101
    [Google Scholar]
  83. 83.  Novembre J, Stephens M 2008. Interpreting principal component analyses of spatial population genetic variation. Nat. Genet. 40:646–49
    [Google Scholar]
  84. 84.  Olalde I, Allentoft ME, Sánchez-Quinto F, Santpere G, Chiang CWK et al. 2014. Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European. Nature 507:225–28
    [Google Scholar]
  85. 85.  Olalde I, Brace S, Allentoft ME, Armit I, Kristiansen K et al. 2018. The Beaker phenomenon and the genomic transformation of northwest Europe. Nature 555190–96
  86. 86.  Olalde I, Schroeder H, Sandoval-Velasco M, Vinner L, Lobón I et al. 2015. A common genetic origin for early farmers from Mediterranean Cardial and central European LBK cultures. Mol. Biol. Evol. 32:3132–42
    [Google Scholar]
  87. 87.  Omrak A, Günther T, Valdiosera C, Svensson EM, Malmström H et al. 2015. Genomic evidence establishes Anatolia as the source of the European Neolithic gene pool. Curr. Biol. 26:270–75
    [Google Scholar]
  88. 88.  Pääbo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J et al. 2004. Genetic analyses from ancient DNA. Annu. Rev. Genet. 38:645–79
    [Google Scholar]
  89. 89.  Pagani L, Lawson DJ, Jagoda E, Mörseburg A, Eriksson A et al. 2016. Genomic analyses inform on migration events during the peopling of Eurasia. Nature 538:238–42
    [Google Scholar]
  90. 90.  Pickrell JK, Patterson N, Barbieri C, Berthold F, Gerlach L et al. 2012. The genetic prehistory of southern Africa. Nat. Commun. 3:1143
    [Google Scholar]
  91. 91.  Pickrell JK, Patterson N, Loh P-R, Lipson M, Berger B et al. 2014. Ancient west Eurasian ancestry in southern and eastern Africa. PNAS 111:2632–37
    [Google Scholar]
  92. 92.  Pickrell JK, Pritchard JK 2012. Inference of population splits and mixtures from genome-wide allele frequency data. PLOS Genet 8:e1002967
    [Google Scholar]
  93. 93.  Posth C, Renaud G, Mittnik A, Drucker DG, Rougier H et al. 2016. Pleistocene mitochondrial genomes suggest a single major dispersal of non-Africans and a Late Glacial population turnover in Europe. Curr. Biol. 26:827–33
    [Google Scholar]
  94. 94.  Posth C, Wißing C, Kitagawa K, Pagani L, van Holstein L et al. 2017. Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals. Nat. Commun. 8:16046
    [Google Scholar]
  95. 95.  Poznik GD, Xue Y, Mendez FL, Willems TF, Massaia A et al. 2016. Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nat. Genet. 48:593–99
    [Google Scholar]
  96. 96.  Prüfer K, de Filippo C, Grote S, Mafessoni F, Korlević P et al. 2017. A high-coverage Neandertal genome from Vindija Cave in Croatia. Science 358:655–58
    [Google Scholar]
  97. 97.  Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S et al. 2014. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505:43–49
    [Google Scholar]
  98. 98.  Prugnolle F, Manica A, Balloux F 2005. Geography predicts neutral genetic diversity of human populations. Curr. Biol. 15:R159–60
    [Google Scholar]
  99. 99.  Racimo F, Berg JJ, Pickrell JK 2017. Detecting polygenic adaptation in admixture graphs. bioRxiv 146043. https://doi.org/10.1101/146043
    [Crossref]
  100. 100.  Raghavan M, DeGiorgio M, Albrechtsen A, Moltke I, Skoglund P et al. 2014. The genetic prehistory of the New World Arctic. Science 345:1255832
    [Google Scholar]
  101. 101.  Raghavan M, Skoglund P, Graf KE, Metspalu M, Albrechtsen A et al. 2014. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505:87–91Analyzed the Mal'ta genome to reveal an ancient lineage connecting Europeans, Siberians, and Native Americans.
    [Google Scholar]
  102. 102.  Raghavan M, Steinrücken 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]
  103. 103.  Ramachandran S, Deshpande O, Roseman CC, Rosenberg NA, Feldman MW, Cavalli-Sforza LL 2005. Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. PNAS 102:15942–47
    [Google Scholar]
  104. 104.  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 506:225–29Described the first ancient American genome and showed that Native Americans descend from the first major founding population on the continent.
    [Google Scholar]
  105. 105.  Rasmussen M, Guo X, Wang Y, Lohmueller KE, Rasmussen S et al. 2011. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science 334:94–98
    [Google Scholar]
  106. 106.  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]
  107. 107.  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]
  108. 108.  Rasmussen S, Allentoft ME, Nielsen K, Orlando L, Sikora M et al. 2015. Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago. Cell 163:571–82
    [Google Scholar]
  109. 109.  Reich D, Green RE, Kircher M, Krause J, Patterson N et al. 2010. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468:1053–60
    [Google Scholar]
  110. 110.  Reich D, Patterson N, Campbell D, Tandon A, Mazieres S et al. 2012. Reconstructing Native American population history. Nature 488:370–74
    [Google Scholar]
  111. 111.  Rodríguez-Varela R, Günther T, Krzewińska M, Storå J, Gillingwater TH et al. 2017. Genomic analyses of pre-European conquest human remains from the Canary Islands reveal close affinity to modern North Africans. Curr. Biol. 27:3396–402
    [Google Scholar]
  112. 112.  Saag L, Varul L, Scheib CL, Stenderup J, Allentoft ME et al. 2017. Extensive farming in Estonia started through a sex-biased migration from the steppe. Curr. Biol. 27:2185–93
    [Google Scholar]
  113. 113.  Sadr K 2015. Livestock first reached southern Africa in two separate events. PLOS ONE 10:e0134215
    [Google Scholar]
  114. 114.  Sánchez-Quinto F, Schroeder H, Ramirez O, Ávila-Arcos María C, Pybus M et al. 2012. Genomic affinities of two 7,000-year-old Iberian hunter-gatherers. Curr. Biol. 22:1494–99
    [Google Scholar]
  115. 115.  Sankararaman S, Mallick S, Dannemann M, Prufer K, Kelso J et al. 2014. The genomic landscape of Neanderthal ancestry in present-day humans. Nature 507:354–57
    [Google Scholar]
  116. 116.  Sankararaman S, Mallick S, Patterson N, Reich D 2016. The combined landscape of Denisovan and Neanderthal ancestry in present-day humans. Curr. Biol. 26:1241–47
    [Google Scholar]
  117. 117.  Sankararaman S, Patterson N, Li H, Pääbo S, Reich D 2012. The date of interbreeding between Neandertals and modern humans. PLOS Genet 8:e1002947
    [Google Scholar]
  118. 118.  Schiffels S, Durbin R 2014. Inferring human population size and separation history from multiple genome sequences. Nat. Genet. 46:919–25
    [Google Scholar]
  119. 119.  Schiffels S, Haak W, Paajanen P, Llamas B, Popescu E et al. 2016. Iron Age and Anglo-Saxon genomes from East England reveal British migration history. Nat. Commun. 7:10408
    [Google Scholar]
  120. 120.  Schlebusch CM, Malmström H, Günther T, Sjödin P, Coutinho A et al. 2017. Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago. Science 358:652–55
    [Google Scholar]
  121. 121.  Schlebusch CM, Skoglund P, Sjödin P, Gattepaille LM, Hernandez D et al. 2012. Genomic variation in seven Khoe-San groups reveals adaptation and complex African history. Science 338:374–79
    [Google Scholar]
  122. 122.  Schroeder H, Ávila-Arcos MC, Malaspinas A-S, Poznik GD, Sandoval-Velasco M et al. 2015. Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean. PNAS 112:3669–73
    [Google Scholar]
  123. 123.  Schuenemann VJ, Peltzer A, Welte B, van Pelt WP, Molak M et al. 2017. Ancient Egyptian mummy genomes suggest an increase of sub-Saharan African ancestry in post-Roman periods. Nat. Commun. 8:15694
    [Google Scholar]
  124. 124.  Seguin-Orlando A, Korneliussen TS, Sikora M, Malaspinas A-S, Manica A et al. 2014. Genomic structure in Europeans dating back at least 36,200 years. Science 346:1113–18
    [Google Scholar]
  125. 125.  Sikora M, Seguin-Orlando A, Sousa VC, Albrechtsen A, Korneliussen T et al. 2017. Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers. Science 358:659–62
    [Google Scholar]
  126. 126.  Simonti CN, Vernot B, Bastarache L, Bottinger E, Carrell DS et al. 2016. The phenotypic legacy of admixture between modern humans and Neandertals. Science 351:737–41
    [Google Scholar]
  127. 127.  Siska V, Jones ER, Jeon S, Bhak Y, Kim H-M et al. 2017. Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago. Sci. Adv. 3:e1601877
    [Google Scholar]
  128. 128.  Skoglund P, Jakobsson M 2011. Archaic human ancestry in East Asia. PNAS 108:18301–6
    [Google Scholar]
  129. 129.  Skoglund P, Mallick S, Bortolini MC, Chennagiri N, Hünemeier T et al. 2015. Genetic evidence for two founding populations of the Americas. Nature 525:104–8
    [Google Scholar]
  130. 130.  Skoglund P, Malmström H, Omrak A, Raghavan M, Valdiosera C et al. 2014. Genomic diversity and admixture differs for Stone-Age Scandinavian foragers and farmers. Science 344:747–50
    [Google Scholar]
  131. 131.  Skoglund P, Malmström H, Raghavan M, Storå J, Hall P et al. 2012. Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe. Science 336:466–69Demonstrated genetic discontinuity between hunter–gatherer and agricultural populations in Europe.
    [Google Scholar]
  132. 132.  Skoglund P, Northoff BH, Shunkov MV, Derevianko AP, Pääbo S et al. 2014. Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. PNAS 111:2229–34
    [Google Scholar]
  133. 133.  Skoglund P, Posth C, Sirak K, Spriggs M, Valentin F et al. 2016. Genomic insights into the peopling of the Southwest Pacific. Nature 538:510–13
    [Google Scholar]
  134. 134.  Skoglund P, Reich D 2016. A genomic view of the peopling of the Americas. Curr. Opin. Genet. Dev. 41:27–35
    [Google Scholar]
  135. 135.  Skoglund P, Thompson JC, Prendergast ME, Mittnik A, Sirak K et al. 2017. Reconstructing prehistoric African population structure. Cell 171:59–71Revealed Holocene population movements and adaptation in Africa.
    [Google Scholar]
  136. 136.  Slon V, Viola B, Renaud G, Gansauge M-T, Benazzi S et al. 2017. A fourth Denisovan individual. Sci. Adv. 3:e1700186
    [Google Scholar]
  137. 137.  Sokal RR, Oden NL, Thomson BA 1999. A problem with synthetic maps. Hum. Biol. 71:1–13
    [Google Scholar]
  138. 138.  Stringer CB 2014. Why we are not all multiregionalists now. Trends Ecol. Evol. 29:248–51
    [Google Scholar]
  139. 139.  Stringer CB, Andrews P 1988. Genetic and fossil evidence for the origin of modern humans. Science 239:1263
    [Google Scholar]
  140. 140.  Terhorst J, Kamm JA, Song YS 2017. Robust and scalable inference of population history from hundreds of unphased whole genomes. Nat. Genet. 49:303–9
    [Google Scholar]
  141. 141.  Tishkoff SA, Reed FA, Friedlaender FR, Ehret C, Ranciaro A et al. 2009. The genetic structure and history of Africans and African Americans. Science 324:1035–44
    [Google Scholar]
  142. 142.  Turchin MC, Chiang CW, Palmer CD, Sankararaman S, Reich D et al. 2012. Evidence of widespread selection on standing variation in Europe at height-associated SNPs. Nat. Genet. 44:1015–19
    [Google Scholar]
  143. 143.  Unterländer M, Palstra F, Lazaridis I, Pilipenko A, Hofmanová Z et al. 2017. Ancestry and demography and descendants of Iron Age nomads of the Eurasian Steppe. Nat. Commun. 8:14615
    [Google Scholar]
  144. 144.  Vernot B, Akey JM 2014. Resurrecting surviving Neandertal lineages from modern human genomes. Science 343:1017–21
    [Google Scholar]
  145. 145.  Vernot B, Tucci S, Kelso J, Schraiber JG, Wolf AB et al. 2016. Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals. Science 352:235–39
    [Google Scholar]
  146. 146.  Wall JD, Yang MA, Jay F, Kim SK, Durand EY et al. 2013. Higher levels of Neanderthal ancestry in East Asians than in Europeans. Genetics 194:199–209
    [Google Scholar]
  147. 147.  Westaway K, Louys J, Awe RD, Morwood M, Price G et al. 2017. An early modern human presence in Sumatra 73,000–63,000 years ago. Nature 548:322–25
    [Google Scholar]
  148. 148.  Wilde S, Timpson A, Kirsanow K, Kaiser E, Kayser M et al. 2014. Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y. PNAS 111:4832–37
    [Google Scholar]
  149. 149.  Wollstein A, Lao O, Becker C, Brauer S, Trent RJ et al. 2010. Demographic history of Oceania inferred from genome-wide data. Curr. Biol. 20:1983–92
    [Google Scholar]
  150. 150.  Yang MA, Gao X, Theunert C, Tong H, Aximu-Petri A et al. 2017. 40,000-year-old individual from Asia provides insight into early population structure in Eurasia. Curr. Biol. 27:3202–8
    [Google Scholar]
/content/journals/10.1146/annurev-genom-083117-021749
Loading
/content/journals/10.1146/annurev-genom-083117-021749
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error