Ancient genomics of modern humans: The first decade

Annual Review of Genomics and Human Genetics

Volumn 19, Issue , 2018, Pages 381-404

  Skoglund, Pontus ^a   Mathieson, Iain ^b  

^a THE FRANCIS CRICK INSTITUTE   (United Kingdom)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

adaptation; ancient DNA; Holocene; human origins; migration; paleogenomics

Indexed keywords

ANCIENT DNA; LACTASE;

AFRICA; ANTIQUITY; ASIA; DIET; EUROPE; GENETIC VARIABILITY; GENETIC VARIATION; GENOMICS; GEOGRAPHIC NAMES; HEIGHT; HISTORY; HOLOCENE; HUMAN; IMMUNE SYSTEM; INDIGENOUS PEOPLE; MIGRATION; MODERN TIMES; PACIFIC ISLANDS; PHENOTYPE; PIGMENTATION; POPULATION GENETIC STRUCTURE; POPULATION GENETICS; REVIEW; RUSSIAN FEDERATION; WESTERN EURASIA; WESTERN HEMISPHERE; ANIMAL; EVOLUTION; GENETICS; HOMINID; HUMAN GENOME;

ANIMALS; BIOLOGICAL EVOLUTION; GENOME, HUMAN; HOMINIDAE; HUMAN MIGRATION; HUMANS;

EID: 85051800466     PISSN: 15278204     EISSN: 1545293X     Source Type: Book Series    
DOI: 10.1146/annurev-genom-083117-021749     Document Type: Review

References (150)

1. Allentoft ME, Sikora M, Sjogren K-G, Rasmussen S, Rasmussen M, et al. 2015. Population genomics of Bronze Age Eurasia. Nature 522:167-72
2. Arcaleni E. 2006. Secular trend and regional differences in the stature of Italians, 1854-1980. Econ. Hum. Biol. 4:24-38
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
4. Berg JJ, Coop G. 2014. A population genetic signal of polygenic adaptation. PLOS Genet. 10:e1004412
5. Berg JJ, Zhang X, Coop G. 2017. Polygenic adaptation has impacted multiple anthropometric traits. bioRxiv 167551. https://doi. org/10. 1101/167551
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
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
8. Bowler JM, JohnstonH, 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
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
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
11. Broushaki F, Thomas MG, Link V, López S, van Dorp L, et al. 2016. Early Neolithic genomes from the eastern Fertile Crescent. Science 353:499
12. Burger J, Kirchner M, Bramanti B, Haak W, Thomas MG. 2007. Absence of the lactase-persistenceassociated allele in early Neolithic Europeans. PNAS 104:3736-41
13. Cann RL, StonekingM, Wilson AC. 1987. MitochondrialDNAand human evolution. Nature 325:31-36
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
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
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
17. Dannemann M, Kelso J. 2017. The contribution of Neanderthals to phenotypic variation in modern humans. Am. J. Hum. Genet. 101:578-89
18. DeGiorgioM, JakobssonM, Rosenberg NA. 2009. Explainingworldwide patterns of human genetic variation using a coalescent-based serial foundermodel ofmigration outward from Africa. PNAS 106:16057-62
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
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
21. Fehren-Schmitz L, Jarman CL, Harkins KM, KayserM, Popp BN, Skoglund P. 2017. Genetic ancestry of Rapanui before and after European contact. Curr. Biol. 27:3209-15
22. Flegontov P, Altinisik NE, Changmai P, RohlandN, Mallick S, et al. 2017. Paleo-Eskimo genetic legacy across North America. bioRxiv 203018. https://doi. org/10. 1101/203018
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
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
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
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
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
28. Fu Q, Posth C, Hajdinjak M, Petr M, Mallick S, et al. 2016. The genetic history of Ice Age Europe. Nature 534:200-5
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
30. Gibbons A. 2011. A new view of the birth of Homo sapiens. Science 331:392-94
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
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
33. Grasgruber P, Cacek J, Kalina T, SeberaM. 2014. The role of nutrition and genetics as key determinants of the positive height trend. Econ. Hum. Biol. 15:81-100
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
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
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
37. Günther T, MalmströmH, SvenssonEM, Omrak A, Sánchez-Quinto F, et al. 2018. Population genomics of Mesolithic Scandinavia: investigating early postglacial migration routes and high-latitude adaptation. PLOS Biol. 16:e2003703
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 522:207-11
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
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
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
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
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
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
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
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. 6:8912
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
48. Kanzawa-KiriyamaH, Kryukov K, JinamTA, HosomichiK, 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
49. KarminM, Saag L, VicenteM, SayresMAW, Järve M, et al. 2015. A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome Res. 25:459-66
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
51. K?l?nç Gülaah 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
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
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
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
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
56. Lazaridis I, NadelD, Rollefson G, Merrett DC, RohlandN, et al. 2016. Genomic insights into the origin of farming in the ancient Near East. Nature 536:419-24
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
58. Li H, Durbin R. 2011. Inference of human population history from individual whole-genome sequences. Nature 475:493-96
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
60. Lindo J, Huerta-Sánchez E, Nakagome S, RasmussenM, Petzelt B, et al. 2016. A time transect of exomes from a Native American population before and after European contact. Nat. Commun. 7:13175
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
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 551:368-72
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
64. LiuW, Martinón-TorresM, Cai Y-J, Xing S, Tong H-W, et al. 2015. The earliest unequivocally modern humans in southern China. Nature 526:696-99
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
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
67. Malaspinas A-S, WestawayMC, MullerC, Sousa VC, LaoO, et al. 2016. A genomic history of Aboriginal Australia. Nature 538:207-14
68. Mallick S, Li H, Lipson M, Mathieson I, GymrekM, et al. 2016. The SimonsGenomeDiversity Project: 300 genomes from 142 diverse populations. Nature 538:201-6
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
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
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
72. Mathieson I, Alpaslan-Roodenberg S, Posth C, Szécsényi-Nagy A, RohlandN, et al. 2018. The genomic history of southeastern Europe. Nature 555:197-203
73. Mathieson I, Lazaridis I, Rohland N, Mallick S, Patterson N, et al. 2015. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528:499-503
74. Meltzer DJ. 2009. First Peoples in a New World: Colonizing Ice Age America. Berkeley: Univ. Calif. Press
75. Menozzi P, Piazza A, Cavalli-Sforza L. 1978. Synthetic maps of human gene frequencies in Europeans. Science 201:786-92
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
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
78. Mittnik A, Wang C-C, Pfrengle S, Daubaras M, Zarina G, et al. 2018. The genetic prehistory of the Baltic Sea region. Nat. Commun. 9:442
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
80. Moreno-Mayar JV, Rasmussen S, Seguin-Orlando A, Rasmussen M, Liang M, et al. 2014. Genomewide ancestry patterns in Rapanui suggest pre-European admixture with Native Americans. Curr. Biol. 24:2518-25
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
82. Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, et al. 2008. Genes mirror geography within Europe. Nature 456:98-101
83. Novembre J, StephensM. 2008. Interpreting principal component analyses of spatial population genetic variation. Nat. Genet. 40:646-49
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
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 555:190-96
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
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
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
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
90. Pickrell JK, Patterson N, Barbieri C, Berthold F, Gerlach L, et al. 2012. The genetic prehistory of southern Africa. Nat. Commun. 3:1143
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
92. Pickrell JK, Pritchard JK. 2012. Inference of population splits and mixtures from genome-wide allele frequency data. PLOS Genet. 8:e1002967
93. PosthC, RenaudG, Mittnik A, Drucker DG, RougierH, et al. 2016. Pleistocenemitochondrial genomes suggest a single major dispersal of non-Africans and a Late Glacial population turnover in Europe. Curr. Biol. 26:827-33
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
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
96. Prüfer K, de Filippo C, Grote S, Mafessoni F, Korlevíc P, et al. 2017. A high-coverage Neandertal genome from Vindija Cave in Croatia. Science 358:655-58
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
98. Prugnolle F, Manica A, Balloux F. 2005. Geography predicts neutral genetic diversity of human populations. Curr. Biol. 15:R159-60
99. Racimo F, Berg JJ, Pickrell JK. 2017. Detecting polygenic adaptation in admixture graphs. bioRxiv 146043. https://doi. org/10. 1101/146043
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
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 505:87-91
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
103. Ramachandran S, DeshpandeO, Roseman CC, RosenbergNA, FeldmanMW, 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
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 506:225-29
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
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
107. RasmussenM, SikoraM, Albrechtsen A, Korneliussen TS, Moreno-Mayar JV, et al. 2015. The ancestry and affiliations of Kennewick Man. Nature 523:455-58
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
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
110. Reich D, Patterson N, Campbell D, Tandon A, Mazieres S, et al. 2012. Reconstructing Native American population history. Nature 488:370-74
111. Rodríguez-Varela R, Günther T, Krzewínska 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
112. Saag L, Varul L, Scheib CL, Stenderup J, AllentoftME, et al. 2017. Extensive farming in Estonia started through a sex-biased migration from the steppe. Curr. Biol. 27:2185-93
113. Sadr K. 2015. Livestock first reached southern Africa in two separate events. PLOS ONE 10:e0134215
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
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
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
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
118. Schiffels S, Durbin R. 2014. Inferring human population size and separation history from multiple genome sequences. Nat. Genet. 46:919-25
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
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
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
122. SchroederH, ávila-ArcosMC, Malaspinas A-S, Poznik GD, Sandoval-VelascoM, et al. 2015. Genomewide ancestry of 17th-century enslaved Africans from the Caribbean. PNAS 112:3669-73
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
124. Seguin-Orlando A, KorneliussenTS, SikoraM, MalaspinasA-S, Manica A, et al. 2014. Genomic structure in Europeans dating back at least 36, 200 years. Science 346:1113-18
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
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
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
128. Skoglund P, Jakobsson M. 2011. Archaic human ancestry in East Asia. PNAS 108:18301-6
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
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
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 336:466-69
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
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
134. Skoglund P, Reich D. 2016. A genomic view of the peopling of the Americas. Curr. Opin. Genet. Dev. 41:27-35
135. Skoglund P, Thompson JC, Prendergast ME, Mittnik A, Sirak K, et al. 2017. Reconstructing prehistoric African population structure. Cell 171:59-71
136. Slon V, Viola B, Renaud G, Gansauge M-T, Benazzi S, et al. 2017. A fourth Denisovan individual. Sci. Adv. 3:e1700186
137. Sokal RR, Oden NL, Thomson BA. 1999. A problem with synthetic maps. Hum. Biol. 71:1-13
138. Stringer CB. 2014. Why we are not all multiregionalists now. Trends Ecol. Evol. 29:248-51
139. Stringer CB, Andrews P. 1988. Genetic and fossil evidence for the origin of modern humans. Science 239:1263
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
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
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
143. UnterländerM, 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
144. Vernot B, Akey JM. 2014. Resurrecting surviving Neandertal lineages from modern human genomes. Science 343:1017-21
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
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
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
148. Wilde S, Timpson A, Kirsanow K, Kaiser E, KayserM, 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
149. Wollstein A, LaoO, Becker C, Brauer S, Trent RJ, et al. 2010. Demographic history of Oceania inferred from genome-wide data. Curr. Biol. 20:1983-92
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