Who We Are and How We Got Here

by David Reich

  9. Langley, Clarkson, and Ulm, “From Small Holes to Grand Narratives”; J. F. Connell and J. Allen, “The Process, Biotic Impact, and Global Implications of the Human Colonization of Sahul About 47,000 Years Ago,” Journal of Archaeological Science 56 (2015): 73–84.

  10. J.-J. Hublin, “The Modern Human Colonization of Western Eurasia: When and Where?,” Quaternary Science Reviews 118 (2015): 194–210.

  11. R. Foley and M. M. Lahr, “Mode 3 Technologies and the Evolution of Modern Humans,” Cambridge Archaeological Journal 7 (1997): 3–36.

  12. M. M. Lahr and R. Foley, “Multiple Dispersals and Modern Human Origins,” Evolutionary Anthropology 3 (1994): 48–60.

  13. H. Reyes-Centeno et al., “Testing Modern Human Out-of-Africa Dispersal Models and Implications for Modern Human Origins,” Journal of Human Evolution 87 (2015): 95–106.

  14. H. S. Groucutt et al., “Rethinking the Dispersal of Homo sapiens Out of Africa,” Evolutionary Anthropology 24 (2015): 149–64.

  15. R. Grün et al., “U-series and ESR Analyses of Bones and Teeth Relating to the Human Burials from Skhul,” Journal of Human Evolution 49 (2005): 316–34.

  16. S. J. Armitage et al., “The Southern Route ‘Out of Africa’: Evidence for an Early Expansion of Modern Humans into Arabia,” Science 331 (2011): 453–56; M. D. Petraglia, “Trailblazers Across Africa,” Nature 470 (2011): 50–51.

  17. M. Kuhlwilm et al., “Ancient Gene Flow from Early Modern Humans into Eastern Neanderthals,” Nature 530 (2016): 429–33.

  18. M. Rasmussen et al., “An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia,” Science 334 (2011): 94–98.

  19. D. Reich et al., “Genetic History of an Archaic Hominin Group from Denisova Cave in Siberia,” Nature 468 (2010): 1053–60; M. Meyer et al., “A High-Coverage Genome Sequence from an Archaic Denisovan Individual,” Science 338 (2012): 222–26.

  20. S. Mallick et al., “The Simons Genome Diversity Project: 300 Genomes from 142 Diverse Populations,” Nature 538 (2016): 201–6.

  21. Q. Fu et al., “Genome Sequence of a 45,000-Year-Old Modern Human from Western Siberia,” Nature 514 (2014): 445–49; S. Sankararaman, S. Mallick, N. Patterson, and D. Reich, “The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans,” Current Biology 26 (2016): 1241–47; P. Moorjani et al., “A Genetic Method for Dating Ancient Genomes Provides a Direct Estimate of Human Generation Interval in the Last 45,000 Years,” Proceedings of the National Academy of Sciences of the U.S.A. 113 (2016): 5652–7.

  22. Mallick et al., “Simons Genome Diversity Project”; M. Lipson and D. Reich, “A Working Model of the Deep Relationships of Diverse Modern Human Genetic Lineages Outside of Africa,” Molecular Biology and Evolution 34 (2017): 889–902.

  23. Mallick et al., “Simons Genome Diversity Project”; A. S. Malaspinas et al., “A Genomic History of Aboriginal Australia,” Nature 538 (2016): 207–14; L. Pagani et al., “Genomic Analyses Inform on Migration Events During the Peopling of Eurasia,” Nature 538 (2016): 238–42.

  24. Hublin, “Modern Human Colonization of Western Eurasia.”

  25. M. Raghavan et al., “Upper Palaeolithic Siberian Genome Reveals Dual Ancestry of Native Americans,” Nature (2013): doi: 10.1038/nature12736.

  26. Hugo Pan-Asian SNP Consortium, “Mapping Human Genetic Diversity in Asia,” Science 326 (2009): 1541–45.

  27. S. Ramachandran et al., “Support from the Relationship of Genetic and Geographic Distance in Human Populations for a Serial Founder Effect Originating in Africa,” Proceedings of the National Academy of Sciences of the U.S.A. 102 (2005): 15942–47; B. M. Henn, L. L. Cavalli-Sforza, and M. W. Feldman, “The Great Human Expansion,” Proceedings of the National Academy of Sciences of the U.S.A. 109 (2012): 17758–64.

  28. J. K. Pickrell and D. Reich, “Toward a New History and Geography of Human Genes Informed by Ancient DNA,” Trends in Genetics 30 (2014): 377–89.

  29. Unpublished results from David Reich’s laboratory.

  30. V. Siska et al., “Genome-Wide Data from Two Early Neolithic East Asian Individuals Dating to 7700 Years Ago,” Science Advances 3 (2017): e1601877.

  31. Peter Bellwood, First Farmers: The Origins of Agricultural Societies (Malden, MA: Blackwell, 2005).

  32. J. Diamond and P. Bellwood, “Farmers and Their Languages: The First Expansions,” Science 300 (2003): 597–603.

  33. S. Xu et al., “Genomic Dissection of Population Substructure of Han Chinese and Its Implication in Association Studies,” American Journal of Human Genetics 85 (2009): 762–74; J. M. Chen et al., “Genetic Structure of the Han Chinese Population Revealed by Genome-Wide SNP Variation,” American Journal of Human Genetics 85 (2009): 775–85.

  34. B. Wen et al., “Genetic Evidence Supports Demic Diffusion of Han Culture,” Nature 431 (2004): 302–5.

  35. F. H. Chen et al., “Agriculture Facilitated Permanent Human Occupation of the Tibetan Plateau After 3600 B.P.,” Science 347 (2015): 248–50.

  36. Unpublished results from David Reich’s laboratory.

  37. T. A. Jinam et al., “Unique Characteristics of the Ainu Population in Northern Japan,” Journal of Human Genetics 60 (2015): 565–71.

  38. Ibid.; P. R. Loh et al., “Inferring Admixture Histories of Human Populations Using Linkage Disequilibrium,” Genetics 193 (2013): 1233–54.

  39. Unpublished results from David Reich’s laboratory; Bellwood, First Migrants.

  40. Diamond and Bellwood, “Farmers and Their Languages.”

  41. M. Lipson et al., “Reconstructing Austronesian Population History in Island Southeast Asia,” Nature Communications 5 (2014): 4689.

  42. R. Blench, “Was There an Austroasiatic Presence in Island Southeast Asia Prior to the Austronesian Expansion?,” Bulletin of the Indo-Pacific Prehistory Association 30 (2010): 133–44.

  43. Bellwood, First Migrants.

  44. A. Crowther et al., “Ancient Crops Provide First Archaeological Signature of the Westward Austronesian Expansion,” Proceedings of the National Academy of Sciences of the U.S.A. 113 (2016): 6635–40.

  45. Lipson et al., “Reconstructing Austronesian Population History.”

  46. A. Wollstein et al., “Demographic History of Oceania Inferred from Genome-Wide Data,” Current Biology 20 (2010): 1983–92; M. Kayser, “The Human Genetic History of Oceania: Near and Remote Views of Dispersal,” Current Biology 20 (2010): R194–201; E. Matisoo-Smith, “Ancient DNA and the Human Settlement of the Pacific: A Review,” Journal of Human Evolution 79 (2015): 93–104.

  47. D. Reich et al., “Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania,” American Journal of Human Genetics 89 (2011): 516–28; P. Skoglund et al., “Genomic Insights into the Peopling of the Southwest Pacific,” Nature 538 (2016): 510–13.

  48. R. Pinhasi et al., “Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone,” PLoS One 10 (2015): e0129102.

  49. Skoglund et al., “Genomic Insights.”

  50. Ibid.

  51. Unpublished results from David Reich’s laboratory and Johannes Krause’s laboratory.

  52. Ibid.

  9 Rejoining Africa to the Human Story

  1. J. Lachance et al., “Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers,” Cell 150 (2012): 457–69.

  2. V. Plagnol and J. D. Wall, “Possible Ancestral Structure in Human Populations,” PLoS Genetics 2 (2006): e105; J. D. Wall, K. E. Lohmueller, and V. Plagnol, “Detecting Ancient Admixture and Estimating Demographic Parameters in Multiple Human Populations,” Molecular Biology and Evolution 26 (2009): 1823–27.

  3. M. F. Hammer et al., “Genetic Evidence for Archaic Admixture in Africa,” Proceedings of the National Academy of Sciences of the U.S.A. 108 (2011): 15123–28.

  4. K. Harvati et al., “The Later Stone Age Calvaria from Iwo Eleru, Nigeria: Morphology and Chronology,” PLoS One 6 (2011): e24024; I. Crevecoeur, A. Broo
ks, I. Ribot, E. Cornelissen, and P. Semal, “The Late Stone Age Human Remains from Ishango (Democratic Republic of Congo): New Insights on Late Pleistocene Modern Human Diversity in Africa,” American Journal of Physical Anthropology 96 (2016): 35–57.

  5. Unpublished results from David Reich’s laboratory.

  6. D. Richter et al., “The Age of the Hominin Fossils from Jebel Irhoud, Morocco, and the Origins of the Middle Stone Age,” Nature 546 (2017): 293–96; J. G. Fleagle, Z. Assefa, F. H. Brown, and J. J. Shea, “Paleoanthropology of the Kibish Formation, Southern Ethiopia: Introduction,” Journal of Human Evolution 55 (2008): 360–65.

  7. H. Li and R. Durbin, “Inference of Human Population History from Individual Whole-Genome Sequences,” Nature 475 (2011): 493–96.

  8. Li and Durbin, “Inference of Human Population History”; K. Prüfer et al., “The Complete Genome Sequence of a Neanderthal from the Altai Mountains,” Nature (2013): doi: 10.1038/nature12886.

  9. P. H. Dirks et al., “The Age of Homo Naledi and Associated Sediments in the Rising Star Cave, South Africa,” eLife 6 (2017): e24231.

  10. I. Gronau et al., “Bayesian Inference of Ancient Human Demography from Individual Genome Sequences,” Nature Genetics 43 (2011): 1031–34.

  11. P. Skoglund et al., “Reconstructing Prehistoric African Population Structure,” Cell 171 (2017): 5694.

  12. S. Mallick et al., “The Simons Genome Diversity Project: 300 Genomes from 142 Diverse Populations,” Nature 538 (2016): 201–6; Gronau et al., “Bayesian Inference.”

  13. S. A. Tishkoff et al., “The Genetic Structure and History of Africans and African Americans,” Science 324 (2009): 1035–44.

  14. C. J. Holden, “Bantu Language Trees Reflect the Spread of Farming Across Sub-Saharan Africa: A Maximum-Parsimony Analysis,” Proceedings of the Royal Society B—Biological Sciences 269 (2002): 793–99; P. de Maret, “Archaeologies of the Bantu Expansion,” in The Oxford Handbook of African Archaeology, ed. Peter Mitchell and Paul J. Lane (Oxford: Oxford University Press, 2013), 627–44.

  15. K. Bostoen et al., “Middle to Late Holocene Paleoclimatic Change and the Early Bantu Expansion in the Rain Forests of Western Central Africa,” Current Anthropology 56 (2016): 354–84; K. Manning et al., “4,500-Year-Old Domesticated Pearl Millet (Pennisetum glaucum) from the Tilemsi Valley, Mali: New Insights into an Alternative Cereal Domestication Pathway,” Journal of Archaeological Science 38 (2011): 312–22.

  16. D. Killick, “Cairo to Cape: The Spread of Metallurgy Through Eastern and Southern Africa,” Journal of World Prehistory 22 (2009): 399–414.

  17. de Maret, “Archaeologies of the Bantu Expansion.”

  18. Holden, “Bantu Language Trees.”

  19. Bostoen et al., “Middle to Late Holocene”; Manning et al., “4,500-Year-Old.”

  20. D. J. Lawson, G. Hellenthal, S. Myers, and D. Falush, “Inference of Population Structure Using Dense Haplotype Data,” PLoS Genetics 8 (2012): e1002453; G. Hellenthal et al., “A Genetic Atlas of Human Admixture History,” Science 343 (2014): 747–51; C. de Filippo, K. Bostoen, M. Stoneking, and B. Pakendorf, “Bringing Together Linguistic and Genetic Evidence to Test the Bantu Expansion,” Proceedings of the Royal Society B—Biological Sciences 279 (2012): 3256–63; E. Patin et al., “Dispersals and Genetic Adaptation of Bantu-Speaking Populations in Africa and North America,” Science 356 (2017): 543–46; G. B. Busby et al., “Admixture Into and Within Sub-Saharan Africa,” eLife 5(2016): e15266.

  21. Tishkoff et al., “Genetic Structure and History”; G. Ayodo et al., “Combining Evidence of Natural Selection with Association Analysis Increases Power to Detect Malaria-Resistance Variants,” American Journal of Human Genetics 81 (2007): 234–42.

  22. C. Ehret, “Reconstructing Ancient Kinship in Africa,” in Early Human Kinship: From Sex to Social Reproduction, ed. Nicholas J. Allen, Hilary Callan, Robin Dunbar, and Wendy James (Malden, MA: Blackwell, 2008), 200–31; C. Ehret, S. O. Y. Keita, and P. Newman, “The Origins of Afroasiatic,” Science 306 (2004): 1680–81.

  23. J. Diamond and P. Bellwood, “Farmers and Their Languages: The First Expansions,” Science 300 (2003): 597–603; P. Bellwood, “Response to Ehret et al. ‘The Origins of Afroasiatic,’ ” Science 306 (2004): 1681.

  24. D. Q. Fuller and E. Hildebrand, “Domesticating Plants in Africa,” in The Oxford Handbook of African Archaeology, ed. Peter Mitchell and Paul J. Lane (Oxford: Oxford University Press, 2013), 507–26; M. Madella et al., “Microbotanical Evidence of Domestic Cereals in Africa 7000 Years Ago,” PLoS One 9 (2014): e110177.

  25. I. Lazaridis et al., “Genomic Insights into the Origin of Farming in the Ancient Near East,” Nature 536 (2016): 419–24; Skoglund et al., “Reconstructing Prehistoric African Population Structure.”

  26. Lazaridis et al., “Genomic Insights”; Skoglund et al., “Reconstructing Prehistoric African Population Structure”; V. J. Schuenemann et al., “Ancient Egyptian Mummy Genomes Suggest an Increase of Sub-Saharan African Ancestry in Post-Roman Periods,” Nature Communications 8 (2017): 15694.

  27. T. Güldemann, “A Linguist’s View: Khoe-Kwadi Speakers as the Earliest Food-Producers of Southern Africa,” Southern African Humanities 20 (2008): 93–132.

  28. J. K. Pickrell et al., “Ancient West Eurasian Ancestry in Southern and Eastern Africa,” Proceedings of the National Academy of Sciences of the U.S.A. 111 (2014): 2632–37.

  29. Pagani et al., “Ethiopian Genetic Diversity.”

  30. Skoglund et al., “Reconstructing Prehistoric African Population Structure.”

  31. Luigi Luca Cavalli-Sforza and Francesco Cavalli-Sforza, The Great Human Diasporas: The History of Diversity and Evolution (Reading, MA: Addison-Wesley, 1995).

  32. M. Gallego Llorente et al., “Ancient Ethiopian Genome Reveals Extensive Eurasian Admixture Throughout the African Continent,” Science 350 (2015): 820–22.

  33. Donald N. Levine, Greater Ethiopia: The Evolution of a Multiethnic Society (Chicago: University of Chicago Press, 2000).

  34. L. Van Dorp et al., “Evidence for a Common Origin of Blacksmiths and Cultivators in the Ethiopian Ari Within the Last 4500 Years: Lessons for Clustering-Based Inference,” PLoS Genetics 11 (2015): e1005397.

  35. D. Reich et al., “Reconstructing Indian Population History,” Nature 461 (2009): 489–94.

  36. Skoglund et al., “Reconstructing Prehistoric African Population Structure.”

  37. Ibid.

  38. Ibid.

  39. J. K. Pickrell et al., “The Genetic Prehistory of Southern Africa,” Nature Communications 3 (2012): 1143; C. M. Schlebusch et al., “Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History,” Science 338 (2012): 374–79; Mallick et al., “Simons Genome Diversity Project.”

  40. M. E. Prendergast et al., “Continental Island Formation and the Archaeology of Defaunation on Zanzibar, Eastern Africa,” PLoS One 11 (2016): e0149565.

  41. Skoglund et al., “Reconstructing Prehistoric African Population Structure.”

  42. P. Ralph and G. Coop, “Parallel Adaptation: One or Many Waves of Advance of an Advantageous Allele?,” Genetics 186 (2010): 647–68.

  43. S. A. Tishkoff et al., “Convergent Adaptation of Human Lactase Persistence in Africa and Europe,” Nature Genetics 39 (2007): 31–40.

  44. Ralph and Coop, “Parallel Adaptation.”

  10 The Genomics of Inequality

  1. Peter Wade, Race and Ethnicity in Latin America (London and New York: Pluto Press, 2010).

  2. Trans-Atlantic Slave Trade Database, www.slavevoyages.org/​assessment/​estimates.

  3. K. Bryc et al., “The Genetic Ancestry of African Americans, Latinos, and European Americans Across the United States,” American Journal of Human Genetics 96 (2015): 37–53.

  4. Piers Anthony, Race Against Time (New York: Hawthorn Books, 1973).

  5. The first federal census in 1790 recorded 292,627 male slaves in Virginia out of a total male population of 747,610; available online at www.nationalgeograp
hic.org/​media/​us-census-1790/.

  6. Joshua D. Rothman, Notorious in the Neighborhood: Sex and Families Across the Color Line in Virginia, 1787–1861 (Chapel Hill: University of North Carolina Press, 2003).

  7. E. A. Foster et al., “Jefferson Fathered Slave’s Last Child,” Nature 396 (1998): 27–28.

  8. “Statement on the TJMF Research Committee Report on Thomas Jefferson and Sally Hemings,” January 26, 2000, available online at https://www.monticello.org/​sites/​default/​files/​inline-pdfs/​jefferson-hemings_report.pdf.

  9. M. Hemings, “Life Among the Lowly, No. 1,” Pike County (Ohio) Republican, March 13, 1873.

  10. E. J. Parra et al., “Ancestral Proportions and Admixture Dynamics in Geographically Defined African Americans Living in South Carolina,” American Journal of Physical Anthropology 114 (2001): 18–29.

  11. Ibid.

  12. Bryc et al., “Genetic Ancestry.”

  13. J. N. Fenner, “Cross-Cultural Estimation of the Human Generation Interval for Use in Genetics-Based Population Divergence Studies,” American Journal of Physical Anthropology 128 (2005): 415–23.

  14. David Morgan, The Mongols (Malden, MA, and Oxford: Blackwell, 2007).

  15. T. Zerjal et al., “The Genetic Legacy of the Mongols,” American Journal of Human Genetics 72 (2003): 717–21.

  16. L. T. Moore et al., “A Y-Chromosome Signature of Hegemony in Gaelic Ireland,” American Journal of Human Genetics 78 (2006): 334–38.

  17. S. Lippold et al., “Human Paternal and Maternal Demographic Histories: Insights from High-Resolution Y Chromosome and mtDNA Sequences,” Investigative Genetics 5 (2014): 13; M. Karmin et al., “A Recent Bottleneck of Y Chromosome Diversity Coincides with a Global Change in Culture,” Genome Research 25 (2015): 459–66.

  18. Ibid.

  19. A. Sherratt, “Plough and Pastoralism: Aspects of the Secondary Products Revolution,” in Pattern of the Past: Studies in Honour of David Clarke, ed. Ian Hodder, Glynn Isaac, and Norman Hammond (Cambridge: Cambridge University Press, 1981), 261–306.