9. Sommer, “Population-Genetic Trees,” 134–139; Sommer, History Within, 379–384.
10. John Novembre, “Pritchard, Stephens, and Donnelly on Population Structure,” Genetics 204, no. 2 (2016): 391–392; Kai Yuan et al., “Models, Methods and Tools for Ancestry Inference and Admixture Analysis,” Quantitative Biology 5, no. 3 (2017): 237–238; Mark Stoneking, An Introduction to Molecular Anthropology (Hoboken, NJ: Wiley-Blackwell, 2017): 169–170; Daniel J. Lawson, Lucy van Dorp, and Daniel Falush, “A Tutorial on How Not to Over-Interpret STRUCTURE and ADMIXTURE Bar Plots,” Nature Communications 9, no. 3258 (2018): 2.
11. Noah A. Rosenberg et al., “Genetic Structure of Human Populations,” Science 298, no. 5602 (2002): 2381–2385.
12. David H. Alexander, John Novembre, and Kenneth Lange, “Fast Model-Based Estimation of Ancestry in Unrelated Individuals,” Genome Research 19, no. 9 (2009): 1655–1656.
13. In this context, ancestry coefficient refers to a statistical measure used to describe the relative degree of shared ancestry.
14. Alexander, Novembre, and Lange, “Fast Model-Based Estimation,” 1655; Jonathan K. Pritchard, Matthew Stephens, and Peter Donnelly, “Inference of Population Structure Using Multilocus Genotype Data,” Genetics 155, no. 2 (2000): 945.
15. Pritchard, Stephens, and Donnelly, “Inference of Population Structure,” 945; Alexander, Novembre, and Lange, “Fast Model-Based Estimation,” 1655.
16. Lawson, van Dorp, and Falush, “Tutorial,” 2.
17. Pritchard, Stephens, and Donnelly, “Inference of Population Structure,” 945.
18. Alexander, Novembre, and Lange, “Fast Model-Based Estimation,” 1656.
19. Rosenberg et al., “Genetic Structure,” 2381–2385.
20. Rosenberg et al., “Genetic Structure,” 2381.
21. Rosenberg et al., “Genetic Structure,” 2381.
22. Pritchard, Stephens, and Donnelly, “Inference of Population Structure,” 945–946.
23. Alexander, Novembre, and Lange, “Fast Model-Based Estimation,” 1663.
24. At the left-hand side of the diagram, there are the number of clusters (abbreviated with the letter K), to which the individual samples are assigned in the corresponding bar plots.
25. Rosenberg et al., “Genetic Structure,” 2382.
26. Lawson, van Dorp, and Falush, “Tutorial,” 2.
27. Lawson, van Dorp, and Falush, “Tutorial,” 10. In a STRUCTURE or ADMIXTURE analysis with “real” data, these simulated populations would be what is commonly called “predefined populations.”
28. Sommer, “Population-Genetic Trees,” 133–135; Sommer, History Within, 380–381.
29. Lawson, van Dorp, and Falush, “Tutorial,” 4.
30. Lawson, van Dorp, and Falush, “Tutorial,” 10; Morten Rasmussen et al., “Ancient Human Genome Sequence of an Extinct Palaeo-Eskimo,” Nature 463, no. 7282 (2010): 760–761; Pontus Skoglund et al., “Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe,” Science 336, no. 6080 (2012): 467.
31. Dienekes Pontikos, “Human Genetic Variation: The First ? Components,” Dienekes’ Anthropology Blog, December 15, 2010, http://dienekes.blogspot.com/2010/12/human-genetic-variation-first.html.
32. See also Sommer, “Population-Genetic Trees,” 26–28; Sommer, History Within, 380–384.
33. Pontikos, “Human Genetic Variation.”
34. Charlotte Lindqvist and Om P. Rajora, eds., Paleogenomics: Genome-Scale Analysis of Ancient DNA (Cham: Springer International, 2019).
35. Michela Leonardi et al., “Evolutionary Patterns and Processes: Lessons from Ancient DNA,” Systematic Biology 66, no. 1 (2017): 1–29.
36. “HG” in the figure stands for “hunter-gatherers.”
37. Mário Vicente and Carina M. Schlebusch, “African Population History: An Ancient DNA Perspective,” Current Opinion in Genetics & Development, Genetics of Human Origin 62 (2020): 12. See also Mário Vicente et al., “Genetic Affinities among Southern Africa Hunter-Gatherers and the Impact of Admixing Farmer and Herder Populations,” Molecular Biology and Evolution 36, no. 9 (2019)): 1849–1861; Pontus Skoglund et al., “Reconstructing Prehistoric African Population Structure,” Cell 171, no. 1 (2017): 59–71.
38. Vicente and Schlebusch, “African Population History,” 12.
39. Vicente and Schlebusch, “African Population History,” 12–13. See also Carina M. Schlebusch et al., “Southern African Ancient Genomes Estimate Modern Human Divergence to 350,000 to 260,000 Years Ago,” Science 358, no. 6363 (2017): 652–655.
40. Skyler D. Resendez et al., “Structural Variants in Ancient Genomes,” in Paleogenomics: Genome-Scale Analysis of Ancient DNA, ed. Charlotte Lindqvist and Om P. Rajora (Cham: Springer International, 2019), 375–391.
41. Leonardi et al., “Evolutionary Patterns and Processes,” 1–29.
42. Vicente and Schlebusch, “African Population History,” 8–15.
43. See below, and also Shyamalika Gopalan et al., “Inferring Archaic Introgression from Hominin Genetic Data,” Evolutionary Anthropology 30, no. 3 (2021): 214–216.
44. Kay Prüfer et al., “The Complete Genome Sequence of a Neanderthal from the Altai Mountains,” Nature 505, no. 7481 (2014): 48.
45. Anders Bergström et al., “Origins of Modern Human Ancestry,” Nature 590, no. 7845 (2021): 233.
46. Bergström et al., “Origins,” 233.
47. Liisa Loog, “Sometimes Hidden but Always There: Assumptions Behind Demographic Inference from Ancient DNA Data,” Philosophical Transactions of the Royal Society B: Biological Sciences 376, no. 1816 (2021): 2.
48. Joseph K. Pickrell and Jonathan K. Pritchard, “Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data,” PLoS Genetics 8, no. 11 (2012): 1–2; Ajai K. Pathak, “Identifying Admixture and Genetic Ancestry in Human Populations via Genetic Drift Pattern,” Polymorphism 4 (2020): 6.
