Текст книги "Кто мы и как сюда попали. Древняя ДНК и новая наука о человеческом прошлом"

Пояснения к иллюстрациям

Источники карт: все карты сделаны с использованием ресурса Natural Earth (http://www.naturalearthdata.com/).

Рисунок 1. Контуры на панели 1а взяты из: L. L. Cavalli-Sforza, P. Menozzi, A. Piazza “Demic Expansions and Human Evolution”, Science 259 (1993): 639–646. Контуры на панели 1б являются интерполяцией численных оценок с илл. 3 в книге: W. Haak et al. “Massive Migration from the Steppe Was a Source for Indo-European Languages in Europe”, Nature 522 (2015): 207–211. Интерполяция выполнена с использованием программы POPSutilities.R из работы: F. Jay et al. “Forecasting Changes in Population Genetic Structure of Alpine Plants in Response to Global Warming, Molecular Ecology (2012): 2354–2368 с параметрами, обоснованными в работе: O. François “Running Structure-like Population Genetic Analyses with R”, June 2016, http:// membres-timc.imag.fr/Olivier.Francois/tutoRstructure.pdf.

Рисунок 2. График показывает данные по 3748 образцам, находящимся во внутренней базе данных моей лаборатории к ноябрю 2017 года; после этого момента данные не добавлялись.

Рисунок 4. Число генеалогических предков, которые внесли свою часть в наследие конкретного сегодняшнего человека, получено с помощью модельных симуляций Грэмом Купом, и результаты переданы автору. Методика симуляций описана в работе: G. Coop “How Many Genetic Ancestors Do I Have”, gcbias blog, November 11, 2013, https://gcbias.org/2013/11/11/how-does-your-number-of-genetic-ancestors-grow-back-over-time/.

Рисунок 5. По числу мутаций, различающихся в сегменте геномов, полученных от отца и от матери, можно оценить, как далеко во времени отстоит общий предок, давший отцу и матери этот конкретный сегмент. Панель 2 показывает оценки времени существования последнего общего предка 250 геномных пар неафриканцев (сплошная линия) и 44 геномные пары индивидов южнее Сахары; для каждой пары время усреднялось по сегментам геномов, с одинаковым сдвигом рамки. Данные оценки опубликованы в: S. Mallick et al. “The Simons Genome Diversity Project: 300 Genomes from 142 Diverse Populations”, Nature 538 (2016): 201–206. Панель 3 показывает максимальные оценки для каждого сегмента 229 геномных пар, данные из той же публикации.

Рисунок 6. Примерное распространение неандертальцев, как показано на илл. 1 в: J. Krause et al. “Neanderthals in Central Asia and Siberia”, Nature 449 (2007): 902–904.

Рисунок 7. Расчет общих мутаций основан на сравнении французов, южноафриканцев и неандертальцев в таблице S48 в: Supplementary Online Materials, R. E. Green et al. “A Draft Sequence of the Neandertal Genome”, Science 328 (2010): 710–722.

Рисунок 8. Иллюстрация выполнена по илл. 2 в: Q. Fu et al. “An Early Modern Human from Romania with a Recent Neanderthal Ancestor”, Nature 524 (2015): 216–219.

Рисунок 9. Иллюстрация выполнена по данным илл. 2. в: Q. Fu et al. “The Genetic History of Ice Age Europe”, Nature 534 (2016): 200–205.

Рисунок 10. Эта круговая диаграмма построена по колонкам AJ и AK в Supplementary Table 2 из: S. Mallick et al. “The Simons Genome Diversity Project: 300 Genomes from 142 Diverse Populations”, Nature 538 (2016): 201–206. Каждая популяция отображается как усреднение по выборке индивидов. Пропорция архаичного наследия посчитана как доля от его максимального значения из всех популяций. Значения меньше 0,03 приравнены к 0, а больше 0,97 – к 1. Из всех проанализированных популяций показаны 47, таким образом, подчеркнуто географическое покрытие и уменьшен визуальный шум.

Рисунок 13. Иллюстрация миграций в Европе дана по: Q. Fu et al. “The Genetic History of Ice Age Europe”, Nature 534 (2016): 200–205. Распространение льда наложено на карту в соответствии с прорисовками в: “Extent of Ice Sheets in Europe”, Map. Encyclopaedia Britannica Online, https://www.britannica.com/place/Scandinavian-Ice-Sheet?oasmId=54573.

Рисунок 14. Панель (а) дана по илл 4. из: Extended Data в W. Haak et al. “Massive Migration from the Steppe Was a Source for Indo-European Lan guages in Europe”, Nature 522 (2015): 207–211. Панель (б) и врезка на рисунке представлена с разрешения: D. W. Anthony и D. Ringe: Fig. 1 и Fig. 2, “The Indo-European Homeland from Linguistic and Archaeological Perspec tives,” Annual Review of Linguistics 1 (2015): 199–219.

Рисунок 15. Графики на всех трех панелях построены на основе анализа главных компонент по илл. 1b в: I. Lazaridis et al. “Genetic Origins of the Minoans and Mycenaeans”, Nature 548 (2017): 214–218.

Рисунок 16. Круговая диаграмма построена по 180 образцам индивидов, принадлежащих к культуре колоколовидных кубков, чью ДНК удалось прочитать с достаточным разрешением для определения уровня степного наследия. Индивидуальные образцы сгруппированы по странам, где они были найдены. Данные взяты из ревизованной версии: I. Olalde et al. “The Beaker Phenom enon and the Genomic Transformation of Northwest Europe”, bioRxiv (2017): doi.org/10.1101/135962.

Рисунок 17. Контуры ареала южноазиатской языковой семьи на панели (а) взяты из: A Historical Atlas of South Asia, ed. Joseph E. Schwartzberg (Oxford: Oxford University Press, 1992). График на панели (б) построен по методу главных компонент в: D. Reich et al. “Reconstruct ing Indian Population History”, Nature 461 (2009): 489–494; Fig. 3. По осям x и y приблизительно выравниваются географические и генетические позиции.

Рисунок 18. Изображение географического распространения земледельческих культур пшеницы и ячменя и соответствующие датировки любезно предоставлены Дорианом Фуллером. Контуры западной половины карты даны в соответствии с илл. 2 в: F. Silva, M. Vander Linden “Amplitude of Travelling Front as Inferred From 14C Pre dicts Levels of Genetic Admixture Among European Early Farmers”, Scientific Reports 7 (2017): 11985.

Рисунок 19. Положение североамериканского ледового щита и береговой линии дано в соответствии с: A. S. Dyke “An Outline of North American Deglaciation with Emphasis on Central and Northern Canada”, Quaternary Glaciations – Extent and Chronology, Part II: North America, ed. J ürgen Ehlers and Philip L. Gibbard (Amsterdam: Elsevier, 2004), p. 373–422, конкретные страницы 380–383. Контуры евразийского ледового щита – в соответствии с илл. 4 в: H. Patton et al. “Deglaciation of the Eurasian Ice Sheet Complex”, Quaternary Science Reviews 169 (2017): 148–172. Южноамериканский ледник и береговая линия взяты из илл. 5.1 в: D. J. Meltzer “The Origins, Antiquity and Dispersal of the First Americans”, The Human Past, 4th Edition, ed. Chris Scarre (London: Thames and Hudson, expected early 2018), 149–171. Древняя береговая линия Сибири интерполирована.

Рисунок 20. Здесь соединена информация с илл. 2 в: D. Reich et al. “Reconstructing Native American Population History”, Nature 488 (2012): 370–374 и илл. 5 в: P. Flegontov et al. “Paleo-Eskimo Genetic Legacy Across North America”, bioRxiv (2017): doi. org/10.1101.203018.

Рисунок 21. Рисунок построен по данным илл. 1 в: P. Skoglund et al. “Genetic Evidence for Two Founding Populations of the Americas”, Nature 525 (2015): 104–108.

Рисунок 23. Вероятные маршруты миграций ранних носителей тай-кадайских, австроазиатских и австронезийских языков показаны в соответствии с илл. 2 в: J. Diamond, P. Bellwood “Farmers and Their Languages: The First Expansions”, Science 300 (2003): 597–603.

Рисунок 24. Древняя береговая линия на панели 1 аппроксимирована в соответствии с картой в: A. Coo per, C. Stringer “Did the Denisovans Cross Wallace's Line?” Science 342 (2013): 321–323.

Рисунок 25. Иллюстрация дана по илл. 3D в: P. Skoglund et al. “Reconstructi ng Prehistoric African Population Structure”, Cell 171 (2017): 59–71.

Рисунок 26. Контуры африканских языковых семей даны по: M. C. Campbell, J. B. Hirbo, J. P. Townsend, S. A. Tishkoff “The Peo pling of the African Continent and the Diaspora into the New World”, Curr ent Opinion in Genetics and Development 29 (2014): 120–132, Fig. 3. Возможные пути миграций народов, ассоциированных с экспансией банту, показаны в соответствии с: Campbell et al. “The Peopling of the African Continent”, а также с учетом мнения Скотта Макичерна и результатов последующего генетического анализа, указывающего на малый вклад в наследие банту-говорящих восточноафриканцев от мигрантов, двигавшихся на север от тропических дождевых лесов (G. B. Busby et al. “Admixture into and Within Sub-Saharan Africa”, eLife 5 (2016): e15266; E. Patin et al. “Dispersals and Genetic Adaptation of Bantu-Speaking Pop ulations in Africa and North America”, Science 356 (2017): 543–546).

Рисунок 27. Здесь объединены данные с илл. 2B и 2C в: P. Skoglund et al. “Reconstructing Prehistoric African Population Structure”, Cell 171 (2017): 59–71.

Рисунок 28. Приведен с разрешения по: M. Karmin et al. “A Recent Bottleneck of Y Chromosome Diversity Coincides with a Global Change in Culture”, Genome Research 25 (2015): 459–466, Fig. 2.

Примечания

Введение

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2 L. L. Cavalli-Sforza, F. Cavalli-Sforza. The Great Human Diasporas: The History of Diversity and Evolution (Reading, MA: Addison-Wesley, 1995).

3 N. A. Rosenberg et al. “Genetic Structure of Human Populations”, Science 298 (2002): 2381–2385.

4 P. Menozzi, A. Piazza, L. L. Cavalli-Sforza. “Synthetic Maps of Human Gene Frequencies in Europeans”, Science 201 (1978): 786–792; L. L. Cavalli-Sforza, P. Menozzi, A. Piazza. “Demic Expansions and Human Evolution”, Science 259 (1993): 639–646.

5 A. J. Ammerman, L. L. Cavalli-Sforza. The Neolithic Transition and the Genetics of Populations in Europe (Princeton, NJ: Princeton University Press, 1984).

6 J. Novembre, M. Stephens. “Interpreting Principal Component Analyses of Spatial Population Genetic Variation”, Nature Genetics 40 (2008): 646–649.

7 O. François et al. “Principal Component Analysis Under Population Genetic Models of Range Expansion and Admixture”, Molecular Biology and Evolution 27 (2010): 1257–68.

8 A. Keller et al. “New Insights into the Tyrolean Iceman’s Origin and Phenotype as Inferred by Whole-Genome Sequencing”, Nature Communications 3 (2012): 698; P. Skoglund et al. “Ori gins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe”, Science 336 (2012): 466–469; I. Lazaridis et al. “Ancient Human Genomes Suggest Three Ancestral Populations for Present-Day Europeans”, Nature 513 (2014): 409–13.

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

10 R. E. Green et al. “A Draft Sequence of the Neandertal Genome”, Science 328 (2010): 710–722.

11 D. Reich et al. “Genetic History of an Archaic Hominin Group from Denisova Cave in Siberia”, Nature 468 (2010): 1053–1060.

12 M. Rasmussen et al. “Ancient Human Genome Sequence of an Extinct Palaeo-Eskimo”, Nature 463 (2010): 757–762.

13 W. Haak et al. “Massive Migration from the Steppe Was a Source for Indo-European Languages in Europe”, Nature 522 (2015): 207–211.

14 M. E. Allentoft et al. “Population Genomics of Bronze Age Eurasia”, Nature 522 (2015): 167–172.

15 I. Mathieson et al. “Genome-Wide Patterns of Selection in 230 Ancient Eurasians”, Nature 528 (2015): 499–503.

16 Q. Fu et al. “DNA Analysis of an Early Modern Human from Tianyuan Cave, China”, Proceedings of the National Academy of Sciences of the U.S.A. 110 (2013): 2223–2227.

17 H. Shang et al. “An Early Modern Human from Tianyuan Cave, Zhoukoudian, China”, Proceedings of the National Academy of Sciences of the U.S.A. 104 (2007): 6573–6578.

18 Haak et al. “Massive Migration”.

19 I. Lazaridis et al. “Genomic Insights into the Origin of Farming in the Ancient Near East”, Nature 536 (2016): 419–424.

20 P. Skoglund et al. “Genomic Insights into the Peopling of the Southwest Pacific”, Nature 538 (2016): 510–513.

21 Lazaridis et al. “Ancient Human Genomes”.

22 Pickrell, Reich. “Toward a New History”.

Глава 1. Как геном объясняет, кто мы такие

1 J. D. Watson and F. H. Crick. “Molecular Structure of Nucleic Acids; a Structure for Deoxyribose Nucleic Acid”, Nature 171 (1953): 737–738.

2 R. L. Cann, M. Stoneking, A. C. Wilson. “Mitochondrial DNA and Human Evolution”, Nature 325 (1987): 31–36.

3 Cann et al. “Mitochondrial DNA and Human Evolution”.

4 Q. Fu et al. “A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes”, Current Biology 23 (2013): 553–559.

5 D. E. Lieberman, B. M. McBratney, G. Krovitz. “The Evolution and Development of Cranial Form in Homo sapiens”, Proceedings of the National Academy of Sciences of the U.S.A. 99 (2002):1134– 39; Richter et al. “The Age of the Hominin Fossils from Jebel Irhoud, Morocco, and the Origins of the Middle Stone Age”, Nature 546 (2017): 293–296.

6 H. S. Groucutt et al. “Rethinking the Dispersal of Homo sapiens Out of Africa”, Evolutionary Anthropology 24 (2015): 149–164.

7 C.-J. Kind et al. “The Smile of the Lion Man: Recent Excavations in Stadel Cave (Baden-Württemberg, South-Western Germany) and the Restoration of the Famous Upper Palaeolithic Figurine”, Quartär 61 (2014): 129–145.

8 T. Higham et al. “The Timing and Spatiotemporal Patterning of Neanderthal Disappearance”, Nature 512 (2014): 306–309.

9 Richard G. Klein, Blake Edgar. The Dawn of Human Culture (New York: Wiley, 2002).

10 J. Doebley. “Mapping the Genes That Made Maize”, Trends in Genetics 8 (1992): 302–307.

11 S. McBrearty, A. S. Brooks. “The Revolution That Wasn’t: A New Interpretation of the Origin of Modern Human Behavior”, Journal of Human Evolution 39 (2000): 453–563.

12 C. S. L. Lai et al. “A Forkhead-Domain Gene Is Mutated in a Severe Speech and Language Disorder”, Nature 413 (2001): 519–523.

13 W. Enard et al. “Molecular Evolution of FOXP2, a Gene Involved in Speech and Language”, Nature 418 (2002): 869–872.

14 W. Enard et al. “A Humanized Version of FOXP2 Affects Cortico-Basal Ganglia Circuits in Mice”, Cell 137 (2009): 961–971.

15 J. Krause et al. “The Derived FOXP2 Variant of Modern Humans Was Shared with Neandertals”, Current Biology 17 (2007): 1908–1912.

16 T. Maricic et al. “A Recent Evolutionary Change Affects a Regulatory Element in the Human FOXP2 Gene”, Molecular Biology and Evolution 30 (2013): 844–852.

17 S. Pääbo. “The Human Condition – a Molecular Approach”, Cell 157 (2014): 216–226.

18 R. E. Green et al. “A Draft Sequence of the Neandertal Genome”, Science 328 (2010): 710–722; K. Prüfer et al. “The Complete Genome Sequence of a Neanderthal from the Altai Mountains”, Nature (2013): doi: 10.1038/nature 1288.

19 R. Lewin. “The Unmasking of Mitochondrial Eve”, Science 238 (1987): 24–26.

20 A. Kong et al. “A High-Resolution Recombination Map of the Human Genome”, Nature Genetics 31 (2002): 241–247.

21 “Descent of Elizabeth II from William I”, Familypedia, http:// familypedia wikia.com/wiki/Descent_of_Elizabeth_II_from_ William_I#Shorter_line_of_descent.

22 S. Mallick et al. “The Simons Genome Diversity Project: 300 Genomes from 142 Diverse Populations”, Nature 538 (2016): 201–206.

23 Green et al. “Draft Sequence”.

24 H. Li, R. Durbin. “Inference of Human Population History from Individual Whole-Genome Sequences”, Nature 475 (2011): 493–496.

25 Там же.

26 S. Schiffels, R. Durbin. “Inferring Human Population Size and Separation History from Multiple Genome Sequences”, Nature Genetics 46 (2014): 919–925.

27 Mallick et al. “Simons Genome Diversity Project”.

28 I. Gronau et al. “Bayesian Inference of Ancient Human Demography from Individual Genome Sequences”, Nature Genetics 43 (2011): 1031–1034.

29 Mallick et al. “Simons Genome Diversity Project”.

30 P. C. Sabeti et al. “Detecting Recent Positive Selection in the Human Genome from Haplotype Structure”, Nature 419 (2002): 832–837; B. F. Voight, S. Kudaravalli, X. Wen, J. K. Pritchard. “A Map of Recent Positive Selection in the Human Genome”, PLoS Biology 4 (2006): e72.

31 K. M. Teshima, G. Coop, M. Przeworski. “How Reliable Are Empirical Genomic Scans for Selective Sweeps?”, Genome Research 16 (2006): 702–712.

32 R. D. Hernandez et al. “Classic Selective Sweeps Were Rare in Recent Human Evolution”, Science 331 (2011): 920–924.

33 S. A. Tishkoff et al. “Convergent Adaptation of Human Lactase Persistence in Africa and Europe”, Nature Genetics 38 (2006): 31–40.

34 M. C. Turchin et al. “Evidence of Widespread Selection on Standing Variation in Europe at Height-Associated SNPs”, Nature Genetics 44 (2012): 1015–1019.

35 I. Mathieson et al. “Genome-Wide Patterns of Selection in 230 Ancient Eurasians”, Nature 528 (2015): 499–503.

36 Y. Field et al. “Detection of Human Adaptation During the Past 2000 Years”, Science 354 (2016): 760–764.

37 D. Welter et al. “The NHGRI GWAS Catalog, a Curated Resource of SNP-Trait Associations”, Nucleic Acids Research 42 (2014): D1001–1006.

38 D. B. Goldstein. “Common Genetic Variation and Human Traits”, New England Journal of Medicine 360 (2009): 1696–1698.

39 A. Okbay et al. “Genome-Wide Association Study Identifies 74 Loci Associated with Educational Attainment”, Nature 533 (2016): 539–542; M. T. Lo et al. “Genome-Wide Analyses for Personality Traits Identify Six Genomic Loci and Show Correlations with Psychiatric Disorders”, Nature Genetics 49 (2017): 152–156; G. Davies et al. “Genome-Wide Association Study of Cognitive Functions and Educational Attainment in UK Biobank (N=112 151)”, Molecular Psychiatry 21 (2016): 758–767.

Глава 2. Встреча с неандертальцами

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2 Erik Trinkaus. The Shanidar Neanderthals (New York: Academic Press, 1983).

3 D. Radovcˇ i, A. O. Sršen, J. Radovcˇ ic´, D. W. Frayer. “Evidence for Neandertal Jewelry: Modified White-Tailed Eagle Claws at Krapina”, PLoS One 10 (2015): e0119802.

4 J. Jaubert et al. “Early Neanderthal Constructions Deep in Bruniquel Cave in Southwestern France”, Nature 534 (2016): 111–114.

5 W. L. Straus, A. J. E. Cave. “Pathology and the Posture of Neanderthal Man”, Quarterly Review of Biology 32 (1957): 348–363.

6 William Golding. The Inheritors (London: Faber and Faber, 1955).

7 Jean M. Auel. The Clan of the Cave Bear (New York: Crown, 1980).

8 T. Higham et al. “The Timing and Spatiotemporal Patterning of Neanderthal Disappearance”, Nature 512 (2014): 306–309.

9 T. Higham et al. “Chronology of the Grotte du Renne (France) and Implications for the Context of Ornaments and Human Remains Within the Châtelperronian”, Proceedings of the National Academy of Sciences of the U.S.A. 107 (2010): 20234–20239; O. Bar-Yosef, J.-G. Bordes. “Who Were the Makers of the Châtelperronian Culture?”, Journal of Human Evolution 59 (2010): 586–593.

10 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): 316–334.

11 H. Valladas et al. “Thermo-Luminescence Dates for the Neanderthal Burial Site at Kebara in Israel”, Nature 330 (1987): 159–160.

12 E. Trinkaus et al. “An Early Modern Human from the Pe¸stera cu Oase, Romania”, Proceedings of the National Academy of Sciences of the U.S.A. 100 (2003): 11231–11236.

13 M. Krings et al. “Neandertal DNA Sequences and the Origin of Modern Humans”, Cell 90 (1997): 19–30.

14 C. Posth et al. “Deeply Divergent Archaic Mitochondrial Genome Provides Lower Time Boundary for African Gene Flow into Neanderthals”, Nature Communications 8 (2017): 16046.

15 Krings et al. “Neandertal DNA Sequences”.

16 M. Currat, L. Excoffier. “Modern Humans Did Not Admix with Neanderthals During Their Range Expansion into Europe”, PLoS Biology 2 (2004): e421; D. Serre et al. “No Evidence of Neandertal mtDNA Contribution to Early Modern Humans”, PLoS Biology 2 (2004): e57; M. Nordborg.“On the Probability of Neanderthal Ancestry”, American Journal of Human Genetics 63 (1998): 1237–1240.

17 R. E. Green et al. “Analysis of One Million Base Pairs of Neanderthal DNA”, Nature 444 (2006): 330–336.

18 J. D. Wall and S. K. Kim. “Inconsistencies in Neanderthal Genomic DNA Sequences”, PLoS Genetics 3 (2007): 1862–1866.

19 Krings et al. “Neandertal DNA Sequences”.

20 S. Sankararaman et al. “The Date of Interbreeding Between Neandertals and Modern Humans”, PLoS Genetics 8 (2012): e1002947.

21 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): 5652–5657.

22 G. Coop. “Thoughts On: The Date of Interbreeding Between Neandertals and Modern Humans”, Haldane’s Sieve, September 18, 2012, https://haldanessieve.org/2012/09/18/thoughts-on-neandertal-article/

23 K. Prüfer et al. “The Complete Genome Sequence of a Neanderthal from the Altai Mountains”, Nature (2013): doi: 10.1038/nature 12886.

24 Там же.

25 Там же; M. Meyer et al. “A High-Coverage Genome Sequence from an Archaic Denisovan Individual”, Science 338 (2012): 222–226; J. D. Wall et al. “Higher Levels of Neanderthal Ancestry in East Asians Than in Europeans”, Genetics 194 (2013): 199–209.

26 Q. Fu et al. “The Genetic History of Ice Age Europe”, Nature 534 (2016): 200–205.

27 I. Lazaridis et al. “Genomic Insights into the Origin of Farming in the Ancient Near East”, Nature 536 (2016): 419–424.

28 Trinkaus et al. “An Early Modern Human”.

29 “An Early Modern Human from Romania with a Recent Neanderthal Ancestor”, Nature 524 (2015): 216–219.

30 N. Teyssandier, F. Bon, and J.-G. Bordes. “Within Projectile Range: Some Thoughts on the Appearance of the Aurignacian in Europe”, Journal of Anthropological Research 66 (2010): 209–229; P. Mellars. “Archeology and the Dispersal of Modern Humans in Europe: Deconstructing the ‘Aurignacian’ ”, Evolutionary Anthropology 15 (2006): 167–182.

31 M. Currat, L. Excoffier. “Strong Reproductive Isolation Between Humans and Neanderthals Inferred from Observed Patterns of Introgression”, Proceedings of the National Academy of Sciences of the U.S.A. 108 (2011): 15129–15134.

32 S. Sankararaman et al. “The Genomic Landscape of Neanderthal Ancestry in Present-Day Humans”, Nature 507 (2014): 354–357; B. Vernot, J. M. Akey. “Resurrecting Surviving Neandertal Lineages from Modern Human Genomes”, Science 343 (2014): 1017–1021.

33 N. Patterson et al. “Genetic Evidence for Complex Speciation of Humans and Chimpanzees”, Nature 441 (2006): 1103–1108.

34 Там же; R. Burgess, Z. Yang. “Estimation of Hominoid Ancestral Population Sizes Under Bayesian Coalescent Models Incorporating Mutation Rate Variation and Sequencing Errors”, Molecular Biology and Evolution 25 (2008): 1975–1994.

35 J. A. Coyne and H. A. Orr. “Two Rules of Speciation”, in Speciation and Its Consequences, ed. Daniel Otte and John A. Endler (Sunderland, MA: Sinauer Associates, 1989), 180–207.

36 P. K. Tucker et al. “Abrupt Cline for Sex-Chromosomes in a Hybrid Zone Between Two Species of Mice”, Evolution 46 (1992): 1146–1163.

37 H. Li, R. Durbin. “Inference of Human Population History from Individual Whole-Genome Sequences”, Nature 475 (2011): 493–496.

38 T. Mailund et al. “A New Isolation with Migration Model Along Complete Genomes Infers Very Different Divergence Processes Among Closely Related Great Ape Species”, PLoS Genetics 8 (2012): e1003125.

39 J. Y. Dutheil et al. “Strong Selective Sweeps on the X Chromosome in the Human-Chimpanzee Ancestor Explain Its Low Divergence”, PLoS Genetics 11 (2015): e1005451.

40 Sankararaman et al. “Genomic Landscape”; B. Jégou et al. “Meiotic Genes Are Enriched in Regions of Reduced Archaic Ancestry”, Molecular Biology and Evolution 34 (2017): 1974–1980.

41 Q. Fu et al. “Ice Age Europe”.

42 I. Juric, S. Aeschbacher, G. Coop. “The Strength of Selection Against Neanderthal Introgression”, PLoS Genetics 12 (2016): e1006340; K. Harris, R. Nielsen. “The Genetic Cost of Neanderthal Introgression”, Genetics 203 (2016): 881–891.

43 G. Bhatia et al. “Genome-Wide Scan of 29, 141 African Americans Finds No Evidence of Directional Selection Since Admixture”, American Journal of Human Genetics 95 (2014): 437–444.

44 Johann G. Fichte. Grundlage der gesamten Wissenschaftslehre (Jena, Germany: Gabler, 1794).

Глава 3. Древняя ДНК открывает шлюзы

1 J. Krause et al. “Neanderthals in Central Asia and Siberia”, Nature 449 (2007): 902–904.

2 J. Krause et al. “The Complete Mitochondrial DNA Genome of an Unknown Hominin from Southern Siberia”, Nature 464 (2010): 894–897.

3 C. Posth et al. “Deeply Divergent Archaic Mitochondrial Genome Provides Lower Time Boundary for African Gene Flow into Neanderthals”, Nature Communications 8 (2017): 16046.

4 Krause et al. “Unknown Hominin”.

5 D. Reich et al. “Genetic History of an Archaic Hominin Group from Denisova Cave in Siberia”, Nature 468 (2010): 1053–1060.

6 K. Prüfer et al. “The Complete Genome Sequence of a Neanderthal from the Altai Mountains”, Nature (2013): doi: 10.1038/nature 12886.

7 Jerry A. Coyne, H. Allen Orr. Speciation (Sunderland, MA: Sinauer Associates, 2004).

8 S. Sankararaman, S. Mallick, N. Patterson, D. Reich. “The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans”, Current Biology 26 (2016): 1241–1247.

9 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): 5652–5657.

10 Sankararaman et al. “Combined Landscape”.

11 D. Reich et al. “Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania”, American Journal of Human Genetics 89 (2011): 516–528.

12 Q. Fu et al. “DNA Analysis of an Early Modern Human from Tianyuan Cave, China”, Proceedings of the National Academy of Sciences of the U.S.A. 110 (2013): 2223–2227; M. Yang et al. “40,000-Year-Old Individual from Asia Provides Insight into Early Population Structure in Eurasia”, Current Biology 27 (2017): 3202–3208.

13 Prüfer et al. “Complete Genome”.

14 C. B. Stringer and I. Barnes. “Deciphering the Denisovans”, Proceedings of the National Academy of Sciences of the U.S.A. 112 (2015): 15542–15543.

15 G. A. Wagner et al. “Radiometric Dating of the Type-Site for Homo Heidelber-gensis at Mauer, Germany”, Proceedings of the National Academy of Sciences of the U.S.A. 107 (2010): 19726–19730.

16 C. Stringer. “The Status of Homo heidelbergensis (Schoetensack 1908)”, Evolutionary Anthropology 21 (2012): 101–107.

17 A. Brumm et al. “Age and Context of the Oldest Known Hominin Fossils from Flores”, Nature 534 (2016): 249–253.

18 Reich et al. “Denisova Admixture”.

19 Prüfer et al. “Complete Genome”.

20 Там же; Sankararaman et al. “Combined Landscape”.

21 E. Huerta-Sánchez et al. “Altitude Adaptation in Tibetans Caused by Introgression of Denisovan-like DNA”, Nature 512 (2014): 194–197.

22 F. H. Chen et al. “Agriculture Facilitated Permanent Human Occupation of the Tibetan Plateau After 3600 B.P.”, Science 347 (2015): 248–250.

23 S. Sankararaman et al. “The Genomic Landscape of Neanderthal Ancestry in PresentDay Humans”, Nature 507 (2014): 354–357; B. Vernot and J. M. Akey. “Resurrecting Surviving Neandertal Lineages from Modern Human Genomes”, Science 343 (2014): 1017–1021.

24 Prüfer et al. “Complete Genome”.

25 G. P. Rightmire. “Homo erectus and Middle Pleistocene Hominins: Brain Size, Skull Form, and Species Recognition”, Journal of Human Evolution 65 (2013): 223–252.

26 M. Martinón-Torres et al. “Dental Evidence on the Hominin Dispersals During the Pleistocene”, Proceedings of the National Academy of Sciences of the U.S.A. 104 (2007): 13279–13282; M. Martinón-Torres, R. Dennell, J. M. B. de Castro. “The Denisova Hominin Need Not Be an Out of Africa Story”, Journal of Human Evolution 60 (2011): 251–255; J. M. B. de Castro, M. Martinón-Torres. “A New Model for the Evolution of the Human Pleistocene Populations of Europe”, Quaternary International 295 (2013): 102–112.

27 De Castro, Martinón-Torres. “A New Model”.

28 J. L. Arsuaga et al. “Neandertal Roots: Cranial and Chronological Evidence from Sima de los Huesos”, Science 344 (2014): 1358–1363; M. Meyer et al. “A Mitochondrial Genome Sequence of a Hominin from Sima de los Huesos”, Nature 505 (2014): 403–406.

29 M. Meyer et al. “Nuclear DNA Sequences from the Middle Pleistocene Sima de los Huesos Hominins”, Nature 531 (2016): 504–507.

30 Meyer et al. “A Mitochondrial Genome”; Meyer et al. “Nuclear DNA Sequences”.

31 Krause et al. “Unknown Hominin”; Reich et al. “Genetic History”.

32 Posth et al. “Deeply Divergent Archaic”.

33 Там же.

34 Prüfer et al. “Complete Genome”.

35 S. McBrearty, A. S. Brooks. “The Revolution That Wasn’t: A New Interpretation of the Origin of Modern Human Behavior”, Journal of Human Evolution 39 (2000): 453–563.

36 M. Kuhlwilm et al. “Ancient Gene Flow from Early Modern Humans into Eastern Neanderthals”, Nature 530 (2016): 429–433.

Глава 4. Призраки человечества

1 Charles R. Darwin. On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life (London: John Murray, 1859).

2 C. Becquet et al. “Genetic Structure of Chimpanzee Populations”, PLoS Genetics 3 (2007): e66.

3 R. E. Green et al. “A Draft Sequence of the Neandertal Genome”, Science 328 (2010): 710–722.

4 N. J. Patterson et al. “Ancient Admixture in Human History”, Genetics 192 (2012): 1065–1093.

5 Ernst Mayr. Systematics and the Origin of Species from the Viewpoint of a Zoologist (New York: Columbia University Press, 1942).

6 J. K. Pickrell, D. Reich. “Toward a New History and Geography of Human Genes Informed by Ancient DNA”, Trends in Genetics 30 (2014): 377–389.

7 A. R. Templeton. “Biological Races in Humans”, Studies in History and Philosophy of Biological and Biomedical Science 44 (2013): 262–271.

8 M. Raghavan et al. “Upper Palaeolithic Siberian Genome Reveals Dual Ancestry of Native Americans”, Nature 505 (2014): 87–91.

9 I. Lazaridis et al. “Ancient Human Genomes Suggest Three Ancestral Populations for Present-Day Europeans”, Nature 513 (2014): 409–413.

10 I. Lazaridis et al. “Genomic Insights into the Origin of Farming in the Ancient Near East”, Nature 536 (2016): 419–424.