10. U2i is clearly home grown . . .: Bamshad, M. et al. (2001) ‘Genetic evidence on the origins of Indian caste populations’ Genome Research 11: 994–1004.
11. Apart from R, U2, and U7, other N groups and subgroups may have a claim of ancient origin in South Asia, in particular W. Groups H, Ö, X, I, J, and T are also found in India. Kivisild et al. (1999) op. cit. pp. 137–50.
12. Between 55,000 and 65,000 years ago the world went through a period of almost unremitting cold and dryness. During this time the Fertile Crescent corridor was shut: For a graphic colour map description of the effect of glacial cycles on the Fertile Crescent corridor see Jonathan Adams’ webpage, http://www.esd.ornl.gov/projects/qen/nercEURASIA.html four warm and wet periods: Interstadials (IS – not OIS) numbered 17–14 and dated as in Dansgaard, W. et al. (1993) ‘Evidence for general instability of past climate from a 250-kyr ice-core record’ Nature 364: 218–20; see also Schultz, H. et al. (1998) ‘Correlation between Arabian Sea and Greenland climate oscillations of the past 110,000 years’ Nature 393: 54–7. The last of these, 51,000 years ago: IS numbered 14 (= Glinde according to Dansgaard et al., op. cit); see also Schultz et al., op. cit. the Indian monsoon was even wetter: See Schultz et al., op. cit. esp. Fig. 2, p. 55. The climatic and archaeological clock timings converge: With correction of the radiocarbon dates – see note 7 above. the earliest daughter lines of Nasreen: I, and the U/Europa derivatives of R/Rohani: U/Europa root and U5, U7 (Richards et al. (2000) op. cit.).
13. The African branch that encompasses all non-Africans is defined by one bi-allelic marker, M168. Underhill, P.A. et al. (2000) ‘Y chromosome sequence variation and the history of human populations’ Nature Genetics 26: 358–61. So far the root type for this ‘Adam’ marker has not been found either within or outside Africa. The three primary branches C, D/E (or YAP), and F, which account for all non-Africans, I have chosen, for simplicity, to call Cain, Abel, and Seth respectively. The letters C–F refer to the new consensus nomenclature. For the consensus nomenclature, see The Y Chromosome Consortium (2002) ‘A nomenclature system for the tree of human Y-chromosomal binary haplogroups’ Genome Research 12: 339–48.
14. J, but I shall call him Jahangir and north-east coast of the Mediterranean: The consensus nomenclature haplogroup J (Jahangir) line is defined by M89, p12f2, and M172 (haplotypes 54–64 in Underhill et al., op. cit.) and is equivalent to Eur9 in Semino, O. et al. (2000) ‘The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: A Y-chromosome perspective’ Science 290: 1155–9, and equivalent to haplogroup 9 according to the nomenclature of Tyler-Smith and Jobling (see Rosser, H.Z. et al. (2000) ‘Y-chromosomal diversity in Europe is clinal and influenced primarily by geography, rather than by language’ American Journal of Human Genetics 67: 1526–43). high frequencies in the Near East: 57% in Syria, 51% in Palestinians, 28–45% in Jews, and 46% among Lebanese (‘Med’ type in Hammer, M. et al. (2000) ‘Jewish and Middle Eastern non-Jewish populations share a common pool of Y-chromosome biallelic haplotypes’ Proceedings of the National Academy of Sciences USA 97: 6769–74) and 33% among Georgians (Semino et al., op. cit.). highest European frequency is in Turkey: ibid. followed by the Balkans and Italy: ibid.; Rosser et al., op. cit. high frequencies in North African countries: ibid.
15. M172 (J/Jahangir) less than 20%, Quintana-Murci, L. et al. (2001) ‘Y-chromosome lineages trace diffusion of people and languages in Southwestern Asia’ American Journal of Human Genetics 68: 537–42; see also Underhill et al., op. cit.; Kivisild, T. (2003b) ‘Genetics of the language and farming spread in India’ in P. Bellwood and C. Renfrew (eds) Examining the Farming/Language Dispersal Hypothesis (McDonald Institute for Archaeology, Cambridge) pp. 215–222.
16. Diversity of Jahangir: Quintana-Murci et al., op. cit. The biggest problem comes in dating the M172 (J/Jahangir) clan. Hammer and colleagues put a date of 15,000–20,000 years on the European expansion, although the original mutation may have been much earlier (Hammer et al., op. cit.). Hammer dated M172’s immediate ancestor (DYS188792) to 60,000 years. However, there are serious problems still with Y-chromosome dating. Kivisild (2003b) op. cit. compares different methods of dating, showing age estimates for the M172 coalescent as much as 54,700 years in Iran and 49,000 years in India, similar to the older Hammer figure. Quintana-Murci in contrast, using ‘pedigree rate’ to estimate time, suggests a Neolithic agricultural expansion, but the origins of this clan clearly go much further back in time and space. The people who have the highest rate of M172, the Kurds, are long-time residents of the hilly part of the Fertile Crescent who until fairly recently were nomadic herders of sheep and goats with only marginal agriculture. Descendants of M172 spread to the East as well, into Central Asia (see Chapters 4 and 5).
17. half of all western and northern European maternal lines: Table 2 in Kivisild et al. (1999) op. cit. The expansion of HV has been dated to 33,500 years ago: Richards et al. (2000) op. cit.
18. Metspalu, E. et al. (1999) ‘The Trans-Caucasus and the expansion of the Caucasoid-specific mitochondrial DNA’ in S.S. Papiha et al. (eds) Genomic Diversity: Applications in Human Population Genetics (Kluwer Academic/Plenum Publishers, New York 1999) pp. 121–134.
19. Inos, after Seth’s son Enos: This consensus haplogroup I (Inos) clan is uniquely identified by bi-allelic marker M170 (haplotypes 49–53) in Underhill et al., op. cit., is synonymous with groups Eur7 and 8 in Semino et al., op. cit., and is largely overlapping with Tyler-Smith’s Haplogroup 2 (Rosser et al., op. cit.). For an explanation of the nomenclature of I (Inos), see The Y Chromosome Consortium op. cit. According to the Leicester-based geneticist Zoë Rosser: Rosser et al., op. cit. Ornella Semino and her colleagues: Semino et al., op. cit.
20. earliest changes from Mousterian: 46,000–47,000 years ago – Bar-Yosef, O. (1994) ‘The contributions of Southwest Asia to the study of the origins of modern humans’ in M.H. Nitecki and D.V. Nitecki (eds) Origins of Modern Humans (Plenum Press, New York, 1994), Chapter 2. These are radiocarbon dates, and – as stated by Bar-Yosef – if correction were possible, could be much older (e.g. as much as 51,000 years ago – see comments on radiocarbon ceiling, note 7 above.) The rock shelter of Ksar ‘Aqil in southern Lebanon has also been suggested as a site of the earliest transition from Mousterian technology to Levantine Aurignacian, possibly (unfortunately the date of the transition of culture could only be inferred stratigraphically) between 50,000 and 52,000 years ago; see Mellars, P. and Tixier, J. (1989) ‘Radiocarbon-accelerator dating of Ksar ‘Aqil (Lebanon) and the chronology of the Upper Palaeolithic sequence in the Middle East’ Antiquity 63: 761–8. hiatus coincided with a climatic worsening: The period spans two warm, wet interstadials, IS 12 and 11, with cold dry snaps preceding each of these. (IS numbering and dates according to Dansgaard op. cit) The first cold event coincided with Heinrich event No. 5. (See also Schultz et al., op. cit.)
21. The progressively worsening cold spell spanned the whole period between (IS) 12 (43,500 years) and IS 8 (34,000 years), the latter IS signalling the onset of re-warming. (Interstadial numbering and dates according to Dansgaard op. cit.) The first cold event coincided with Heinrich event No. 5. See also Schultz et al., op. cit.
22. For details of the Shanidar burial and the Baradostian culture, see Solecki, R. (1972) Shanidar: The Humanity of Neanderthal Man (Allen Lane, London).
23. Table 6.1 in Gamble op. cit.
24. Earliest Upper Palaeolithic, 33,000–45,000 years ago: Table 6.5 in Gamble op. cit. Occupation peaks for this phase occur between 40,000 and 44,000 years ago (calibrated 14C dates, ibid. p. 285). Cultures taking off from around 30,000 years ago: Table 6.5 ibid. third phase of high occupation: These (the Gravettian technocomplex) correspond with a third occupation peak (or Middle Upper Palaeolithic) between 25,000 and 29,000 years ago (uncalibrated dates, Fig. 6.5 ibid.). 33,000 years ago, for example at Kostenki: ibid. pp. 287–92.
25. cultural additions innovations of the Gravettian: Gamble op. cit. pp. 287–92, esp. p. 290; Soffer,
O. (1993) ‘Upper Paleolithic adaptations in Central and Eastern Europe and man-mammoth interactions’ in O. Soffer and N. Praslov (eds) From Kostenki to Clovis: Upper Paleolithic-Paleo-Indian Adaptations (Plenum, New York) pp. 31–49. may also have represented an intrusion of peoples carrying the seeds of such cultural practices from eastern Europe: Otte, M. (2000) ‘The history of European populations as seen by archaeology’ in C. Renfrew and K. Boyle (eds) Archaeogenetics: DNA and the Population Prehistory of Europe (MacDonald Institute for Archaeological Research, Cambridge) pp. 139–41.
26. Torroni, A. et al. (2001) ‘A signal, from human mtDNA, of postglacial recolonization in Europe’ American Journal of Human Genetics 69: 844–52.
27. perfectly preserved Caucasoid mummies: The point about the 3,000-year-old Caucasoid mummies on the Silk Road is merely to emphasise that there is no a priori reason to assume that the first populations of this part of Central Asia were Mongoloid: Barber, E.W. (2000) The Mummies of Urumchi (Pan, London); Mallory, J.P. and Mair, V. (2000) The Tarim Mummies: Ancient China and the Mystery of the Earliest Peoples from the West (Thames & Hudson, London). two sites in the Russian Altai: Otte, M. and Derevianko, A. (2001) ‘The Aurignacian in Altai’ Antiquity 75: 44–8; Goebel, T. et al. (1993) ‘Dating the Middle-to-Upper-Palaeolithic transition at Kara Bom’ Current Anthropology 34: 452–8; Goebel, T. and Aksenov, M. (1995) ‘Accelerator radiocarbon dating of the intial Upper Palaeolithic in Southeast Siberia’ Antiquity 69: 349–57.
28. Half of these consist of HV stock: Metspalu et al., op. cit.; Kivisild et al. (1999) op. cit. recent eastward European emigration: Comas, D. et al. (1998) ‘Trading genes along the Silk Road; mitochondrial DNA sequences and the origin of Central Asian populations’ Molecular Biology and Evolution 13: 1067–77. absent from Central Asia: although there are matches for most European H founders. most of the other ‘west Eurasian Nasreen lines’: U, J, and T haplogroups – U2i, U7, U5a, 1a, U4, U1, and K; see Fig. 2 in Metspalu et al., op. cit.; Kivisild et al. (1999) op. cit. HV could have originally come from South Asia: and J1, U1, and T.
29. Dates of branches vary enormously: e.g. Kivisild (2003b) op. cit.; Forster, P. et al. (2000) ‘A short tandem repeat-based phylogeny for the human Y chromosome’ American Journal of Human Genetics 67: 182–96. careful analysis of founder lines and mtDNA dating: Richards et al. (2000) op. cit.; Metspalu et al., op. cit.; Kivisild et al. (1999) op. cit.
30. Underhill et al., op. cit.; Semino et al., op. cit.
31. The root haplotype 87 defined by M9 in Underhill et al., op. cit. This clade has been reclassified as K/Krishna (while M89 is F/Seth): see The Y Chromosome Consortium op. cit.
32. the Oxford-based geneticist: Zergal, T. et al. (1997) ‘Genetic relationships of Asians and Northern Europeans, revealed by Y-chromosomal DNA analysis’ American Journal of Human Genetics 60: 1174–83. his genetic father and grandfather: haplotypes 87 and 71 respectively, defined by M9 and M89 in Underhill et al., op. cit. a migration from Central Asia: possibly only since the last glaciation – see Rosser et al., op. cit.; Semino et al., op. cit.
33. Hungarians achieve the highest frequency: followed closely by Poland, the Ukraine, and Russia at 56, 54, and 47%, respectively: Semino et al., op. cit.; Rosser et al., op. cit. especially the Altai: 52%, Quintana-Murci et al., op. cit.; Underhill et al., op. cit.
34. the ultimate origin of M17: Kivisild et al. (2003a,b) op. cit. highest rates and diversity of the M17 line in Pakistan, India, and eastern Iran, and low rates in the Caucasus: respectively 32, 20, 31, and 2% – Quintana-Murci et al., op. cit.; Rosser et al., op. cit. For a tabulation of the relative diversity of M17 (R1a) showing the highest diversity in South Asia, particularly Iran, see Table 5 in Kivisild et al. (2003a) op. cit. 36,000 years: measured at 35,700 years – Kivisild (2003b) op. cit.; other methods of calculation yield much lower estimates.
35. movement from the east to the west 30,000 years ago: Semino et al., op. cit. Phylogenetic analysis produces a realistic age, for M17 in Europe, of 27,000 years, see: Kivisild (2003b) op. cit. In contrast, Quintana-Murci et al. (op. cit.) tentatively suggests that the expansion into Europe started only around 5,000 years ago with the advent of farming. Ruslan: M173 root type, i.e. Haplotype 104, in Underhill et al., op. cit. Reclassified as ‘R’ in: The Y Chromosome Consortium (2002) op. cit.
36. according to one study: M173/ht 104, in Underhill et al., op. cit. Ruslan’s genetic father, P: Haplotype 111 in ibid.; reclassified as P in The Y Chromosome Consortium op. cit.
37. Semino et al., op. cit. It should be noted that the coalescent estimate for M17, M173, and M172 at M89 (Underhill haplotype 71) in India may be as old as 88,300 years – estimated by phylogenetic analysis, see Kivisild (2003b) op. cit.
Chapter 4
1. For a full discussion of the phylogeographic approach and founder analysis see Richards, M. et al. (1998) ‘Phylogeography of mitochondrial DNA in western Europe’ American Journal of Human Genetics 67: 241–60; Richards, M. et al. (2000) ‘Tracing European founder lineages in the Near Eastern mtDNA pool’ American Journal of Human Genetics 67: 1251–76.
2. much more recent African admixture: Richards, M. et al. (2003) ‘Extensive female-mediated gene flow from sub-Saharan Africa into Near Eastern Arab populations’ American Journal of Human Genetics 72: 1058–64. a number of other South Asian aboriginal groups: India also has so-called proto-Asian groups, such as Maria Gond, Khonda Dora, and Kattuniaken. Some of these are probably, like the Munda/Mundari groups, more recent east-west re-entrants from Indo-China: see Figs 14 and 21 in Oppenheimer, S.J. (1998) Eden in the East (Weidenfeld & Nicolson, London). For an anthropological/genetic description of the Indian aboriginal groups see also Watkins, W.S. et al. (1999) ‘Multiple origins of the mtDNA 9-bp deletion in populations of South India’ American Journal of Physical Anthropology 109: 147–58; Watkins, W.S. et al. (2001) ‘Patterns of ancestral human diversity: An analysis of Aluinsertion and restriction-site polymorphisms’ American Journal of Human Genetics 68: 738–52. beach-settling ancestors from Africa: Kivisild. T. et al. (2003) ‘The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations’ American Journal of Human Genetics 72: 313–32.
3. two ancient and unique Indian Manju clans, M2 and M4: for these groups in Andamanese, see Endicott, P. et al. (2003) ‘The genetic origins of the Andaman Islanders’ American Journal of Human Genetics 72: 178–84; Thangaraj, K. et al. (2003) ‘Genetic affinities of the Andaman Islanders, a vanishing human population’ Current Biology published online, 26 November 2002. commonest mtDNA component among the Indian aboriginal groups: Kivisild et al., op. cit. On the paternal side: for Y types in Andamanese, see Thangaraj et al., op. cit.
4. Pre-F1: Hill, C. et al. (2003) ‘Mitochondrial DNA variation in the Orang Asli of the Malay Peninsula’ (in preparation). For similar Pre-F1 haplotypes in Andamanese and Nicobars, see Andaman haplotypes 9 and 10 and Nicobar haplotype 1 in: Thangaraj et al., op.cit.; Prasad, B.V. et al. (2001). ‘Mitochondrial DNA variation in Nicobarese Islanders’ Human Biology 73: 715–25.
5. Nasreen and Manju mtDNA lines in New Guinea and Australia (see also Fig. 8.2 in Appendix 1): New Guinea has three main mtDNA clades, labelled PNG 1–3 in Redd, A.J. and Stoneking, M. (1999) ‘Peopling of Sahul: mtDNA variation in Aboriginal Australian and Papua New Guinean populations’ American Journal of Human Genetics 65: 808–28. The name labels of these three clades in the above paper corresponding to the nomenclature used in this book (Table 8.1 in Appendix 1) are as follows. PNG1 = Haplogroup B (of R haplogroup); PNG2 = local subgroup (of R haplogroup, also Group P in Forster, P. et al. (2003) ‘Asian and Papuan mtDNA evolution’ in P. Bellwood and C. Renfrew (eds) Examining the Farming/Language Dispersal Hypothesis (McDonald Institute for Archaeological Research, Cambridge) pp. 89–98); PNG3 = Q in Forster et al. (2003) op. cit., and M11 in Richards, M. and Macaulay, V. (2000) ‘Genetic data and colonization of Europe: Genealogies and founders’ in C. Renfrew and K. Boyle (eds) Archaeogenetics: DNA and
the Population Prehistory of Europe (McDonald Institute for Archaeological Research, Cambridge) pp. 139–41, Fig. 14.1. These three clades can also be confirmed unambiguously using typing data from several other publications, e.g. PNG2 = Haplotypes 6–8 and PNG3 = Haplotype 22, in Ingman, M. et al. (2000) ‘Mitochondrial genome variation and the origin of modern humans’ Nature 408: 708–13; PNG1 = Haplogroup 1 and PNG3 = Haplogroup 2, in Sykes, B. et al. (1995) ‘The origins of the Polynesians: An intepretation from mitochondrial lineage analysis’ American Journal of Human Genetics 57: 1463–75. For further Papuan details, see also Forster et al. (2003) op. cit.
Australian lineages have been rather less well characterized, but Redd and Stoneking (op. cit.) group them with Asians (specifically Indians – with rather less justification), rather than with Africans (see e.g. their Fig. 4). See also Ingman et al. (op. cit.), who show that Haplogroups 2 and 3 form a unique N subgroup and that Haplogroup 23 is a unique M type. No non-M/non-N Australian lineages have been demonstrated so far.
6. A recent article co-authored by Alan Thorne, a leading multiregionalist, suggested, on the basis of mtDNA results from ancient Australian bones, that some Australians may have left Africa in an earlier migration: Adcock, G.J. et al. (2001) ‘Mitochondrial DNA sequences in ancient Australians: Implications for modern human origins’ Proceedings of the National Academy of Sciences USA 98(2): 537–42. An immediate response from scientists working in the same field roundly condemned the study on the basis of methods, data presented, and underlying argument: Cooper, A. et al. (2001) ‘Human origins and ancient DNA’ Science 292: 1655–6. The discussion is rather technical and involved, and I mostly agree with the counterarguments given in the response by Cooper, A. et al. Mainly at issue was mtDNA extracted from one of the oldest sets of skeletal remains (possibly 62,000 years old – a date challenged again recently) found at Lake Mungo in the Willandra Lakes region of south-west Australia (LM3). Adcock and co-authors (op. cit.) argued that this mtDNA came from an earlier human branch. Cooper et al. (op. cit.) convincingly undermined their claim.
Out of Eden: The Peopling of the World Page 38
