A structured ancestral population for the evolution of modern humans

Current Opinion in Genetics and Development

Volumn 14, Issue 6, 2004, Pages 667-674

  Harding, Rosalind M ^a   McVean, Gil ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BOTTLENECK POPULATION; CHIMPANZEE; EVOLUTION; GENETIC ANALYSIS; GENETIC VARIABILITY; HUMAN; METAPOPULATION; NONHUMAN; PHENOTYPE; PLEISTOCENE; POPULATION; POPULATION MODEL; POPULATION STRUCTURE; PRIORITY JOURNAL; REVIEW;

AFRICA; DEMOGRAPHY; EVOLUTION; GENETICS, POPULATION; HISTORY, ANCIENT; HUMANS; PALEONTOLOGY; VARIATION (GENETICS);

HOMO; PAN TROGLODYTES;

EID: 8644263161     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gde.2004.08.010     Document Type: Review

References (83)

1. T.D. White, B. Asfaw, D. DeGusta, H. Gilbert, G.D. Richards, G. Suwa, and F.C. Howell Pleistocene Homo sapiens from Middle Awash, Ethiopia Nature 423 2003 742 747
2. C. Stringer Out of Ethiopia Nature 423 2003 692 695
3. C. Stringer Modern human origins: progress and prospects Philos Trans R Soc Lond B Biol Sci 357 2002 563 579
4. M. Balter What made humans modern? Science 295 2002 1219 1225
5. D.E. Lieberman, B.M. McBratney, and G. Krovitz The evolution and development of cranial form in Homo sapiens Proc Natl Acad Sci USA 99 2002 1134 1139
6. C. Dean, M.G. Leakey, D. Reid, F. Schrenk, G.T. Schwartz, C. Stringer, and A. Walker Growth processes in teeth distinguish modern humans from Homo erectus and earlier hominins Nature 414 2001 628 631
7. L.J. Hlusko Integrating the genotype and phenotype in hominid paleontology Proc Natl Acad Sci USA 101 2004 2653 2657
8. M.H. Wolpoff, J. Hawks, D.W. Frayer, and K. Hunley Modern human ancestry at the peripheries: a test of the replacement theory Science 291 2001 293 297
9. R. Potts, A.K. Behrensmeyer, A. Deino, P. Ditchfield, and J. Clark Small mid-Pleistocene hominin associated with East African Acheulean technology Science 305 2004 75 78
10. L.L. Cavalli-Sforza, and M.W. Feldman The application of molecular genetic approaches to the study of human evolution Nat Genet 33 2003 266 275
11. D.B. Goldstein, and L. Chikhi Human migrations and population structure: what we know and why it matters Annu Rev Genomics Hum Genet 3 2002 129 152
12. L. Excoffier Human demographic history: refining the recent African origin model Curr Opin Genet Dev 12 2002 675 682
13. M.A. Beaumont Recent developments in genetic data analysis: what can they tell us about human demographic history? Heredity 92 2004 365 379 A useful review of model-based likelihood methods for interpreting genetic data, motivated by the increasing awareness of complications caused by population structure and selection.
14. W.H. Li, and L.A. Sadler Low nucleotide diversity in Man Genetics 129 1991 513 523
15. R.C. Lewontin The apportionment of human diversity J Evol Biol 6 1972 381 398
16. W.S. Watkins, A.R. Rogers, C.T. Ostler, S. Wooding, M.J. Bamshad, A.-M.E. Brassington, M.L. Carroll, S.V. Nguyen, J.A. Walker, and B.V.R. Prasad Genetic variation among world populations: inferences from 100 Alu insertion polymorphisms Genome Res 13 2003 1607 1618
17. C. Romualdi, D. Balding, I.S. Nasidze, G. Risch, M. Robichaux, S.T. Sherry, M. Stoneking, M.A. Batzer, and G. Barbujani Patterns of human diversity, within and among continents, inferred from biallelic DNA polymorphisms Genome Res 12 2002 602 612
18. N.A. Rosenberg, J.K. Pritchard, J.L. Weber, H.M. Cann, K.K. Kidd, and L.A. Zhivotovsky Genetic structure of human populations Science 298 2002 2381 2385
19. D. Falush, T. With, B. Linz, J.K. Pritchard, M. Stephens, M. Kidd, M.J. Blaser, D.Y. Graham, S. Vacher, and G.I. Perez-Perez Traces of human migrations in H. pylori populations Science 299 2003 1582 1585 This analysis of diversity in Helicobacter pylori distinguishes five ancestral human populations: two in Africa, one in East Asia and two in Europe, with one of the African populations evolving before the others split. Having defined these ancestral gene pools, the authors identify several ancient and modern human migrations, including an early range expansion within Africa, and a complex admixture history for Europe, as well as the colonization of remote Oceania and the Americas. The high phylo-geographic resolution is as good as that provided by mtDNA and Y chromosomes, demonstrating a new and previously unsuspected source of DNA markers for tracking human migrations.
20. P.A. Underhill, P. Shen, A.A. Lin, L. Jin, G. Passarino, W.H. Yang, E. Kauffman, B. Bonné-Tamir, J. Bertranpetit, and P. Francalacci Y chromosome sequence variation and the history of human populations Nat Genet 26 2000 358 361
21. P. Forster Ice ages and the mitochondrial DNA chronology of human dispersals: a review Philos Trans R Soc Lond B Biol Sci 359 2004 255 264
22. M. Ingman, and U. Gyllensten Mitochondrial genome variation and evolutionary history of Australian and New Guinea Aborigines Genome Res 13 2003 1600 1606
23. P. Shen, F. Wang, P.A. Underhill, C. Franco, W.-H. Yang, A. Roxas, R. Sung, A.A. Lin, R.W. Hyman, and D. Vollrath Population genetic implications from sequence variation in four Y chromosome genes Proc Natl Acad Sci USA 97 2000 7354 7359
24. R. Thomson, J.K. Pritchard, P. Shen, P. Oefner, and M.W. Feldman Recent common ancestry of human Y chromosomes: evidence from DNA sequence data Proc Natl Acad Sci USA 97 2000 7360 7365
25. L. Frisse, R.R. Hudson, A. Bartoszewicz, J.D. Wall, J. Donfack, and A. Di Rienzo Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels Am J Hum Genet 69 2001 831 843
26. G. Marth, G. Schuler, R. Yeh, R. Davenport, R. Agarwala, D. Church, S. Wheelan, J. Baker, M. Ward, and M. Kholodov Sequence variations in the public human genome data reflect a bottlenecked population history Proc Natl Acad Sci USA 100 2003 376 381 A good example of the use of multi-locus single nucleotide polymorphism data in a model-based approach. These data provide a strong signal for a population size collapse that the authors identify as the initial modern human colonization of Europe. The addition of a recent phase of mild size recovery makes a modest improvement to the fit of the model.
27. B.J. Hayes, P.M. Visscher, H.C. McPartlan, and M.E. Goddard Novel multilocus measure of linkage disequilibrium to estimate past effective population size Genome Res 13 2003 635 643 A good example of the use of multi-locus haplotypes in a model-based approach. In this study, linkage disequilibrium and chromosome segment homozygosity provide information to detect the recent growth phase in European population size.
28. J. Wakeley, R. Nielsen, S.N. Liu-Cordero, and K. Ardlie The discovery of single-nucleotide polymorphisms - and inferences about human demographic history Am J Hum Genet 69 2001 1332 1347
29. N. Ray, M. Currat, and L. Excoffier Intra-deme molecular diversity in spatially expanding populations Mol Biol Evol 20 2003 76 86 This is a fascinating simulation study that examines the effect of a recent spatial expansion out of a single deme on patterns of molecular diversity. Population structure is modeled as a two-dimensional 50 × 50 stepping-stone lattice. Parameter values are set in order to focus attention on the implications for patterns in mitochondrial DNA of range expansions out of an African source population.
30. L. Excoffier Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite-island model Mol Ecol 13 2004 853 864 Presentation of analytical results for an infinite-island migration model that is well-suited for representing a recent speciation event or recent range expansion out of a substantial bottleneck.
31. R.L. Cann, M. Stoneking, and A.C. Wilson Mitochondrial DNA and human evolution Nature 325 1987 31 36
32. H. Tang, D.O. Siegmund, P. Shen, P.J. Oefner, and M.W. Feldman Frequentist estimation of coalescence times from nucleotide sequence data using a tree-based partition Genetics 161 2002 447 459
33. N. Yu, F.-C. Chen, S. Ota, L.B. Jorde, P. Pamilo, L. Patthy, M. Ramsay, T. Jenkins, S.-K. Shyue, and W.-H. Li Larger genetic differences within Africans than between Africans and Eurasians Genetics 161 2002 269 274
34. C. Lonjou, W. Zhang, A. Collins, W.J. Tapper, E. Elahi, N. Maniatis, and N.E. Morton Linkage disequilibrium in human populations Proc Natl Acad Sci USA 100 2003 6069 6074 Patterns of linkage disequilibrium are found to be consistent with population size reduction ∼173 500 years ago, possibly - but not necessarily - associated with speciation, if the out-of-Africa bottleneck was 100 000 years ago. Assuming 173 500 years to be 7000 generations and a measure of genetic association among founders, an estimate for effective population size as the harmonic mean per generation is 21 600.
35. J. Zhang, W.L. Rowe, A.G. Clark, and K.H. Buetow Genomewide distribution of high-frequency, completely mismatching SNP haplotype pairs observed to be common across human populations Am J Hum Genet 73 2003 1073 1081 This fascinating study describes a pattern of abundant diversity featuring two high-frequency haplotypes marked by different alleles at every single nucleotide polymorphism. 75% to 85% of the human genome could be spanned by these yin yang haplotypes. Drosophila melanogaster reveal a similar pattern.
36. S.E. Ptak, and M. Przeworski Evidence for population growth in humans is confounded by fine-scale population structure Trends Genet 18 2002 559 563
37. M.F. Hammer, F. Blackmer, D. Garrigan, M.W. Nachman, and J.A. Wilder Human population structure and its effects on sampling Y chromosome sequence variation Genetics 164 2003 1495 1509
38. J. Hey, and C.A. Machado The study of structured populations - new hope for a difficult and divided science Nat Rev Genet 4 2003 535 543
39. D. Labuda, E. Ziȩtkiewicz, and V. Yotova Archaic lineages in the history of modern humans Genetics 156 2000 799 808
40. Y. Satta, and N. Takahata The distribution of the ancestral haplotype in finite stepping-stone models with population expansion Mol Ecol 13 2004 877 886 An analysis of why ancestral haplotypes (i.e. least derived from an outgroup sequence) across many loci are present almost exclusively in African samples. The conclusions are that African populations have been more strongly subdivided, and that some were not directly involved in the Late Pleisocene range expansions out of Africa. The model approach taken cannot distinguish between a recent African origin with complete replacement and multiregional evolution.
41. R.M. Harding, S.M. Fullerton, R.C. Griffiths, J. Bond, M.J. Cox, J.A. Schneider, D.S. Moulin, and J.B. Clegg Archaic African and Asian lineages in the genetic ancestry of modern humans Am J Hum Genet 60 1997 772 789
42. E.E. Harris, and J. Hey X chromosome evidence for ancient human histories Proc Natl Acad Sci USA 96 1999 3320 3324
43. Z. Zhao, L. Jin, Y.-X. Fu, M. Ramsay, T. Jenkins, E. Leskinen, P. Pamilo, M. Trexler, L. Patthy, and L.B. Jorde Worldwide DNA sequence variation in a 10-kilobase noncoding region on human chromosome 22 Proc Natl Acad Sci USA 97 2000 11354 11358
44. N. Yu, Z. Zhao, Y.-X. Fu, N. Sambuughin, M. Ramsay, T. Jenkins, E. Leskinen, L. Patthy, L.B. Jorde, T. Kuromori, and W.-H. Li Global patterns of human DNA sequence variation in a 10-kb region on chromosome 1 Mol Biol Evol 18 2001 214 222
45. N. Yu, Y.-X. Fu, and W.-H. Li DNA polymorphism in a worldwide sample of human X chromosomes Mol Biol Evol 19 2002 2131 2141
46. E. Ziȩtkiewicz, V. Yotova, D. Gehl, T. Wambach, I. Arrieta, M. Batzer, D.E.C. Cole, P. Hechtman, F. Kaplan, and D. Modiano Haplotypes in the dystrophin DNA segment point to a mosaic origin of modern human diversity Am J Hum Genet 73 2003 994 1015 This study suggests that not all contemporary human genetic diversity is of recent African origin. One of the subpopulations contributing to haplotype diversity for the dystrophin locus may have been located outside of Africa as much as 160 000 years ago.
47. ST.
48. ST values, possibly reflecting balancing selection.
49. P. Gagneux The genus Pan: population genetics of an endangered outgroup Trends Genet 18 2002 327 330
50. A. Fischer, V. Wiebe, S. Pääbo, and M. Przeworski Evidence for a complex demographic history of chimpanzees Mol Biol Evol 21 2004 799 808 A complex demography is caused by population structure within and between subspecies. DNA sequence variation from nine ∼2 kb intergenic, autosomal regions in 14 central chimpanzees provides an estimate for nucleotide diversity (π) of 0.17. A subset of seven intergenic regions is used to compare diversity between central and western chimpanzees (Table 1). This study shows that diversity estimates depend on geographic sampling of chimpanzees as well as on choice of loci.
51. J.D. Wall, L.A. Frisse, R.R. Hudson, and A. Di Rienzo Comparative linkage-disequilibrium analysis of the β-globin hotspot in primates Am J Hum Genet 73 2003 1330 1340
52. A. Eyre-Walker, P.D. Keightley, N.G. Smith, and D. Gaffney Quantifying the slightly deleterious mutation model of molecular evolution Mol Biol Evol 19 2002 2142 2149
53. N. Yu, M.I. Jensen-Seaman, L. Chemnick, J.R. Kidd, A.S. Deinard, O. Ryder, K.K. Kidd, and W.-H. Li Low nucleotide diversity in chimpanzees and bonobos Genetics 164 2003 1511 1518 This fascinating sequel to Li and Sadler's paper [14] reports levels of nucleotide diversity for chimpanzees (n = 17) that are not much greater than found for humans and lowest levels for bonobos (n = 9). Small, geographically restricted sample sizes might be a factor, but the genomic coverage is the greatest so far for a comparative diversity study.
54. Y. Gilad, C.D. Bustamante, D. Lancet, and S. Pääbo Natural selection on the olfactory receptor gene family in humans and chimpanzees Am J Hum Genet 73 2003 489 501 Selective pressures on the olfactory receptor (OR) genes vary between chimpanzees and humans. Whereas Ka/Ks ratios suggest that purifying selection on chimpanzee OR genes maintains function, human OR genes have accumulated more fixed amino-acid coding differences than expected from polymorphism, suggesting positive selection during divergence history. Relaxation of functional constraint on human OR genes but not on chimpanzee OR genes is unlikely; rather, the evidence implies similar levels of functional constraint across primate species.
55. H. Kaessmann, V. Wiebe, and S. Pääbo Extensive nuclear DNA sequence diversity among chimpanzees Science 286 1999 1159 1162
56. H. Kaessmann, F. Heißig, A. von Haeseler, and S. Pääbo DNA sequence variation in a non-coding region of low recombination on the human X chromosome Nat Genet 22 1999 78 81
57. H. Kaessmann, V. Wiebe, G. Weiss, and S. Pääbo Great ape DNA sequences reveal a reduced diversity and an expansion in humans Nat Genet 27 2001 155 156
58. T. Kitano, C. Schwarz, B. Nickel, and S. Pääbo Gene diversity patterns at 10 X chromosomal loci in humans and chimpanzees Mol Biol Evol 20 2003 1281 1289
59. A.C. Stone, R.C. Griffiths, S.L. Zegura, and M.F. Hammer High levels of Y-chromosome nucleotide diversity in the genus Pan Proc Natl Acad Sci USA 99 2002 43 48
60. Z. Yang Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci Genetics 162 2002 1811 1823
61. F.-C. Chen, and W.-H. Li Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees Am J Hum Genet 68 2001 444 456
62. J.D. Wall Estimating ancestral population sizes and divergence times Genetics 163 2003 395 404
63. D. Caramelli, C. Lalueza-Fox, C. Vernesi, M. Lari, A. Casoli, F. Mallegni, B. Chiarelli, I. Dupanloup, J. Bertranpetit, G. Barbujani, and G. Bertorelle Evidence of a genetic discontinuity between Neandertals and 24,000-year-old anatomically modern Europeans Proc Natl Acad Sci USA 100 2003 6593 6597
64. M. Krings, C. Capelli, F. Tschentscher, H. Geisert, S. Meyer, A. von Haeseler, K. Grossschmidt, G. Possnert, M. Paunovic, and S. Pääbo A view of Neandertal genetic diversity Nat Genet 26 2000 144 146
65. M. Nordborg On the probability of Neanderthal ancestry Am J Hum Genet 63 1998 1237 1240
66. D. Serre, A. Langaney, M. Chech, M. Teschler-Nicola, M. Paunovic, P. Mennecier, M. Hofreiter, G. Possnert, and S. Pääbo No evidence of Neandertal mtDNA contribution to early modern humans PLoS Biology 2 2004 E57
67. A. Cooper, A.J. Drummond, and E. Willerslev Ancient DNA: would the real Neandertal please stand up? Curr Biol 14 2004 R431 R433
68. J.L. Elson, D.M. Turnbull, and N. Howell Comparative genomics and the evolution of human mitochondrial DNA: assessing the effects of selection Am J Hum Genet 74 2004 229 238 Evidence for mainly purifying selection on non-synonymous variation in human mitochondrial DNA is presented, although the data assume that the AT6 gene specifically has been subject to positive selection. Of particular interest is the analysis that compares embedded 'haplogroup associated' single nucleotide polymorphisms from inside the mitochondrial DNA network, with 'private polymorphisms' from the tips. A relative loss from the first set, owing to selective constraint, becomes apparent by comparison with the latter set. A strong signal for the African data contributes to a significant discrepancy. Outside of Africa, where more of the variation is younger, purifying selection is not detectable and probably has been weakened by drift. This analysis does not support a simple model in which climatic adaptation has been a major force during human mitochondrial DNA evolution.
69. M. Hasegawa, Y. Cao, and Z. Yang Preponderance of slightly deleterious polymorphism in mitochondrial DNA: nonsynonymous/synonymous rate ratio is much higher within species than between species Mol Biol Evol 15 1998 1499 1505
70. M.T. Koskinen, T.O. Haugen, and C.R. Primmer Contemporary fisherian life-history evolution in small salmonid populations Nature 419 2002 826 830
71. D.E. Wildman, M. Uddin, G. Liu, L.I. Grossman, and M. Goodman Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: enlarging genus Homo Proc Natl Acad Sci USA 100 2003 7181 7188
72. M.-C. King, and A.C. Wilson Evolution at two levels in humans and chimpanzees Science 188 1975 107 188
73. M.V. Olson, and A. Varki Sequencing the chimpanzee genome: insights into human evolution and disease Nat Rev Genet 4 2003 20 28
74. The International Chimpanzee Chromosome 22 Consortium: DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature 2004, 429:382-388.
75. H.H. Stedman, B.W. Kozyak, A. Nelson, D.M. Thesier, L.T. Su, D.W. Low, C.R. Bridges, J.B. Shrager, N. Minaugh-Purvis, and M.A. Mitchell Myosin gene mutation correlates with anatomical changes in the human lineage Nature 428 2004 415 418 A mutation for gracilization that appeared 2.4 million years ago, predating the appearance of modern human body size and emigration of Homo from Africa. Such studies raise the hope that DNA changes associated with divergence between modern and archaic anatomy may be found in future.
76. W. Enard, M. Przeworski, S.E. Fisher, C.S.L. Lai, V. Wiebe, T. Kitano, A.P. Monaco, and S. Pääbo Molecular evolution of FOXP2, a gene involved in speech and language Nature 418 2002 869 872
77. J. Zhang, D.M. Webb, and O. Podlaha Accelerated protein evolution and origins of human-specific features: FOXP2 as an example Genetics 162 2002 1825 1835
78. J. Zhang Evolution of the human ASPM gene, a major determinant of brain size Genetics 165 2003 2063 2070
79. P.D. Evans, J.R. Anderson, E.J. Vallender, S.L. Gilbert, C.M. Malcolm, S. Dorus, and B.T. Lahn Adaptive evolution of ASPM, a major determinant of cerebral cortical size in humans Hum Mol Genet 13 2004 489 494
80. Y. Wang, and B. Su Molecular evolution of microcephalin, a gene determining brain size Hum Mol Genet 13 2004 1131 1137
81. P.D. Evans, J.R. Anderson, E.J. Vallender, S.S. Choi, and B.T. Lahn Reconstructing the evolutionary history of microcephalin, a gene controlling human brain size Hum Mol Genet 13 2004 1139 1145
82. A.G. Clark, S. Glanowski, R. Nielsen, P.D. Thomas, A. Kejariwal, M.A. Todd, D.M. Tanenbaum, D. Civello, F. Lu, and B. Murphy Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios Science 302 2003 1960 1963
83. A.A. Gimelbrant, H. Skaletsky, and A. Chess Selective pressures on the olfactory receptor repertoire since the human-chimpanzee divergence Proc Natl Acad Sci USA 101 2004 9019 9022