Estimating the impact of prehistoric admixture on the genome of Europeans

Molecular Biology and Evolution

Volumn 21, Issue 7, 2004, Pages 1361-1372

  Dupanloup, Isabelle ^a,c   Bertorelle, Giorgio ^a   Chikhi, Lounès ^b   Barbujani, Guido ^a  

^a UNIVERSITY OF FERRARA   (Italy)

^b École Nationale de Formation Agronomique   (France)

^c UNIVERSITY OF LAUSANNE   (Switzerland)

Author keywords

Admixture; Europe; Human populations; Neolithic; Paleolithic

Indexed keywords

ARTICLE; CORRELATION COEFFICIENT; DEMOGRAPHY; EUROPE; GENE POOL; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOME ANALYSIS; GEOGRAPHIC DISTRIBUTION; HYBRIDIZATION; MITOCHONDRION; MOLECULAR MODEL; NONHUMAN; POPULATION; PREDICTION;

CHROMOSOMES, HUMAN, Y; DNA, MITOCHONDRIAL; ETHNIC GROUPS; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENETICS, POPULATION; GENOME, HUMAN; HUMANS;

EID: 3042648025     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msh135     Document Type: Article

References (66)

1. Ammerman, A. J., and L. L. Cavalli-Sforza. 1984. The Neolithic transition and the genetics of populations in Europe. Princeton University Press, Princeton.
2. Barbujani, G. 1997. DNA variation and language affinities. Am. J. Hum. Genet. 61:1011-1014.
3. Barbujani, G., and G. Bertorelle. 2001. Genetics and the population history of Europe. Proc. Natl. Acad. Sci. USA 98:22-25.
4. Barbujani, G., G. Bertorelle, and L. Chikhi. 1998. Evidence for Paleolithic and Neolithic gene flow in Europe. Am. J. Hum. Genet. 62:488-492.
5. Barbujani, G., A. Pilastro, S. De Domenico, and C. Renfrew. 1994. Genetic variation in North Africa and Eurasia: Neolithic demic diffusion vs. Paleolithic colonisation. Am. J. Phys. Anthropol. 95:137-154.
6. Barbujani, G., R. R. Sokal, and N. L. Oden. 1995. Indo-European origins: a computer-simulation test of five hypotheses. Am. J. Phys. Anthropol. 96:109-132.
7. Bertorelle, G., and L. Excoffier. 1998. Inferring admixture proportions from molecular data. Mol. Biol. Evol. 15:1298-1311.
8. Bertranpetit, J., and L. L. Cavalli-Sforza. 1991. A genetic reconstruction of the history of the population of the Iberian Peninsula. Ann. Hum. Genet. 55:51-56.
9. Bertranpetit, J., J. Sala, F. Calafell, P. A. Underhill, P. Moral, and D. Comas. 1995. Human mitochondrial DNA variation and the origin of Basques. Ann. Hum. Genet. 59:63-81.
10. Bosch, E., F. Calafell, D. Comas, P. J. Oefner, P. A. Underhill, and J. Bertranpetit. 2001. High-resolution analysis of human Y-chromosome variation shows a sharp discontinuity and limited gene flow between northwestern Africa and the Iberian Peninsula. Am. J. Hum. Genet. 68:1019-1029.
11. Caramelli, D., C. Lalueza-Fox, C. Vemesi, M. Lari, A. Casoli, F. Mallegni, B. Chiarelli, I. Dupanloup, J. Bertranpetit, G. Barbujani, and G. Bertorelle. 2003. Evidence for a genetic discontinuity between Neandertals and 24,000-year-old anatomically modem Europeans. Proc. Natl. Acad. Sci. USA 100:6593-6597.
12. Cavalli-Sforza, L. L., and W. F. Bodmer. 1971. The genetics of human populations. W.H. Freeman and Company, San Francisco, Calif.
13. Cavalli-Sforza, L. L., P. Menozzi, and A. Piazza. 1993. Demic expansions and human evolution. Science 259:639-646.
14. Cavalli-Sforza, L. L., and A. Piazza. 1993. Human genomic diversity in Europe: a summary of recent research and prospects for the future. Eur. J. Hum. Genet. 1:3-18.
15. Chakraborty, R. 1986. Gene admixture in human populations: models and predictions. Yearb. Phys. Anthropol. 29:1-43.
16. Chikhi, L., G. Destro-Bisol, G. Bertorelle, V. Pascali, and G. Barbujani. 1998. Clines of nuclear DNA markers suggest a largely Neolithic ancestry of the European gene pool. Proc. Natl. Acad. Sci. USA 95:9053-9058.
17. Chikhi, L., R. A. Nichols, G. Barbujani, and M. A. Beaumont. 2002. Y genetic data support the Neolithic demic diffusion model. Proc. Natl. Acad. Sci. USA 99:10008-10013.
18. Dupanloup, I., and G. Bertorelle. 2001. Inferring admixture proportions from molecular data: extension to any number of parental populations. Mol. Biol. Evol. 18:672-675.
19. Dupanloup, I., L. Pereira, G. Bertorelle, F. Calafell, M. J. Prata, A. Amorim, and G. Barbujani. 2003. A recent shift from polygyny to monogamy in humans is suggested by the analysis of worldwide Y-chromosome diversity. J. Mol. Evol. 57:85-97.
20. Edwards, S. V., and P. Beerli. 2000. Gene divergence, population divergence, and the variance in coalescence times in phylogeographic studies. Evolution 54:1839-1854.
21. Efron, B. 1982. The jacknife, the bootstrap and other resampling plans. Regional Conference Series in Applied Mathematics, Society for Industrial and Applied Mathematics, Philadelphia.
22. Estivill, X., C. Bancells, and C. Ramos. 1997. Geographic distribution and regional origin of 272 cystic fibrosis mutations in European populations. The Biomed CF Mutation Analysis Consortium. Hum. Mutat. 10:135-154.
23. Excoffier, L., and S. Schneider. 1999. Why hunter-gatherer populations do not show signs of Pleistocene demographic expansions. Proc. Natl. Acad. Sci. USA 96:10597-10602.
24. Excoffier, L., P. Smouse, and J. M. Quattro. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479-491.
25. Goldstein, D. B., and L. Chikhi. 2002. Human migration and population structure: what we know and why it matters. Annu. Rev. Genom. Hum. Genet. 3:129-152.
26. Hammer, M. F. 1995. A recent common ancestry for human Y chromosomes. Nature 378:376-378.
27. Harris, E. E., and J. Hey. 1999. Human demography in the Pleistocene: do mitochondrial and nuclear genes tell the same story? Evol. Anthropol. 8:81-86.
28. Holtkemper, U., B. Rolf, C. Hohoff, P. Forster, and B. Brinkmann. 2001. Mutation rates at two human Y-chromosomal microsatellite loci using small pool PCR techniques. Hum. Mol. Genet. 10:629-633.
29. Jobling, M. A., A. Pandya, and C. Tyler-Smith. 1997. The Y chromosome in forensic analysis and paternity testing. Int. J. Legal Med. 110:118-124.
30. Jobling, M. A., and C. Tyler-Smith. 2000. New uses for new haplotypes. The human Y chromosome, disease and selection. Trends. Genet. 16:356-362.
31. Krings, M., C. Capelli, F. Tschentscher, H. Geisert, S. Meyer, A. von Haeseler, K. Grossschmidt, G. Possnert, M. Paunovic, and S. Pääbo. 2000. A view of Neandertal genetic diversity. Nature Genet. 26:144-146.
32. Luikart, G., P. R. England, D. Tallmon, S. Jordan, and P. Taberlet. 2003. The power and promise of population genomics: From genotyping to genome typing. Nature Rev. Genet. 4:981-994.
33. Macaulay, V., M. Richards, E. Hickey, E. Vega, F. Cruciani, V. Guida, R. Scozzari, B. Bonne-Tamir, B. Sykes, and A. Torroni. 1999. The emerging tree of West Eurasian mtDNAs: a synthesis of control-region sequences and RFLPs. Am. J. Hum. Genet. 64:232-249.
34. Menozzi, P., A. Piazza, and L. L. Cavalli-Sforza. 1978. Synthetic maps of human gene frequencies in Europeans. Science 201:786-792 .
35. Mishmar, D., E. Ruiz-Pesini, P. Golik et al. (13 co-authors). 2003. Natural selection shaped regional mtDNA variation in humans. Proc. Natl. Acad. Sci. USA 100:171-176.
36. Nichols, R. 2001. Gene trees and species trees are not the same. Trends Ecol. Evol. 16:358-364.
37. Otte, M. 2000. The history of European populations as seen by archaeology. Pp 41-44 in C. Renfrew and H. Boyle, eds. Archaeogenetics: DNA and the population prehistory of Europe. McDonald Institute for Archaeological Research, Cambridge.
38. Pääbo, S. 1999. Human evolution. Trends. Cell. Biol. 9:13-16.
39. Pinhasi, R., R. A. Foley, and M. Mirazòn Lahr. 2000. Spatial and temporal patterns in the Mesolithic-Neolithic archaeological record of Europe. Pp 45-56 in C. Renfrew and H. Boyle, eds. Archaeogenetics: DNA and the population prehistory of Europe. McDonald Institute for Archaeological Research, Cambridge.
40. Rando, J. C., F. Pinto, A. M. Gonzalez, M. Hernandez, J. M. Larruga, V. M. Cabrera, and H. J. Bandelt. 1998. Mitochondrial DNA analysis of northwest African populations reveals genetic exchanges with European, near-eastern, and sub-Saharan populations. Ann. Hum. Genet. 62:531-550.
41. Relethford, J. A. 2001. Absence of regional affinities of Neandertal DNA with living humans does not reject multiregional evolution. Am. J. Phys. Anthropol. 115:95-98.
42. Renfrew, C. 1987. Archaeology and language: the puzzle of Indo-European origins. Jonathan Cape, London.
43. Richards, M., H. Corte-Real, P. Forster, V. Macaulay, H. Wilkinson-Herbots, A. Demaine, S. Papiha, R. Hedges, H. J. Bandelt, and B. Sykes. 1996. Paleolithic and neolithic lineages in the European mitochondrial gene pool. Am. J. Hum. Genet. 59:185-203.
44. Richards, M., V. Macaulay, E. Hickey et al. (34 co-authors). 2000. Tracing European founder lineages in the Near Eastern mtDNA pool. Am. J. Hum. Genet. 67:1251-1276.
45. Richards, M., V. Macaulay, A. Torroni, and H. J. Bandelt. 2002. In search of geographical patterns in European mitochondrial DNA. Am. J. Hum. Genet. 71:1168-1174.
46. Romualdi, C., D. Balding, I. S. Nasidze, G. Risch, M. Robichaux, S. T. Sherry, M. Stoneking, M. A. Batzer, and G. Barbujani. 2002. Patterns of human diversity, within and among continents, inferred from biallelic DNA polymorphisms. Genome Res. 12:602-612.
47. Rosenberg, N. A., J. K. Pritchard, J. L. Weber, H. M. Cann, K. K. Kidd, L. A. Zhivotovsky, and M. W. Feldman. 2002. Genetic structure of human populations. Science 298:2381-2385.
48. Rosser, Z. H., T. Zerjal, M. E. Hurles et al. (63 co-authors). 2000. Y-chromosomal diversity in Europe is clinal and influenced primarily by geography, rather than by language. Am. J. Hum. Genet. 67:1526-1543.
49. Sajantila, A., P. Lahermo, T. Anttinen et al. (13 co-authors). 1995. Genes and languages in Europe: an analysis of mitochondrial lineages. Genome Res. 5:42-52.
50. Seielstad, M. T., E. Minch, and L. L. Cavalli-Sforza. 1998. Genetic evidence for a higher female migration rate in humans. Nat. Genet. 20:278-280.
51. Semino, O., G. Passarino, A. Brega, M. Fellous, and S. Santachiara-Benerecetti. 1996. A view of the Neolithic demic diffusion in Europe through two Y chromosome-specific markers. Am. J. Hum. Genet. 59:964-968.
52. Semino, O., G. Passarino, P. J. Oefner et al. (17 co-authors). 2000. The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perspective. Science 290:1155-1159.
53. Simoni, L., F. Calafell, D. Pettener, J. Bertranpetit, and G. Barbujani. 2000. Geographic patterns of mtDNA diversity in Europe. Am. J. Hum. Genet. 66:262-278.
54. Simoni, L., P. Gueresi, D. Pettener, and G. Barbujani. 1999. Patterns of gene flow inferred from genetic distances in the Mediterranean region. Hum. Biol. 71:399-415.
55. Sokal, R. R., N. L. Oden, M. S. Rosenberg, and D. DiGiovanni. 1997. Ethnohistory, genetics, and cancer mortality in Europeans. Proc. Natl. Acad. Sci. USA 94:12728-12731.
56. Sokal, R. R., N. L. Oden, and C. Wilson. 1991. Genetic evidence for the spread of agriculture in Europe by demic diffusion. Nature 351:143-145.
57. Sokal, R. R., and F. J. 1995. Biometry. W. H. Freeman and Company, New York.
58. Stringer, C. 2003. Out of Ethiopia. Nature 423:692-694.
59. Stumpf, M. P., and D. B. Goldstein. 2001. Genealogical and evolutionary inference with the human Y chromosome. Science 291:1738-1742.
60. Terwilliger, J. D., S. Zollner, M. Laan, and S. Pääbo. 1998. Mapping genes through the use of linkage disequilibrium generated by genetic drift: 'Drift mapping' in small populations with no demographic expansion. Hum. Hered. 48: 138-154.
61. Torroni, A., H. J. Bandelt, V. Macaulay et al. (33 co-authors). 2001. A signal, from human mtDNA, of postglacial recolonization in Europe. Am. J. Hum. Genet. 69:844-852.
62. Underhill, P. A., P. Shen, A. A. Lin et al. (24 co-authors). 2000. Y chromosome sequence variation and the history of human populations. Nat. Genet. 26:358-361.
63. Vemesi, C., S. Fuselli, L. Castri, G. Bertorelle, and G. Barbujani. 2002. Mitochondrial diversity in linguistic isolates of the Alps: a reappraisal. Hum. Biol. 74:725-730.
64. Wilson, J. F., D. A. Weiss, M. Richards, M. G. Thomas, N. Bradman, and D. B. Goldstein 2001. Genetic evidence for different male and female roles during cultural transitions in the British Isles. Proc. Natl. Acad. Sci. USA 98:5078-5083.
65. Wiuf, C. 2001. Do AF508 heterozygotes have a selective advantage? Genet. Res. 78:41-47.
66. Zvelebil, M. 1986. Mesolithic prelude and Neolithic revolution. Pp 5-16 in M. Zvelebil, ed. Hunters in transition: Mesolithic societies of temperate Eurasia and their transition to farming. Cambridge University Press, Cambridge.