Recovering the geographic origin of early modern humans by realistic and spatially explicit simulations

Genome Research

Volumn 15, Issue 8, 2005, Pages 1161-1167

  Ray, Nicolas ^a   Currat, Mathias ^a   Berthier, Pierre ^a   Excoffier, Laurent ^a  

^a UNIVERSITY OF BERN   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

AFRICA; ARTICLE; DEMOGRAPHY; EVOLUTION; GENETIC DATABASE; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GEOGRAPHIC ORIGIN; HUMAN; MULTILOCUS SEQUENCE TYPING; NORTH AFRICA; PRIORITY JOURNAL; SIMULATION; STATISTICAL MODEL;

AFRICA; EUROPE; EVOLUTION; GENETICS, POPULATION; GEOGRAPHY; HUMANS; MODELS, GENETIC; POPULATION DYNAMICS; TANDEM REPEAT SEQUENCES; VARIATION (GENETICS);

EID: 23744491421     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.3708505     Document Type: Article

References (47)

1. Beaumont, M.A., Zhang, W., and Balding, D.J. 2002. Approximate Bayesian computation in population genetics. Genetics 162: 2025-2035.
2. Brauer, G., Collard, M., and Stringer, C. 2004. On the reliability of recent tests of the Out of Africa hypothesis for modern human origins. Anat. Rec. 279A: 701-707.
3. Cavalli-Sforza, L.L. and Feldman, M.W. 2003. The application of molecular genetic approaches to the study of human evolution. Nat. Genet. 33: 266-275.
4. Cavalli-Sforza, L.L., Menozzi, P., and Piazza, A. 1994. The history and geography of human genes. Princeton University Press, Princeton, NJ.
5. Chikhi, L., Nichols, R.A., Barbujani, G., and Beaumont, M.A. 2002. Y genetic data support the Neolithic demic diffusion model. Proc. Natl. Acad. Sci. 99: 11008-11013.
6. Cordaux, R., Deepa, E., Vishwanathan, H., and Stoneking, M. 2004. Genetic evidence for the demic diffusion of agriculture to India. Science 304: 1125.
7. Currat, M. and Excoffier, L. 2004. Modern humans did not admix with Neanderthals during their range expansion into Europe. PLoS Biol. 2: 2264-2274.
8. Currat, M., Ray, N., and Excoffier, L. 2004. SPLATCHE: A program to simulate genetic diversity taking into account environmental heterogeneity. Mol. Ecol. Notes 4: 139-142.
9. Donnelly, P., Tavare, S., Balding, D.J., and Griffiths, R.C. 1996. Estimating the age of the common ancestor of men from the ZFY intron. Science 272: 1357-1359.
10. Excoffier, L. 2002. Human demographic history: Refining the recent African origin model. Curr. Opin. Genet. Dev. 12: 675-682.
11. Gabriel, S.B., Schaffner, S.F., Nguyen, H., Moore, J.M., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M., et al. 2002. The structure of haplotype blocks in the human genome. Science 296: 2225-2229.
12. Gage, T.B. 1998. The comparative demography of primates: With some comments on the evolution of life histories. Annu. Rev. Anthropol. 27: 197-221.
13. Hammer, M.F., Garrigan, D., Wood, E., Wilder, J.A., Mobasher, Z., Bigham, A., Krenz, J.G., and Nachman, M.W. 2004. Heterogeneous patterns of variation among multiple human X-linked loci: The possible role of diversity-reducing selection in non-Africans. Genetics 167: 1841-1853.
14. Harding, R.M. and McVean, G. 2004. A structured ancestral population for the evolution of modern humans. Curr. Opin. Genet. Dev. 14: 667-674.
15. Harpending, H. and Rogers, A. 2000. Genetic perspectives on human origins and differentiation. Ann. Rev. Gen. Hum. Gen. 1: 361-385.
16. Hawks, J., Hunley, K., Lee, S.H., and Wolpoff, M. 2000. Population bottlenecks and Pleistocene human evolution. Mol. Biol. Evol. 17: 2-22.
17. Helgason, A., Hrafnkelsson, B., Gulcher, J.R., Ward, R., and Stefansson, K. 2003. A populationwide coalescent analysis of Icelandic matrilineal and patrilineal genealogies: Evidence for a faster evolutionary rate of mtDNA lineages than Y chromosomes. Am. J. Hum. Genet. 72: 1370-1388.
18. Ingman, M., Kaessmann, H., Paabo, S., and Gyllensten, U. 2000. Mitochondrial genome variation and the origin of modern humans. Nature 408: 708-713.
19. Kaessmann, H. and Paabo, S. 2002. The genetical history of humans and the great apes. J. Intern. Med. 251: 1-18.
20. Marjoram, P., Molitor, J., Plagnol, V., and Tavare, S. 2003. Markov chain Monte Carlo without likelihoods. Proc. Natl. Acad. Sci. 100: 15324-15328.
21. Mellars, P. 2004. Neanderthals and the modern human colonization of Europe. Nature 432: 461-465.
22. Michalakis, Y. and Excoffier, L. 1996. A generic estimation of population subdivision using distances between alleles with special reference for microsatellite loci. Genetics 142: 1061-1064.
23. Pritchard, J., Seielstad, M., Perez-Lezaun, A., and Feldman, M. 1999. Population growth of human Y chromosomes: A study of Y chromosome microsatellites. Mol. Biol. Evol. 16: 1791-1798.
24. Prugnolle, F., Manica, A., and Balloux, F. 2005. Geography predicts neutral genetic diversity of human populations. Curr. Biol. 15: R159-R160.
25. Przeworski, M., Hudson, R.R., and Di Rienzo, A. 2000. Adjusting the focus on human variation. Trends Genet. 16: 296-302.
26. Ray, N. 2003. "Modélisation de la démographie des populations humaines préhistoriques à l'aide de données environnementales et génétiques." Ph.D. thesis, Université de Genève, Geneva, Switzerland.
27. Ray, N., Currat, M., and Excoffier, L. 2003. Intra-deme molecular diversity in spatially expanding populations. Mol. Biol. Evol. 20: 76-86.
28. Rogers, A.R. and Jorde, L.B. 1996. Ascertainment bias in estimates of average heterozygosity. Am. J. Hum. Genet. 58: 1033-1041.
29. Rosenberg, N.A., Pritchard, J.K., Weber, J.L., Cann, H.M., Kidd, K.K., Zhivotovsky, L.A., and Feldman, M.W. 2002. Genetic structure of human populations. Science 298: 2381-2385.
30. Satta, Y. and Takahata, N. 2004. The distribution of the ancestral haplotype in finite stepping-stone models with population expansion. Mol. Ecol. 13: 877-886.
31. Schneider, S., Roessli, D., and Excoffier, L. 2000. Arlequin: A software for population genetics data analysis. User manual ver. 2.000. Genetics and Biometry Lab, Department of Anthropology, University of Geneva, Geneva, Switzerland.
32. Slatkin, M. 1995. A measure of population subdivision based on microsatellite allele frequencies. Genetics 139: 457-462.
33. Steele, J., Adams, J.M., and Sluckin, T. 1998. Modeling Paleoindian dispersals. World Arch. 30: 286-305.
34. Storz, J.F., Payseur, B.A., and Nachman, M.W. 2004. Genome scans of DNA variability in humans reveal evidence for selective sweeps outside of Africa. Mol. Biol. Evol. 21: 1800-1811.
35. Stringer, C. 2002. Modern human origins: Progress and prospects. Phil. Trans. Roy. Soc. London (B) 357: 563-579.
36. Takahata, N., Lee, S.H., and Satta, Y. 2001. Testing multiregionality of modern human origins. Mol. Biol. Evol. 18: 172-183.
37. Templeton, A. 2002. Out of Africa again and again. Nature 416: 45-51.
38. Tishkoff, S.A. and Williams, S.M. 2002. Genetic analysis of African populations: Human evolution and complex disease. Nat. Rev. Genet. 3: 611-621.
39. Tishkoff, S.A., Dietzsch, E., Speed, W., Pakstis, A.J., Kidd, J.R., Cheung, K., Bonne-Tamir, B., Santachiara-Benerecetti, A.S., Moral, P., and Krings, M. 1996. Global patterns of linkage disequilibrium at the CD4 locus and modern human origins. Science 271: 1380-1387.
40. Tremblay, M. and Vezina, H. 2000. New estimates of intergenerational time intervals for the calculation of age and origins of mutations. Am. J. Hum. Genet. 66: 651-658.
41. Vigilant, L., Stoneking, M., Harpending, H., Hawkes, K., and Wilson, A.C. 1991. African populations and the evolution of mitochondrial DNA. Science 253: 1503-1507.
42. Wall, J.D. and Przeworski, M. 2000. When did the human population size start increasing? Genetics 155: 1865-1874.
43. Wen, B., Li, H., Lu, D., Song, X., Zhang, F., He, Y., Li, F., Gao, Y., Mao, X., Zhang, L., et al. 2004. Genetic evidence supports demic diffusion of Han culture. Nature 431: 302-305.
44. White, T.D., Asfaw, B., DeGusta, D., Gilbert, H., Richards, G.D., Suwa, G., and Howell, F.C. 2003. Pleistocene Homo sapiens from Middle Awash, Ethiopia. Nature 423: 742-747.
45. Wolpoff, M.H. 1989. Multiregional evolution: The fossil alternative to Eden. In The human revolution: Biological perspectives in the origins of modern humans (eds. P. Mellars and C. Stringer), pp. 62-108. Princeton University Press, Princeton, NJ.
46. Wolpoff, M.H., Hawks, J., and Caspari, R. 2000. Multiregional, not multiple origins. Am. J. Phys. Anthrop. 112: 129-136.
47. Yu, N., Zhao, Z., Fu, Y.X., Sambuughin, N., Ramsay, M., Jenkins, T., Leskinen, E., Patthy, L., Jorde, L.B., Kuromori, T., et al. 2001. Global patterns of human DNA sequence variation in a 10-kb region on chromosome 1. Mol. Biol. Evol. 18: 214-222.