Principal component analysis under population genetic models of range expansion and admixture

Molecular Biology and Evolution

Volumn 27, Issue 6, 2010, Pages 1257-1268

  Franois, Olivier ^a   Currat, Mathias ^b   Ray, Nicolas ^b,c,d   Han, Eunjung ^b   Excoffier, Laurent ^c,d   Novembre, John ^e,f  

^a GRENOBLE INSTITUTE OF TECHNOLOGY   (France)

^b UNIVERSITY OF GENEVA   (Switzerland)

^c UNIVERSITY OF BERN   (Switzerland)

^d SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Admixture; Demic diffusion model; Population structure; Principal component analysis; Range expansion

Indexed keywords

AGRICULTURAL WORKER; ALLELE; ARTICLE; BREEDING; GENE FREQUENCY; GENETIC MODEL; HUMAN; NEOLITHIC; POPULATION GENETICS; PRINCIPAL COMPONENT ANALYSIS; SIMULATION;

ALLELES; COMPUTER SIMULATION; EUROPE; EUROPEAN CONTINENTAL ANCESTRY GROUP; EVOLUTION, MOLECULAR; GENETICS, POPULATION; HUMANS; MODELS, GENETIC; PRINCIPAL COMPONENT ANALYSIS; REGRESSION ANALYSIS;

EID: 77952840471     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msq010     Document Type: Article

References (58)

1. Ammerman AJ, Cavalli-Sforza LL. 1984. The neolithic transition and the genetics of populations in Europe. Princeton (NJ): Princeton University Press.
2. Auton A, Bryc K, Lohmueller KE, et al. (13 co-authors). 2009. Global distribution of genomic diversity underscores rich complex history of continental human populations. Genome Res. 19:795-803.
3. Barbujani G, Sokal RR, Oden NL. 1995. Indo-European origins: a computer-simulation test of five hypotheses. Am J Phys Anthropol. 96:109-132.
4. Barbujani GG, Goldstein DB. 2004. Africans and Asians abroad: genetic diversity in Europe. Annu Rev Genomics Hum Genet. 5:119-150.
5. Barbujani GG, Pilastro A. 1993. Genetic evidence on origin and dispersal of human populations speaking languages of the Nostratic macrofamily. Proc Natl Acad Sci USA. 90:4670-4673.
6. Bauchet M, McEvoy B, Pearson LN, Quillen EE, Sarkisian T, Hovhannesyan K, Deka R, Bradley DG, Shriver MD. 2007. Measuring European population stratification with microarray genotype data. Am J Hum Genet. 80:948-956.
7. Beaumont MA, Rannala B. 2004. The Bayesian revolution in genetics. Nat Rev Genet. 5:251-261.
8. Bramanti B, Thomas MG, Haak W, et al. (16 co-authors). 2009. Genetic discontinuity between local hunter-gatherers and central Europe's first farmers. Science 26(5949):137-140.
9. Burton OJ, Travis JM. 2008. Landscape structure and boundary effects determine the fate of mutations occurring during range expansions. Heredity 101(4):329-340.
10. Cavalli-Sforza LL, Edwards AWF. 1963. Analysis of human evolution. In: Geerts SJ, editor. Genetics today: Proceedings of the 11th International Congress of Genetics, The Hague, The Netherlands. New York: Pergamon. Vol.3. p. 923-993
11. Cavalli-Sforza LL, Menozzi P, Piazza A. 1993. Demic expansions and human evolution. Science 259:639-646.
12. Cavalli-Sforza LL, Menozzi P, Piazza A. 1994. The history and geography of human genes. Princeton (NJ): Princeton University Press.
13. Chen C, Durand E, Forbes F, Franxcois O. 2007. Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison study. Mol Ecol Notes. 7:747-756.
14. Chiaroni J, Underhill PA, Cavalli-Sforza LL. 2009. Y chromosome diversity, human expansion, drift, and cultural evolution. Proc Natl Acad Sci USA. 106:20174-20179.
15. Chikhi L, Destro-Bisol G, Bertorelle G, Pascali V, Barbujani G. 1998. Clines of nuclear DNA markers suggest a recent Neolithic ancestry of the European gene pool. Proc Natl Acad Sci USA. 95:9053-9058.
16. Chikhi L, Nichols RA, Barbujani G, Beaumont MA. 2002. Y genetic data support the Neolithic demic diffusion model. Proc Natl Acad Sci USA. 99:11008-11013.
17. Cressie NAC. 1993. Statistics for spatial data. Wiley, New York.
18. Currat M, Excoffier L. 2004. Modern humans did not admix with Neanderthals during their range expansion into Europe. PLoS Biol. 2:2264-2274.
19. Currat M, Excoffier L. 2005. The effect of the Neolithic expansion on European molecular diversity. Proc R Soc B. 272:679-688.
20. Currat M, Ray N, Excoffier L. 2004. SPLATCHE: a program to simulate genetic diversity taking into account environmental heterogeneity. Mol Ecol Notes. 4(1):139-142.
21. Currat M, Ruedi M, Petit RJ, Excoffier L. 2008. The hidden side of invasions: massive introgression by local genes. Evolution 62:1908-1920.
22. Davies N. 1998. Europe: a history. Harper Perennial, New York.
23. Diamond J, Bellwood P. 2003. Farmers and their languages: the first expansions. Science 300:597-603.
24. Dupanloup I, Bertorelle G, Chikhi L, Barbujani G. 2004. Estimating the impact of prehistoric admixture on the genome of Europeans. Mol Biol Evol 21:1361-1372.
25. Durand E, Jay F, Gaggiotti OE, Franxcois O. 2009. Spatial inference of admixture proportions and secondary contact zones. Mol Biol Evol. 26:1963-1973.
26. Edmonds CA, Lillie AS, Cavalli-Sforza LL. 2004. Mutations arising in the wave front of an expanding population. Proc Natl Acad Sci USA. 101:975-979.
27. Excoffier L, Ray N. 2008. Surfing during population expansions promotes genetic revolutions and structuration. Trends Ecol Evol. 23:347-351.
28. Hallatschek O, Hersen P, Ramanathan S, Nelson DR. 2007. Genetic drift at expanding frontiers promotes gene segregation. Proc Natl Acad Sci USA. 104:19926-19930.
29. Hallatschek O, Nelson DR. 2008. Gene surfing in expanding populations. Theor Popul Biol. 73:158-170.
30. Harpending HC, Jenkins T. 1973. Genetic distance among southern African populations. In: Crawford M, Workman P, editors. Method and theory in anthropological genetics. Albuquerque (NM): University of New Mexico Press.
31. Heath SC, Gut IG, Brennan P, et al. (27 co-authors). 2008. Investigation of the fine structure of European populations with applications to disease association studies. Eur J Hum Genet 16:1413-1429.
32. Hudson RR, Slatkin M, Maddison WP. 1992. Estimation of levels of gene flow from DNA sequence data. Genetics 132(2):583-589.
33. Jakobsson M, Scholz SW, Scheet P, et al. (24 co-authors). 2008. Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451:998-1003.
34. Jobling MA, Hurles ME, Tyler-Smith C. 2004. Human evolutionary genetics: origins, peoples and disease. London: Garland Science Publishing.
35. Klopfstein S, Currat M, Excoffier L. 2006. The fate of mutations surfing on the wave of a range expansion. Mol Biol Evol. 23:482-490.
36. Lao O, Lu TT, Nothnagel M, et al. (33 co-authors). 2008. Correlation between genetic and geographic structure in Europe. Curr Biol. 18:1241-1248.
37. Li JZ, Abscher DM, Tang H, et al. (11 co-authors). 2008. Worldwide human relationships inferred from genome-wide patterns of variation. Science 319:1100-1104.
38. McVean G. 2009. A genealogical interpretation of principal components analysis. PLoS Genet. 5(10):e1000686.
39. Mellars P. 2004. Neanderthals and the modern human colonization of Europe. Nature 432:461-465.
40. Mellars P. 2006. Archeology and the dispersal of modern humans in Europe: deconstructing the "Aurignacian". Evol Anthropol. 15:167-182.
41. Menozzi P, Piazza A, Cavalli-Sforza L. 1978. Synthetic maps of human gene frequencies in Europeans. Science 201:786-792.
42. Novembre J, Johnson T, Bryc K, et al. (12 co-authors). 2008. Genes mirror geography within Europe. Nature 456:98-101.
43. Novembre J, Stephens M. 2008. Interpreting principal components analyses of spatial population genetic variation. Nat Genet. 40:646-649.
44. Patterson NJ, Price AL, Reich D. 2006. Population structure and eigenanalysis. PLoS Genet. 2:e190.
45. Pinhasi R, Fort J, Ammerman AJ. 2005. Tracing the origin and spread of agriculture in Europe. PLoS Biol. 3:e410.
46. Price AL, Helgason A, Palsson S, Stefansson H, St Clair D, Andreassen OA, Reich D, Kong A, Stefansson K. 2009. The impact of divergence time on the nature of population structure: an example from Iceland. PLoS Genet. 5(6):e1000505.
47. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. 2006. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet. 8:904-909.
48. Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
49. Rendine S, Piazza A, Cavalli-Sforza LL. 1986. Simulation and separation by principal components of multiple demic expansions in Europe. Am Nat. 128:681-706.
50. Rosser ZH, Zerjal T, Hurles ME, 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.
51. Rowley-Conwy P. 2009. Human prehistory: hunting for the earliest farmers. Curr Biol. 19:R948-R949.
52. Sabatti C, Service SK, Hartikainen AL, et al. (25 co-authors). 2009. Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. Nat Genet. 41:35-46.
53. Slatkin M. 1993. Isolation-by-distance in equilibrium and non-equilibrium populations. Evolution 47:264-279.
54. Sokal RR, Harding RM, Oden NL. 1989. Spatial patterns of human gene frequencies in Europe. Am J Phys Anthropol. 80:267-294.
55. Sokal RR, Menozzi P. 1982. Spatial autocorrelation of HLA frequencies in Europe support demic diffusion of early farmers. Am Nat. 119:1-17.
56. Sokal RR, Oden NL, Thomson BA. 1999. A problem with synthetic maps. Hum Biol. 71:1-13.
57. Steele J, Adams JM, Sluckin T. 1998. Modeling Paleoindian dispersals. World Archaeol. 30:286-305.
58. Tian C, Plenge RM, Ransom M, et al. (11 co-authors). 2008. Analysis and application of European genetic substructure using 300 K SNP information. PLoS Genet. 4:e4.