The Geography of Recent Genetic Ancestry across Europe

PLoS Biology

Volumn 11, Issue 5, 2013, Pages

  Ralph, Peter ^a,b   Coop, Graham ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AGE; ARTICLE; CAUCASIAN; CONSANGUINITY; ETHNIC GROUP; EUROPE; GENEALOGY; GENETIC ANCESTOR; GENOMICS; GEOGRAPHY; HUMAN; HUNNIC; ITALY; MIGRATION; ORGANISMS BY PHYLOGENETIC POSITION; POPULATION GENETICS; SLAVIC; SPAIN;

EUROPE; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENEALOGY AND HERALDRY; GENETIC VARIATION; GENETICS, POPULATION; GEOGRAPHY; HUMANS; PHYLOGENY; POPULATION DYNAMICS;

EID: 84878314759     PISSN: 15449173     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.1001555     Document Type: Article

References (75)

1. Cann RL, Stoneking M, Wilson AC, (1987) Mitochondrial DNA and human evolution. Nature 325: 31-36.
2. Takahata N, (1993) Allelic genealogy and human evolution. Molecular Biology and Evolution 10: 2-22.
3. Li H, Durbin R, (2011) Inference of human population history from individual whole-genome sequences. Nature 475: 493-496.
4. Moorjani P, Patterson N, Hirschhorn JN, Keinan A, Hao L, et al. (2011) The history of African gene flow into Southern Europeans, Levantines, and Jews. PLoS Genet 7: e1001373 doi:10.1371/journal.pgen.1001373.
5. Henn BM, Botigué LR, Gravel S, Wang W, Brisbin A, et al. (2012) Genomic ancestry of North Africans supports back-to-Africa migrations. PLoS Genet 8: e1002397 doi:10.1371/journal.pgen.1002397.
6. Chang J, (1999) Recent common ancestors of all present-day individuals. Advances in Applied Probability 31: 1002-1026.
7. Rohde DLT, Olson S, Chang JT, (2004) Modelling the recent common ancestry of all living humans. Nature 431: 562-566.
8. Donnelly KP, (1983) The probability that related individuals share some section of genome identical by descent. Theor Popul Biol 23: 34-63.
9. Gillett A, (2006) Ethnogenesis: a contested model of early medieval Europe. History Compass 4: 241-260.
10. Soares P, Achilli A, Semino O, Davies W, Macaulay V, et al. (2010) The archaeogenetics of Europe. Curr Biol 20: 174-183.
11. Novembre J, Ramachandran S, (2011) Perspectives on human population structure at the cusp of the sequencing era. Annu Rev Genomics Hum Genet 12: 245-274.
12. Menozzi P, Piazza A, Cavalli-Sforza L, (1978) Synthetic maps of human gene frequencies in Europeans. Science 201: 786-792.
13. Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, et al. (2008) Genes mirror geography within Europe. Nature 456: 98-101.
14. Lao O, Lu TT, Nothnagel M, Junge O, Freitag-Wolf S, et al. (2008) Correlation between genetic and geographic structure in Europe. Curr Biol 18: 1241-1248.
15. Novembre J, Stephens M, (2008) Interpreting principal component analyses of spatial population genetic variation. Nat Genet 40: 646-649.
16. Auton A, Bryc K, Boyko AR, Lohmueller KE, Novembre J, et al. (2009) Global distribution of genomic diversity underscores rich complex history of continental human populations. Genome Res 19: 795-803.
17. Nelson MR, Wegmann D, Ehm MG, Kessner D, St Jean P, et al. (2012) An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science 337 (6090) (): 100-104.
18. O'Dushlaine CT, Morris D, Moskvina V, Kirov G, (2010) International Schizophrenia Consortium, (2010) et al. Population structure and genome-wide patterns of variation in Ireland and Britain. Eur J Hum Genet 18: 1248-1254.
19. Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, et al. (2012) Ancient admixture in human history. Genetics 192: 1065-1093.
20. Skoglund P, Malmström H, Raghavan M, Storá J, Hall P, et al. (2012) Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe. Science 336: 466-469.
21. Keller A, Graefen A, Ball M, Matzas M, Boisguerin V, et al. (2012) New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing. Nat Commun 3: 698-698.
22. Lawson DJ, Hellenthal G, Myers S, Falush D, (2012) Inference of population structure using dense haplotype data. PLoS Genet 8: e1002453 doi: 10.1371/journal.pgen.1002453.
23. Palamara PF, Lencz T, Darvasi A, Pe'er I, (2012) Length distributions of identity by descent reveal fine-scale demographic history. Am J Hum Genet 91 (5) (): 809-822.
24. Harris K, Nielsen R, (in press) Inferring demographic history from a spectrum of shared haplotype lengths. PLoS Genetics.
25. Pool JE, Nielsen R, (2009) Inference of historical changes in migration rate from the lengths of migrant tracts. Genetics 181: 711-719.
26. Gravel S, (2012) Population genetics models of local ancestry. Genetics 191: 607-619.
27. Fisher RA, (1954) A fuller theory of 'Junctions' in inbreeding. Heredity 8: 187-197.
28. Chapman NH, Thompson EA, (2002) The effect of population history on the lengths of ancestral chromosome segments. Genetics 162: 449-458.
29. Powell JE, Visscher PM, Goddard ME, (2010) Reconciling the analysis of IBD and IBS in complex trait studies. Nat Rev Genet 11: 800-805.
30. Brown MD, Glazner CG, Zheng C, Thompson EA, (2012) Inferring coancestry in population samples in the presence of linkage disequilibrium. Genetics 190 (4) (): 1447-1460.
31. Browning BL, Browning SR, (2011) A fast, powerful method for detecting identity by descent. American Journal of Human Genetics 88: 173-182.
32. Gusev, Lowe JK, Stoffel M, Daly MJ, Altshuler D, et al. (2009) Whole population, genome-wide mapping of hidden relatedness. Genome Res 19: 318-326.
33. Hudson R, (1990) Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology 7: 44.
34. Nelson MR, Bryc K, King KS, Indap A, Boyko AR, et al. (2008) The Population Reference Sample, POPRES: a resource for population, disease, and pharmacological genetics research. Am J Hum Genet 83: 347-358.
35. Albrechtsen A, Moltke I, Nielsen R, (2010) Natural selection and the distribution of identity-bydescent in the human genome. Genetics 186: 295-308.
36. Giglio S, Broman KW, Matsumoto N, Calvari V, Gimelli G, et al. (2001) Olfactory receptor-gene clusters, genomic-inversion polymorphisms, and common chromosome rearrangements. Am J Hum Genet 68: 874-883.
37. Gusev A, Palamara PF, Aponte G, Zhuang Z, Darvasi A, et al. (2012) The architecture of longrange haplotypes shared within and across populations. Molecular Biology and Evolution 29: 473-486.
38. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38: 904-909.
39. Fenner JN, (2005) Cross-cultural estimation of the human generation interval for use in geneticsbased population divergence studies. American Journal of Physical Anthropology 128: 415-423.
40. Petrov Y, Sizikov V, (2005) Well-posed, ill-posed, and intermediate problems with applications, volume 49. Walter de Gruyter.
41. Malécot G (1969) The mathematics of heredity. Freeman. Translated from the French edition, 1948.
42. Slatkin M, (1991) Inbreeding coefficients and coalescence times. Genet Res 58: 167-175.
43. Rousset F, (2002) Inbreeding and relatedness coefficients: what do they measure? Heredity 88: 371-380.
44. McVean G, (2009) A genealogical interpretation of principal components analysis. PLoS Genet 5: e1000686 doi:10.1371/journal.pgen.1000686.
45. Price AL, Helgason A, Palsson S, Stefansson H, St Clair D, et al. (2009) The impact of divergence time on the nature of population structure: an example from Iceland. PLoS Genet 5: e1000505 doi:10.1371/journal.pgen.1000505.
46. Jakkula E, Rehnström K, Varilo T, Pietiläinen OP, Paunio T, et al. (2008) The genome-wide patterns of variation expose significant substructure in a founder population. Am J Hum Genet 83: 787-794.
47. Tyler-Smith C, Xue Y, (2012) A British approach to sampling. Eur J Hum Genet 20: 129-130.
48. Winney B, Boumertit A, Day T, Davison D, Echeta C, et al. (2011) People of the British Isles: preliminary analysis of genotypes and surnames in a UK-control population. Eur J Hum Genet 20 (2) (): 203-210.
49. Huff CD, Witherspoon DJ, Simonson TS, Xing J, Watkins WS, et al. (2011) Maximum-likelihood estimation of recent shared ancestry (ERSA). Genome Res 21: 768-774.
50. Henn BM, Hon L, Macpherson JM, Eriksson N, Saxonov S, et al. (2012) Cryptic distant relatives are common in both isolated and cosmopolitan genetic samples. PLoS ONE 7: e34267 doi:10.1371/journal.pone.0034267.
51. Davies N (2010) Europe: A history. Random House.
52. Barford P (2001) The early Slavs: culture and society in early medieval Eastern Europe. Ithaca, NY: Cornell University Press.
53. Hamp E (1966) The position of Albanian. In Ancient Indo-European Dialects, pp. 97-121.
54. Halsall G (2005) The Barbarian invasions. In: Fouracre P, editor, The New Cambridge Medieval History, Cambridge University Press, number v. 1 in The New Cambridge Medieval History, chapter 2. pp. 38-55.
55. Kobyliński Z (2005) The Slavs. In: Fouracre P, editor, The New Cambridge Medieval History, Cambridge University Press, number v. 1 in The New Cambridge Medieval History, chapter 19. pp. 524-544.
56. Tennessen JA, Bigham AW, O'Connor TD, Fu W, Kenny EE, et al. (2012) Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 337 (6090) (): 64-69.
57. Patterson N, Price AL, Reich D, (2006) Population structure and eigenanalysis. PLoS Genet 2: e190 doi:10.1371/journal.pgen.0020190.
58. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81: 559-575.
59. R Development Core Team (2012) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Available at http://www.R-project.org/. ISBN 3-900051-07-0.
60. Zeileis A, Hornik K, Murrell P, (2009) Escaping RGBland: selecting colors for statistical graphics. Computational Statistics & Data Analysis 53 (9) (): 3259-3270.
61. Plate T (2011) RSVGTipsDevice: an R SVG graphics device with dynamic tips and hyperlinks. URL http://CRAN.R-project.org/package=RSVGTipsDevice. R package version 1.0-2, based on RSvgDevice by T Jake Luciani.
62. Ralph P, Coop G (2013). Data from: the geography of recent genetic ancestry across Europe. Available at http://dx.doi.org/10.5061/dryad.57kc5.
63. International HapMap Consortium (2007) Frazer KA, Ballinger DG, Cox DR, Hinds DA, et al. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851-861.
64. McCullagh P, Nelder J (1989) Generalized Linear Models, Second Edition. Chapman and Hall/CRC Monographs on Statistics and Applied Probability Series. Chapman & Hall.
65. Carmi S, Palamara PF, Vacic V, Lencz T, Darvasi A, et al. (2012) The variance of identity-bydescent sharing in the Wright-Fisher model. Genetics 193: 911-928.
66. Kingman JFC, (1982) On the genealogy of large populations. Journal of Applied Probability 19: 27-43.
67. Wakeley J (2005) Coalescent theory, an introduction. Greenwood Village, CO: Roberts and Company.
68. Grimmett G, Stirzaker D (2001) Probability and random processes. New York: Oxford University Press.
69. Epstein CL, Schotland J, (2008) The bad truth about Laplace's transform. SIAM Review 50: 504-520.
70. Stuart AM, (2010) Inverse problems: a Bayesian perspective. Acta Numer 19: 451-559.
71. Cowan G (1998) Statistical data analysis. New York: Oxford University Press.
72. Tikhonov AN, Arsenin VY (1977) Solutions of ill-posed problems. Washington, DC: John Wiley & Sons, New York: V. H. Winston & Sons, xiii+258 pp.
73. Hoerl AE, Kennard RW, (1970) Ridge regression: biased estimation for nonorthogonal problems. Technometrics 12: 55-67.
74. Edwards A (1984) Likelihood. Cambridge Science Classics. New York: Cambridge University Press.
75. Turlach BA, Weingessel A (2011) quadprog: functions to solve Quadratic programming problems. Available at http://CRAN.R-project.org/package=quadprog.