Inferring admixture histories of human populations using linkage disequilibrium

Genetics

Volumn 193, Issue 4, 2013, Pages 1233-1254

  Loh, Po Ru ^a   Lipson, Mark ^a   Patterson, Nick ^b   Moorjani, Priya ^b,c   Pickrell, Joseph K ^c   Reich, David ^b,c   Berger, Bonnie ^a,b  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; CHROMOSOME; COMPUTER PROGRAM; ETHNICITY; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC ADMIXTURE; HAPLOTYPE; HUMAN; HUMAN GENOME PROJECT; JAPANESE; PHYLOGENY; POPULATION GENETICS; POPULATION STRUCTURE; PRIORITY JOURNAL; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGICAL MODEL; CENTRAL AFRICA; GENETICS; ITALY; JAPAN; MIGRATION; POPULATION; POPULATION GROUP;

AFRICA, CENTRAL; HUMAN MIGRATION; HUMANS; ITALY; JAPAN; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; PHYLOGENY; POPULATION; POPULATION GROUPS; SOFTWARE;

EID: 84876362318     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.112.147330     Document Type: Article

References (45)

1. Bramanti, B., M. Thomas, W. Haak, M. Unterlaender, P. Jores et al., 2009 Genetic discontinuity between local hunter-gatherers and Central Europe's first farmers. Science 326 (5949): 137-140.
2. Chakraborty, R., and K. Weiss, 1988 Admixture as a tool for finding linked genes and detecting that difference from allelic association between loci. Proc. Natl. Acad. Sci. USA 85(23): 9119-9123.
3. Chen, G., P. Marjoram, and J. Wall, 2009 Fast and flexible simulation of DNA sequence data. Genome Res. 19(1): 136-142.
4. Chikhi, L., M. Bruford, and M. Beaumont, 2001 Estimation of admixture proportions: a likelihood-based approach using Markov chain Monte Carlo. Genetics 158: 1347-1362.
5. Davies, R., 1977 Hypothesis testing when a nuisance parameter is present only under the alternative. Biometrika 64(2): 247-254.
6. Dupanloup, I., G. Bertorelle, L. Chikhi, and G. Barbujani, 2004 Estimating the impact of prehistoric admixture on the genome of Europeans. Mol. Biol. Evol. 21(7): 1361-1372.
7. Gravel, S., 2012 Population genetics models of local ancestry. Genetics 191: 607-619.
8. Gravel, S., B. Henn, R. Gutenkunst, A. Indap, G. Marth et al., 2011 Demographic history and rare allele sharing among human populations. Proc. Natl. Acad. Sci. USA 108(29): 11983-11988.
9. Green, R., J. Krause, A. Briggs, T. Maricic, U. Stenzel et al., 2010 A draft sequence of the Neandertal genome. Science 328(5979): 710-722.
10. Hammer, M., and S. Horai, 1995 Y chromosomal DNA variation and the peopling of Japan. Am. J. Hum. Genet. 56(4): 951-962.
11. Hammer, M., T. Karafet, H. Park, K. Omoto, S. Harihara et al., 2006 Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes. J. Hum. Genet.51(1): 47-58.
12. International HapMap Consortium, 2007 A second generation human haplotype map of over 3.1 million SNPs. Nature 449 (7164): 851-861.
13. International HapMap Consortium, 2010 Integrating common and rare genetic variation in diverse human populations. Nature 467(7311): 52-58.
14. Jarvis, J., L. Scheinfeldt, S. Soi, C. Lambert, L. Omberg et al., 2012 Patterns of ancestry, signatures of natural selection, and genetic association with stature in western African Pygmies. PLoS Genet. 8(4): e1002641.
15. Laval, G., E. Patin, L. Barreiro, and L. Quintana-Murci, 2010 Formulating a historical and demographic model of recent human evolution based on resequencing data from noncoding regions. PLoS ONE 5(4): e10284.
16. Lawson, D., G. Hellenthal, S. Myers, and D. Falush, 2012 Inference of population structure using dense haplotype data. PLoS Genet. 8(1): e1002453.
17. Li, J., D. Absher, H. Tang, A. Southwick, A. Casto et al., 2008 Worldwide human relationships inferred from genomewide patterns of variation. Science 319(5866): 1100-1104.
18. Lipson, M., P. Loh, A. Levin, D. Reich, N. Patterson et al., 2012 Efficient moment-based inference of admixture parameters and sources of gene flow, arXiv arXiv:1212.2555 (in press).
19. Moorjani, P., N. Patterson, J. Hirschhorn, A. Keinan, L. Hao et al., 2011 The history of African gene flow into Southern Europeans, Levantines, and Jews. PLoS Genet. 7(4): e1001373.
20. Moorjani, P., N. Patterson, P. Loh, M. Lipson, P. Kisfali et al., 2012 Reconstructing Roma history from genome-wide data., arXiv arXiv:1212.1696 (in press).
21. Ohta, T., and M. Kimura, 1971 Linkage disequilibrium between two segregating nucleotide sites under the steady flux of mutations in a finite population. Genetics 68: 571-580.
22. Patin, E., G. Laval, L. Barreiro, A. Salas, O. Semino et al., 2009 Inferring the demographic history of African farmers and Pygmy hunter-gatherers using a multilocus resequencing data set. PLoS Genet. 5(4): e1000448.
23. Patterson, N., N. Hattangadi, B. Lane, K. Lohmueller, D. Hafler et al., 2004 Methods for high-density admixture mapping of disease genes. Am. J. Hum. Genet. 74(5): 979-1000.
24. Patterson, N., A. Price, and D. Reich, 2006 Population structure and eigenanalysis. PLoS Genet. 2(12): e190.
25. Patterson, N., P. Moorjani, Y. Luo, S. Mallick, N. Rohland et al., 2012 Ancient admixture in human history. Genetics 192: 1065-1093.
26. Pickrell, J., and J. Pritchard, 2012 Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8(11): e1002967.
27. Pickrell, J., N. Patterson, C. Barbieri, F. Berthold, L. Gerlach et al., 2012 The genetic prehistory of southern Africa. Nat. Commun.3(1): 1143.
28. Pinhasi, R., M. Thomas, M. Hofreiter, M. Currat, and J. Burger, 2012 The genetic history of Europeans. Trends Genet. 28 (10): 496-505.
29. Pool, J., and R. Nielsen, 2009 Inference of historical changes in migration rate from the lengths of migrant tracts. Genetics 181: 711-719.
30. Price, A., M. Weale, N. Patterson, S. Myers, A. Need et al., 2008 Long-range LD can confound genome scans in admixed populations. Am. J. Hum. Genet. 83(1): 132-135.
31. Price, A., A. Tandon, N. Patterson, K. Barnes, N. Rafaels et al., 2009 Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet. 5(6): e1000519.
32. Pritchard, J., M. Stephens, and P. Donnelly, 2000 Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
33. Pugach, I., R. Matveyev, A. Wollstein, M. Kayser, and M. Stoneking, 2011 Dating the age of admixture via wavelet transform analysis of genome-wide data. Genome Biol. 12(2): R19.
34. Quintana-Murci, L., H. Quach, C. Harmant, F. Luca, B. Massonnet et al., 2008 Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter-gatherers and Bantu-speaking farmers. Proc. Natl. Acad. Sci. USA 105(5): 1596.
35. Rasteiro, R., and L. Chikhi, 2009 Revisiting the peopling of Japan: an admixture perspective. J. Hum. Genet. 54(6): 349-354.
36. Reich, D., M. Cargill, S. Bolk, J. Ireland, P. Sabeti et al., 2001 Linkage disequilibrium in the human genome. Nature 411(6834): 199-204.
37. Reich, D., K. Thangaraj, N. Patterson, A. Price, and L. Singh, 2009 Reconstructing Indian population history. Nature 461 (7263): 489-494.
38. Rosenberg, N., J. Pritchard, J. Weber, H. Cann, K. Kidd et al., 2002 Genetic structure of human populations. Science 298 (5602): 2381-2385.
39. Sankararaman, S., S. Sridhar, G. Kimmel, and E. Halperin, 2008 Estimating local ancestry in admixed populations. Am. J. Hum. Genet. 82(2): 290-303.
40. Soares, P., A. Achilli, O. Semino, W. Davies, V. Macaulay et al., 2010 The archaeogenetics of Europe. Curr. Biol. 20(4): R174-R183.
41. Sousa, V., M. Fritz, M. Beaumont, and L. Chikhi, 2009 Approximate Bayesian computation without summary statistics: the case of admixture. Genetics 181: 1507-1519.
42. Tang, H., M. Coram, P. Wang, X. Zhu, and N. Risch, 2006 Reconstructing genetic ancestry blocks in admixed individuals. Am. J. Hum. Genet. 79 (1): 1-12.
43. Verdu, P., F. Austerlitz, A. Estoup, R. Vitalis, M. Georges et al., 2009 Origins and genetic diversity of Pygmy hunter-gatherers from western Central Africa. Curr. Biol. 19(4): 312-318.
44. Wall, J., K. Lohmueller, and V. Plagnol, 2009 Detecting ancient admixture and estimating demographic parameters in multiple human populations. Mol. Biol. Evol. 26(8): 1823-1827.
45. Wang, J., 2003 Maximum-likelihood estimation of admixture proportions from genetic data. Genetics 164: 747-765.