Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies

Genetics

Volumn 164, Issue 4, 2003, Pages 1567-1587

  Falush, Daniel ^a   Stephens, Matthew ^b   Pritchard, Jonathan K ^c  

^a MAX PLANCK INSTITUTE FOR INFECTION BIOLOGY   (Germany)

^b UNIVERSITY OF WASHINGTON   (United States)

^c UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA MODIFICATION; DROSOPHILA MELANOGASTER; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC LINKAGE; GENETIC REGULATION; HELICOBACTER PYLORI; HUMAN; NONHUMAN; POPULATION STRUCTURE; PRIORITY JOURNAL;

AFRICAN CONTINENTAL ANCESTRY GROUP; ALGORITHMS; ALLELES; ANIMALS; BAYES THEOREM; CHROMOSOMES; COMPUTER SIMULATION; DROSOPHILA MELANOGASTER; EVOLUTION, MOLECULAR; FEMALE; GENE FREQUENCY; GENETIC DRIFT; GENETIC MARKERS; GENETICS, POPULATION; GENOTYPE; HELICOBACTER PYLORI; HUMANS; LINKAGE (GENETICS); MALE; MARKOV CHAINS; MODELS, GENETIC; MONTE CARLO METHOD; RECOMBINATION, GENETIC;

DROSOPHILA MELANOGASTER; HELICOBACTER; HELICOBACTER PYLORI; MELANOGASTER;

EID: 0041817568     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (43)

1. AGIS, M., and C. SCHLÖTTERER, 2001 Microsatellite variation in natural Drosophila melanogaster populations from New South Wales (Australia) and Tasmania. Mol. Ecol. 10: 1197-1205.
2. ANDERSON, E. C., 2001 Monte Carlo methods for inference in population genetic models. Ph.D. Thesis, University of Washington, Seattle.
3. ANDERSON, E. C., and E. A. THOMPSON, 2002 A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160: 1217-1229.
4. BALDING, D. J., and R. A. NICHOLS, 1997 Significant genetic correlations among Caucasians at forensic DNA loci. Heredity 78: 583-589.
5. BARTON, N. H., and G. M. HEWITT, 1989 Adaptation, speciation and hybrid zones. Nature 341: 497-503.
6. BEAUMONT, M., D. GOTTELLI, E. M. BARRATT, A. C. KITCHENER, M. J. DANIELS et al., 2001 Genetic diversity and introgression in the Scottish wildcat. Mol. Ecol. 10: 319-336.
7. BERTORELLE, G., and L. EXCOFFIER, 1998 Inferring admixture proportions from molecular data. Mol. Biol. Evol. 15: 1298-1311.
8. BROMAN, K. W., J. C. MURRAY, V. C. SHEFFIELD, R. L. WHITE and J. L. WEBER, 1998 Comprehensive human genetic maps: individual and sex-specific variation in recombination. Am. J. Hum. Genet. 63: 861-869.
9. CHAKRABORTY, R., and K. M. 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: 9119-9123.
10. CHIKHI, L., M. W. BRUFORD and M. A. BEAUMONT, 2001 Estimation of admixture proportions: a likelihood-based approach using Markov chain Monte Carlo. Genetics 158: 1347-1362.
11. COOPER, R. S., A. LUKE, X. ZHU, D. KAN, A. ADEYEMO et al., 2002 A genome-wide scan among Nigerians linking blood pressure to regions on chromosomes 2, 3, and 19. Hypertension 40: 629-633.
12. DALY, M. J., J. D. RIOUX, S. F. SCHAFFNER, T. J. HUDSON and E. S. LANDER, 2001 High-resolution haplotype structure in the human genome. Nat. Genet. 29: 229-232.
13. DAWSON, K. J., and K. BELKHIR, 2001 A Bayesian approach to the identification of panmictic populations and the assignment of individuals. Genet. Res. 78: 59-77.
14. EROSHEVA, E. A., 2002 Grade of membership and latent structure models with application to disability survey data. Ph.D. Thesis, Department of Statistics, Carnegie Mellon University, Pittsburgh.
15. EXCOFFIER, L., 2001 Analysis of population subdivision, pp. 271-307 in Handbook of Statistical Genetics, edited by D. BALDING, M. BISHOP and C. CANNINGS. John Wiley & Sons, New York.
16. FALUSH, D., C. KRAFT, N. S. TAYLOR, P. CORREA, J. G. FOX et al. 2001 Recombination and mutation during long-term gastric colonization by Helicobacter pylori: estimates of clock rates, recombination size, and minimal age. Proc. Natl. Acad Sci. USA 98: 1505-1561.
17. FALUSH, D., T. WIRTH, B. LINZ, J. K. PRITCHARD, M. STEPHENS et al., 2003 Traces of human migrations in Helicobacter pylori populations. Science 299: 1582-1585.
18. GILKS, W. R., S. RICHARDSON and D.J. SPIEGELHALTER (Editors), 1996 Markov Chain Monte Carlo in Practice. Chapman & Hall, London.
19. GUGLIELMINO, C. R., A. PIAZZA, P. MENOZZI and L. L. CAVALLI-SFORZA, 1990 Uralic genes in Europe. Am. J. Phys. Anthropol. 83: 57-68.
20. KNOWLER, W. C., R. C. WILLIAMS, D.J. PETTITT and A. G. STEINBERG, 1988 Gm3;5,13,14 and type 2 diabetes mellitus: an association in American Indians with genetic admixture. Am. J. Hum. Genet. 43: 520-526.
21. KONG, A., D. F. GUDBJARTSSON, J. SAINZ, G. M. JONSDOTTIR, S. A. GUDJONSSON et al., 2002 A high-resolution recombination map of the human genome. Nat. Genet. 31: 241-247.
22. KUMAR, S., K. TAMURA, I. B. JAKOBSEN and M. NEI, 2001 MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17: 1244-1245.
23. LONG, J. C., 1991 The genetic structure of admixed population. Genetics 127: 417-428.
24. MARCHINI, J. L., and L. R. CARDON, 2002 Discussion on statistical modelling and genetic data. J. R. Stat. Soc. B 64: 740-741.
25. McKEIGUE, P. M., 1998 Mapping genes that underlie ethnic differences in disease risk: methods for detecting linkage in admixed populations, by conditioning on parental admixture. Am. J. Hum. Genet. 63: 241-251.
26. McKEIGUE, P. M., J. R. CARPENTER, E. J. PARRA and M. D. SHRIVER, 2000 Estimation of admixture and detection of linkage in admixed populations by a Bayesian approach: application to African-American populations. Ann. Hum. Genet. 64: 171-186.
27. NEI, M., and W.-H. LI, 1979 Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 76: 5269-5273.
28. NICHOLSON, G., A. V. SMITH, F. JÓNSSON, O. GÜSTAFSSON, K. STEFANSSON et al., 2002 Assessing population differentiation and isolation from single nucleotide polymorphism data. J. R. Stat. Soc. B 64: 695-715.
29. PARRA, E. J., A. MARCINI, J. AKEY, J. MARTINSON, M. A. BATZER et al., 1998 Estimating African American admixture proportions by use of population-specific alleles. Am. J. Hum. Genet. 63: 1839-1851.
30. PFAFF, C. L., E. J. PARRA, C. BONILLA, K. HIESTER, P. M. McKEIGUE et al., 2001 Population structure in admixed populations: effect of admixture dynamics on the pattern of linkage disequilibrium. Am. J. Hum. Genet. 68: 198-207.
31. PRITCHARD, J. K., M. STEPHENS and P. DONNELLY, 2000 Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
32. RABINER, L. R., 1989 A tutorial on hidden Markov models and selected applications in speech recognition. Proc. IEEE 77 (2): 257-286.
33. RIESEBERG, L. H., J. WHITTON and K. GARDNER, 1999 Hybrid zones and the genetic architecture of a barrier to gene flow between two sunflower species. Genetics 152: 713-727.
34. ROSENBERG, N. A., J. K. PRITCHARD, J. L. WEBER, H. M. CANN, K. K. KIDD et al., 2002 Genetic structure of human populations. Science 298: 2381-2385.
35. SATTEN, G. A., W. D. FLANDERS and Q. YANG, 2001 Accounting for unmeasured population structure in case-control studies of genetic association using a novel latent-class model. Am. J. Hum. Genet. 68: 466-477.
36. SILLAMPÄÄ, M.J., R. KILPIKARI, S. RIPATTI, P. ONKAMO and P. UIMARI, 2001 Bayesian association mapping for quantitative traits in a mixture of two populations. Genet. Epidemiol. 21: 692-699.
37. SITES, J. W., N. H. BARTON and K. M. REED, 1995 The genetic-structure of a hybrid zone between 2 chromosome races of the Sceloporus grammicus complex (Sauria, Phrynosomatidae) in central Mexico. Evolution 49: 9-36.
38. STEPHENS, J. C., D. BRISCOE and S.J. O'BRIEN, 1994 Mapping admixture linkage disequilibrium in human populations: limits and guidelines. Am. J. Hum. Genet. 55: 809-824.
39. STEPHENS, M., N.J. SMITH and P. DONNELLY, 2001 A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68: 978-989.
40. THIEL, B. A., A. CHAKRAVARTI, R. S. COOPER, A. LUKE, S. LEWIS et al., 2003 A genome wide linkage analysis investigating the determinants of blood pressure in Caucasians and African Americans. Am. J. Hypertens. 16: 151-153.
41. THOMPSON, E. A., 1973 The Icelandic admixture problem. Ann. Hum. Genet. 37: 69-80.
42. THORNSBERRY, J. M., M. M. GOODMAN, J. DOEBLEY, S. KRESOVICH, D. NIELSEN et al., 2001 Dwarf8 polymorphisms associate with variation with flowering time. Nat. Genet. 28: 286-289.
43. WRIGHT, S., 1951 The genetical structure of populations. Ann. Eugen. 15: 323-354.