Inference of population structure under a dirichlet process model

Genetics

Volumn 175, Issue 4, 2007, Pages 1787-1802

  Huelsenbeck, John P ^a,b   Andolfatto, Peter ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of California at San Diego   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAYES THEOREM; GENETIC MODEL; MATHEMATICAL COMPUTING; MATHEMATICAL GENETICS; MATHEMATICAL MODEL; MONTE CARLO METHOD; POPULATION GENETIC STRUCTURE; POPULATION STRUCTURE; PRIORITY JOURNAL; PROBABILITY;

ALGORITHMS; ALLELES; ANIMALS; BAYES THEOREM; COMPUTER SIMULATION; GENE FREQUENCY; GENETICS, POPULATION; MARKOV CHAINS; MICE; MODELS, GENETIC; MODELS, STATISTICAL; MONTE CARLO METHOD; RUMINANTS; SONGBIRDS;

EID: 34249066206     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.106.061317     Document Type: Article

References (48)

1. AKAIKE, H., 1973 Information theory as an extension of the maximum likelihood principle, pp. 267-281 in Second International Symposium on Information Theory, edited by B. N. PETROV and F. CSAKI. Akademiai Kiado, Budapest.
2. ANDOLFATTO, P., and M. PRZEWORSKI, 2000 A genome-wide departure from the standard neutral model in natural populations of Drosophila. Genetics 156: 257-268.
3. ANTONIAK, C. E., 1974 Mixtures of Dirichlet processes with applications to non-parametric problems. Ann. Stat. 2: 1152-1174.
4. BALDING, D. J., and R. A. NICHOLS, 1995 A method for quantifying differentiation between populations at multi-allelic loci and its implications for investigating identity and paternity. Genetica 96: 3-12.
5. BELL, E. T., 1934 Exponential numbers. Am. Math. Mon. 41: 411-419.
6. CORANDER, J., P. WALDMANN and M. J. SILLANPÄÄ, 2003 Bayesian analysis of genetic differentiation between populations. Genetics 163: 367-374.
7. CORANDER, J., P. WALDMANN, P. MARTTINEN and M. J. SILLANPÄÄ, 2004 BAPS2: enhanced possibilities for the analysis of population structure. Bioinformatics 20: 2363-2369.
8. 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.
9. EVANNO, G., S. REGNAUT and J. GOUDET, 2005 Detecting the number of clusters of individuals using the software Structure: a simulation study. Mol. Ecol. 14: 2611-2620.
10. FALUSH, D., M. STEPHENS and J. K. PRITCHARD, 2003 Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
11. FERGUSON, T. S., 1973 A Bayesian analysis of some nonparametric problems. Ann. Stat. 1: 209-230.
12. GALBUSERA, P., L. LENS, E. WAIYAKI, T. SCHENCK and E. MATTYSEN, 2000 Effective population size and gene flow in the globally, critically endangered Taita thrush, Turdus helleri. Conserv. Genet. 1: 45-55.
13. GEYER, C. J., 1991 Markov chain Monte Carlo maximum likelihood, pp. 156-163 in Computing Science and Statistics: Proceedings of the 23rd Symposium on the Interface, edited by E. M. Keramidas. Interface Foundation, Fairfax Station, VA.
14. GREEN, P. J., 1995 Reversible jump MCMC computation and Bayesian model determination. Biometrika 82: 711-732.
15. GUSFIELD, D., 2002 Partition-distance: a problem and class of perfect graphs arising in clustering. Inform. Process. Lett. 82: 159-164.
16. HAMMER, M. F., F. BLACKMER, D. GARRIGAN, M. W. NACHMAN and J. A. WILDER, 2003 Human population structure and its effects on sampling Y chromosome sequence variation. Genetics 164: 1495-1509.
17. HOLSINGER, K. E., P. O. LEWIS and D. K. DEY, 2002 A Bayesian approach to inferring population structure from dominant markers. Mol. Ecol. 11: 1157-1164.
18. HUDSON, R. R., 2002 Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
19. JEFFREYS, H., 1961 Theory of Probability, Ed. 3. Oxford University Press, Oxford.
20. LAVINE, M., and M. J. SCHERVISH, 1999 Bayes factors: what they are and what they are not. Am. Stat. 53: 119-122.
21. LEO, N. P., J. M. HUGHES, X. YANG, S. K. S. POUDEL, W. G. BROGDON et al., 2005 The head and body lice of humans are genetically distinct (Insecta: Phthiraptera, Pediculidae): evidence from double infestations. Heredity 95: 34-40.
22. LORENZEN, E. D., and H. R. SIEGISMUND, 2004 No suggestion of hybridization between the vulnerable black-faced impala (Aepyceros melampus petersi) and the common impala (A. m. melampus) in Etosha NP, Namibia. Mol. Ecol. 13: 3007-3019.
23. LORENZEN, E. D., P. ARCTANDER and H. R. SIEGISMUND, 2006 Regional genetic structuring and evolutionary history of the impala Aepyceros melampus. J. Hered. 97: 119-132.
24. MALÉCOT, G., 1948 Les Mathématiques D l' Hérédité. Massonet Cie, Paris.
25. MICHEL, A. P., M. J. INGRASCI, B. J. SCHEMERHORN, M. KERN, G. LE GOFF et al., 2005 Rangewide population genetic structure of the African malaria vector Anopheles funestus. Mol. Ecol. 14: 4235-4248.
26. MOODLEY, Y., and E. H. HARLEY, 2005 Population structuring in mountain zebras (Equus zebra): the molecular consequences of divergent demographic histories. Conserv. Genet. 6: 953-968.
27. NEAL, R. M., 2000 Markov chain sampling methods for Dirichlet process mixture models. J. Comput. Graph. Stat. 9: 249-265.
28. NEJSUM, P., E. D. PARKER, J. FRYDENBERG, A. ROEPSTORFF, J. BOES et al., 2005 Ascariasis is a zoonosis in Denmark. J. Clin. Microbiol. 43: 1142-1148.
29. NEWTON, M. A., and A. E. RAFTERY, 1994 Approximate Bayesian inference with the weighted likelihood bootstrap. J. R. Stat. Soc. B 56: 3-48.
30. NIELSEN, R., 2001 Statistical tests of neutrality in the age of genomics. Heredity 86: 641-647.
31. OCHSENREITHER, S., K. KUHLS, M. SCHAAR, W. PRESBER and G. SCHONIAN, 2006 Multilocus microsatellite typing as a new tool for discrimination of Leishmania infantum MON-1 strains. J. Clin. Microbiol. 44: 495-503.
32. ORTH, A., T. ADAMA, W. DIN and F. BONHOMME, 1998 Hybridation naturelle entre deux sous espéces de souris domestique Mus musculus domesticus et Mus musculus castaneus prés de Lake Casitas (Californie). Genome 41: 104-110.
33. PELLA, J., and M. MASUDA, 2006 The Gibbs and split-merge sampler for population mixture analysis from genetic data with incomplete baselines. Can. J. Fish. Aquat. Sci. 63: 576-596.
34. PRITCHARD, J. K., M. STEPHENS and P. DONNELLY, 2000 Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
35. PRZEWORSKI, M., 2002 The signature of positive selection at randomly chosen loci. Genetics 160: 1179-1189.
36. RAFTERY, A. E., M. A. NEWTON, J. M. SATAGOPAN and P. N. KRIVITSKY, 2006 Estimating the Integrated Likelihood via Posterior Simulation Using the Harmonic Mean Identity (Memorial Sloan-Kettering Cancer Center Department of Epidemiology and Biostatistics Working Paper Series, Working Paper 6).
37. RANNALA, B., and J. L. MOUNTAIN, 1997 Detecting immigration by using multilocus genotypes. Proc. Natl. Acad. Sci. USA 94: 9197-9201.
38. 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: 2981-2985.
39. SMALL, M. P., A. E. FRYE, J. F. VON BARGEN and S. F. YOUNG, 2006 Genetic structure of chum salmon (Oncorhynchus keta) populations in the lower Columbia River: Are chumsalmon in Cascade tributaries remnant populations? Conserv. Genet. 7: 65-78.
40. SONG, K. J., and R. C. ELSTON, 2006 A powerful method of combining measures of association and Hardy-Weinberg disequilibrium for fine-mapping in case-control studies. Stat. Med. 25: 105-126.
41. STANTON, D., and D. WHITE, 1986 Constructive Combinatorics. Springer-Verlag, New York.
42. STEPHENS, M., 2000 Dealing with label-switching in mixture models. J. R. Stat. Soc. Ser. B 62: 795-809.
43. TIERNEY, L., 1996 Introduction to general state-space Markov chain theory, pp. 59-74 in Markov Chain Monte Carlo in Practice. Chapman & Hall, London.
44. TSAI, H. J., J. Y. KHO, N. SHAIKH, S. CHOUDHRY, M. NAQVI et al., 2006 Admixture-matched case-control study: a practical approach for genetic association studies in admixed populations. Hum. Genet. 118: 626-639.
45. WRIGHT, S., 1940 Breeding structure of populations in relation to speciation. Am. Nat. 74: 232-248.
46. WRIGHT, S., 1943 Isolation by distance. Genetics 28: 114-138.
47. WRIGHT, S., 1951 The genetical structure of populatons. Ann. Eugen. 15: 323-354.
48. YU, J. M., G. PRESSOIR, W. H. BRIGGS, I. V. BI, M. YAMASAKI et al., 2006 A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat. Genet. 38: 203-208.