Structurama: Bayesian inference of population structure

Evolutionary Bioinformatics

Volumn 2011, Issue 7, 2011, Pages 55-59

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

^a UNIVERSITY OF CALIFORNIA   (United States)

^b PRINCETON UNIVERSITY   (United States)

Author keywords

Bayesian estimaion; Dirichlet process prior; Markov chain monte carlo; Population structure; References

Indexed keywords

ARTICLE; BAYES THEOREM; COMPUTER MEMORY; COMPUTER MODEL; COMPUTER PROGRAM; GENE FREQUENCY; GENE LOCUS; GENETIC ALGORITHM; GENETIC LINKAGE; GENOTYPE; MATHEMATICAL VARIABLE; MONTE CARLO METHOD; POPULATION DENSITY; POPULATION GENETIC STRUCTURE; PROBABILITY;

EID: 79958851503     PISSN: None     EISSN: 11769343     Source Type: Journal    
DOI: 10.4137/EBO.S6761     Document Type: Article

References (22)

1. Nielsen R. Statistical tests of selective neutrality in the age of genomics. Heredity. 2001;86:641-647.
2. Ewens WJ, Spielman RS. The transmission/disequilibrium test: history, subdivision, and admixture. American Journal of Human Genetics. 1995;57: 455-464.
3. Corander JP, Waldmann MJ, Sillanpää. Bayesian analysis of genetic differentiation between populations. Genetics. 2003;163:367-74.
4. Corander JP, Waldmann P, Marttinen MJ, Sillanpää. BAPS2: Enhanced possiblities for the analysis of population structure. Bioinformatics. 2004;20: 2363-2369.
5. Falush DM, Stephens JK, Pritchard. Inference of population structure using multi-locus genotype data: Linked loci and correlated allele frequencies. Genetics. 2003;164:1567-1587.
6. Holsinger KE, Lewis PO, Dey DK. A Bayesian approach to inferring population structure from dominant markers. Molecular Ecology. 2002;11: 1157-1164.
7. Pella J, Masuda M. The Gibbs and split-merge sampler for population mixture analysis from genetic data with incomplete baselines. Canadian Journal of Fisheries and Aquatic Sciences. 2006;63:576-596.
8. Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000;155:945-959.
9. Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software Structure: a simulation study. Molecular Ecology. 2005;14:2611-2620.
10. Raftery AE, Newton MA, Satagopan JM, Krivitsky PN. Estimating the integrated likelihood via posterior simulation using the harmonic mean identity. Bayesian Statistics. 2007;8:1-45.
11. Huelsenbeck JP, Andolfatto P. Inference of population structure under a Dirichlet process model. Genetics. 2007;175:1787-1802.
12. Teh YW, Jordan MI, Beal MJ, Blei DM. Hierarchical Dirichlet processes. Journal of the American Statistical Association. 2006;101:1566-1581.
13. Antoniak CE. Mixtures of Dirichlet processes with applications to non-parametric problems. Annals of Statistics. 1974;2:1152-1174.
14. Ferguson TS. A Bayesian analysis of some nonparametric problems. Annals of Statistics. 1973;1:209-230.
15. Neal RM. Markov chain sampling methods for Dirichlet process mixture models. Journal of Computational and Graphical Statistics. 2000;9:249-265.
16. Aldous D. Exchangeability ad related topics. In École d'Eté de Probabilités de Saint-Flour XIII-1983, Springer, Berlin; 1985:1-198.
17. Pitman J. Combinatorial stochastic processes. Technical Report 621, University of California at Berkeley, lecture notes for St. Flour Summer School; 2002.
18. Stanton D, White D. Constructive Combinatorics. Springer-Verlag, New York, 1986.
19. Gusfield D. Partition-distance: A problem and class of perfect graphs arising in clustering. Information Processing Letters. 2002;82:159-164.
20. Maddison DR, Swofford DL, Maddison WP. NEXUS: an extensible file format for systematic information. Systematic Biology. 1997;46:590-621.
21. Lorenzen ED, Arctander P, Siegismund HR. Regional genetic structuring and evolutionary history of the impala Aepyceros melampus. Journal of Heredity. 2006;97:119-132.
22. Lorenzen ED, Siegismund HR. No suggestion of hybridization between the vulnerable black-faced impala (Aepyceros melampus petersi) and the common impala (A.m. melampus) in Etosha NP, Namibia. Molecular Ecology. 2004;13:3007-3019.