ObStruct: A method to objectively analyse factors driving population structure using Bayesian ancestry profiles

PLoS ONE

Volumn 9, Issue 1, 2014, Pages

  Gayevskiy, Velimir ^a   Klaere, Steffen ^a,b   Knight, Sarah ^a   Goddard, Matthew R ^a  

^a UNIVERSITY OF AUCKLAND   (New Zealand)

^b UNIVERSITY OF AUCKLAND   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAYES THEOREM; COMPUTER PROGRAM; GENETIC DATABASE; GENETIC VARIABILITY; HUMAN; MICROSATELLITE MARKER; NEW ZEALAND; NONHUMAN; PARTITION COEFFICIENT; POPULATION DIFFERENTIATION; POPULATION STRUCTURE; SACCHAROMYCES CEREVISIAE; STRUCTURE ANALYSIS;

BAYES THEOREM; CONTINENTAL POPULATION GROUPS; GENETIC VARIATION; HUMANS; MICROSATELLITE REPEATS; MODELS, GENETIC; NEW ZEALAND; PHYLOGEOGRAPHY; POPULATION DYNAMICS; SACCHAROMYCES CEREVISIAE; SOFTWARE;

EID: 84897464804     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0085196     Document Type: Article

References (21)

1. Hartl DL, Clark AG (1997) Principles of population genetics. Sinauer Associates, Incorporated, 3rd edition.
2. Charlesworth B (1998) Measures of divergence between populations and the effect of forces that reduce variability. Molecular Biology and Evolution 15: 538-543.
3. Coyne JA, Orr HA (2004) Speciation. Sinauer Associates.
4. Schluter D (2009) Evidence for ecological speciation and its alternative. Science (New York, NY) 323: 737-741.
5. Gray JC, Goddard MR (2012) Gene-flow between niches facilitates local adaptation in sexual populations. Ecology Letters 15: 955-962.
6. Smadja CM, Butlin RK (2011) A framework for comparing processes of speciation in the presence of gene ow. Molecular Ecology 20: 5123-5140.
7. Papadopulos AST, Baker WJ, Crayn D, Butlin RK, Kynast RG, et al. (2011) Speciation with gene flow on Lord Howe Island. Proceedings of the National Academy of Sciences 108: 13188-13193.
8. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959. (Pubitemid 30397141)
9. Gao H, Williamson S, Bustamante CD (2007) A Markov Chain Monte Carlo approach for joint inference of population structure and inbreeding rates from multilocus genotype data. Genetics 176: 1635-1651. (Pubitemid 47105223)
10. Corander J, Waldmann P, Marttinen P, Sillanpaa MJ (2004) BAPS 2: enhanced possibilities for the analysis of genetic population structure. Bioinformatics 20: 2363-2369. (Pubitemid 39429907)
11. Corander J, Marttinen P, Sirén J, Tang J (2008) Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC Bioinformatics 9: 539.
12. Evanno G, Regnaut S, Goutdet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 2611-2620. (Pubitemid 40886055)
13. Rosenberg NA (2003) distruct: a program for the graphical display of population structure. Molec-ular Ecology Notes 4: 137-138.
14. Gittins R (1985) Canonical analysis: a review with applications in ecology. Springer-Verlag : 351 pp.
15. Anderson MJ (2001) A new method for nonparametric multivariate analysis of variance. Austral Ecology 26: 32-46.
16. Friendly M (2007) HE plots for multivariate linear models. Journal of Computational and Graphical Statistics 16: 421-444.
17. Excoffier L, Foll M (2011) fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios. Bioinformatics 27: 1332-1334.
18. Wang S, Lewis CM, Jakobsson M, Ramachandran S, Ray N, et al. (2007) Genetic variation and population structure in Native Americans. PLoS Genetics 3: e185.
19. Gayevskiy V, Goddard MR (2012) Geographic delineations of yeast communities and populations associated with vines and wines in New Zealand. The ISME Journal 6: 1281-1290.
20. Martiny JBH, Bohannan BJM, Brown JH, Colwell RK, Fuhrman JA, et al. (2006) Microbial biogeography: putting microorganisms on the map. Nature Reviews Microbiology 4: 102-112. (Pubitemid 43158153)
21. McGovern PE, Zhang J, Tang J, Zhang Z, Hall GR, et al. (2004) Fermented beverages of pre-and proto-historic China. Proceedings of the National Academy of Sciences of the United States of America 101: 17593-17598. (Pubitemid 40051931)