Cryptic population genetic structure: The number of inferred clusters depends on sample size

Molecular Ecology Resources

Volumn 10, Issue 2, 2010, Pages 314-323

  Fogelqvist, Johan ^a   Niittyvuopio, Anne ^b   Ågren, Jon ^a   Savolainen, Outi ^b   Lascoux, Martin ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b UNIVERSITY OF OULU   (Finland)

Author keywords

Arabidopsis thaliana; Population structure; Sampling; STRUCTURE

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 77949336419     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2009.02756.x     Document Type: Article

References (42)

1. Abbott RJ, Gomes MF. Population genetic structure and outcrossing rate of Arabidopsis thaliana (L.) Heynh. Heredity 1989, 62:411-418.
2. Bakker EG, Stahl EA, Toomajian C, Nordborg M, Kreitman M, Bergelson J. Distribution of genetic variation within and among local populations of Arabidopsis thaliana over its species range. Molecular Ecology 2006, 15:1405-1418.
3. Balloux F. easypop (version 1.7): a computer program for population genetic simulations. Journal of Heredity 2001, 92:301-302.
4. Beck JB, Schmuths H, Schaal BA. Native range genetic variation in Arabidopsis thaliana is strongly geographically structured and reflects Pleistocene glacial dynamics. Molecular Ecology 2008, 17:902-915.
5. Bell CJ, Ecker JR. Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics 1994, 19:137-144.
6. Bergelson J, Stahl E, Dudek S, Kreitman M. Genetic variation within and among populations of Arabidopsis thaliana. Genetics 1998, 148:1311-1323.
7. Caicedo AL, Stinchcombe JR, Olsen KM, Schmitt J, Purugganan MD. Epistatic interaction between Arabidopsis FRI and FLC flowering time genes generates a latitudinal cline in a life history trait. Proceedings of the National Academy of Sciences of the United States of America 2004, 101:15670-15675.
8. Chen C, Durand E, Forbes F, Francois O. Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison study. Molecular Ecology Notes 2007, 7:747-756.
9. Clauss MJ, Cobban H, Mitchell-Olds T. Cross-species microsatellite markers for elucidating differences in population genetic structure in Arabidopsis and Arabis (Brassicaceae). Molecular Ecology 2002, 11:591-601.
10. Corander J, Waldmann P, Marttinen P, Mäntyniemi S. baps 2: enhanced possibilities for the analysis of genetic population structure. Bioinformatics 2003, 20:2363-2369.
11. Corander J, Marttinen P, Mäntyniemi S. Bayesian identification of stock mixtures from molecular marker data. Fishery Bulletin 2006, 104:550-558.
12. 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.
13. Falush D, Stephens M, Pritchard JK. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 2003, 164:1567-1587.
14. Falush D, Stephens M, Pritchard JK. Inference of population structure using multilocus genotype data: dominant markers and null alleles. Molecular Ecology Notes 2007, 7:574-578.
15. Francois O, Blum MGB, Jakobsson M, Rosenberg NA. Demographic history of European populations of Arabidopsis thaliana. PLoS Genetics 2008, 4:e1000075.
16. François O, Ancelet S, Guillot G. Bayesian clustering using hidden Markov random fields in spatial population genetics. Genetics 2006, 174:805-816.
17. Gao H, Williamson S, Bustamante CD. A Markov Chain Monte Carlo approach for joint inference of population structure and inbreeding rates from multi-locus genotype data. Genetics 2007, 176:1635-1651.
18. Guillot G, Mortier F, Estoup A. Geneland: a program for landscape genetics. Molecular Ecology Notes 2005, 5:712-715.
19. Hudson RR. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 2002, 18:337-338.
20. Huelsenbeck JP, Andolfatto P. Inference of population structure under a Dirichlet process model. Genetics 2007, 175:1787-1802.
21. Jakobsson M, Rosenberg NA. clumpp: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 2007, 23:1801-1806.
22. Kaeuffer R, Réale D, Coltman DW, Pontier D. Detecting population structure using structure software: effect of background linkage disequilibrium. Heredity 2007, 99:374-380.
23. Kim S, Plagnol V, Hu TT. Recombination and linkage disequilibrium in Arabidopsis thaliana. Nature Genetics 2007, 39:1151-1155.
24. Kimura M, Crow JF. The number of alleles that can be maintained in a finite population. Genetics 1964, 49:725-738.
25. Korves TM, Schmid KJ, Caicedo AL. Fitness effects associated with the major flowering time gene FRIGIDA in Arabidopsis thaliana in the field. The American Naturalist 2007, 169:141-157.
26. Kuittinen H, Mattila A, Savolainen O. Genetic variation at marker loci and in quantitative traits in natural populations of Arabidopsis thaliana. Heredity 1997, 79:144-152.
27. Latch EK, Dharmarajan G, Glaubitz JC, Rhodes OE. Relative performance of Bayesian clustering software for inferring population substructure and individual assignment at low levels of population differentiation. Conservation Genetics 2006, 7:295-302.
28. Lawson-Handley LJ, Manica A, Goudet J, Balloux F. Going the distance: human population genetics in a clinal world. Trends in Genetics 2007, 23:432-439.
29. Nordborg M, Borevitz JO, Bergelson J. The extent of linkage disequilibrium in Arabidopsis thaliana. Nature Genetics 2002, 30:190-193.
30. Nordborg M, Hu TT, Ishino Y. The pattern of polymorphism in Arabidopsis thaliana. PLoS Biology 2005, 3:1289-1299.
31. Ohta T, Kimura M. A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genetical Research 1973, 22:201-204.
32. Olsen KM, Haldorsdottir S, Stinchcombe J, Weinig C, Schmitt J, Purugganan MD. Linkage disequilibrium mapping of Arabidopsis CRY2 flowering time alleles. Genetics 2004, 167:1361-1369.
33. Ostrowski MF, David J, Santoni S. Evidence for a large-scale population structure among accessions of Arabidopsis thaliana: possible causes and consequences for the distribution of linkage disequilibrium. Molecular Ecology 2006, 15:1507-1517.
34. Ponce MR, Robles P, Micol JL. High-throughput genetic mapping in Arabidopsis thaliana. Molecular and General Genetics 1999, 261:408-415.
35. Pritchard JK, Stephens M, Donnelly PJ. Inference of population structure using multilocus genotype data. Genetics 2000, 155:945-959.
36. Rosenberg NA, Burke T, Elo K. Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds. Genetics 2001, 159:699-713.
37. Rousset F. genepop'007: a complete re-implementation of the genepop software for Windows and Linux. Molecular Ecology Resources 2008, 8:103-106.
38. Schmid KJ, Törjék O, Meyer R, Schmuts H, Hoffmann MH, Altmann T. Evidence for a large-scale population structure of Arabidopsis thaliana from genome-wide single-nucleotide polymorphism markers. Theoretical Applied Genetics 2006, 112:1104-1114.
39. Setakis E, Stirnadel H, Balding DJ. Logistic regression protects against population structure in genetic association studies. Genome Research 2006, 16:290-296.
40. Stenøien HK, Fenster CB, Tonteri A, Savolainen O. Genetic variability in natural populations of Arabidopsis thaliana from northern Europe. Molecular Ecology 2005, 14:137-148.
41. Waples RS, Gaggiotti OE. What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Molecular Ecology 2006, 15:1419-1439.
42. Zhao K, Aranzana MJ, Kim S. An Arabidopsis example of association mapping in structured samples. PLoS Genetics 2007, 3:e4.