Assessing population structure: FST and related measures

Molecular Ecology Resources

Volumn 11, Issue 1, 2011, Pages 5-18

  Meirmans, Patrick G ^a   Hedrick, Philip W ^b  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

^b ARIZONA STATE UNIVERSITY   (United States)

Author keywords

D; F statistics; Fixation; G'ST; Heterozygosity; Population differentiation

Indexed keywords

BIOLOGICAL MODEL; FACTORIAL ANALYSIS; GENETIC VARIABILITY; METHODOLOGY; POPULATION GENETICS; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL MODEL; STATISTICS;

FACTOR ANALYSIS, STATISTICAL; GENETIC VARIATION; GENETICS, POPULATION; MODELS, GENETIC; MODELS, STATISTICAL; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 78650079113     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2010.02927.x     Document Type: Review

References (61)

1. Balloux F (2001) easypop (Version 1.7): a Computer Program for Population Genetics Simulations. Journal of Heredity, 92, 301-302.
2. Balloux F, Goudet J (2002) Statistical properties of population differentiation estimators under stepwise mutation in a finite island model. Molecular Ecology, 11, 771-783.
3. Balloux F, Lugon-Moulin N (2002) The estimation of population differentiation with microsatellite markers. Molecular Ecology, 11, 155-165.
4. Balloux F, Brunner H, Lugon-Moulin N, Hausser J, Goudet J (2000) Microsatellites can be misleading: an empirical and simulation study. Evolution, 54, 1414-1422.
5. Beaumont MA, Balding D (2004) Identifying adaptive genetic divergence among populations from genome scans. Molecular Ecology, 13, 969-980.
6. Caballero A, Rodríguez-Ramilo S, Ávila V, Fernández J (2010). Management of genetic diversity of subdivided populations in conservation programmes. Conservation Genetics, DOI .
7. Carreras-Carbonell J, Macpherson E, Pascual M (2006) Population structure within and between subspecies of the Mediterranean triplefin fish Tripterygion delaisi revealed by highly polymorphic microsatellite loci. Molecular Ecology, 15, 3527-3539.
8. Chao A, Jost L, Chiang S, Jiang Y, Chazdon R (2008) A two-stage probabilistic approach to multiple-community similarity indices. Biometrics, 64, 1178-1186.
9. Chao A, Shen T-J (2009) Program SPADE (Species Prediction and Diversity Estimation). Program and user's guide at .
10. Charlesworth B (1998) Measures of divergence between populations and the effect of forces that reduce variability. Molecular Biology and Evolution, 15, 538-543.
11. Cockerham CC (1973) Analysis of gene frequencies. Genetics, 74, 679-700.
12. Cockerham CC, Weir BS (1993) Estimation of gene flow from F-statistics. Evolution, 47, 855-863.
13. Crawford N (2010) smogd: software for the measurement of genetic diversity. Molecular Ecology Resources, 10, 556-557.
14. ST, a genetic measure of population differentiation. American Journal of Botany, 89, 460-465.
15. Excoffier L, Hamilton G (2003) Comment on "Genetic structure of human populations.". Science, 300, 1877.
16. Excoffier L, Lischer H (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10, 564-567.
17. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes - application to human mitochondrial-DNA restriction data. Genetics, 131, 479-491.
18. Excoffier L, Hofer T, Foll M (2009) Detecting loci under selection in a hierarchically structured population. Heredity, 103, 285-298.
19. Goudet J (1995) fstat (Version 1.2): a computer program to calculate F-statistics. Journal of Heredity, 86, 485-486.
20. Gregorius HR (2010) Linking diversity and differentiation. Diversity, 2, 370-394.
21. Gregorius HR, Degen B, Koenig A (2007) Problems in the analysis of genetic differentiation among populations - a case study in Quercus robur. Silvae Genetica, 56, 190-199.
22. Hamrick JL, Godt MJW (1996) Effects of life history traits on genetic diversity in plant species. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences, 351, 1291-1298.
23. Hedrick PW (1999) Perspective: highly variable loci and their interpretation in evolution and conservation. Evolution, 53, 313-318.
24. Hedrick PW (2005) A standardized genetic differentiation measure. Evolution, 59, 1633-1638.
25. ST: how wrong have we been? Molecular Ecology, 18, 2080-2083.
26. ST. Nature Reviews Genetics, 10, 639-650.
27. Hubalek Z (2000) Measures of species diversity in ecology: An evaluation. Folia Zoologica, 49, 241-260.
28. Jost L (2006) Entropy and diversity. Oikos, 113, 363-375.
29. Jost L (2007) Partitioning diversity into independent alpha and beta components. Ecology, 88, 2427-2439.
30. ST and its relatives do not measure differentiation. Molecular Ecology, 17, 4015-4026.
31. ST: response to Heller and Siegismund (2009) and Ryman and Leimar (2009). Molecular Ecology, 18: 2088-2091.
32. Kronholm I, Loudet O, De Mieux J (2010) Influence of mutation rate on estimators of genetic differentiation-lessons from Arabidopsis thaliana. BMC Genetics, 11, 33.
33. Lehtonen P, Laaksonen T, Artemyev A et al. (2009) Geographic patterns of genetic differentiation and plumage colour variation are different in the pied flycatcher (Ficedula hypoleuca). Molecular Ecology, 18, 4463-4476.
34. Lewontin RC (1964) The interaction of selection and linkage. I. General considerations; heterotic models. Genetics, 49, 49-67.
35. Lewontin R, Krakauer J (1973) Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics, 74, 175.
36. Li W (1976) Effect of migration on genetic distance. American Naturalist, 110, 841-847.
37. Long JC, Kittles RA (2003) Human genetic diversity and the nonexistence of biological races. Human Biology, 75, 449-471.
38. Lowe WH, Allendorf FW (2010) What can genetics tell us about population connectivity? Molecular Ecology, 19, 3038-3051.
39. Meirmans PG (2006) Using the AMOVA framework to estimate a standardized genetic differentiation measure. Evolution, 60, 2399-2402.
40. Meirmans PG, Van Tienderen PH (2004) GenoType and GenoDive: two programs for the analysis of genetic diversity of asexual organisms. Molecular Ecology Notes, 4, 792-794.
41. Merilä J, Crnokrak P (2001) Comparison of genetic differentiation at marker loci and quantitative traits. Journal of Evolutionary Biology, 14, 892-903.
42. Neff B, Fraser B (2010) A program to compare genetic differentiation statistics across loci using resampling of individuals and loci. Molecular Ecology Resources, 10, 546-550.
43. Nei M (1973) Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences of the United States of America, 70, 3321-3323.
44. Nei M (1975). Molecular Population Genetics and Evolution. North-Holland Publishing Co., Amsterdam, The Netherlands.
45. Nei M (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
46. Nei M, Chesser R (1983) Estimation of fixation indexes and gene diversities. Annals of Human Genetics, 47, 253-259.
47. ST obsolete? Conservation Genetics, 3, 167-173.
48. Nybom H (2004) Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Molecular Ecology, 13, 1143-1155.
49. O'Reilly PT, Canino MF, Bailey KM, Bentzen P (2004) Inverse relationship between FST and microsatellite polymorphism in the marine fish, walleye pollock (Theragra chalcogramma): implications for resolving weak population structure. Molecular Ecology, 13, 1799-1814.
50. Peakall R, Smouse PE (2005) GenAlEx 6: Genetic Analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6, 288-295.
51. Peijnenburg KTCA, Breeuwer JAJ, Pierrot-Bults AC, Menken SBJ (2004) Phylogeography of the planktonic chaetognath Sagitta setosa reveals isolation in European seas. Evolution, 58, 1472-1487.
52. Peijnenburg KTCA, Fauvelot C, Breeuwer AJ, Menken SBJ (2006) Spatial and temporal genetic structure of the planktonic Sagitta setosa (Chaetognatha) in European seas as revealed by mitochondrial and nuclear DNA markers. Molecular Ecology, 15, 3319-3338.
53. Ryman N, Leimar O (2008) Effect of mutation on genetic differentiation among nonequilibrium populations. Evolution, 62, 2250-2259.
54. ST is still a useful measure of genetic differentiation - a comment on Jost's D. Molecular Ecology, 18, 2084-2087.
55. Slatkin M (1995) A measure of population subdivision based on microsatellite allele frequencies. Genetics, 139, 457-462.
56. Spitze K (1993) Population structure in Daphnia obtusa: quantitative genetic and allozymic variation. Genetics, 135, 367-374.
57. Weir BS, Cockerham C (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358-1370.
58. ST!= 1/(4Nm+1). Heredity, 82, 117-125.
59. Wright S (1943a) Isolation by distance. Genetics, 28, 114.
60. Wright S (1943b) An analysis of local variability of flower color in Linanthus parryae. Genetics, 28, 139.
61. Wright S (1965) The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution, 19, 395-420.