Comparisons between Q ST and F ST-how wrong have we been?

Molecular Ecology

Volumn 20, Issue 23, 2011, Pages 4830-4839

  Edelaar, Pim ^a   Burraco, Pablo ^a   Gomez Mestre, Ivan ^a,b  

^a DEPARTMENT OF CONSERVATION BIOLOGY   (Spain)

^b CSIC   (Spain)

Author keywords

ST; divergent selection; F ST; microsatellites; neutral marker mutation rate; Q ST

Indexed keywords

BIOLOGICAL MODEL; COMPARATIVE STUDY; GENE FLOW; GENETIC MARKER; GENETIC SELECTION; METHODOLOGY; MOLECULAR EVOLUTION; MUTATION RATE; POPULATION GENETICS; REVIEW;

EVOLUTION, MOLECULAR; GENE FLOW; GENETIC MARKERS; GENETICS, POPULATION; MODELS, GENETIC; MUTATION RATE; SELECTION, GENETIC;

EID: 81855164599     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2011.05333.x     Document Type: Review

References (80)

1. Antoniazza S, Burri R, Fumagalli L, Goudet J, Roulin A, (2010) Local adaptation maintains clinal variation in melanin-based coloration of European barn owls (Tyto alba). Evolution, 64, 1944-1954.
2. Arnqvist G, Kolm N, (2010) Population differentiation in the swordtail characin (Corynopoma riisei): a role for sensory drive? Journal of Evolutionary Biology, 23, 1907-1918.
3. Balloux F, Lugon-Moulin N, (2002) The estimation of population differentiation with microsatellite markers. Molecular Ecology, 11, 155-165.
4. Brumfield RT, Beerli P, Nickerson DA, Edwards SV, (2003) The utility of single nucleotide polymorphisms in inferences of population history. Trends in Ecology and Evolution, 18, 249-256.
5. Campillo S, García-Roger EM, Carmona MJ, Gómez A, Serra M, (2009) Selection on life-history traits and genetic population divergence in rotifers. Journal of Evolutionary Biology, 22, 2542-2553.
6. Cano JM, Mäkinen HS, Leinonen T, Freyhof J, Merilä J, (2008) Extreme neutral genetic and morphological divergence supports classification of Adriatic three-spined stickleback (Gasterosteus aculeatus) populations as distinct conservation units. Biological Conservation, 141, 1055-1066.
7. Conde-Padín P, Carvajal-Rodríguez A, Carballo M, Caballero A, Rolán-Alvarez E, (2006) Genetic variation for shell traits in a direct-developing marine snail involved in a putative sympatric ecological speciation process. Evolutionary Ecology, 23, 635-650.
8. Demont M, Blanckenhorn WU, Hosken DJ, Garner TWJ, (2008) Molecular and quantitative genetic differentiation across Europe in yellow dung flies. Journal of Evolutionary Biology, 21, 1492-1503.
9. Drake JW, Charlesworth B, Charlesworth D, Crow JF, (1998) Rates of spontaneous mutation. Genetics, 148, 1667-1686.
10. Edelaar P, Björklund M, (2011) If Fst does not measure neutral genetic differentiation, then comparing it with Qst is misleading. Or is it?. Molecular Ecology, 20, 1805-1812.
11. Edmands S, Harrison S, (2003) Molecular and quantitative trait variation within and among populations of the intertidal copepod Tigriopus californicus. Evolution, 57, 2277-2285.
12. Ellegren H, (2004) Microsatellites: simple sequences with complex evolution. Nature Reviews Genetics, 5, 435-445.
13. Excoffier L, (2007) Analysis of Population Subdivision. In: Handbook of Statistical Genetics, 3rd edn, Vol. II. (eds, Balding DJ, Bishop M, and, Cannings C,), pp. 980-1020. Wiley, Chichester, UK.
14. 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.
15. st but not all of statistics!. Molecular Ecology, 19, 3845-3852.
16. Gilbert SF, Epel D, (2009) Ecological Developmental Biology: Integrating Epigenetics, Medicine, and Evolution. Sinauer Associates, Sunderland, Massachusetts.
17. Glover KA, Hanse MM, Lien S, Als TD, Høyheim B, Skaala Ø, (2010) A comparison of SNP and STR loci for delineating population structure and performing individual assignment. BMC Genetics, 11, 2.
18. Gomez-Mestre I, Tejedo M, (2004) Contrasting patterns of quantitative and neutral genetic variation in locally adapted populations of the Natterjack toad, Bufo calamita. Evolution, 58, 2343-2352.
19. Gravuer K, von Wettberg E, Schmitt J, (2005) Population differentiation and genetic variation inform translocation decisions for Liatris scariosa var. novae-angliae, a rare New England grassland perennial. Biological Conservation, 124, 155-167.
20. Gregorius H-R, (2010) Linking diversity and differentiation. Diversity, 2, 370-394.
21. Hardy OJ, Charbonnel N, Fréville H, Myriam H, (2003) Microsatellite allele sizes: a simple test to assess their significance on genetic differentiation. Genetics, 163, 1467-1482.
22. Hartl DL, Clark AG, (1997) Principles of Population Genetics, 3rd edn. Sinauer Associates, Sunderland, Massachusetts.
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. Hendry AP, (2002) Qst>=
27. Herrera CM, Bazaga P, (2010) Epigenetic differentiation and relationship to adaptive genetic divergence in discrete populations of the violet Viola cazorlensis. New Phytologist, 187, 867-876.
28. Holsinger KE, Weir BS, (2009) Genetics in geographically structured populations: defining, estimating and interpreting Fst. Nature Reviews Genetics, 10, 639-650.
29. Jaramillo-Correa JP, Beaulieu J, Bousquet J, (2001) Contrasting evolutionary forces driving population structure at expressed sequence tag polymorphisms, allozymes and quantitative traits in white spruce. Molecular Ecology, 10, 2729-2740.
30. Jensen LF, Hansen MM, Pertoldi C, Holdensgaard G, Mensberg KLD, Loeschcke V, (2008) Local adaptation in brown trout early life-history traits: implications for climate change adaptability. Proceedings of the Royal Society B, 275, 2859-2868.
31. Jimenez-Ambriz G, Petit C, Bourrie I, Dubois S, Olivieri I, Ronce O, (2007) Life history variation in the heavy metal tolerant plant Thlaspi caerulescens growing in a network of contaminated and noncontaminated sites in southern France: role of gene flow, selection and phenotypic plasticity. New Phytologist, 173, 199-215.
32. Jost L, (2008) Gst and its relatives do not measure differentiation. Molecular Ecology, 17, 4015-4026.
33. Kalinowski ST, (2002) How many alleles per locus should be used to estimate genetic distances? Heredity, 88, 62-65.
34. Knopp T, Cano JM, Crochet PA, Merilä J, (2007) Contrasting levels of variation in neutral and quantitative genetic loci on island populations of Moor frogs (Rana arvalis). Conservation Genetics, 8, 45-56.
35. Koskinen MT, Haugen TO, Primmer CR, (2002) Contemporary fisherian life-history evolution in small salmonid populations. Nature, 419, 826-830.
36. Kronholm I, Loudet O, De Meaux J, (2010) Influence of mutation rate on estimators of genetic differentiation-lessons from Arabidopsis thaliana. BMC Genetics, 11, 33.
37. Kuittinen H, Mattila A, Savolainen O, (1997) Genetic variation at marker loci and in quantitative traits in natural populations of Arabidopsis thaliana. Heredity, 79, 144-152.
38. Lascoux M, Thorsen J, Gullberg U, (1996) Population structure of a riparian willow species, Salix viminalis. Genetics Research, 68, 45-54.
39. Le Corre V, (2005) Variation at two flowering time genes within and among populations of Arabidopsis thaliana: comparison with markers and traits. Molecular Ecology, 14, 4181-4192.
40. Lehtonen PK, Laaksonen T, Aleksandr VA, 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.
41. Leinonen T, Cano JM, Mäkinen H, Merilä J, (2006) Contrasting patterns of body shape and neutral genetic divergence in marine and lake populations of threespine sticklebacks. Journal of Evolutionary Biology, 19, 1803-1812.
42. Leinonen T, O'Hara RB, Cano JM, Merilä J, (2008) Comparative studies of quantitative trait and neutral marker divergence: a meta-analysis. Journal of Evolutionary Biology, 21, 1-17.
43. Li YC, Korol AB, Fahima T, Beiles A, Nevo E, (2002) Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Molecular Ecology, 11, 2453-2465.
44. Liang Z-C, Huang P, Yang J, Rao G-Y, (2009) Population divergence in the amphicarpic species Amphicarpaea edgeworthii Benth. (Fabaceae): microsatellite markers and leaf morphology. Biological Journal of the Linnean Society, 96, 505-516.
45. Lynch M, Spitze K, (1994) Evolutionary genetics of Daphnia. In: Ecological Genetics (ed, Real LA,), pp. 109-128. Princeton University Press, Princeton, New Jersey.
46. Lynch M, Pfrender M, Spitze K, et al. (1999) The quantitative and molecular genetic architecture of a subdivided species. Evolution, 53, 100-110.
47. McKay JK, Latta RG, (2002) Adaptive population divergence: markers, QTL and traits. Trends in Ecology and Evolution, 17, 285-291.
48. Meirmans PG, (2006) Using the AMOVA framework to estimate a standardized genetic differentiation measure. Evolution, 60, 2399-2402.
49. Meirmans PG, Hedrick PW, (2010) Assessing population structure: Fst and related measures. Molecular Ecology Resources, 11, 5-18.
50. Merilä J, (1997) Quantitative trait and allozyme divergence in the greenfinch (Carduelis chloris, Aves: Fringillidae). Biological Journal of the Linnean Society, 61, 243-266.
51. Merilä J, Crnokrak P, (2001) Comparison of genetic differentiation at marker loci and quantitative traits. Journal of Evolutionary Biology, 14, 892-903.
52. Michalakis Y, Excoffier L, (1996) A generic estimation of population subdivision using distances between alleles with special reference for microsatellite loci. Genetic, 142, 1061-1064.
53. Morgan KK, Hicks J, Spitze K, et al. (2001) Patterns of genetics architecture for life-history traits and molecular markers in a subdivided species. Evolution, 55, 1753-1761.
54. Nachman MW, Crowell SL, (2000) Estimate of the mutation rate per nucleotide in humans. Genetics, 156, 297-304.
55. OHara RB, Merilä J, (2005) Bias and precision in Qst estimate: problems and some solutions. Genetics, 171, 1331-1339.
56. Østbye K, Næsje TF, Bernatchez L, Sandlund OT, Hindar K, (2005) Morphological divergence and origin of sympatric populations of European whitefish (Coregonus lavaretus L.) in Lake Femund, Norway. Journal of Evolutionary Biology, 18, 683-702.
57. Ouborg NJ, Pertoldi C, Loeschcke V, Bijlsma R (Kuke), Hedrick PW, (2010) Conservation genetics in transition to conservation genomics. Trends in Genetics, 26, 177-187.
58. Ovaskainen O, Karhunen M, Zheng C, Cano Arias JM, Merilä J, (2011) A new method to uncover signatures of divergent and stabilizing selection in quantitative traits. Genetics, 189, 621-632.
59. Palo JU, O'Hara RB, Laugen AT, Laurila A, Primmer CR, Merilä J, (2003) Latitudinal divergence of common frog (Rana temporaria) life history traits by natural selection: evidence from a comparison of molecular and quantitative genetic data. Molecular Ecology, 12, 1963-1978.
60. Perry GML, Audet C, Bernatchez L, (2005) Maternal genetic effects on adaptive divergence between anadromous and resident brook charr during early life history. Journal of Evolutionary Biology, 18, 1348-1361.
61. Petit C, Freville H, Mignot A, et al. (2001) Gene flow and local adaptation in two endemic plant species. Biological Conservation, 100, 21-34.
62. Raeymaekers JAM, Van Houdt JKJ, Larmuseau MHD, Geldof S, Volckaert FAM, (2007) Divergent selection as revealed by PST and QTL-based FST in three-spined stickleback (Gasterosteus aculeatus) populations along a coastal-inland gradient. Molecular Ecology, 16, 891-905.
63. Richter-Boix A, Teplitsky C, Rogell B, Laurila A, (2010) Local selection modifies phenotypic divergence among Rana temporaria populations in the presence of gene flow. Molecular Ecology, 19, 716-731.
64. Ritland K, (2000) Marker-inferred relatedness as a tool for detecting heritability in nature. Molecular Ecology, 9, 1195-1204.
65. Roach JC, Glusman G, Smit AFA, et al. (2010) Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science, 328, 636-639.
66. Saint-Laurent R, Legault M, Bernatchez L, (2003) Divergent selection maintains high gene flow between sympatric rainbow smelt ecotypes (Osmerus mordax Mitchill). Molecular Ecology, 12, 315-330.
67. Sanou H, Lovett PN, Bouvet JM, (2005) Comparison of quantitative and molecular variation in agroforestry populations of the shea tree (Vitellaria paradoxa C.F. Gaertn) in Mali. Molecular Ecology, 14, 2601-2610.
68. Santure AW, Ewen JG, Sicard D, Roff DA, Møller AP, (2010) Population structure in the barn swallow, Hirundo rustica: a comparison between neutral DNA markers and quantitative traits. Biological Journal of the Linnean Society, 99, 306-314.
69. Slatkin M, (1995) A measure of population subdivision based on microsatellite allele frequencies. Genetics, 139, 457-462.
70. Spitze K, (1993) The population structure in Daphnia obtusa: quantitative genetic and allozymic variation. Genetics, 135, 367-374.
71. Steane DA, Conod N, Jones RC, Vaillancourt RE, Potts BM, (2006) A comparative analysis of population structure of a forest tree, Eucalyptus globulus (Myrtaceae), using microsatellite markers and quantitative traits. Tree Genetics & Genomes, 2, 30-38.
72. Stenøien HK, Fenster CB, Tonteri A, Savolainen O, (2005) Genetic variability in natural populations of Arabidopsis thaliana in northern Europe. Molecular Ecology, 14, 137-148.
73. Storz JF, (2002) Contrasting patterns of divergence in quantitative traits and neutral DNA markers: analysis of clinal variation. Molecular Ecology, 11, 2537-2551.
74. Tautz D, Ellegren H, Weigel D, (2010) Next generation molecular ecology. Molecular Ecology, 19, S1: 1-3.
75. Volis S, Yakubov B, Shulgina I, Ward D, Mendlinger S, (2005) Distinguishing adaptive from nonadaptive genetic differentiation: comparison of QST and FST at two spatial scales. Heredity, 95, 466-475.
76. Waldmann P, Andersson S, (1998) Comparison of quantitative genetic variation and allozyme diversity within and between populations of Scabiosa canescens and S. columbaria. Heredity, 81, 79-86.
77. ST. Molecular Ecology, 17, 1885-1896.
78. ST and D do not replace Fst. Molecular Ecology, 20, 1083-1091.
79. Wojcik AM, Polly PD, Sikorski MD, Wojcik JM, (2006) Selection in a cycling population: differential response among skeletal traits. Evolution, 60, 1925-1935.
80. Yoshida Y, Honjo M, Kitamoto N, Ohsawa R, (2009) Reconsideration for conservation units of wild Primula sieboldii in Japan based on adaptive diversity and molecular genetic diversity. Genetics Research, 91, 225-235.