Distinguishing adaptive from nonadaptive genetic differentiation: Comparison of QST and FST at two spatial scales

Heredity

Volumn 95, Issue 6, 2005, Pages 466-475

  Volis, S ^a   Yakubov, B ^b   Shulgina, I ^a   Ward, D ^c   Mendlinger, S ^a  

^a BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

^b PURDUE UNIVERSITY   (United States)

^c UNIVERSITY OF KWAZULU NATAL   (South Africa)

Author keywords

Adaptation; Hordeum spontaneum; Molecular markers; Population genetic structure

Indexed keywords

ISOENZYME;

ADAPTATION; BARLEY; GENETIC DIFFERENTIATION; GENETIC STRUCTURE; POPULATION GENETICS;

ADAPTATION; ARTICLE; BARLEY; GENETIC MARKER; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; POPULATION GENETICS; QUANTITATIVE TRAIT; QUANTITATIVE TRAIT LOCUS; RANDOM AMPLIFIED POLYMORPHIC DNA;

ADAPTATION, BIOLOGICAL; GENETIC MARKERS; GENETICS, POPULATION; HORDEUM; ISOENZYMES; QUANTITATIVE TRAIT LOCI; QUANTITATIVE TRAIT, HERITABLE; RANDOM AMPLIFIED POLYMORPHIC DNA TECHNIQUE; SELECTION (GENETICS); VARIATION (GENETICS);

HORDEUM VULGARE SUBSP. SPONTANEUM; HORDEUM VULGARE SUBSP. VULGARE;

EID: 28344442950     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/sj.hdy.6800745     Document Type: Article

References (87)

1. Aagaard J, Krutovskii KV, Strauss SH (1998). RAPDs and allozymes exhibit similar levels of diversity and differentiation among populations and races of Douglas-fir. Heredity 81: 69-78.
2. Allendorf FW, Seeb LW (2000). Concordance of genetic divergence among sockeye salmon populations at allozyme, nuclear DNA, and mitochondrial DNA markers. Evolution 54: 640-651.
3. Ayres DR, Ryan FJ (1997). The clonal and population structure of a rare endemic plant, Wyethia reticulata (Asteraceae): allozyme and RAPD analysis. Mol Ecol 6: 761-772.
4. Bartish IV, Garkava LP, Rumpunen K, Nybom H (2000a). Phylogenetic relationships and differentiation among and within populations of Chaenomeles Lindl. (Rosaceae) estimated with RAPDs and isozymes. Theoret Appl Genet 101: 554-563.
5. Bartish IV, Jeppsson N, Bartish GI, Lu R, Nybom H (2000b). Inter- and intraspecific genetic variation in Hippophae (Elaeagnaceae) investigated by RAPD markers. Plant Syst Evol 225: 85-101.
6. Barton NH (1995). Linkage and the limits to natural selection. Genetics 140: 821-841.
7. Baum BR, Nevo E, Johnson DA, Beiles A (1997). Genetic diversity in wild barley (Hordeum spontaneum C. Koch) in the Near East: a molecular analysis using Random Amplified Polymorphic DNA (RAPD) markers. Genet Resources Crop Evol 44: 147-157.
8. Black-Samuelsson S, Eriksson G, Gustafsson L, Gustafsson P (1997). RAPD and morphological analysis of the rare plant species Vicia pisiformis (Fabaceae). Biol J Linnean Soc 61: 325-343.
9. Bonnin I, Prosperi JM, Olivieri I (1996). Genetic markers and quantitative genetic variation in Medicago truncatula (Leguminosae): a comparative analysis of population structure. Genetics 143: 1795-1805.
10. Bossart JL, Pashley Prowell D (1998). Genetic estimates of population structure and gene flow: limitations, lessons and new directions. Trends Ecol Evol 13: 202-206.
11. Brown AHD, Nevo E, Zohary D, Dagan O (1978a). Genetic variation in natural populations of wild barley (Hordeum spontaneum). Genetica 49: 97-108.
12. Brown AHD, Zohary D, Nevo E (1978b). Outcrossing rates and heterozygosity in natural populations of Hordeum spontaneum Koch in Israel. Heredity 41: 49-62.
13. Cavalli-Sforza L (1966). Population structure and human evolution. Proc R Soc London, Ser B 164: 362-379.
14. Chan Y, Arcese P (2003). Morphological and microsatellite differentiation in Melospiza melodia (Aves) at a microgeographic scale. J Evol Biol 16: 939-947.
15. Charlesworth D (2003). Effects of inbreeding on the genetic diversity of populations. Philos Trans R Soc London Ser B-Biol Sci 358: 1051-1070.
16. Charlesworth B, Nordborg M, Charlesworth D (1997). The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations. Genet Res 70: 155-174.
17. Comes HP, Abbott RJ (2000). Random amplified polymorphic DNA (RAPD) and quantitative trait analyses across a major phylogeographic break in the Mediterranean ragwort Senesio gallicus (Asteraceae). Mol Ecol 9: 61-76.
18. Edmands S, Harrison JS (2003). Molecular and quantitative trait variation within and among populations of the intertidal copepod Tigriopus californicus. Evolution 57: 2277-2285.
19. 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.
20. Falconer DS, Mackay TFC (1996). Introduction to Quantitative Genetics, 4th edn. Longman: Harlow, UK.
21. Heaton HJ, Whitkus R, Gomez PA (1999). Extreme ecological and phenotypic differences in the tropical tree chicozapote (Manilkara zapota (L.) P. Royen) are not matched by genetic divergence: a random amplified polymorphic DNA (RAPD) analysis. Mol Ecol 8: 627-632.
22. Heun M, Murphy JP, Phillips TD (1994). A comparison of RAPD and isozyme analyses for determining the genetic relationships among Avena sterilis L. accessions. Theoret Appl Genet 87: 689-696.
23. Isabel N, Beaulieu J, Bousquet J (1995). Complete congruence between gene diversity estimates derived from genotypic data at enzyme and random amplified polymorphic DNA loci in black spruce. PNAS 92: 6369-6373.
24. 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. Mol Ecol 10: 2729-2740.
25. Jenczewski E, Prosperi JM, Ronfort J (1999). Differentiation between natural and cultivated populations of Medicago sativa (Leguminosae) from Spain: Analysis with random amplified polymorphic DNA (RAPD) markers and comparison to allozymes. Mol Ecol 8: 1317-1330.
26. JMP (1995). SAS Institute Inc. Cary, NC.
27. Karhu A, Hurme P, Karjalainen M, Karvonen P, Kärkkäinen K, Neale D et al (1996). Do molecular markers reflect pattern of differentiation in adaptive traits of conifers? Theoret Appl Genet 93: 215-221.
28. Karl SA, Avise JC (1992). Balancing selection at allozyme loci in oysters: implications from nuclear RFLPs. Science 256: 100-102.
29. Kawecki TJ (1997). Sympatric speciation via habitat specialization driven by deleterious mutations. Evolution 51: 1751-1763.
30. Kimura M (1983). The neutral theory of molecular evolution. In: Mei M, Koehn RK (eds) Evolution of Genes and Proteins. Sinauer Associates: Sunderland, MA. pp 208-233.
31. Knapp EE, Rice KJ (1998). Comparison of isozymes and quantitative traits for evaluating patterns of genetic variation in purple needlegrass (Nassella pulchra). Conservation Biol 12: 1031-1041.
32. Kovach W (1999). Multi-Variate Statistical Package 3.11b. Kovach Computing Services: Aberystwyth, Wales, UK.
33. 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.
34. Lagercrantz U, Ryman N (1990). Genetic structure of Norway spruce (Picea abies): concordance of morphological and allozymic variation. Evolution 44: 38-53.
35. Latta RG, Mitton JB (1997). A comparison of population differentiation across four classes of gene marker in limber pine (Pinus flexilis James). Genetics 146: 1153-1163.
36. Le Corre V, Dumolin-Lapegue S, Kremer A (1997). Genetic variation at allozyme and RAPD loci in sessile oak Quercus petraea (Matt) Liebl: the role of history and geography. Mol Ecol 6: 519-529.
37. Lewontin RC (1991). Electrophoresis in the development of evolutionary genetics: milestone or millstone? Genetics 128: 657-662.
38. Lewontin RC, Krakauer J (1973). Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74: 175-195.
39. Lifante ZD, Aguinagalde I (1996). The use of random amplified polymorphic DNA (RAPD) markers for the study of taxonomical relationships among species of Asphodelus sect. Verinea (Asphodelaceae). Am J Botany 83: 949-953.
40. Luttikhuizen PC, Drent J, van Delden W, Piersma T (2003). Spatially structured genetic variation in a broadcast spawning bivalve: quantitative vs molecular traits. J Evol Biol 16: 260-272.
41. Lynch M (1988). The divergence of neutral quantitative characters among partially isolated populations. Evolution 42: 455-466.
42. Lynch M (1994). The neutral theory of phenotypic evolution. In: Real L (ed) Ecological Genetics. Princeton University Press: Princeton, NJ. pp 86-108.
43. Lynch M, Walsh B (1998). Genetics and Analysis of Quantitative Traits. Sinauer Associates: Sunderland, MA.
44. Mamuris Z, Stamatis C, Triantaphyllidis C (1999). Intraspecific genetic variation of striped red mullet (Mullus surmuletus L.) in the Mediterranean Sea assessed by allozyme and random amplified polymorphic DNA (RAPD) analysis. Heredity 83: 30-38.
45. Maynard Smith J, Haigh J (1974). The hitch-hiking effect of a favorable gene. Genet Res 23: 23-35.
46. McDonald JH (1994). Detecting natural selection by comparing geographic variation in protein and DNA polymorphisms. In: Golding B (ed) Non-Neutral Evolution. Theories and Molecular Data. Chapman & Hall: New York. pp 88-100.
47. McKay JK, Bishop JG, Lin JZ, Richards JH, Sala A, Mitchell-Olds T (2001). Local adaptation across a climatic gradient despite small effective population size in the rare sapphire rockcress. Proc R Soc London Ser B-Biol Sci 268: 1715-1721.
48. Merila J, Crnokrak P (2001). Comparison of genetic differentiation at marker loci and quantitative traits. J Evol Biol 14: 892-903.
49. Morgan KK, Hicks J, Spitze K, Latta L, Pfrender ME, Weaver CS et al (2001). Patterns of genetic architecture for life-history traits and molecular markers in a subdivided species. Evolution 55: 1753-1761.
50. Nei M (1973). Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci 70: 3321-3323.
51. Nei M (1978). Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89: 583-590.
52. Nybom H (2004). Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Mol Ecol 13: 1143-1155.
53. Pakniyat H, Powell W, Baird E, Handley LL, Robinson D, Scrimgeour CM et al (1997). AFLP variation in wild barley (Hordeum spontaneum). Genome 40: 332-341.
54. Peakall R, Smouse PE, Huff DR (1995). Evolutionary implications of allozyme and RAPD variation in diploid populations of dioecious buffalograss Buchloe dactyloides. Mol Ecol 4: 135-147.
55. Petit C, Freville H, Mignot A, Colas B, Riba M, Imbert E et al (2001). Gene flow and local adaptation in two endemic plant species. Biol Conservation 100: 21-34.
56. Podolsky RH (2001). Genetic variation for morphological and allozyme variation in relation to population size in Clarkia dudleyana, an endemic annual. Conservation Biol 15: 412-423.
57. Podolsky RH, Holtsford TP (1995). Population structure of morphological traits in Clarkia dudleyana.1. Comparison of Fst between allozymes and morphological traits. Genetics 140: 733-744.
58. Rogers AR, Harpending HC (1983). Population structure and quantitative characters. Genetics 105: 985-1002.
59. Rohlf FJ (1998). NTSYSpc Numerical Taxonomy and Multivariate Analysis System, version 2.0. Eeter Software: Setauket, New York.
60. Ross KG (1997). Multilocus evolution in fire ants: effects of selection, gene flow and recombination. Genetics 145: 961-974.
61. Ross KG, Krieger MJB, Shoemaker DD, Vargo EL, Keller L (1997). Hierarchical analysis of genetic structure in native fire ant populations: results from three classes of molecular markers. Genetics 147: 643-655.
62. Ross KG, Shoemaker DD, Krieger MJB, DeHeer CJ, Keller L (1999). Assessing genetic structure with multiple classes of molecular markers: a case study involving the introduced fire ant Solenopsis invicta. Mol Biol Evol 16: 525-543.
63. Simon JL (1995). Resampling: the New Statistics. Julian L Simon.
64. Slatkin M (1987). Gene flow and the geographic structure of natural populations. Science 236: 787-792.
65. Slatkin M, Wiehe T (1998). Genetic hitch-hiking in a subdivided population. Genet Res 71: 155-160.
66. Snow L, Brody T (1984). Genetic variation of Hordeum spontaneum in Israel: eco-geographical races, detected by trait measurements. Plant Syst Evol 145: 15-28.
67. Sokal RR, Wartenburg DE (1983). A test of spatial autocorrelation analysis using an isolation-by-distance model. Genetics 105: 219-237.
68. Spitze K (1993). Population structure in Daphnia obtusa: quantitative genetic and allozymic variation. Genetics 135: 367-374.
69. Steinger T, Haldimann P, Leiss KA, Muller-Scharer H (2002). Does natural selection promote population divergence? A comparative analysis of population structure using amplified fragment length polymorphism markers and quantitative traits. Mol Ecol 11: 2583-2590.
70. Storz JF (2002). Contrasting patterns of divergence in quantitative traits and neutral DNA markers: analysis of clinal variation. Mol Ecol 11: 2537-2551.
71. Sun M, Wong KC (2001). Genetic structure of three orchid species with contrasting breeding systems using RAPD and allozyme markers. Am J Botany 88: 2180-2188.
72. Szmidt AE, Wang XR, Lu MZ (1996). Empirical assessment of allozyme and RAPD variation in Pinus sylvestris (L) using haploid tissue analysis. Heredity 76: 412-420.
73. Turpeinen T, Tenhola T, Manninen O, Nevo E, Nissila E (2001). Microsatellite diversity associated with ecological factors in Hordeum spontaneum populations in Israel. Mol Ecol 10: 1577-1591.
74. Vandewoestijne S, Baguette M (2002). The genetic structure of endangered populations in the Cranberry Fritillary, Boloria aquilonaris (Lepidoptera, Nymphalidae): RAPDs vs allozymes. Heredity 89: 439-445.
75. Verhoeven KJF, Vanhala TK, Biere A, Nevo E, Van Damme JMM (2004). The genetic basis of adaptive population differentiation: a quantitative trait locus analysis of fitness traits in two wild barley populations from contrasting habitats. Evolution 58: 270-283.
76. Volis S, Mendlinger S, Turuspekov Y, Esnazarov U (2002a). Phenotypic and allozyme variation in Mediterranean and desert populations of wild barley, Hordeum spontaneum Koch. Evolution 56: 1403-1415.
77. Volis S, Mendlinger S, Ward D (2002b). Adaptive traits of wild barley plants of Mediterranean and desert origin. Oecologia 133: 131-138.
78. Volis S, Mendlinger S, Ward D (2002c). Differentiation along a gradient of environmental productivity and predictability in populations of Hordeum spontaneum Koch: multilevel selection analysis. Biol J Linnean Soc 75: 313-318.
79. Volis S, Mendlinger S, Ward D (2002d). Differentiation in populations of Hordeum spontaneum along a gradient of environmental productivity and predictability: life history and local adaptation. Biol J Linnean Soc 77: 479-490.
80. Volis S, Mendlinger S, Ward D (2002e). Differentiation in populations of Hordeum spontaneum Koch along a gradient of environmental productivity and predictability: plasticity in response to water and nutrient stress. Biol J Linnean Soc 75: 301-312.
81. Volis S, Shulgina I, Ward D, Mendlinger S (2003). Regional allozyme variation in wild barley, Hordeum spontaneum: adaptive or neutral? J Hered 94: 341-351.
82. Volis S, Verhoeven K, Mendlinger S, Ward D (2004). Phenotypic selection and regulation of reproduction in different environments in wild barley. J Evol Biol 17: 1121-1131.
83. Volis S, Yakubov B, Shulgina I, Ward D, Zur V, Mendlinger S (2001). Tests for adaptive RAPD variation in population genetic structure of wild barley, Hordeum spontaneum Koch. Biol J Linnean Soc 74: 289-303.
84. 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.
85. Wu J, Krutovskii KV, Strauss SH (1999). Nuclear DNA diversity, population differentiation, and phylogenetic relationships in the California closed-cone pines based on RAPD and allozyme markers. Genome 42: 893-908.
86. ST. Genetics 142: 1045-1052.
87. Yeh FC, Rong-Cai Y, Boyle T (1998). POPGENE VERSION 1.31. University of Alberta, Center for International Forestry Research: Edmonton, Alberta, Canada.