Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata

PLoS ONE

Volumn 3, Issue 6, 2008, Pages

  Ross Ibarra, Jeffrey ^a   Wright, Stephen I ^b   Foxe, John Paul ^b   Kawabe, Akira ^c   DeRose Wilson, Leah ^a   Gos, Gesseca ^b   Charlesworth, Deborah ^c   Gaut, Brandon S ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b YORK UNIVERSITY   (Canada)

^c UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS LYRATA; ARTICLE; CONTROLLED STUDY; DEMOGRAPHY; DNA SEQUENCE; EFFECT SIZE; EVOLUTIONARY ADAPTATION; GENE IDENTIFICATION; GENE LOCUS; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GEOGRAPHIC ORIGIN; GERMANY; LOCAL ADAPTATION; NATURAL SELECTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENETICS; SEQUENCE ANALYSIS; UNINDEXED SEQUENCE; ADAPTATION; GENE; GENETICS; PHYSIOLOGY;

ARABIDOPSIS LYRATA; ARABIDOPSIS THALIANA;

PLANT DNA;

ADAPTATION, PHYSIOLOGICAL; ARABIDOPSIS; DNA, PLANT; GENES, PLANT; POLYMORPHISM, GENETIC;

EID: 48749130911     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0002411     Document Type: Article

References (95)

1. Thornton KR, Jensen JD, Becquet C, Andolfatto P (2007) Progress and prospects in mapping recent selection in the genuine. Heredity 98: 340-348.
2. Begun DJ, Holloway AK, Stevens K, Hillier LW, et al. (2007) Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biol 5: e310 EP -.
3. Williamson SH, Hubisz MJ, Clark AG, Payseur BA, Bustamante CD, et al. (2007) Localizing recent adaptive evolution in the human genome. PLoS Genet 3: e90.
4. Clark RM, Schweikert G, Toomajian C, Ossowski S, et al. (2007) Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science 317: 338-342.
5. Wright SI, Bi IV, Schroeder SG, Yamasaki M, Doebley JF, et al. (2005) The effects of artificial selection on the maize genome. Science 308: 1310-1314.
6. Wakeley J, Aliacar N (2001) Gene genealogies in a metapopulation. Genetics 159: 893-905.
7. Eyre-Walker A, Gaut RL, Hilton H, Feldman DL, Gaut BS (1998) Investigation of the bottleneck leading to the domestication of maize. Proc Natl Acad Sci U S A 95: 4441-4446.
8. Haddrill PR, Thornton KR, Charlesworth B, Andolfatto P (2005) Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Res 15: 790-799.
9. Voight BF, Adams AM, Frisse LA, Qian Y, Hudson RR, et al. (2005) Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes. Proc Natl Acad Sci U S A 102: 18508-18513.
10. Zhu Q, Zheng X, Luo J, Gaut BS, et al. (2007) Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Mol Biol Evol 24: 875-888.
11. Hamrick JL, Godt MJW (1996) Effects of life history traits on genetic diversity in plant species. Philosophical Transactions of the Royal Society of London B Biological Sciences 351: 1291-1298.
12. Nybom H (2004) Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Molecular Ecology 13: 1143-1155.
13. Arunyawat U, Stephan W, Städler T (2007) Using multilocus sequence data to assess population structure, natural selection, and linkage disequilibrium in wild tomatoes. Mol Biol Evol 24: 2310-2322.
14. Eveno E, Collada C, Guevara MA, Valérie, et al. (2008) Contrasting patterns of selection at Pinus pinaster Ait. drought stress candidate genes as revealed by genetic differentiation analyses. Mol Biol Evol 25: 417-437.
15. Heuertz M, De Paoli E, Kallman T, Larsson H, Jurman I, et al. (2006) Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce [Picea abies (L.) Karst]. Genetics 174: 2095-2105.
16. Liu F, Charlesworth D, Kreitman M (1999) The effect of mating system differences on nucleotide diversity at the phosphoglucose isomerase locus in the plant genus Leavenworthia. Genetics 151: 343-357.
17. Liu F, Zhang L, Charlesworth D (1998) Genetic diversity in Leavenworthia populations with different inbreeding levels. Proc R Soc Lond B Biol Sci 265: 293-301.
18. Ma X-F, Szmidt AE, Wang X-R (2006) Genetic structure and evolutionary history of a diploid hybrid pine Pinus densata inferred from the nucleotide variation at seven gene loci. Mol Biol Evol 23: 807-816.
19. Moeller DA, Tenaillon MI, Tiffin P (2007) Population structure and its effects on patterns of nucleotide polymorphism in teosinte (Zea mays ssp. parviglumis). Genetics 176: 1799-1809.
20. Pyhajarvi T, Garcia-Gil MR, Knurr T, Mikkonen M, Wachowiak W, et al. (2007) Demographic history has influenced nucleotide diversity in European Pinus sylvestris populations. Genetics 177: 1713-1724.
21. Stadler T, Arunyawat U, Stephan W (2008) Population genetics of speciation in two closely related wild tomatoes (Solanum section Lycopersicon). Genetics 178: 339-350.
22. Pritchard JK, Przeworski M (2001) Linkage disequilibrium in humans: models and data. Am J Hum Genet 69: 1-14.
23. Tishkoff SA, Dietzsch E, Speed W, Pakstis AJ, Kidd JR, et al. (1996) Global patterns of linkage disequilibrium at the CD4 locus and modern human origins. Science 271: 1380-1387.
24. Clauss MJ, Mitchell-Olds T (2006) Population genetic structure of Arabidopsis lyrata in Europe. Molecular Ecology 15: 2753-2766.
25. Koch MA, Matschinger M (2007) Evolution and genetic differentiation among relatives of Arabidopsis thaliana. Proc Natl Acad Sci U S A 104: 6272-6277.
26. Ramos-Onsins SE, Stranger BE, Mitchell-Olds T, Aguade M (2004) Multilocus analysis of variation and speciation in the closely related species Arabidopsis halleri and A. lyrata. Genetics 166: 373-388.
27. Savolainen O, Langley CH, Lazzaro BP, Fréville H (2000) Contrasting patterns of nucleotide polymorphism at the alcohol dehydrogenase locus in the outcrossing Arabidopsis lyrata and the selfing Arabidopsis thaliana. Mol Biol Evol 17: 645-655.
28. Wright SI, Foxe JP, DeRose-Wilson L, Kawabe A, Looseley M, et al. (2006) Testing for effects of recombination rate on nucleotide diversity in natural populations of Arabidopsis lyrata. Genetics 174: 1421-1430.
29. Wright SI, Lauga B, Charlesworth D (2003) Subdivision and haplotype structure in natural populations of Arabidopsis lyrata. Molecular Ecology 12: 1247-1263.
30. Kivimäki M, Kärkkäinen K, Gaudeul M, Geir, et al. (2007) Gene, phenotype and function: GLABROUS1 and resistance to herbivory in natural populations of Arabidopsis lyrata. Molecular Ecology 16: 453-462.
31. Kärkkäinen K, Løe G, Agren J (2004) Population structure in Arabidopsis lyrata: evidence for divergent selection on trichome production. Evolution 58: 2831-2836.
32. Riihimäki M, Podolsky R, Kuittinen H, Koelewijn H, et al. (2005) Studying genetics of adaptive variation in model organisms: flowering time variation in Arabidopsis lyrata. Genetica 123: 63-74.
33. Sandring S, Riihimaki M-A, Savolainen O, Agren J (2007) Selection on flowering time and floral display in an alpine and a lowland population of Arabidopsis lyrata. Journal of Evolutionary Biology 20: 558-567.
34. Charlesworth D, Wright SI (2001) Breeding systems and genuine evolution. Current Opinion in Genetics & Development 11: 685-690.
35. Charlesworth D (2003) Effects of inbreeding on the genetic diversity of populations. Philos Trans R Soc Lond B Biol Sci 358: 1051-1070.
36. Muller MH, Leppala J, Savolainen O (2008) Genome-wide effects of postglacial colonization in Arabidopsis lyrata. Heredity 100: 47-58.
37. Clauss MJ, Mitchell-Olds T (2003) Population genetics of tandem trypsin inhibitor genes in Arabidopsis species with contrasting ecology and life history. Molecular Ecology 12: 1287-1299.
38. Wright SI, Lauga B, Charlesworth D (2002) Rates and patterns of molecular evolution in inbred and outbred Arabidopsis. Mol Biol Evol 19: 1407-1420.
39. Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theoretical Population Biology 7: 256-276.
40. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
41. Thornton K (2003) libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics 19: 2325-2327.
42. Weir BS (1990) Genetic data analysis: methods for discrete population genetic data. Sunderland, Mass: Sinauer Associates. pp xii, 377.
43. McVean G, Awadalla P, Fearnhead P (2002) A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160: 1231-1241.
44. Hudson RR (2001) Two-locus sampling distributions and their application. Genetics 159: 1805-1817.
45. Stephens M, Donnelly P (2003) A comparison of Bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet 73: 1162-1169.
46. Stephens M, Smith NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68: 978-989.
47. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
48. Hansson B, Kawabe A, Preuss S, Kuittinen H, et al. (2006) Comparative gene mapping in Arabidopsis lyrata chromosomes 1 and 2 and the corresponding A. thaliana chromosome 1: recombination rates, rearrangements and centromere location. Genet Res 87: 75-85.
49. Kawabe A, Hansson B, Forrest A, Hagenblad J, et al. (2006) Comparative gene mapping in Arabidopsis lyrata chromosomes 6 and 7 and A. thaliana chromosome IV: evolutionary history, rearrangements and local recombination rates. Genet Res 88: 45-56.
50. Koch MA, Haubold B, Mitchell-Olds T (2000) Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol Biol Evol 17: 1483-1498.
51. Becquet C, Przeworski M (2007) A new approach to estimate parameters of speciation models with application to apes. Genome Res 17: 1505-1519.
52. Fagundes NJR, Ray N, Beaumont M, Samuel, et al. (2007) Statistical evaluation of alternative models of human evolution. Proc Natl Acad Sci U S A 104: 17614-17619.
53. Wakeley J, Hey J (1997) Estimating ancestral population parameters. Genetics 145: 847-855.
54. Beaumont MA, Zhang W, Balding DJ (2002) Approximate Bayesian computation in population genetics. Genetics 162: 2025-2035.
55. Hamilton G, Stoneking M, Excoffier L (2005) Molecular analysis reveals tighter social regulation of immigration in patrilocal populations than in matrilocal populations. Proc Natl Acad Sci U S A 102: 7476-7480.
56. Hudson RR (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
57. Bakker EG, Toomajian C, Kreitman M, Bergelson J (2006) A genome-wide survey of R gene polymorphisms in Arabidopsis. Plant Cell 18: 1803-1818.
58. Thornton K, Andolfatto P (2006) Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster. Genetics 172: 1607-1619.
59. Beaumont MA (2005) Adaptation and speciation: what can Fst tell us? Trends in Ecology & Evolution 20: 435-440.
60. Beaumont MA, Balding DJ (2004) Identifying adaptive genetic divergence among populations from genome scans. Molecular Ecology 13: 969-980.
61. 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.
62. Li H, Stephan W (2006) Inferring the demographic history and rate of adaptive substitution in Drosophila. PLoS Genet 2: e166.
63. Caicedo AL, Williamson SH, Hernandez RD, Boyko A, Fledel-Alon A, et al. (2007) Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet 3: 1745-1756.
64. Balana-Alcaide D, Ramos-Onsins SE, Boone Q, Aguade M (2006) Highly structured nucleotide variation within and among Arabidopsis lyrata populations at the FAH1 and DFR gene regions. Molecular Ecology 15: 2059-2068.
65. Mable BK, Adam A (2007) Patterns of genetic diversity in outcrossing and selfing populations of Arabidopsis lyrata. Molecular Ecology 16: 3565-3580.
66. Wright S (1943) Isolation by Distance. Genetics 28: 114-138.
67. Kawabe A, Nasuda S, Charlesworth D (2006) Duplication of centromeric histone H3 (HTR12) gene in Arabidopsis halleri and A. lyrata, plant species with multiple centromeric satellite sequences. Genetics 174: 2021-2032.
68. Fay JC, Wu CI (2000) Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
69. Schlötterer C (2002) A microsatellite-based multilocus screen for the identification of local selective sweeps. Genetics 160: 753-763.
70. Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, et al. (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832-837.
71. Macknight R, Duroux M, Laurie R, Dijkwel P, Simpson G, et al. (2002) Functional significance of the alternative transcript processing of the Arabidopsis floral promoter FCA. Plant Cell 14: 877-888.
72. Macknight R, Bancroft I, Page T, Lister C, Schmidt R, et al. (1997) FCA, a gene controlling flowering time in Arabidopsis, encodes a protein containing RNA-binding domains. Cell 89: 737-745.
73. Quesada V, Macknight R, Dean C, Simpson GG (2003) Autoregulation of FCA pre-mRNA processing controls Arabidopsis flowering time. EMBO Journal 22: 3142-3152.
74. Li Y, Roycewicz P, Smith E, Borevitz JO (2006) Genetics of local adaptation in the laboratory: flowering time quantitative trait loci under geographic and seasonal conditions in Arabidopsis. PLoS ONE 1: e105.
75. Bergelson J, Dwyer JG, Emerson JJ (2001) Models and data on plant-enemy coevolution. Annu Rev Genet 35: 469-499.
76. Holub EB (2001) The arms race is ancient history in Arabidopsis, the wildflower. Nat Rev Genet 2: 516-527.
77. Tian D, Traw MB, Chen JQ, Kreitman M, Bergelson J (2003) Fitness costs of R-gene-mediated resistance in Arabidopsis thaliana. Nature 423: 74-77.
78. Touzet P, Budar F (2004) Unveiling the molecular arms race between two conflicting genomes in cytoplasmic male sterility? Trends in Plant Science 9: 568-570.
79. Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, et al. (2005) The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol 3: e196.
80. Schmid KJ, Törjék O, Meyer R, Schmuths H, Hoffmann MH, et al. (2006) Evidence for a large-scale population structure of Arabidopsis thaliana from genome-wide single nucleotide polymorphism markers. Theoretical and Applied Genetics 112: 1104-1114.
81. Bakker EG, Stahl EA, Toomajian C, Nordborg M, Kreitman M, et al. (2006) Distribution of genetic variation within and among local populations of Arabidopsis thaliana over its species range. Molecular Ecology 15: 1405-1418.
82. Kuittinen H, Haan AAd, Vogl C, Oikarinen S, et al. (2004) Comparing the linkage maps of the close relatives Arabidopsis lyrata and A. thaliana. Genetics 168: 1575-1584.
83. Kim S, Plagnol V, Hu TT, Toomajian C, et al. (2007) Recombination and linkage disequilibrium in Arabidopsis thaliana. Nat Genet 39: 1151-1155.
84. Plagnol V, Padhukasahasram B, Wall JD, Marjoram P, Nordborg M (2006) Relative influences of crossing over and gene conversion on the pattern of linkage disequilibrium in Arabidopsis thaliana. Genetics 172: 2441-2448.
85. Abbott RJ, Gomes MF (1989) Population genetic structure and outcrossing rate of Arabidopsis thaliana (L.) Heynh. Heredity 62: 411-418.
86. 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.
87. Hamrick JL, Nason JD (1996) Consequences of dispersal in plants. In: Rhodes OE, Chester RK, Smith MH, eds. Population Dynamics in Ecological Space and Time University of Chicago Press. pp 203-236.
88. Ingvarsson PK (2002) A metapopulation perspective on genetic diversity and differentiation in partially self-fertilizing plants. Evolution Int J Org Evolution 56: 2368-2373.
89. Nordborg M, Donnelly P (1997) The coalescent process with selfing. Genetics 146: 1185-1195.
90. Sharbel TF, Haubold B, Mitchell-Olds T (2000) Genetic isolation by distance in Arabidopsis thaliana: biogeography and postglacial colonization of Europe. Molecular Ecology 9: 2109-2118.
91. Innan H, Stephan W (2000) The coalescent in an exponentially growing metapopulation and its application to Arabidopsis thaliana. Genetics 155: 2015-2019.
92. Schmid KJ, Ramos-Onsins S, Ringys-Beckstein H, Weisshaar B, Mitchell-Olds T (2005) A multilocus sequence survey in Arabidopsis thaliana reveals a genome-wide departure from a neutral model of DNA sequence polymorphism. Genetics 169: 1601-1615.
93. Bergelson J, Stahl E, Dudek S, Kreitman M (1998) Genetic variation within and among populations of Arabidopsis thaliana. Genetics 148: 1311-1323.
94. Borevitz JO, Hazen SP, Michael TP, Morris GP, Baxter IR, et al. (2007) Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana. Proc Natl Acad Sci U S A 104: 12057-12062.
95. Toomajian C, Hu TT, Aranzana MJ, Lister C, Tang C, et al. (2006) A nonparametric test reveals selection for rapid flowering in the Arabidopsis genome. PLoS Biol 4: e137.