The relationship of nucleotide polymorphism, recombination rate and selection in wild tomato species

Genetics

Volumn 171, Issue 2, 2005, Pages 753-763

  Roselius, Kerstin ^a   Stephan, Wolfgang ^a   Städler, Thomas ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; GENE LOCUS; GENE MUTATION; GENETIC RECOMBINATION; GENETIC VARIABILITY; HAPLOTYPE; MUTATION RATE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIFFERENCE; TOMATO;

BASE SEQUENCE; GENETICS, POPULATION; HAPLOTYPES; LYCOPERSICON ESCULENTUM; MOLECULAR SEQUENCE DATA; MUTATION; POLYMORPHISM, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULATION DENSITY; RECOMBINATION, GENETIC; REPRODUCTION; SELECTION (GENETICS); SEQUENCE ANALYSIS, DNA;

LYCOPERSICON; LYCOPERSICON ESCULENTUM; LYCOPERSICON PERUVIANUM; SOLANUM;

EID: 31544473725     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.105.043877     Document Type: Article

References (77)

1. AGUADÉ, M., N. MIYASHITA and C. H. LANGLEY, 1989 Reduced variation in the yellow-achaete-scute region in natural populations of Drosophila melanogaster. Genetics 122: 607-615.
2. AWADALLA, P., and K. RITLAND, 1997 Microsatellite variation and evolution in the Mimulus guttatus species complex with contrasting mating systems. Mol. Biol. Evol. 14: 1023-1034.
3. BARRETT, S. C. H., 2003 Mating strategies in flowering plants: the outcrossing-selfing paradigm and beyond. Philos. Trans. R. Soc. Lond. B Biol. Sci. 358: 991-1004.
4. BAUDRY, E., C. KERDELHUÉ, H. INNAN and W. STEPHAN, 2001 Species and recombination effects on DNA variability in the tomato genus. Genetics 158: 1725-1735.
5. BEGUN, D. J., and C. F. AQUADRO, 1992 Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature 356: 519-520.
6. BROWN, G. R., G. P. GILL, R. J. KUNTZ, C. H. LANGLEY and D. B. NEALE, 2004 Nucleotide diversity and linkage disequilibrium in loblolly pine. Proc. Natl. Acad. Sci. USA 101: 15255-15260.
7. CAICEDO, A. L., and B. A. SCHAAL, 2004 Population structure and phylogeography of Solanum pimpinellifolium inferred from a nuclear gene. Mol. Ecol. 13: 1871-1882.
8. CHARLESWORTH, B., M. T. MORGAN and D. CHARLESWORTH, 1993 The effect of deleterious mutations on neutral molecular variation. Genetics 134: 1289-1303.
9. CHARLESWORTH, D., 2003 Effects of inbreeding on the genetic diversity of populations. Philos. Trans. R. Soc. Lond. B Biol. Sci. 358: 1051-1070.
10. CHARLESWORTH, D., B. CHARLESWORTH and M. T. MORGAN, 1995 The pattern of neutral molecular variation under the background selection model. Genetics 141: 1619-1632.
11. 1 Lycopersicon esculentum × Solanum lycopersicoides reveals overall synteny but suppressed recombination between these homeologous genomes. Genetics 154: 857-867.
12. DEVRIES, T. J., 1987 A review of geological evidence for ancient El Niño activity in Peru. J. Geophys. Res. 92: 14471-14479.
13. DVORAK, J., M.-C. LUO and Z.-L. YANG, 1998 Restriction fragment length polymorphism and divergence in the genomic regions of high and low recombination in self-fertilizing and cross-fertilizing Aegilops species. Genetics 148: 423-434.
14. DVORNYK, V., A. SIRVIÖ, M. MIKKONEN AND O. SAVOLAINEN, 2002 Low nucleotide diversity at the pal1 locus in the widely distributed Pinus sylvestris. Mol. Biol. Evol. 19: 179-188.
15. FU, Y.-X., and W. H. LI, 1993 Statistical tests of neutrality of mutations. Genetics 133: 693-709.
16. GANAL, M. W., R. CZIHAL, U. HANNAPPEL, D.-U. KLOOS, A. POLLEY et al., 1998 Sequencing of cDNA clones from the genetic map of tomato (Lycopersicon esculentum). Genome Res. 8: 842-847.
17. GEORGIADY, M. S., R. W. WHITKUS and E. M. LORD, 2002 Genetic analysis of traits distinguishing outcrossing and self-pollinating forms of currant tomato, Lycopersicon pimpinellifolium (Jusl.) Mill. Genetics 161: 333-344.
18. GRAUSTEIN, A., J. M. GASPAR, J. R. WALTERS and M. F. PALOPOLI, 2002 Levels of DNA polymorphism vary with mating system in the nematode genus Caenorhabditis. Genetics 161: 99-107.
19. GREGORY-WODZICKI, K. M., 2000 Uplift history of the central and northern Andes: a review. GSA Bull. 112: 1091-1105.
20. GUTIÉRREZ, J. R., and P. L. MESERVE, 2003 El Niño effects on soil seed bank dynamics in north-central Chile. Oecologia 134: 511-517.
21. HAMRICK, J. L., and M. J. W. GODT, 1990 Allozyme diversity in plant species, pp. 43-63 in Plant Population Genetics, Breeding, and Genetic Resources, edited by A. H. D. BROWN, M. T. CLEGG, A. L. KAHLER and B. S. WEIR. Sinauer Associates, Sunderland, MA.
22. HARTLEY, A. J., 2003 Andean uplift and climate change. J. Geol. Soc. Lond. 160: 7-10.
23. HELLMANN, I., I.EBERSBERGER, S. E. PTAK, S. PÄÄBO and M. PRZEWORSKI, 2003 A neutral explanation for the correlation of diversity with recombination rates in humans. Am. J. Hum. Genet. 72: 1527-1535.
24. HEY, J., and J. WAKELEY, 1997 A coalescent estimator of the population recombination rate. Genetics 145: 833-846.
25. HUDSON, R. R., 1987 Estimating the recombination parameter of a finite population model without selection. Genet. Res. 50: 245-250.
26. HUDSON, R. R., 2001 Two-locus sampling distributions and their application. Genetics 159: 1805-1817.
27. HUDSON, R. R., M. KREITMAN and M. AGUADÉ, 1987 A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
28. IGIC, B., L. BOHS and J. R. KOHN, 2004 Historical inferences from the self-incompatibility locus. New Phytol. 161: 97-105.
29. INGVARSSON, P. K., 2002 A metapopulation perspective on genetic diversity and differentiation in partially self-fertilizing plants. Evolution 56: 2368-2373.
30. INNAN, H., and W. STEPHAN, 2003 Distinguishing the hitchhiking and background selection models. Genetics 165: 2307-2312.
31. KIMURA, M., 1983 The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge, UK.
32. KRAFT, T., T. SÄLL, I. MAGNUSSON-RADING, N.-O. NILSSON and C. HALLDÉN, 1998 Positive correlation between recombination rates and levels of genetic variation in natural populations of sea beet (Beta vulgaris subsp. maritima). Genetics 150: 1239-1244.
33. LI, Y. J., Y. SATTA and N. TAKAHATA, 1999 Paleo-demography of the Drosophila melanogaster subgroup: application of the maximum likelihood method. Genes Genet. Syst. 74: 117-127.
34. LIU, F., D. CHARLESWORTH and M. KREITMAN, 1999 The effect of mating system differences on nucleotide diversity at the phosphoglucose isomerase locus in the plant genus Leavenworthia. Genetics 151: 343-357.
35. MADDISON, W. P., and D. R. MADDISON, 1992 MacClade3: Analysis of Phylogeny and Character Evolution. Sinauer Associates, Sunderland, MA.
36. MAYNARD SMITH, J., and J. HAIGH, 1974 The hitch-hiking effect of a favourable gene. Genet. Res. 23: 23-35.
37. McDONALD, J. H., and M. KREITMAN, 1991 Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
38. McVEAN, G., P. AWADALLA and P. FEARNHEAD, 2002 A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160: 1231-1241.
39. MILLER, J. C., and S. D. TANKSLEY, 1990 RFLP analysis of phylogenetic relationships and genetic variation in the genus Lycopersicon. Theor. Appl. Genet. 80: 437-448.
40. MONIZ DE SÁ, M., and G. DROUIN, 1996 Phylogeny and substitution rates of angiosperm actin genes. Mol. Biol. Evol. 13: 1198-1212.
41. NACHMAN, M. W., 1997 Patterns of DNA variability at X-linked loci in Mus domesticus. Genetics 147: 1303-1316.
42. NACHMAN, M. W., V. L. BAUER, S. L. CROWELL and C. F. AQUADRO, 1998 DNA variability and recombination rates at X-linked loci in humans. Genetics 150: 1133-1141.
43. NEI, M., 1987 Molecular Evolutionary Genetics. Columbia University Press, New York.
44. NORDBORG, M., and P. DONNELLY, 1997 The coalescent process with selfing. Genetics 146: 1185-1195.
45. NUNNEY, L., 2002 The effective size of annual plant populations: the interaction of a seed bank with fluctuating population size in maintaining genetic variation. Am. Nat. 160: 195-204.
46. PERALTA, I. E., and D. M. SPOONER, 2001 Granule-bound starch synthase (GBSSI) gene phylogeny of wild tomatoes (Solanum L. section Lycopersicon [Mill.] Wettst. subsection Lycopersicon). Am. J. Bot. 88: 1888-1902.
47. POLLAK, E., 1987 On the theory of partially inbreeding finite populations. I. Partial selfing. Genetics 117: 353-360.
48. RICK, C. M., 1979 Biosystematic studies in Lycopersicon and closely related species of Solanum, pp. 667-678 in The Biology and Taxonomy of the Solanaceae, edited by J. G. HAWKES, R. N. LESTER and A. D. SKELDING. Academic Press, New York.
49. RICK, C. M., 1983 Evolution of mating systems: evidence from allozyme variation, pp. 215-221 in Genetics: New Frontiers (Proc. XV International Congress of Genetics). Oxford and IBH Publishing, New Delhi.
50. RICK, C. M., and R. LAMM, 1955 Biosystematic studies on the status of Lycopersicon chilense. Am. J. Bot. 42: 663-675.
51. RICK, C. M., and J. I. YODER, 1988 Classical and molecular genetics of tomato: highlights and perspectives. Annu. Rev. Genet. 22: 281-300.
52. RICK, C. M., E. KESICKI, J. F. FOBES and M. HOLLE, 1976 Genetic and biosystematic studies on two new sibling species of Lycopersicon from Interandean Peru. Theor. Appl. Genet. 47: 55-68.
53. RICK, C. M., J. F. FOBES and M. HOLLE, 1977 Genetic variation in Lycopersicon pimpinellifolium: evidence of evolutionary change in mating system. Plant Syst. Evol. 127: 139-170.
54. RICK, C. M., M. HOLLE and R. W. THORP, 1978 Rates of cross-pollination in Lycopersicon pimpinellifolium: impact of genetic variation in floral characters. Plant Syst. Evol. 129: 31-44.
55. RICK, C. M., J. F. FOBES and S. D. TANKSLEY, 1979 Evolution of mating systems in Lycopersicon hirsutum as deduced from genetic variation in electrophoretic and morphological characters. Plant Syst. Evol. 132: 279-298.
56. ROSE, L., 2002 The population genetics and functional analysis of the Pto disease resistance gene in Lycopersicon spp. and the RPP13 gene in Arabidopsis thaliana. Ph.D. Thesis, University of California, Davis, CA.
57. ROZAS, J., J. C. SANCHÉZ-DELBARRIO, X. MESSEGUER and R. ROZAS, 2003 DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496-2497.
58. SAVOLAINEN, O., C. H. LANGLEY, B. P. LAZZARO and H. FRÉVILLE, 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.
59. SCHOEN, D. J., and A. H. D. BROWN, 1991 Intraspecific variation in population gene diversity and effective population size correlates with the mating system in plants. Proc. Natl. Acad. Sci. USA 88: 4494-4497.
60. SPOONER, D. M., G. J. ANDERSON and R. K. JANSEN, 1993 Chloroplast DNA evidence for the interrelationships of tomatoes, potatoes, and pepinos (Solanaceae). Am. J. Bot. 80: 676-688.
61. SPOONER, D. M., I. E. PERALTA and S. KNAPP, 2005 Comparison of AFLPs with other markers for phylogenetic inference in wild tomatoes. [Solanum L. section Lycopersicon (Mill.) Wettst.]. Taxon 54: 43-61.
62. STÄDLER, T., K. ROSELIUS and W. STEPHAN, 2005 Genealogical footprints of speciation processes in wild tomatoes: demography and evidence for historical gene flow. Evolution 59: 1268-1279.
63. STEPHAN, W., and C. H. LANGLEY, 1989 Molecular genetic variation in the centromeric region of the X chromosome in three Drosophila ananassae populations. I. Contrasts between the vermilion and forked loci. Genetics 121: 89-99.
64. STEPHAN, W., and C. H. LANGLEY, 1998 DNA polymorphism in Lycopersicon and crossing-over per physical length. Genetics 150: 1585-1593.
65. SWEIGART, A. L., and J. H. WILLIS, 2003 Patterns of nucleotide diversity in two species of Mimulus are affected by mating system and asymmetric introgression. Evolution 57: 2490-2506.
66. TAJIMA, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
67. TANKSLEY, S. D., M. W. GANAL, J. P. PRINCE, M. C. DE VICENTE, M. W. BONIERBALE et al., 1992 High density molecular linkage map of the tomato and potato genomes. Genetics 132: 1141-1160.
68. TAYLOR, I. B., 1986 Biosystematics of the tomato, pp. 1-34 in The Tomato Crop: A Scientific Basis for Improvement, edited by J. G. ATHERTON and J. RUDICH. Chapman & Hall, London.
69. TENAILLON, M. I., M. C. SAWKINS, A. D. LONG, R. L. GAUT, J. F. DOEBLEY et al., 2001 Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc. Natl. Acad. Sci. USA 98: 9161-9166.
70. TENAILLON, M. I., M. C. SAWKINS, L. K. ANDERSON, S. M. STACK, J. DOEBLEY et al., 2002 Patterns of diversity and recombination along chromosome 1 of maize (Zea mays ssp. mays L.). Genetics 162: 1401-1413.
71. TENAILLON, M. I., J. U'REN, O. TENAILLON and B. S. GAUT, 2004 Selection versus demography: a multilocus investigation of the domestication process in maize. Mol. Biol. Evol. 21: 1214-1225.
72. THOMPSON, J. D., D. G. HIGGINS and T. J. GIBSON, 1994 ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
73. TUDHOPE, S., and M. COLLINS, 2003 The past and future of El Niño. Nature 424: 261-262.
74. WALL, J. D., 2000 A comparison of estimators of the population recombination rate. Mol. Biol. Evol. 17: 156-163.
75. WANG, R. L., J. WAKELEY and J. HEY, 1997 Gene flow and natural selection in the origin of Drosophila pseudoobscura and close relatives. Genetics 147: 1091-1106.
76. WATTERSON, G. A., 1975 On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7: 256-276.
77. WRIGHT, S. I., B. LAUGA and D. CHARLESWORTH, 2002 Rates and patterns of molecular evolution in inbred and outbred Arabidopsis. Mol. Biol. Evol. 19: 1407-1420.