Local recombination and mutation effects on molecular evolution in Drosophila

Genetics

Volumn 153, Issue 3, 1999, Pages 1285-1296

  Takano Shimizu, Toshiyuki ^a  

^a NATIONAL INSTITUTE OF GENETICS   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; DNA SEQUENCE; DROSOPHILA MELANOGASTER; FEMALE; GENE MUTATION; GENETIC RECOMBINATION; IN SITU HYBRIDIZATION; MALE; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; TELOMERE; X CHROMOSOME;

ANIMALS; BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORS; CHROMOSOME MAPPING; DNA; DNA MUTATIONAL ANALYSIS; DNA-BINDING PROTEINS; DROSOPHILA; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; EVOLUTION, MOLECULAR; GENETIC MARKERS; INSECT PROTEINS; MUTATION; PHYLOGENY; RECOMBINATION, GENETIC; TRANSCRIPTION FACTORS; X CHROMOSOME;

DROSOPHILA ERECTA; DROSOPHILA MELANOGASTER; DROSOPHILA ORENA; DROSOPHILA YAKUBA; MELANOGASTER;

EID: 0032758253     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (81)

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. AKASHI, H., 1994 Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics 136: 927-935.
3. AKASHI, H., 1995 Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA. Genetics 139: 1067-1076.
4. AKASHI, H., 1996 Molecular evolution between Drosophila melanogasler and D. simulans: reduced codon bias, faster rates of amino acid substitution, and larger proteins in D. melanogaster. Genetics 144: 1297-1307.
5. AKASHI, H., and S. W. SCHAEFFER, 1997 Natural selection and the frequency distributions of "silent" DNA polymorphism in Drosophila. Genetics 146: 295-307.
6. ALONSO, M. C., and C. V. CABRERA, 1988 The achaete-scute gene complex of Drosophila melanogaster comprises four homologous genes. EMBO J. 7: 2585-2591.
7. ANDERSSON, D. I., and D. HUGHES, 1996 Muller's ratchet decreases fitness of a DNA-based microbe. Proc. Natl. Acad. Sci. USA 93: 906-907.
8. BARTON, N. H., 1995 Linkage and the limits to natural selection. Genetics 140: 821-841.
9. 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.
10. BENNETZEN, J. L., and B. D. HALL, 1982 Codon selection in yeast. J. Biol. Chem. 257: 3026-3031.
11. BIRKY, C. W., JR., and J. B. WALSH, 1988 Effects of linkage on rates of molecular evolution. Proc. Natl. Acad. Sci. USA 85: 6414-6418.
12. BULMER, M., 1991 The selection-mutation-drift theory of synonymous codon usage. Genetics 129: 897-907.
13. CARIOU, M. L., 1987 Biochemical phylogeny of the eight species in the Drosophila melanogaster subgroup, including D. sechellia and D. orena. Genet. Res. 50: 181-185.
14. CARULLI, J. P., D. E. KRANE, D. L. HARTL and H. OCHMAN, 1993 Compositional heterogeneity and patterns of molecular evolution in the Drosophila genome. Genetics 134: 837-845.
15. CHAO, L., 1990 Fitness of RNA virus decreased by Muller's ratchet. Nature 348: 454-455.
16. CHARLESWORTH, B., 1994 The effect of background selection against deleterious mutations on weakly selected, linked variants. Genet. Res. 63: 213-227.
17. CHARLESWORTH, B., M. T. MORGAN and D. CHARLESWORTH, 1993 The effect of deleterious mutations on neutral molecular variation. Genetics 134: 1289-1303.
18. CHOU, T.-B., Z. ZACHAR and P. M. BINGHAM, 1987 Developmental expression of a regulatory gene is programmed at the level of splicing. EMBO J. 6: 4095-4104.
19. COMERON, J. M., M. KREITMAN and M. AGUADÉ, 1999 Natural selection on synonymous sites is correlated with gene length and recombination in Drosophila. Genetics 151: 239-249.
20. DUARTE, K., D. CLARKE, A. MOYA, E. DOMINGO and J. HOLLAND, 1992 Rapid fitness losses in mammalian RNA virus clones due to Muller's ratchet. Proc. Natl. Acad. Sci. USA 89: 6015-6019.
21. DVOŘÁK, J., M.-C. LUO and Z.-I., 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.
22. ELLIS, H. M., D. R. SPANN and J. W. POSAKONY, 1990 extramacrochaetae, a negative regulator of sensory organ development in Drosophila, defines a new class of helix-loop-helix proteins. Cell 61: 27-38.
23. EYRE-WALKER, A., and M. BULMER, 1993 Synonymous substitution rates in Enterobacteria. Genetics 140: 1407-1412.
24. FELSENSTEIN, J., 1974 The evolutionary advantage of recombination. Genetics 78: 737-756.
25. FISHER, R. A., 1930 The Genetical Theory of Natural Selection. Clarendon Press, Oxford.
26. GARRELL, J., and J. MODOLELL, 1990 The Drosophila extramacrochaetae locus, an antagonist of proneural genes that, like these genes, encodes a helix-loop-helix protein. Cell 61: 39-48.
27. GEYER, P. K., and V. G. CORCES, 1987 Separate regulatory elements are responsible for the complex pattern of tissue-specific and developmental transcription of the yellow locus in Drosophila melanognster. Genes Dev. 1: 996-1004.
28. GEYER, P. K., C. SPANA and V. G. CORCES, 1986 On the molecular mechanism of gypsy-induced mutations at the yellow locus of Drosophila melanogaster. EMBO J. 5: 2657-2662.
29. GILLESPIE, J. H., 1994 Substitution processes in molecular evolution. III. Deleterious alleles. Genetics 138: 943-952.
30. GRANTHAM, R., C. GAUTIER, M. GOUY, R. MERCIER and A. PAVÉ, 1980 Codon catalog usage and the genome hypothesis. Nucleic Acids Res. 8: r49-r62.
31. HILL, W. G., and A. ROBERTSON, 1966 The effect of linkage on limits to artificial selection. Genet. Res. 8: 269-294.
32. HONGYO, T., G. S. BUZARD, R. J. CALVERT and C. M. WEGHORST, 1993 'Cold SSCP': a simple, rapid and non-radioactive method for optimized single-strand conformation polymorphism analyses. Nucleic Acids Res. 21: 3637-3642.
33. IKEMURA, T., 1981a Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in ils protein genes. J. Mol. Biol. 146: 1-21.
34. IKEMURA, T., 1981b Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J. Mol. Biol. 151: 389-409.
35. IKEMURA, T., 1982 Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes: differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs. J. Mol. Biol. 158: 573-597.
36. IWASA, Y., 1993 Overdispersed molecular evolution in constant environments. J. Theor. Biol. 164: 373-393.
37. JEFFS, P. S., E. C. HOLMES and M. ASHBURNER, 1994 The molecular evolution of the alcohol dehydrogenase and alcohol dehydrogenase-related genes in the Drosophila melanogaster species subgroup. Mol. Biol. Evol. 11: 287-304.
38. KAPLAN, N. L., R. R. HUDSON and C. H. LANGLEY, 1989 The "hitchhiking effect" revisited. Genetics 123: 887-899.
39. KIMURA, M., 1981 Possibility of extensive neutral evolution under stabilizing selection with special reference to nonrandom usage of synonymous codons. Proc. Natl. Acad. Sci. USA 78: 5773-5777.
40. KLIMAN, R. M., and A. EYRE-WALKER, 1998 Patterns of base composition within the genes of Drosophila melanogaster. J. Mol. Evol. 46: 534-541.
41. KLIMAN, R. M., and J. HEY, 1993 Reduced natural selection associated with low recombination in Drosophila melanogaster. Mol. Biol. Evol. 10: 1239-1258.
42. KLIMAN, R. M., and J. HEY, 1994 The effects of mutation and natural selection on codon bias in the genes of Drosophila. Genetics 137: 1049-1056.
43. LEMEUNIER, F., and M. ASHBURNER, 1976 Relationships within the melanogaster species subgroup of the genus Drosophila (Sophophora). II. Phylogenetic relationships between six species based upon polytene chromosome banding sequences. Proc. R. Soc. Lond. Ser. B 193: 275-294.
44. LI, W.-H., 1987 Models of nearly neutral mutations with particular implications for nonrandom usage of synonymous codons. J. Mol. Evol. 24: 337-345.
45. LINDSLEY, D. L., and L. SANDLER, 1977 The genetic analysis of meiosis in female Drosophila melanogaster. Philos. Trans. R. Soc. Lond. Biol. Sci. 277: 295-312.
46. LINDSLEY, D. L., and G. G. ZIMM, 1992 The Genome of Drosophila melanogaster. Academic Press, San Diego.
47. LYNCH, M., 1997 Mutation accumulation in nuclear, organelle, and prokaryotic transfer RNA genes. Mol. Biol. Evol. 14: 914-925.
48. MARTÍN-CAMPOS, J. M., J. M. COMERÓN, N. MIYASHITA and M. AGUADÉ, 1992 Intraspecific and interspecific variation at the y-ac-sc region of Drosophila simulans and Drosophila melanogaster. Genetics 130: 805-816.
49. MAYNARD SMITH, J., and J. HAIGH, 1974 The hitch-hiking effect of a favourable gene. Genet. Res. 23: 23-35.
50. MELNICK, M. B., E. NOLL and N. PERRIMON, 1993 The Drosophila stubarista phenotype is associated with a dosage effect of the putative ribosome-associated protein D-p40 on spineless. Genetics 135: 553-564.
51. MIYATA, T., and T. YASUNAGA, 1980 Molecular evolution of mRNA: a method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application. J. Mol. Evol. 16: 23-36.
52. MORIYAMA, E. N., and T. GOJOBORI, 1992 Rates of synonymous substitution and base composition of nuclear genes in Drosophila. Genetics 130: 855-864.
53. MORIYAMA, K. N., and J. R. POWELL, 1997 Codon usage bias and tRNA abundance in Drosophila. J. Mol. Evol. 45: 514-523.
54. MOSCOSO DEL PRADO, J., and A. GARCIA-BELLIDO, 1984 Genetic regulation of the achaete-scute complex of Drosophila melanogaster. Roux's Arch. Dev. Biol. 193: 242-245.
55. MUNTÉ, A., M. AGUADÉ and C. SEGARRA, 1997 Divergence of the yellow gene between Drosophila melanogaster and D. subobscura: recombination rate, codon bias and synonymous substitutions. Genetics 147: 165-175.
56. NACHMAN, M. W., 1997 Patterns of DNA variability at X-linked loci in Mus domesticus. Genetics 147: 1303-1316.
57. OHTA, T., 1992 The nearly neutral theory of molecular evolution. Annu. Rev. Ecol. Syst. 23: 263-286.
58. ORITA, M., H. IWAHANA, M. KANAZAWA, K. HAYASHI and T. SEKIYA, 1989 Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc. Natl. Acad. Sci. USA 86: 2706-2770.
59. PECK, J. R., 1994 A ruby in the rubbish: beneficial mutations, deleterious mutations and the evolution of sex. Genetics 137: 597-606.
60. RICE, W. R., 1994 Degeneration of a nonrecombining chromosome. Science 263: 230-232.
61. SANTIAGO, E., and A. CABALLERO, 1998 Effective size and polymorphism of linked neutral loci in populations under directional selection. Genetics 149: 2105-2117.
62. SCHULTZ, J., and H. REDFIELD, 1951 Interchromosomal effects on crossing over in Drosophila. Cold Spring Harbor Symp. Quant. Biol. 16: 175-197.
63. SHARP, P. M., and W.-H. LI, 1986 An evolutionary perspective on synonymous codon usage in unicellular organisms. J. Mol. Evol. 24: 28-38.
64. SHARP, P. M., and W.-H. LI, 1989 On the rate of DNA sequence evolution in Drosophila. J. Mol. Evol. 28: 398-402.
65. SHIBATA, H., and T. YAMAZAKI, 1995 Molecular evolution of the duplicated Amy locus in the Drosophila melanogaster species subgroup: concerted evolution only in the coding region and an excess of nonsynonymous substitutions in speciation. Genetics 141: 223-236.
66. SHIELDS, D. C., P. M. SHARP, D. G. HIGGINS and K. WRIGHT, 1988 "Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Mol. Biol. Evol. 5: 704-716.
67. SNIEGOWSKI, P. D., A. PRINGLE and K. A. HUGHES, 1994 Effects of autosomal inversions on meiotic exchange in distal and proximal regions of the X chromosome in a natural population of Drosophila melanogaster. Genet. Res. 63: 57-62.
68. SOLIGNAC, M., M. MONNEROT and J.-C. MOUNOLOU, 1986 Mitochondrial DNA evolution in the melanogaster species subgroup of Drosophila. J. Mol. Evol. 23: 31-40.
69. 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.
70. STEPHAN, W., and C. H. LANGLEY, 1998 DNA polymorphism in Lycopersicon and crossing-over per physical length. Genetics 150: 1585-1593.
71. STEVENS, W. L., 1942 Accuracy of mutation rates. J. Genet. 43: 301-307.
72. SUEOKA, N., 1993 Directional mutation pressure, mutator mutations, and dynamics of molecular evolution. J. Mol. Evol. 37: 137-153.
73. TAJIMA, F., 1993 Simple methods for testing the molecular evolutionary clock hypothesis. Genetics 135: 599-607.
74. TAKAHATA, N., 1987 On the overdispersed molecular clock. Genetics 116: 169-179.
75. TAKANO, T. S., 1998 Rate variation of DNA sequence evolution in the Drosophila lineages. Genetics 149: 959-970.
76. THIERY, J.-P., G. MACAYA and G. BERNARDI, 1976 An analysis of eukaryotic genomes by density gradient centrifugation. J. Mol. Biol. 108: 219-235.
77. THOMPSON, J. D., D. G. HIGGINS and T. J. GIBSON, 1994 GLUSTAL W: 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.
78. TRUE, J. R., J. M. MERCER and C. C. LAURIE, 1996 Differences in crossover frequency and distribution among three sibling species of Drosophila. Genetics 142: 507-523.
79. VILLARES, R., and C. V. CABRERA, 1987 The achaete-scute gene complex of D. melanogaster: conserved domains in a subset of genes required for neurogenesis and their homology to myc. Cell 50: 415-424.
80. WRIGHT, S., 1931 Evolution in Mendelian populations. Genetics 16: 97-159.
81. ZENG, L.-W., J. M. COMERON, B. CHEN and M. KREITMAN, 1998 The molecular clock revisited: the rate of synonymous vs. replacement change in Drosophila. Genetica 102/103: 369-382.