Effect of inversion polymorphism on the neutral nucleotide variability of linked chromosomal regions in drosophila

Genetics

Volumn 155, Issue 2, 2000, Pages 685-698

  Navarro, Arcadio ^a,b   Barbadilla, Antonio ^a   Ruiz, Alfredo ^a  

^a UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME INVERSION; CHROMOSOME POLYMORPHISM; COMPUTER SIMULATION; DROSOPHILA; GENE EXPRESSION; GENE MUTATION; GENETIC RECOMBINATION; GENETIC VARIABILITY; NONHUMAN; PRIORITY JOURNAL;

ANIMALS; DROSOPHILA; INVERSION, CHROMOSOME; LINKAGE (GENETICS); MODELS, GENETIC; POLYMORPHISM, GENETIC;

EID: 0034096314     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (78)

1. AGUADÉ, M., 1988 Restriction map variation at the Adh locus of Drosophila melanogaster in inverted an noninverted chromosomes. Genetics 119: 135-140.
2. AKASHI, H., 1996 Molecular evolution between Drosophila melanogaster and D. simulans: reduced codon bias, faster rates of amino acid substitution, and larger proteins in D. melanogaster. Genetics 144: 1297-1307.
3. ANDOLFATTO, P., J. D. WALL and M. KRETTMAN, 1999 Unusual haplotype structure at the proximal breakpoint of In(2L)t in a natural population of Drosophila melanogaster. Genetics 153: 1297-1311.
4. AQUADRO, C. F., and D. J. BEGUN, 1993 Evidence for an implication of genetic hitchhiking in the Drosophila genome, pp. 159-178 in Mechanisms of Molecular Evolution, edited by N. TAKAHATA and A. G. CLARK. Sinauer Associates, Sunderland, MA.
5. AQUADRO, C. F., S. F. DESSE, M. M. BLAND, C. H. LANGLEY and C. C. LAURIE-AHLBERG, 1986 Molecular population genetics of the alcohol dehydrogenase gene region of Drosophila melanogaster. Genetics 114: 1165-1190.
6. AQUADRO, C. F., D. J. BEGUN and E. C. KINDAHL, 1994 Selection, recombination and DNA polymorphism in Drosophila, pp. 46-56 in Non-Neutral Evolution, edited by B. GOLDING, Chapman & Hall, New York.
7. ASHBURNER, M., 1989 Drosophila: A Laboratory Handbook. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
8. BEGUN, D. J., 1996 Population genetics of silent and replacement variation in Drosophila simulans and D. melanogaster: X/autosomes differences? Mol. Biol. Evol. 13: 1405-1407.
9. BÉNASSI, V., S. AULARD, S. MAZEAU and M. VEUILLE, 1993 Molecular variation of Adh and P6 genes in an African population of Drosophila melanogaster and its relation to chromosomal inversions. Genetics 134: 789-799.
10. BRAVERMAN, J. M., R. R. HUDSON, N. L. KAPLAN C. H. LANGLEY and W. STEPHAN, 1995 The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. Genetics 140: 783-796.
11. CÁCERES, M., J. M. RANZ, A. BARBADILLA, M. LONG and A. RUIZ, 1999 Generation of a widespread Drosophila inversion by a transposable element. Science 285: 415-418.
12. CHARLESWORTH, B., 1974 Inversion polymorphism in a two-locus genetic system. Genet. Res. 23: 259-280.
13. CHARLESWORTH, B., 1994 The effect of background selection against deleterious mutations on weakly selected, linked variants. Genet. Res. 63: 213-227.
14. CHARLESWORTH, B., and D. CHARLESWORTH, 1973 Selection of new inversions in multilocus genetic systems. Genet. Res. 21: 167-183.
15. CHARLESWORTH, B., M. T. MORGAN and D. CHARLESWORTH, 1993 The effect of deleterious mutations on neutral molecular variation. Genetics 134: 1289-1303.
16. CHOVNICK, A., 1973 Gene conversion and transfer of genetic information within the inverted region of inversion heterozygotes. Genetics 75: 123-131.
17. DEPAULIS, F., L. BRAZIER and M. VEUILLE, 1999 Selective sweep at the Drosophila melanogaster Supressor of Hairless locus and its association with the In(2L)t inversion polymorphism. Genetics 152: 1017-1024.
18. DOBZHANSKY, TH., 1970 Genetics of the Evolutionary Process. Columbia University Press, New York.
19. HASSON, E., and W. EANES, 1996 Contrasting histories of three gene regions associated with In(3L) Payne of Drosophila melanogaster. Genetics 144: 1565-1575.
20. HEY, J., 1991 A multi-dimensional coalescent process applied to multiallelic selection models and migration models. Theor. Popul. Biol. 39: 30-48.
21. HUDSON, R. R., 1983 Properties of a neutral alleles model with intragenic recombination. Theor. Popul. Biol. 23: 183-201.
22. HUDSON, R. R., 1990 Gene genealogies and the coalescent process. Oxf. Surv. Evol. Biol. 7: 1-44.
23. HUDSON, R. R., 1993 The how and why of generating gene genealogies, pp. 23-36 in Mechanisms of Molecular Evolution, edited by N. TAKAHATA and A. G. CLARK. Sinauer Associates, Sunderland, MA.
24. HUDSON, R. R., 1994 How can the low levels of Drosophila sequence variation in regions of the genome with low levels of recombination be explained. Proc. Natl. Acad. Sci. USA 91: 6815-6818.
25. HUDSON, R. R., and N. L. KAPLAN. 1988 The coalescent process in models with selection and recombination. Genetics 120: 831-840.
26. HUDSON, R. R., and N. L. KAPLAN, 1995 Deleterious background selection with recombination. Genetics 141: 1605-1617.
27. KAPLAN, N. L., T. DARDEN and R. R. HUDSON, 1988 The coalescent process in models with selection. Genetics 120: 841-848.
28. KAPLAN, N. L., R. R. HUDSON and C. H. LANGLEY, 1989 The "hitchhiking effect" revisited. Genetics 123: 887-899.
29. KIMURA, M., 1969 The rate of molecular evolution considered from the standpoint of population genetics. Proc. Natl. Acad. Sci. USA 63: 1181-1188.
30. KREITMAN, M., 1983 Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster. Nature 304: 412-417.
31. KREITMAN, M., and M. L. WAYNE, 1994 Organization of genetic variation at the molecular level: lessons from Drosophila, pp. 157-183 in Molecular Ecology and Evolution: Approaches and Implications, edited by D. SCHIERWATER, B. STREIT, G. P. WAGNER and R. DE SALLE. Birkhäuser, Basel.
32. KRIMBAS, C. B., and J. R. POWELL. 1992 Drosophila Inversion Polymorphism. CRC Press, Boca Raton, FL.
33. LABATE, J. A., C. H. BIERMANN and W. F. EANES, 1999 Nucleotide variation at the runt locus in Drosophila melanogaster and Drosophila simulans. Mol. Biol. Evol. 16: 724-731.
34. LEWONTIN, R. C., 1981 The scientific work of Th. Dobzhansky, pp. 93-115 Dobzhansky's Genetics of Natural Populations, edited by R. C. LEWONTIN, J. A. MOORE, W. B. PROVINE and B. WALLACE. Columbia University Press, New York.
35. LINDSLEY, D. L., and L. SANDLER, 1977 The genetic analysis of meiosis in female Drosophila melanogaster. Philos. Trans. R. Soc. Lond. B Biol. Sci. 277: 295-312.
36. MAYURAMA, T., 1971 An invariant property of a structured population. Genet. Res. 18: 81-84.
37. MORIYAMA, E. N., and J. R. POWELL., 1996 Intraspecific nuclear DNA variation in Drosophila. Mol. Biol. Evol. 13: 261-277.
38. NACHMAN, M. W., 1997 Patterns of DNA variability at X-linked loci in Mus domesticus. Genetics 147: 1303-1316.
39. 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.
40. NAGYLAKI, T., 1982 Geographical invariance in population genetics. J. Theor. Biol. 99: 159-172.
41. NAGYLAKI, T., 1992 Introduction to Theoritical Population Genetics. Springer-Verlag, Berlin.
42. NAVARRO, A., and A. RUIZ, 1997 On the fertility effects of pericentric inversions. Genetics 147: 931-933.
43. NAVARRO, A., E. BETRÁN, C. ZAPATA and A. RUIZ, 1996 Dynamics of gametic disequilibria between loci linked to chromosome inversions: the recombination redistributing effect of inversions. Genet. Res. 67: 67-76.
44. NAVARRO, A., E. BETRÁN, A. BARBADILLA and A. RUIZ, 1997 Recombination and gene flux caused by crossing over and gene conversion in inversion heterokaryotypes. Genetics 146: 695-709.
45. NEI, M., 1987 Molecular Evolutionary Genetics. Columbia University Press, New York.
46. NEI, M., K.-I. KOJIMA and H. E. SCHAEFFER, 1967 Frequency changes of new inversions in populations under mutation-selection equilibria. Genetics 57: 741-750.
47. NORDBORG, M., 1997 Structured coalescent processes on different time scales. Genetics 146: 1501-1514.
48. NOTOHARA, M., 1990 The coalescent and the genealogical process in geographically structured populations. J. Math. Biol. 29: 59-75.
49. OHTA, T., and K.-I. KOJIMA, 1968 Survival probabilities of new inversions in large populations. Biometrics 24: 501-516.
50. PAYNE, F., 1924 Crossover modifiers in the third chromosome of Drosophila melanogaster. Genetics 9: 327-342.
51. POPADIĆ, A., and W. ANDERSON, 1995 Evidence of gene conversion in the Amylase multigene family of Drosophila pseudoobscura. Mol. Biol. Evol. 12: 564-572.
52. POPADIĆ, A., D. POPADIĆ and W. ANDERSON, 1995 Interchromosomal exchange of genetic information between gene arrangements on the third chromosome of Drosophila pseudoobscura. Mol. Biol. Evol. 12: 938-943.
53. POWELL, J. R., 1997 Progress and Prospects in Evolutionary Biology: The Drosophila Model. Oxford University Press, Oxford.
54. PRAKASH, S., and R. C. LEWONTIN, 1968 A molecular approach to the study of genetic heterozygosity in natural populations. III. Direct evidence of coadaptation in gene arrangements of Drosophila. Proc. Natl. Acad. Sci. USA 59: 398-405.
55. RANZ, J. M., C. SEGARRA and A. RUIZ, 1997 Chromosomal homology and molecular organization of Muller's elements D and E in the Drosophila repleta species group. Genetics 145: 281-295.
56. RANZ, J. M., M. CÁCERES and A. RUÍZ, 1999 Comparative mapping of cosmids and gene clones from a 1.6 Mb chromosomal region of Drosophila melanogaster in three species of the distantly related subgenus Drosophila. Chromosoma 108: 32-43.
57. ROZAS, J., and M. AGUADÉ, 1993 Transfer of genetic information in the rp49 region of Drosophila subobscura between different chromosomal gene arrangements. Proc. Natl. Acad. Sci. USA 90: 8083-8087.
58. ROZAS, J., and M. AGUADÉ, 1994 Gene conversion is involved in the transfer of genetic information between naturally occurring inversions of Drosophila. Proc. Natl. Acad. Sci. USA 91: 11517-11521.
59. ROZAS, J., C. SEGARRA, G. RIBÓ and M. AGUADÉ, 1999 Molecular population genetics of the rp49 gene region in different chromosomal inversions of Drosophila subobscura. Genetics 151: 189-202.
60. SLATKIN, M., 1987 The average number of sites separating DNA sequences drawn from a subdivided population. Theor. Popul. Biol. 32: 42-49.
61. SORSA, V., 1988 Polytene Chromosomes in Genetic Research. John Wiley & Sons, New York.
62. SPERLICH, D., and P. PERIEM, 1986 Chromosomal polymorphism in natural and experimental populations, pp. 257-309 in The Genetics and Biology of Drosophila, edited by M. ASHBURNER, H. L. CARSON and J. N. THOMPSON JR., Vol. 3e, Academic Press, London.
63. STEPHAN, W., and C. H. LANGLEY, 1998 DNA polymorphism in Lycopersicon and crossing-over per physical length. Genetics 150: 1585-1593.
64. STEPHAN W., T. H. E. WIEHE and M. W. LENZ, 1992 The effect of strongly selected substitutions on neutral polymorphism: analytical results based on diffusion theory. Theor. Popul. Biol. 41: 237-254.
65. STROBECK, C., 1983 Expected linkage disequilibrium for a neutral locus linked to a chromosomal arrangement. Genetics 103: 545-555.
66. STROBECK, C., 1987 Average number of nucleotide differences in a sample from a single subpopulation: a test for population subdivision. Genetics 117: 149-153.
67. STURTEVANT, A. H., and G. W. BEADLE, 1936 The relations of inversions in the X chromosome of Drosophila melanogaster to crossing over and disjunction. Genetics 21: 544-604.
68. TAJIMA, F., 1983 Evolutionary relalionship of DNA sequences in finite populations. Genetics 105: 437-460.
69. TAJIMA, F., 1989a DNA polymorphism in a subdivided population: the expected number of segregating sites in the two-subpopulation model. Genetics 123: 229-240.
70. TAJIMA, F., 1989b Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
71. TAJIMA, F., 1993 Measurement of DNA polymorphism, pp. 37-59 in Mechanisms of Molecular Evolution, edited by N. TAKAHATA and A. G. CLARK. Sinauer Associates, Sunderland, MA.
72. 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.
73. WAKELEY, J., 1996 The variance of pairwise nucleotide differences in two populations with migration. Theor. Popul. Biol. 49: 39-57.
74. WATTERSON, G. A., 1975 On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7: 256-276.
75. WESLEY, C. S., and W. F. EANES, 1994 Isolation and analysis of the breakpoint sequences of chromosome inversion In(3L)Payne in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 91: 3132-3136.
76. ZAPATA, C., and G. ÁLVAREZ, 1987 Gametic disequilibrium in populations of Drosophila subobscura: a review of experimental evidence. Genét. Ibér. 39: 593-616.
77. ZAPATA, C., and G. ÁLVAREZ, 1992 The detection of gametic disequilibrium between allozyme loci in natural populations of Drosophila. Evolution 46: 1900-1917.
78. ZAPATA, C., and G. ÁLVAREZ, 1993 On the detection of nonrandom associations between DNA polymorphism in natural populations. Mol. Biol. Evol. 10: 823-841.