The lack of recombination drives the fixation transposable elements on the fourth chromosome of Drosophila melanogaster

Genetical Research

Volumn 83, Issue 2, 2004, Pages 91-100

  Bartolomé, Carolina ^a   Maside, Xulio ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME 4; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; FEMALE; GENE FREQUENCY; GENE INSERTION; GENE SEGREGATION; GENETIC RECOMBINATION; GENETIC VARIABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; RETROPOSON; TRANSPOSON;

ANIMALS; CHROMOSOME MAPPING; DNA TRANSPOSABLE ELEMENTS; DNA, INTERGENIC; DROSOPHILA MELANOGASTER; EVOLUTION, MOLECULAR; GENE FREQUENCY; INTRONS; RECOMBINATION, GENETIC; SEQUENCE ANALYSIS, DNA;

DROSOPHILA MELANOGASTER; ILEX COOKII; MELANOGASTER;

EID: 2942689361     PISSN: 00166723     EISSN: None     Source Type: Journal    
DOI: 10.1017/S0016672304006755     Document Type: Article

References (47)

1. Adams, M. D., Celniker, S. E., Holt, R. A., Evans, C. A., Gocayne, J. D., Amanatides, P. G., Scherer, S. E., Li, P. W., Hoskins, R. A., Galle, R. F., et al. (2000). The genome sequence of Drosophila melanogaster. Science 287, 2185-2195.
2. Akashi, H. (1995). Inferring weak selection from patterns of polymorphism and divergence at silent sites in Drosophila DNA. Genetics 139, 1067-1076.
3. 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.
4. Andolfatto, P. (2001). Contrasting patterns of X-linked and autosomal nucleotide variation in Drosophila melanogaster and Drosophila simulans. Molecular Biology and Evolution 18, 279-290.
5. Bachtrog, D. (2003). Adaptation shapes patterns of genome evolution on sexual and asexual chromosomes in Drosophila. Nature Genetics 34, 215-219.
6. Bachtrog, D. & Charlesworth, B. (2002). Reduced adaptation of a non-recombining neo-Y chromosome. Nature 416, 323-326.
7. Bartolomé, C., Maside, X. & Charlesworth, B. (2002). On the abundance and distribution of transposable elements in the genome of Drosophila melanogaster. Molecular Biology and Evolution 19, 926-937.
8. Berry, A. J., Ajioka, J. W. & Kreitman, M. (1991). Lack of polymorphism on the Drosophila fourth chromosome resulting from selection. Genetics 129, 1111-1117.
9. Betancourt, A. J., Presgraves, D. C. & Swanson, W. J. (2002). A test for faster X evolution in Drosophila. Molecular Biology and Evolution 19, 1816-1819.
10. Biémont, C., Lemeunier, F., Garcia Guerreiro, M. P., Brookfield, J. F., Gautier, C., Aulard, S. & Pasyukova, E. G. (1994). Population dynamics of the copia, mdg1, mdg3, gypsy, and P transposable elements in a natural population of Drosophila melanogaster. Genetical Research 63, 197-212.
11. Blumenstiel, J. P., Hartl, D. L. & Lozovsky, E. R. (2002). Patterns of insertion and deletion in contrasting chromatin domains. Molecular Biology and Evolution 19, 2211-2225.
12. Brookfield, J. F. (1986). A model for DNA sequence evolution within transposable element families. Genetics 112, 393-407.
13. Brookfield, J. F. (1996). Models for the spread of nonautonomous selfish transposable elements when transposition and fitness are coupled. Genetical Research 67, 199-210.
14. Carmena, M. & Gonzalez, C. (1995). Transposable elements map in a conserved pattern of distribution extending from beta-heterochromatin to centromeres in Drosophila melanogaster. Chromosoma 103, 676-684.
15. Carr, M., Soloway, J. R., Robinson, T. E. & Brookfield, J. F. (2001). An investigation of the cause of low variability on the fourth chromosome of Drosophila melanogaster. Molecular Biology and Evolution 18, 2260-2269.
16. Charlesworth, B. (1986). Genetic divergence between transposable elements. Genetical Research 48, 111-118.
17. Charlesworth, B. & Charlesworth, D. (1983). The population dynamics of transposable elements. Genetical Research 42, 1-27.
18. Charlesworth, B., Lapid, A. & Canada, D. (1992a). The distribution of transposable elements within and between chromosomes in a population of Drosophila melanogaster. I. Element frequencies and distribution. Genetical Research 60, 103-114.
19. Charlesworth, B., Lapid, A. & Canada, D. (1992b). The distribution of transposable elements within and between chromosomes in a population of Drosophila melanogaster. II. Inferences on the nature of selection against elements. Genetical Research 60, 115-130.
20. Charlesworth, D., Morgan, M. T. & Charlesworth, B. (1993). The effect of deleterious mutations on neutral molecular variation. Genetics 134, 1289-1303.
21. Comeron, J. M. & Kreitman, M. (2000). The correlation between intron length and recombination in Drosophila. Dynamic equilibrium between mutational and selective forces. Genetics 156, 1175-1190.
22. David, J. R. & Capy, P. (1988). Genetic variation of Drosophila melanogaster natural populations. Trends in Genetics 4, 106-111.
23. Doolitle, W. F. & Sapienza, D. (1980). Selfish genes, the phenotype paradigm and genome evolution. Nature 284, 601-603.
24. Duret, L., Marais, G. & Biémont, C. (2000). Transposons but not retrotransposons are located preferentially in regions of high recombination rate in Caenorhabditis elegans. Genetics 156, 1661-1669.
25. Hill, W. G. & Robertson, A. (1966). The effect of linkage on limits to artificial selection. Genetical Research 8, 269-294.
26. Hochman, B. (1976). The fourth chromosome of Drosophila melanogaster. In The Genetics and Biology of Drosophila (ed. M. Ashburner & E. Novitski), pp. 903-928. London and New York: Academic Press.
27. Hudson, R. R. & Kaplan, N. L. (1985). Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111, 147-164.
28. Jensen, M. A., Charlesworth, B. & Kreitman, M. (2002). Patterns of genetic variation at a chromosome 4 locus of Drosophila melanogaster and D. simulans. Genetics 160, 493-507.
29. Kaminker, J. S., Bergman, C. M., Kronmiller, B., Carlson, J., Svirskas, R., Patel, S., Frise, E., Wheeler, D. A., Lewis, S. E., Rubin, G. M., et al. (2002). The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biology 3, RESEARCH 0084-0084.
30. Keightley, P. D. & Johnson, T. (2004). MCALIGN: stochastic alignment of noncoding DNA sequences based on an evolutionary model of sequence evolution. Genome Research, in press
31. Kumar, A., Tamura, K., Jakobsen, I. B. & Nei, M. (2001). MEGA2: Molecular Evolutionary Genetics Analysis software. Arizona State University, Tempe, Arizona, USA.
32. Kurek, R., Reugels, A. M., Lammermann, U. & Bunemann, H. (2000). Molecular aspects of intron evolution in dynein encoding mega-genes on the heterochromatic Y chromosome of Drosophila sp. Genetica 109, 113-123.
33. Langley, C. H., Montgomery, E., Hudson, R., Kaplan, N. & Charlesworth, B. (1988). On the role of unequal exchange in the containment of transposable element copy number. Genetical Research 52, 223-235.
34. Lerat, E., Rizzon, C. & Biemont, C. (2003). Sequence divergence within transposable element families in the Drosophila melanogaster genome. Genome Research 13, 1889-1896.
35. Maside, X., Bartolomé, C. & Charlesworth, B. (2002). S-element insertions are associated with the evolution of the Hsp70 genes in Drosophila melanogaster. Current Biology 12, 1686-1691.
36. Maside, X., Bartolomé, C. & Charlesworth, B. (2003). Inferences on the evolutionary history of the S-element family of Drosophila melanogaster. Molecular Biology and Evolution 20, 1183-1187.
37. Maynard Smith, J. M. & Haigh, J. (1974). The hitch-hiking effect of a favourable gene. Genetical Research 23, 23-35.
38. Merriman, P. J., Grimes, C. D., Ambroziak, J., Hackett, D. A., Skinner, P. & Simmons, M. J. (1995). S elements: a family of Tc1-like transposons in the genome of Drosophila melanogaster. Genetics 141, 1425-1438.
39. Muller, H. (1964). The relation of recombinational to mutational advance. Mutational Research 1, 2-9.
40. Orgel, L. E. & Crick, F. H. C. (1980). Selfish DNA: the ultimate parasite. Nature 284, 604-607.
41. Petrov, D. A., Aminetzach, Y. T., Davis, J. C., Bensasson, D. & Hirsh, A. E. (2003). Size matters: non-LTR retrotransposable elements and ectopic recombination in Drosophila. Molecular Biology and Evolution 20, 880-892.
42. Rizzon, C., Marais, G., Gouy, M. & Biemont, C. (2002). Recombination rate and the distribution of transposable elements in the Drosophila melanogaster genome. Genome Research 12, 400-407.
43. Steinemann, M. & Steinemann, S. (1992). Degenerating Y chromosome of Drosophila miranda: a trap for retrotransposons. Proceedings of the National Academy of Sciences of the USA 89, 7591-7595.
44. Steinemann, M., Steinemann, S. & Lottspeich, F. (1993). How Y chromosomes become genetically inert. Proceedings of the National Academy of Sciences of the USA 90, 5737-5741.
45. Takano, T. S. (1998). Rate variation of DNA sequence evolution in the Drosophila lineages. Genetics 149, 959-970.
46. Wang, W., Thornton, K., Berry, A. & Long, M. (2002). Nucleotide variation along the Drosophila melanogaster fourth chromosome. Science 295, 134-137.
47. Wright, S. I., Agrawal, N. & Bureau, T. E. (2003). Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana. Genome Research 13, 1897-1903.