Rapid divergence of microsatellite abundance among species of Drosophila

Molecular Biology and Evolution

Volumn 20, Issue 7, 2003, Pages 1143-1157

  Ross, Charles L ^a   Dyer, Kelly A ^a   Erez, Tamar ^a   Miller, Susan J ^a   Jaenike, John ^a   Markow, Therese A ^a  

^a NONE

Author keywords

D. arizonae; D. mojavensis; D. neotestacea; D. pachea; D. recens; Drosophila; Microsatellite evolution

Indexed keywords

DIMER; MICROSATELLITE DNA; REPETITIVE DNA;

ARTICLE; DROSOPHILA; DROSOPHILA ARIZONAE; DROSOPHILA MELANOGASTER; DROSOPHILA MOJAVENSIS; DROSOPHILA NEOTESTACEA; DROSOPHILA PACHEA; DROSOPHILA RECENS; DROSOPHILA VIRILIS; GENE FREQUENCY; GENE MUTATION; GENETIC CONSERVATION; GENETIC VARIABILITY; GENUS; MICROSATELLITE INSTABILITY; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; PROTEIN ANALYSIS; PROTEIN MOTIF; SOPHOPHORA; SPECIES; SPECIES COMPARISON; STATISTICAL SIGNIFICANCE; TAXONOMY;

ARACHNIDA; DROSOPHILA; DROSOPHILA ARIZONAE; DROSOPHILA MELANOGASTER; DROSOPHILA MOJAVENSIS; DROSOPHILA NEOTESTACEA; DROSOPHILA PACHEA; DROSOPHILA RECENS; DROSOPHILA VIRILIS; HEXAPODA; MELANOGASTER; SOPHOPHORA;

EID: 0038081260     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msg137     Document Type: Article

References (62)

1. Bachtrog, D., M. Agis, M. Imhof, and C. Schlötterer. 2000. Microsatellite variability differs between dinucleotide repeat motifs: evidence from Drosophila melanogaster. Mol. Biol. Evol. 17:1277-1285.
2. Bachtrog, D., S. Weiss, B. Zangerl, G. Brem, and C. Schlötterer. 1999. Distribution of dinucleotide microsatellites in the Drosophila melanogaster genome. Mol. Biol. Evol. 16: 602-610.
3. Beckmann, J. S., and J. L. Weber. 1992. Survey of human and rat microsatellites. Genomics 12:627-631.
4. Benson, G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27:573-580.
5. Benson, G., and L. Dong. 1999. Reconstructing the duplication history of a tandem repeat. Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology ISMB-99:44-53.
6. Beverley, S. M., and A. C. Wilson. 1984. Molecular evolution in Drosophila and the higher Diptera. II: a time scale for fly evolution. J. Mol. Evol. 21:1013.
7. Brooker, A. L., D. Cook, P. Bentzen, J. M. Wright, and R. W. Doyle. 1994. Organization of microsatellites differs between mammals and cold-water teleost fishes. Can. J. Fish. Aquat. Sci. 51:1959-1966.
8. Calabrese, P. P., R. T. Durrett, and C. F. Aquadro. 2001. Dynamics of microsatellite divergence under stepwise mutation and proportional slippage/point mutation models. Genetics 159:839-852.
9. Dallas, J. F. 1992. Estimation of microsatellite mutation rates in recombinant inbred strains of mouse. Mamm. Genome 3:452-456.
10. Degtyareva, N. P., P. Greenwell, E. R. Hofmann, M. O. Hengartner, L. Zhang, J. G. Culotti, and T. D. Petes. 2002. Caenorhabditis elegans DNA mismatch repair gene msh-2 is required for microsatellite stability and maintenance of genome integrity. Proc. Natl. Acad. Sci. USA 99:2158-2163.
11. Ellegren, H. 1995. Mutation rates at porcine microsatellite loci. Mamm. Genome 6:376-377.
12. n microsatellites: a new class of genetic markers for Salmo trutta L. (brown trout). Heredity 71:488-496.
13. Estoup, A., M. Solignac, M. Harry, and J. M. Cornuet. 1993b. Characterization of (GT)n and (CT)n microsatellites in two insect species: Apis melifera and Bombus terrestris. Nucleic Acids Res. 21:1427-1431.
14. Ewing, B., L. Hillier, M. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:175-185.
15. Feldman, M. W., A. Bergman, D. D. Pollock, and D. B. Goldstein. 1997. Microsatellite genetic distances with range constraints: analytic description and problems of estimation. Genetics 145:207-216.
16. Fellows, D. P., and W. B. Heed. 1972. Factors affecting host plant selection in desert-adapted cactophilic Drosophila. Ecology 53:850-858.
17. Field, D., and C. Wills. 1996. Long, polymorphic microsatellites in simple organisms. Proc. R. Soc. Lond. Ser. B. 263:209-215.
18. -. 1998. Abundant microsatellite polymorphism in Saccharomyces cerevisiae, and the different distributions of microsatellites in eight prokaryotes and S. cerevisiae, result from strong mutation pressures and a variety of selective forces. Proc. Natl. Acad. Sci. USA 95:1647-1652.
19. Garza, J. C., M. Slatkin, and N. B. Freimer. 1995. Microsatellite allele frequencies in humans and chimpanzees, with implications for constraint on allele size. Mol. Biol. Evol. 12:594-603.
20. Goldstein, D., and C. Schlötterer. 1999. Microsatellites: evolution and applications. Oxford University Press, New York.
21. Grimaldi, D., A. C. James, and J. Jaenike. 1992. Systematics and modes of reproductive isolation in the holarctic Drosophila testacea species group (Diptera: Drosophilidae). Ann. Entomol. Soc. Am. 85:671-685.
22. Gryfe, R., C. Swallow, B. Bapat, M. Redston, S. Gallinger, and J. Couture. 1997. Molecular biology of colorectal cancer. Curr. Probl. Cancer 21:238.
23. Hamilton, M. B., E. L. Pincus, A. DiFiore, and R. C. Fleischer. 1999. BioTechniques 27:500-507. Protocol may be found at: http://www.georgetown.edu/faculty/hamiltm1/lab.html.
24. Hancock, J. M. 1995. The contribution of slippage-like processes to genome evolution. J. Mol. Evol. 41:1038-1047.
25. -. 1996. Simple sequences and the expanding genome. BioEssays 18:421-425.
26. Harr, B., and C. Schlötterer. 2000. Long microsatellite alleles in Drosophila melanogaster have a downward mutation bias and short persistence times, which cause their genome-wide underrepresentation. Genetics 155:1213-1220.
27. Heed, W. B., and R. L. Mangan. 1986. Community ecology of the Sonoran Desert USA Mexico Drosophila. Pp. 311-346 in M. Ashburner, H. L. Carson, and J. N. Thompson, Jr., eds. The genetics and biology of Drosophila, Vol. 3E. Academic Press, Orlando, Fla.
28. Hutter, C. M., M. D. Schug, and C. F. Aquadro. 1998. Microsatellite variation in Drosophila melanogaster and Drosophila simulans: a reciprocal test of the ascertainment bias hypothesis. Mol. Biol. Evol. 15:1620-1638.
29. Jaenike J. 1978. Resource predictability and niche breadth in Drosophila Quinaria species group. Evolution 32:676-678.
30. Jurka, J., and C. Pethiyagoda. 1995. Simple receptive DNA sequences from primates: compilation and analysis. J. Mol. Evol. 40:120-126.
31. Katti, M. V., P. K. Ranjekar, and V. S. Gupta. 2001. Differential distribution of simple sequence repeats in eukaryotic genome sequences. Mol. Biol. Evol. 18:1161-1167.
32. Kruglyak, S., R. T. Durrett, M. D. Schug, and C. F. Aquadro. 1998. Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations. Proc. Natl. Acad. Sci. USA 95:10774-10778.
33. -. 2000. Distribution and abundance of microsatellites in the yeast genome can be explained by a balance between slippage events and point mutations. Mol. Biol. Evol. 17:1210-1219.
34. Lagercrantz, U., H. Ellegren, and L. Andersson. 1993. The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acids Res. 21:1111-1115.
35. Markow, T. A., and G. D. Hocutt. 1998. Reproductive isolation in Sonoran Desert Drosophila: testing the limits of the rules. Pp. 234-244 in D. J. Howard and S. H. Berlocher, eds. Endless forms: species and speciation. Oxford University Press, New York.
36. Miller, S., and E. Myers. 1999. The FAKtory DNA sequence fragment assembly system. Technical Report 99-03, Department of Computer Science, University of Arizona, Tucson. 85721. Available at http://www.cs.arizona.edu/research/reports.html.
37. Mooers A. O. and E. C. Holmes. 2000. The evolution of base composition and phylogenetic inference. Trends Ecol. Evol. 15:365-369.
38. Neff, B. D., and M. R. Gross. 2001. Microsatellite evolution in vertebrates: inference from AC dinucleotide repeats. Evolution 55:1717-1733.
39. Noor, M. A. F., R. M. Kliman, and C. A. Machado. 2001. Evolutionary history of microsatellites in the Obscura group of Drosophila. Mol. Biol. Evol. 18:551-556.
40. Noor, M. A. F., M. D. Schug, and C. F. Aquadro. 1999. Microsatellite variation in populations of Drosophila pseudoobscura and Drosophila persimilis. Genet. Res. 75:25-35.
41. Ortí, G., D. E. Pearse, and J. C. Avise. 1997. Phylogenetic assessment of length variation at a microsatellite locus. Proc. Natl. Acad. Sci. USA 94:10745-10749.
42. Pascual, M., M. D. Schug, and C. F. Aquadro. 2000. High density of long dinucleotide microsatellites in Drosophila subobscura. Mol. Biol. Evol. 17:1259-1267.
43. Pitnick, S. 1993. Operational sex ratios and sperm limitation in populations of Drosophila pachea. Behav. Ecol. Sociobiol. 33:383-391.
44. Pitnick, S., G. S. Spicer, and T. Markow. 1997. Phylogenetic examination of female incorporation of ejaculate in Drosphila. Evolution 51:833-845.
45. Powell, J. R. 1997. Progress and prospects in evolutionary biology: the Drosophila model. Oxford University Press, New York.
46. Powell, J. R., and E. N. Moriyama. 1997. Evolution of codon usage bias in Drosophila. Proc. Natl. Acad. Sci. USA 94:7784-7790.
47. Primmer, C. R., T. Raudsepp, G. P. Chowdhary, A. P. Möller, and H. Ellegren. 1997. Low frequency of microsatellites in the avian genome. Genome Res. 7:471-482.
48. Ruiz, A., and W. B. Heed. 1978. Host plant specificity in the cactophilic Drosophila mulleri species complex. J. Anim. Ecol. 57:237-249.
49. Ruiz, A., W. B. Heed, and M. Wasserman. 1990. Evolution of the mojavensis species cluster of cactophilic Drosophila, with descriptions of two new species. J. Hered. 81:30-42.
50. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual. 2nd edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
51. Schlötterer, C., and B. Harr. 2000. Drosophila virilis has long and highly polymorphic microsatellites. Mol. Biol. Evol. 17:1641-1646.
52. Schug, M. D., C. M. Hutter, K. A. Wetterstrand, M. S. Gaudette, T. F. C. Mackay, and C. F. Aquadro. 1998a. The mutation rates of di-, tri- and tetranucleotide repeats in Drosophila melanogaster. Mol. Biol. Evol. 15:1751-1760.
53. Schug, M. D., K. A. Wetterstrand, M. S. Gaudette, R. H. Lim, C. M. Hutter, M. S. Gaudette, and C. F. Aquadro. 1998b. The distribution and frequency of microsatellite loci in Drosophila melanogaster. Mol. Ecol. 7:57-70.
54. Shoemaker D. D. W., and J. Jaenike. 1997. Habitat continuity and the genetic structure of Drosophila populations. Evolution 51:1326-1332.
55. Sia, E. A., S. Jinks-Robertson, and T. D. Petes. 1997. Genetic control of microsatellite stability. Mutat. Res. - DNA Repair 383:61-70.
56. Slatkin, M. 1995. A measure of population subdivision based on microsatellite allele frequencies. Genetics 139:457-462.
57. n repetitive sequences in mammalian genomes. Genomics 10:807-815.
58. n microsatellite loci in a yellow-jacket wasp, Vespula rufa (L.) (Hymenoptera: Vespidae). Insect Mol. Biol. 4:141-148.
59. Toth, G., Z. Gáspári, and J. Jurka. 2000. Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res. 10:967-981.
60. Van Den Bussche, R. A., J. L. Longmire, and R. J. Baker. 1995. How bats achieve a small C-value: frequency of repetitive DNA in Macrotus. Genome 6:521-525.
61. Wilder, J., and H. Hollocher. 2001. Mobile elements and the genesis of microsatellites in dipterans. Mol. Biol. Evol. 18:384-392.
62. Zhu, Y., D. C. Queller, and J. E. Strassmann. 2000. A phylogenetic perspective on sequence evolution in microsatellite loci. J. Mol. Evol. 50:324-338.