Microsatellite variation in Drosophila melanogaster and Drosophila simulans: A reciprocal test of the ascertainment bias hypothesis

Molecular Biology and Evolution

Volumn 15, Issue 12, 1998, Pages 1620-1636

  Hutter, Carolyn M ^a   Schug, Malcolm D ^a   Aquadro, Charles F ^a  

^a Department of Population Medicine and Diagnostic Sciences   (United States)

Author keywords

Ascertainment bias; Dinucleotide repeat; Drosophila melanogaster; Drosophila simulans; Microsatellite; Simple sequence length polymorphism

Indexed keywords

DNA; MICROSATELLITE DNA;

ARTICLE; DINUCLEOTIDE REPEAT; DNA SEQUENCE; DROSOPHILA MELANOGASTER; GENETIC VARIABILITY; GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; POPULATION GENETICS; SPECIES DIFFERENTIATION;

DROSOPHILA MELANOGASTER; DROSOPHILA SIMULANS; MELANOGASTER;

EID: 0031796424     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a025890     Document Type: Article

References (50)

1. AKASHI, H. 1996. Molecular evolution between D. melanogaster and D. simulans: Reduced codon bias, faster rates of amino acid substitution and larger proteins in D. melanogaster. Genetics 144:1297-1307.
2. ALTSCHUL, S. F., W. GISH, W. MILLER, E. W. MYERS, and D. J. LIPMAN. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
3. AMOS, W., and J. HARWOOD. 1998. Factors affecting levels of genetic diversity in natural populations. Philos. Trans. R. Soc. Lond B. Biol. Sci. 353:177-186.
4. AMOS, W., and D. C. RUBINSZTEIN. 1996. Microsatellites are subject to directional evolution. Nat. Genet. 12:13-14.
5. AMOS, W., S. J. SAWCER, R. W. FEAKES, and D. C. RUBINSZTEIN. 1996. Microsatellites show mutational bias and heterozygote instability. Nat. Genet. 13:390-391.
6. ANGERS, B., and L. BERNATCHEZ. 1997. Complex evolution of a samonid microsatellite locus and its consequences in inferring allelic divergence from size information. Mol. Biol. Evol. 14:230-238.
7. AQUADRO, C. F., K. M. LADO, and W. A. NOON. 1988. The rosy region of Drosophila melanogaster and Drosophila simulans. I. Contrasting levels of naturally occurring DNA restriction map variation and divergence. Genetics 119:875-888.
8. BEGUN, D. J., and C. F. AQUADRO. 1994. Evolutionary inferences from DNA variation at the 6-phosphogluconate dehydrogenase locus in natural populations of Drosophila: selection and geographic differentiation. Genetics 136:155-171.
9. _. 1995. Molecular variation at the vermilion locus in geographically diverse populations of Drosophila melanogaster and D. simulans. Genetics 140:1019-1032.
10. BLANQUER-MAUMONT, A., and B. CROUAU-ROY. 1995. Polymorphism, monomorphism, and sequences in conserved microsatellites in primate species. J. Mol. Evol. 41:492-497.
11. CRAWFORD, A. M., S. M. KAPPES, K. A. PATERSON, M. J. DEGOTARI, K. G. DODDS, B. A. FREKING, R. T. STONE, and C. W. BEATTIE. 1998. Microsatellite evolution: testing the ascertainment bias hypothesis. J. Mol. Evol. 46:256-260.
12. DOWSETT, A. P., and M. W. YOUNG. 1982. Differing levels of dispersed repetitive DNA among closely related species of Drosophila. Proc. Natl. Acad. Sci. USA 79:4570-4574.
13. DUBY, A. 1988. Using synthetic oligonucleotides as probes. Pp. 6.4.3-6.4.10 in F. M. AUSUBEL, R. BRENT, R. KINSTON, D. D. MOORE, J. G. SEIDMAN, J. A. SMITH, and K. STRUHL, eds. Current protocols in molecular biology. Vol. 1. John Wiley and Sons, New York.
14. ELLEGREN, H., S. MOORE, N. ROBINSON, K. BYRNE, W. WARD, and B. C. SHELDON. 1997. Microsatellite evolution: a reciprocal study of repeat lengths at homologous loci in cattle and sheep. Mol. Biol. Evol. 14:854-860.
15. ELLEGREN, H., C. R. PRIMMER, and B. C. SHELDON. 1995. Microsatellite 'evolution': directionality or bias? Nat. Genet. 11:360-362.
16. ESTOUP, A., C. TAILLIEZ, J. M. CORNUET, and M. SOLIGNAC. 1995. Size homoplasy and mutational process of interrupted microsatellites in two bee species, Apis mellifera and Bombus terrestris (Apidae). Mol. Biol. Evol. 12:1074-1084.
17. FITZSIMMONS, N. N., C. MORITZ, and S. S. MOORE. 1995. Conservation and dynamics of microsatellite loci over 300 million years of marine turtle evolution. Mol. Biol. Evol. 12: 432-440.
18. FORBES, S. H., J. T. HOGG, F. C. BUCHANAN, A. M. CRAWFORD, and F. W. ALLENDORF. 1995. Microsatellite evolution in congeneric mammals: domestic and bighorn sheep. Mol. Bio. Evol. 12:1106-1113.
19. GARZA, J. C., M. SLATKIN, and N. B. FREIMER. 1995. Microsatellite allele frequencies in humans and chimpanzees, with implications for constraints on allele size. Mol. Biol. Evol. 12:594-603.
20. GLOOR, G. B., C. R. PRESTON, D. M. JOHNSON-SCHLITZ, N. A. NASSIF, R. W. PHILLIS, W. K. BENZ, H. M. ROBERTSON, and W. R. ENGELS. 1993. Type I repressors of P element mobility. Genetics 135:81-95.
21. GOLDSTEIN, D. B., and A. G. CLARK. 1995. Microsatellite variation in North American populations of Drosophila melanogaster. Nucleic Acids Res. 23:3882-3886.
22. GOLDSTEIN, D. B., A. R. LINARES, L. L. CAVALLI-SFORZA, and M. W. FELDMAN. 1995. An evaluation of genetic distances for use with microsatellite loci. Genetics 139:463-471.
23. GOLDSTEIN, D. B., and D. D. POLLOCK. 1997. Launching microsatellites: a review of mutation processes and methods of phylogenetic inference. J. Hered. 88:335-342.
24. HARR, B., B. ZANGERL, G. BREM, and C. SCHLÖTTERER. 1998. Conservation of locus-specific microsatellite variability across species: a comparison of two Drosophila sibling species, D. melanogaster and D. simulans. Mol. Biol. Evol. 15: 176-184.
25. HEY, J., and R. M. KLIMAN. 1993. Population genetics and phylogenetics of DNA sequence variation of multiple loci within the Drosophila melanogaster species complex. Mol. Biol. Evol. 10:804-822.
26. JARNE, P., and P. J. L. LAGODA. 1996. Microsatellites, from molecules to populations and back. TREE 11:424-429.
27. JIN, L., C. MACAUBAS, J. HALLMAYER, A. KIMURA, and E. MIGNOT. 1996. Mutation rate varies among alleles at a microsatellite locus: Phylogenetic evidence. Proc. Natl. Acad. Sci. USA 93:15285-15288.
28. KIMMEL, M., and R. CHAKRABORTY. 1996. Measures of variation at DNA repeat loci under a general stepwise mutation model. Theor. Popul. Biol. 50:345-367.
29. 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.
30. LACHAISE, D., M.-L. CARIOU, J. R. DAVID, F. LEMEUNIER, L. TSACAS, and M. ASHBURNER. 1988. Historical biogeography of the Drosophila melaongaster species subgroup. Pp. 159-225 in M. K. HECHT, B. WALLACE, and G. H. PRANCE, eds. Evolutionary biology. Vol. 22. Plenum Press, New York.
31. MORAN, P. A. P. 1975. Wandering distributions and electrophoretic profile. Theor. Popul. Biol. 8: 318-330.
32. MORIYAMA, E. N., and J. R. POWELL. 1996. Intraspecific nuclear DNA variation in Drosophila. Mol. Biol. Evol. 13: 261-277.
33. ORTÍ, G., D. E. PEARSE, and J. C. AVISE. 1997. Phylogenetic assessment of length variation at a microsatellite loci. Proc. Natl. Acad. Sci. USA 94:10745-10749.
34. PARDUE, M. L., K. LOWENHAUPT, A. RICH, and A. NORDHEIM. 1987. (dC-dA)ṅ(dG-dT)n sequences have evolutionarily conserved chromosomal locations in Drosophila with implications for roles in chromosome structure and function. EMBO J. 6:1781-1789.
35. PÉPIN, L., Y. AMIGUES, A. LÉPINGLE, J. L. BERTHIER, A. BENSAID, and D. VAIMAN. 1995. Sequence conservation of microsatellites between Bos taurus (cattle), Capra hircus (goat) and related species. Examples of use in parentage testing and phylogeny analysis. Heredity 74:53-61.
36. PETROV, D. A., and D. L. HARTL. 1998. High rate of DNA loss in Drosophila melanogaster and Drosophila virilus species groups. Mol. Biol. Evol. 15:293-302.
37. PRIMMER, C. R., H. ELLENGREN, N. SAINO, and A. P. MOLLER. 1996. Directional evolution in germline microsatellite mutations. Nat. Genet. 13:391-393.
38. PRITCHARD, J. K., and M. W. FELDMAN. 1996. Statistics for microsatellite variation based on coalescence. Theor. Popul. Biol. 50:325-344.
39. RICO, C., I. RICO, and G. HEWITT. 1996. 470 million years of conservation of microsatellite loci among fish species. Proc. R. Soc. Lond. B Biol. Sci. 263:549-557.
40. RUBINSZTEIN, D. C., W. AMOS, J. LEGGO, S. GOODBURN, S. JAIN, S. H. LI, R. L. MARGOLIS, C. A. ROSS, and M. A. FERGUSON-SMITH. 1995. Microsatellite evolution - evidence for directionality and variation in rate between species. Nat. Genet. 10:337-343.
41. RUBINSZTEIN, D. C., J. LEGGO, and W. AMOS. 1995. Microsatellites evolve more rapidly in humans than in chimpanzees. Genomics 30:610-612.
42. RUSSO, C. A., N. TAKEZAKI, and M. NEI. 1995. Molecular phylogeny and divergence times of Drosophilid species. Mol. Biol. Evol. 12:391-404.
43. SAMBROOK, J., E. F. FRITSCH, and T. MANIATIS. 1989. Molecular cloning: a laboratory manual. 2nd edition. Cold Spring Harbor Laboratory Press, New York.
44. SCHUG, M. D., C. M. HUTTER, M. A. F. NOOR, and C. F. AQUADRO. 1998a. Mutation and evolution of microsatellites in Drosophila melanogaster. Genetica 102/103:359-367.
45. SCHUG, M. D., C. M. HUTTER, K. A. WETTERSTRAND, M. S. GAUDETTE, T. F. C. MACKAY, and C. F. AQUADRO. 1998c. The mutation rates of di-, tri-, and tetranucleotide repeats in Drosophila melanogaster. Mol. Biol. Evol. 15:1751-1760.
46. SCHUG, M. D., T. F. C. MACKAY, and C. F. AQUADRO. 1997. Low mutation rates of microsatellite loci in Drosophila melanogaster. Nat. Genet. 15:99-102.
47. SCHUG, M. D., K. A. WETTERSTRAND, M. S. GAUDETTE, R. H. LIM, C. M. HUTTER, and C. F. AQUADRO. 1998b. The distribution and frequency of microsatellite loci in Drosophila melanogaster. Mol. Ecol. 7:57-70.
48. WEBER, J. L. 1990. Informativeness of human (dC-dA)ṅ(dG-dT)n polymorphisms. Genomics 7:524-530.
49. WETTERSTRAND, K. A. 1997. Microsatellite polymorphism and divergence in worldwide populations of D. melanogaster and D. simulans. Masters thesis, Cornell University, Ithaca, N.Y.
50. ZAR, J. H. 1996. Biostatistical analysis. 3rd edition. Prentice Hall, Upper Saddle River, N.J.