An episodic change of rDNA nucleotide substitution rate has occurred during the emergence of the insect order diptera

Molecular Biology and Evolution

Volumn 14, Issue 6, 1997, Pages 644-653

  Friedrich, Markus ^a,b   Tautz, Diethard ^a  

^a UNIVERSITY OF MUNICH   (Germany)

^b CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Diptera; directional mutation pressure; evolutionary rates; insects; molecular clock; phylogeny; ribosomal DNA; stationarity of base composition

Indexed keywords

RIBOSOME DNA;

AMINO ACID COMPOSITION; AMINO ACID SUBSTITUTION; ANALYTIC METHOD; ARTICLE; DROSOPHILA MELANOGASTER; FLY; GENETIC ANALYSIS; INSECT; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROTEIN SYNTHESIS REGULATION; STRAIN DIFFERENCE;

DIPTERA; DROSOPHILA MELANOGASTER; HEXAPODA; INSECTA; MELANOGASTER;

EID: 0030985312     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a025804     Document Type: Article

References (69)

1. CAMPBELL, B. C., J. D. STEFFEN-CAMPBELL, and J. H. WERREN. 1993. Phylogeny of Nasonia species complex (Hymenoptera: Pteromalidae) inferred from an internal transcribed spacer (ITS2) and 28S rDNA sequences. Insect Mol. Biol. 2:225-237.
2. CARMEAN, D., and J. B. CRESPI. 1995. Do long branches attract flies? Nature 373:666.
3. CARMEAN, D., L. S. KIMSEY, and M. L. BERBEE. 1992. 18S rDNA sequences and the holometabolous insects. Mol. Phylogenet. Evol. 2:270-278.
4. CASANOVA, J. L., C. PANNETIER, C. JAULIN, and P. KOURILSKY. 1990. Optimal conditions for directly sequencing double-stranded PCR products with Sequenase. Nucleic Acids Res. 18:4028.
5. CHALWATZIS, N., A. BAUR, E. STETZER, R. KINZELBACH, and F. K. ZIMMERMANN. 1994. Strongly expanded 18S ribosomal-RNA genes correlated with a peculiar morphology in the insect order of Strepsiptera. Zoology 98:115-126.
6. CLARK, C. G., B. W. TAGUE, V. C. WARE, and S. A. GERBI. 1984. Xenopus laevis 28S ribosomal RNA: a secondary structure model and its evolutionary and functional implications. Nucleic Acids Res. 12:6197-6220.
7. DAHLBERG, A. E. 1989. The functional role of ribosomal RNA in protein synthesis. Cell 57:525-529.
8. DE RIJK, P., Y. VAN DE PEER, I. VAN DEN BROECK, and R. DE WACHTER. 1995. Evolution according to large ribosomal subunit RNA. J. Mol. Evol. 41:366-375.
9. DIXON, M. T., and D. M. HILLIS. 1993. Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis. Mol. Biol. Evol. 10:256-267.
10. EVENHUIS, N. L. 1994. Catalogue of the fossil flies of the world (Insecta, Diptera). Backhuys, Leiden.
11. FELDMAN, D., J. GAGNON, R. HOFMANN, and J. SIMPSON. 1988. StatView™SE+ Graphics. Version 1.02. Abacus Concepts Inc., Berkeley, Calif.
12. FELSENSTEIN, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 19: 401-410.
13. _. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
14. _. 1985. Confidence limits on phytogenies: an approach using the bootstrap. Evolution 39:783-791.
15. _. 1989. Phylogenetic inference programs (PHYLIP). University of Washington, Seattle and University Herbarium, University of California, Berkeley.
16. FITCH, D. H., G. B. BUGAJ, and S. W. EMMONS. 1995. 18S ribosomal RNA gene phylogeny for some Rhabditidae related to Caenorhabditis. Mol. Biol. Evol 12:346-358.
17. FITCH, W. M. 1971. Toward defining the course of evolution: minimal change for a specific tree topology. Syst. Zool. 20: 406-416.
18. FRASER, N. C., D. A. GRIMALDI, P. E. OLSEN, and B. AXSMITH. 1996. A triassic lagerstätte from eastern North America. Nature 380:615-619.
19. FRIEDRICH, M. 1995. Phylogenetischer Informationsgehalt und evolutionäre Eigenschaften von kernkodierten ribosomalen Genen innerhalb der Euarthropoda. Ph.D. thesis, Ludwig-Maximilians-Universität, München.
20. FRIEDRICH, M., and D. TAUTZ. 1995. Ribosomal DNA phylogeny of the major extant arthropod classes and the evolution of myriapods. Nature 376:165-167.
21. GILLESPIE, J. H. 1984. The molecular clock may be an episodic clock. Proc. Natl. Acad. Sci. USA 81:8009-8013.
22. _. 1986. Rates of molecular evolution. Annu. Rev. Ecol. Syst. 17:637-665.
23. GOLDMAN, N. 1994. Variance to mean ratio, R(t), for poisson processes on phylogenetic trees. Mol. Phylogenet. Evol. 3: 230-239.
24. GUTELL, R. R., M. W. GRAY, and M. N. SCHNARE. 1993. A compilation of large subunit (23S and 23S-like) ribosomal RNA structures. Nucleic Acids Res. 21:3055-3074.
25. GUTELL, R. R., N. LARSEN, and C. R. WOESE. 1994. Lessons from evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol. Rev. 58:10-26
26. GUTELL, R. R., B. WEISER, C. R. WOESE, and H. F. NOLLER. 1985. Comparative anatomy of 16S-like ribosomal RNA. Prog. Nucleic Acid Res. Mol. Biol. 32:155-216.
27. HANCOCK, J. M., and G. A. DOVER. 1988. Molecular coevolution among cryptically simple expansion segments of eukaryotic 26S/28S rRNAs. Mol. Biol. Evol. 5:377-392.
28. HASEGAWA, M., and T. HASHIMOTO. 1993. Ribosomal RNA trees misleading? Nature 361:23.
29. HASEGAWA, M., H. KISHINO, and T. A. YANO. 1985. Dating of the human ape splitting by a molecular clock of mitochondrial-DNA. J. Mol. Evol. 22:160-174.
30. HENNIG, W. 1981. Insect phylogeny. Chichester, New York, N.Y.
31. HIGGINS, D. G. 1994. CLUSTAL V: multiple alignment of DNA and protein sequences. Methods Mol. Biol 25:307-318.
32. HILLIS, D. M., and M. T. DIXON. 1991. Ribosomal DNA: molecular evolution and phylogenetic inference. Q. Rev. Biol. 66:411-453.
33. HUGHES, A. L., and M. NEI. 1988. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335:167-170.
34. JIN, L., and M. NEI. 1990. Limitations of the evolutionary parsimony method of phylogenetic analysis. Mol. Biol. Evol. 7:607-633.
35. JOHNSON, N. L., and S. KOTZ. 1973. Distributions in statistics; discrete distributions. Houghton-Mifflin, Boston, Mass.
36. JORDAN, B. R., M. LATIL-DAMOTTE, and R. JOURDAN. 1980. Coding and spacer sequences in the 5.8S-2S region of Bradysia coprophila ribosomal DNA. Nucleic Acids Res. 8: 3565-3572.
37. KIM, J., J. F. ROHLF, and R. R. SOKAL. 1993. The accuracy of phylogenetic estimation using the neighbor-joining method. Evolution 47:471-486.
38. KIMURA, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
39. KRISTENSEN, N. P. 1991. Phylogeny of extant hexapods. Pp. 125-140 in I. D. NAUMANN, ed. The insects of Australia. Vol. 1. Melbourne University Press, Melbourne.
40. KUHNER, M. K., and J. FELSENSTEIN. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11:459-468.
41. KUKALOVA-PECK, J. 1991. Fossil history and evolution of hexapod structures. Pp. 141-179. in I. D. NAUMANN, ed. The insects of Australia. Vol. 1. Melbourne University Press, Melbourne.
42. KUPERUS, W. R., and W. CHAPKO. 1994. Usefulness of internal transcribed spacer regions of ribosomal DNA in Melanopine (Orthoptera: Acrididae) systematics. Ann. Entomol. Soc. Am. 87:751-754.
43. MADDISON, W. P., and D. R. MADDISON. 1992. MacClade. Sinauer, Sunderland, Mass.
44. MARTIN, A. P., and S. R. PALUMBI. 1993. Body size, metabolic rate, generation time, and the molecular clock. Proc. Natl. Acad. Sci. USA 90:4087-4091.
45. MILLER, B. R., M. B. CRABTREE, and H. M. SAVAGE. 1996. Phylogeny of 14 culex mosquito species, including the culex-pipiens complex, inferred from the internal transcribed spacers of ribosomal DNA. Insect Mol. Biol. 5:93-107.
46. NICHOL, S. T., J. E. ROWE, and W. M. FITCH. 1993. Punctuated equilibrium and positive Darwinian evolution in vesicular stomatitis virus. Proc. Natl. Acad. Sci. USA 90:10424-10428.
47. OCHMAN, H., and A. C. WILSON. 1987. Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J. Mol. Evol. 26:74-86.
48. OOSTERBROEK, P. F. L. S., and G. COURTNEY. 1995. Phylogeny of nematocerous families of Diptera (Insecta). Zool. J. Linn. Soc. 115:267-311.
49. PHILIPPE, H., A. CHENUIL, and A. ADOUTTE. 1994. Can the Cambrian explosion be inferred through molecular phylogeny? Pp. 15-25 in M. AKAM, P. HOLLAND, P. INGHAM, and G. WRAY, eds. Development 1994 supplement. The Company of Biologists Limited, Cambridge.
50. ROHLF, I. F., W. S. CHANG, R. R. SOKAL, and J. KIM. 1990. Accuracy of estimated phylogenies: effects of tree topology and evolutionary model. Evolution 44:1671-1684.
51. RZHETSKY, A., and M. NEI. 1995. Tests of applicability of several substitution models for DNA sequence data. Mol. Biol. Evol. 12:131-151.
52. SAIKI, R, K., D. H. GELFAND, S. STOFFEL, S. J. SCHARF, R. HIGUCHI, G. T. HORN, K. B. MULLIS, and H. A. ERLICH. 1988. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487-491.
53. SAITOU, N., and M. NEI. 1987. The neighbour-joining method: a method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
54. SARICH, V. M., and A. C. WILSON. 1973. Generation time and genomic evolution in primates. Science 179:1144-1147.
55. SCHLÖTTERER, C., M.-T. HAUSER, A. V. HAESELER, and D. TAUTZ. 1994. Comparative evolutionary analysis of rDNA ITS regions in Drosophila. Mol. Biol. Evol. 11:513-522.
56. SPEARS, T., L. ABELE, and W. KIM. 1993. The monophyly of brachyuran crabs: a phylogentic study based on 18S rDNA. Syst. Biol. 41:446-461.
57. SPRINGER, M. S., L. J. HOLLAR, and A. BURK. 1995. Compensatory substitutions and the evolution of the mitochondrial 12S rRNA gene in mammals. Mol. Biol. Evol. 12:1138-1150.
58. STEWART, C.-B., J. W. SCHILLING, and A. C. WILSON. 1987. Adaptive evolution in the stomach lysozymes of foregut fermenters. Nature 330:401-404.
59. SUEOKA, N. 1988. Directional mutation pressure and neutral molecular evolution. Proc. Natl. Acad. Sci. USA 85:2653-2657.
60. _. 1993. Directional mutation pressure, mutator mutations, and the dynamics of molecular evolution. J. Mol. Evol. 37:137-153.
61. SWOFFORD, D. L. 1993. PAUP: phylogenetic analysis using parsimony. Illinois Natural History Survey, Champaign.
62. SWOFFORD, D. L., and G. J. OLSEN. 1990. Phylogeny reconstruction. Pp. 411-502 in D. M. HILLIS and C. MORITZ, eds. Molecular systematics. Sinauer, Sunderland, Mass.
63. TANG, J. M., L. TOE, C. BACK, and T. R. UNNASCH. 1996. Intra-specific heterogeneity of the rDNA internal transcribed spacer in the Simulium-Damnosum (Diptera, Simuliidae) complex. Mol. Biol. Evol. 13:244-252.
64. TAUTZ, D., J. M. HANCOCK, D. A. WEBB, C. TAUTZ, and G. A. DOVER. 1988. Complete sequences of the rRNA genes of Drosophila melanogaster. Mol. Biol. Evol 5:366-376.
65. VAWTER, L., and W. M. BROWN. 1993. Rates and patterns of base change in the small subunit ribosomal RNA gene. Genetics 134:597-608.
66. WHITING, M. F., and W. C. WHEELER. 1994. Insect homeotic transformation. Nature 368:696.
67. WILLMANN, R. 1989. Rediscovered: Permotipula patricia, the oldest known fly. Naturwissenschaften 76:375-377.
68. WOOTTON, R. J., and A. R. ENNOS. 1989. The implications of function on the origin and homologies of the dipterous wing. Syst. Entomol. 14:507-520.
69. WU, C.-I., and W.-H. Li. 1985. Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Natl. Acad. Sci. USA 82:1741-1745.