How slippage-derived sequences are incorporated into rRNA variable-region secondary structure: Implications for phylogeny reconstruction

Molecular Phylogenetics and Evolution

Volumn 14, Issue 3, 2000, Pages 366-374

  Hancock, John M ^a   Vogler, Alfried P ^b,c  

^a HAMMERSMITH HOSPITAL   (United Kingdom)

^b DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

Cicindelidae; Compensatory slippage; DNA sequence alignment; Ribosomal RNA; RNA secondary structure evolution; Self organization; Slipped strand mispairing

Indexed keywords

ANIMALIA; CICINDELIDAE; COLEOPTERA; PANTHERA TIGRIS;

EID: 0034087551     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1006/mpev.1999.0709     Document Type: Article

References (31)

1. Aguinaldo A. M. A., Turbeville J. M., Linford L. S., Rivera M. C., Garey J. R., Raff R. A., Lake J. A. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature. 387:1997;489-493.
2. Brower A. V. Z., Schawaroch V. Three steps of homology assessment. Cladistics. 12:1996;265-272.
3. De Pinna M. C. C. Concepts and tests of homology in the cladistic paradigm. Cladistics. 7:1991;367-394.
4. Dover G. A. Molecular drive: A cohesive mode of species evolution. Nature. 299:1982;111-117.
5. Gerbi S. The evolution of eukaryotic ribosomal DNA. Biosystems. 19:1986;247-258.
6. Gutell R. R., Larson N., Woese C. R. Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol. Rev. 58:1994;10-26.
7. Hancock J. M. The contribution of slippage-like processes to genome evolution. J. Mol. Evol. 41:1995;1038-1047.
8. Hancock J. M., Dover G. A. Molecular coevolution among cryptically simple expansion segments of eukaryotic 26S/28S rRNAs. Mol. Biol. Evol. 5:1988;377-391.
9. Hancock J. M., Dover G. A. Nucleic Acids Res. 18:1990;5949-5954.
10. Hancock J. M., Vogler A. P. Modelling the secondary structures of slippage-prone hypervariable RNA regions using suboptima folding and statistical testing: The example of the tiger beetle 18S rRNA variable region V4. Nucleic Acids Res. 26:1998;1689-1699.
11. Hancock J. M., Shaw J., Bonneton F., Dover G. A. High sequence turnover in the regulatory regions of the developmental gene hunchback in insects. Mol. Biol. Evol. 16:1999;253-265.
12. Hickson R. E., Simon C., Cooper A., Spicer G. S., Sullivan J., Penny D. Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA. Mol. Biol. Evol. 13:1996;150-169.
13. Hillis D. M., Dixon M. T. Ribosomal DNA: Molecular evolution and phylogenetic inference. Q. Rev. Biol. 66:1991;411-453.
14. Jaeger J. A., Turner D. H., Zuker M. Predicting optimal and suboptimal secondary structure for RNA. Methods Enzymol. 183:1990;281-306.
15. Kjer K. M. Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: An example of alignment and data presentation from the frogs. Mol. Phylogenet. Evol. 4:1995;314-330.
16. Levinson G., Gutman G. A. Slipped-strand mispairing: A major mechanism for DNA sequence evolution. Mol. Biol. Evol. 4:1987;203-221.
17. Morrison D. A., Ellis J. T. Effects of nucleotide sequence alignment on phylogeny estimation: A case study of 18S rDNAs of Apicomplexa. Mol. Biol. Evol. 14:1997;428-441.
18. Nunn G. B., Theisen B. F., Christensen B., Arctander P. Simplicity-correlated size growth of the nuclear 28S ribosomal RNA D3 expansion segment in the Crustacean order Isopoda. J. Mol. Evol. 42:1996;211-223.
19. RuizTrillo I., Riutort M., Littlewood D. T. J., Herniou E. A., Baguna J. Acoel flatworms: Earliest extant bilaterian metazoans, not members of Platyhelminthes. Science. 283:1999;1919-1923.
20. Titus T. A., Frost D. R. Molecular homology assessment and phylogeny in the lizard family Opluridae (Squamata: Iguania). Mol. Phylogenet. Evol. 6:1996;49-62.
21. Vawter L., Brown W. M. Rates and patterns of srDNA change. Genetics. 134:1993;597-608.
22. Vogler A. P., Pearson D. L. A molecular phylogeny of the tiger beetles (Cicindelidae): Congruence of mitochondrial and nuclear rDNA data sets. Mol. Phylogenet. Evol. 6:1996;321-338.
23. Vogler A. P., Welsh A., Hancock J. M. Phylogenetic analysis of slippage-like sequence variation in the V4 rRNA expansion segment in tiger beetles (Cicindelidae). Mol. Biol. Evol. 14:1997;6-19.
24. Wheeler W. C., Honeycutt R. L. Paired sequence difference in ribosomal RNAs: Evolutionary and phylogenetic implications. Mol. Biol. Evol. 5:1988;90-96.
25. Whiting M. F. Long branch distraction and the Strepsiptera. Syst. Biol. 47:1998;134-137.
26. Whiting M. F., Carpenter J. C., Wheeler W. D., Wheeler W. C. The Strepsiptera problem: Phylogeny of the holometabolous insect orders inferred from 18S and 28S ribosomal DNA sequences and morphology. Syst. Biol. 46:1997;1-68.
27. Zuker M. On finding all suboptimal foldings of an RNA molecule. Science. 244:1989;48-52.
28. Zuker M. Prediction of RNA secondary structure by energy minimization. Methods Mol. Biol. 25:1994;267-294.
29. Zuker M., Jacobson A. B. "Well-determined" regions in RNA secondary structure predictions: Analysis of small subunit ribosomal RNA. Nucleic Acids Res. 23: 1995;2791-2798.
30. Zuker M., Jacobson A. B. Using reliability information to annotate RNA secondary structures. RNA. 4:1998;669-679.
31. Zuker M., Jaeger J. A., Turner D. H. A comparison of optimal and suboptimal RNA secondary structures predicted by free energy minimization with structures determined by phylogenetic comparison. Nucleic Acids Res. 19:1991;2707-2714.