Comparative analysis of mt LSU rRNA secondary structures of Odonates: Structural variability and phylogenetic signal

Insect Molecular Biology

Volumn 12, Issue 6, 2003, Pages 535-548

  Misof, B ^a   Fleck, G ^a  

^a Museum of Zoology   (Germany)

Author keywords

16S ribosomal RNA; Comparative analyses; Insect systematics; Odonata; Secondary structure

Indexed keywords

ANIMALIA; DROSOPHILA MELANOGASTER; EPHEMERA; EPHEMEROPTERA; INSECTA; MELANOGASTER; ODONATA;

EID: 0344664006     PISSN: 09621075     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2583.2003.00432.x     Document Type: Article

References (48)

1. Ban, N., Nissen, P., Hansen, J., Moore, RB. and Steitz, T.A. (2000) The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 289: 905-920.
2. Bechly, G. (1996) Morphologische Untersuchungen am Flügelgeä der der rezenten Libellen und deren Stammgruppenvertreter (Insecta: Odonatoptera), unter besonderer Berücksichtigung der Phylogenetischen Systematik und des Grundplanes der Odonata. Petalura 2 (Sp. Vol.): 1-402.
3. Bechly, G., Nel, A., Martínez-Delclòs, X. and Fleck, G. (1998) Four new dragonflies from the upper Jurassic of Germany and the lower Cretaceous of Mongolia (Anisoptera: Hemeroscopidae, Sonidae, and Proterogomphidae fam. nov.). Odonatologica 27: 149-187.
4. Billoud, B., Guerucci, M.-A., Masselot, M. and Deutsch, J.S. (2000) Cirripede phylogeny using a novel approach: molecular morphometrics. Mol Biol Evol 17: 1435-1445.
5. Boudreaux, H.B. (1979) Arthropod Phylogeny with Special Reference to Insects. Wiley, New York.
6. Buckley, T.R., Simon, C., Flook, P.K. and Misof, B. (2000) Secondary structure and conserved motifs of the frequently sequenced domains IV and V of the insect mitochondrial large subunit rRNA gene. Insect Mol Biol 9: 565-580.
7. Cannone, J.J., Subramanian, S., Schnare, M.N., Collett, J.R., Du D'Souza, L.M.Y., Feng, B., Lin, N., Madabusi, L.V., Muller, K.M., Pande, N., Shang, Z., Yu, N. and Gutell, R.R. (2002) The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BioMed Central Bioinformatics 3: 2. [Correction. Biomed Central Bioinformatics 3: 15.] http://www.rna.icmb.utexas.edu/.
8. Carle, F.L. (1982) The wing vein homologies and phylogeny of Odonata: a continuing debate. Soc Intis Odonatologica, Rapid Comms 4: 1-66.
9. Carle, F.L. (1995) Evolution, taxonomy, and biogeography of ancient Gondwanian libelluloides, with comments on anisopteroid evolution and phylogenetic systematics (Anisoptera: Libelluloidea). Odonatologica 24: 383-506.
10. Collins, L.J., Moulton, V. and Penny, D. (2000) Use of RNA secondary structure for studying the evolution of RNase P and RNase MRP. J Mol Evol 51: 194-204.
11. Corpet, F. and Michot, B. (1994) RNAlign program: alignment of RNA sequences using both primary and secondary structures. Comput Applic Biosci 10: 389-399.
12. De Rijk, P. and De Wachter, R. (1997) RnaViz, a program for the visualisation of RNA secondary structure. Nucl Acids Res 25: 4679-4684.
13. Fleck, G., Nel, A., Bechly, G. and Martínez-Delclòs, X. (2001) Revision and phylogenetic affinities of the Jurassic Steleopteridae Handlirsch, 1906 (Odonata: Zygoptera). Insect Syst Evol 32: 285-305.
14. Fraser, F.C. (1957) A Reclassification of the Order Odonata. Royal Zoological Society of New South Wales, Sydney.
15. Gutell, R.R., Larsen, N. and Woese, C.R. (1994) Lessons from an evolving rRNA: mt LSU and 23S structures from a comparative perspective. Microbiol Rev 58: 10-26.
16. Gutell, R.R., Lee, J.C. and Cannone, J.J. (2002) The accuracy of ribosomal RNA comparative structure models. Curr Opin Struct Biol 12: 301-310.
17. Hennig, W. (1969) Die Stammesgeschichte der Insekten. Kramer, Frankfurt am Main.
18. Hickson, R.E., Simon, C. and Perrey, S.W. (2000) The performance of several multiple-sequence alignment programs in relation to secondary-structure features for an rRNA sequence. Mol Biol Evol 17: 530-539.
19. Higgs, P.G. (2000) RNA secondary structure: physical and computational aspects. Quart Rev Biophys 33: 199-253.
20. Hofacker, I.L., Fekete, M. and Stadler, P. (2002) Secondary structure prediction for aligned RNA sequences. J Mol Biol 319: 1059-1066.
21. Hofacker, I.L., Fontana, W., Stadler, P.F., Bonhoeffer, L.S., Tacker, M. and Schuster, P. (1994) Fast folding and comparison of RNA secondary structures. Monatsh Chem 125: 167-188.
22. Hovmöller, R., Pape, T. and Källersjö, M. (2002) The palaeoptera problem: basal pterygote phylogeny inferred from 18S and 28S rDNA sequences. Cladistics 18: 313-323.
23. Kjer, K.M. (1995) Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from frogs. Mol Phyl Evol 4: 314-330.
24. Kristensen, N.P. (1975) The phylogeny of the hexapod 'orders': a critical review of recent accounts. Z Zool Syst Evol 13: 1-44.
25. Kristensen, N.P. (1997) The groundplan and basal diversification of hexapods. In Arthropod Relationships (Fortey, R.A. and Thomas, R.H., eds), Systematics Association Special Volume Series 55, pp. 281-293. Chapman & Hall, London.
26. Kukalová-Peck, J. (1997) Arthropod phylogeny and 'basal' morphological structures. In Arthropod Relationships (Fortey, R.A. and Thomas, R.H., eds), Systematics Association Special Volume Series 55, pp. 249-268. Chapman & Hall, London.
27. Lenhof, H.-P., Reinert, K. and Vingron, M. (1998) A polyhedral approach to RNA sequence structure alignment. J Comput Biol 5: 517-530.
28. Lydeard, C., Holznagel, W.E., Schnare, M.N. and Gutell, R.R. (2000) Phylogenetic analysis of molluscan mitochondrial LSU rDNA sequences and secondary structures. Mol Phyl Evol 15: 83-102.
29. McCaskill, J.S. (1990) The equilibrium partition function and base-pair binding probabilities for RNA secondary structure. Biopolymers 29: 1105-1119.
30. Misof, B., Anderson, C.L., Buckley, T.R., Erpenbeck, D., Rickert, A. and Misof, K. (2002) An empirical analysis of mt 16S rRNA covarion-like evolution in insects: site-specific rate variation is clustered and frequently detected. J Mol Evol 55: 460-469.
31. Misof, B., Rickert, A.M., Buckley, T.H., Fleck, G. and Sauer, K.P. (2001) Phylogenetic signal and its decay in mitochondrial SSU and LSU rRNA gene fragments of dragonflies. Mol Biol Evol 18: 27-37.
32. Nel, A., Bechly, G., Jarzembowski, E.A. and Martínez- Delclós, X. (1998) A revision of the recent and fossil petalurid dragonflies (Insecta, Odonata, Anisoptera, Petalurida taxon n.). Paleontogr Lombarda (Milano, Nuova Serie) 10: 1-68.
33. Nel, A., Martínez-Delclós, X., Paicheler, J.-C. and Henrotay, M. (1993) Les 'Anisozygoptera' fossiles - Phylogénie et classification (Odonata). Martinia, Numéro Hors-Série 3, juin 1993. S.F.O. Bois-d'Arcy, France.
34. Notredame, C., O'Brien, E.A. and Higgins, D.G. (1997) RAGA: RNA sequence alignment by genetic algorithm. Nucl Acids Res 25: 4570-4580.
35. Ouvrard, D., Campbell, B.C., Bourgoin, T. and Chan, K.L. (2000) 18S rRNA secondary structure and phylogenetic position of Peloridiidae (Insecta, Hemiptera). Mol Phyl Evol 16: 403-417.
36. Page, R.D.M., Cruickshank, R. and Johnson, K.P. (2002) Louse (Insecta: Phthiraptera) mitochondrial 12S rRNA secondary structure is highly variable. Insect Mol Biol 11: 361-369.
37. Pfau, H.K. (1991) Contributions of functional morphology to the phylogenetic systematics of Odonata. Adv Odonatol 5: 109-141.
38. Rehn, A. (2003) Phylogenetic analysis of higher-level relationships of Odonata. Syst Entomol 28: 181-239.
39. Sankoff, D. (1985) Simultaneous solutions of the RNA folding, alignment, and proto-sequence problems. SIAM J Appl Math 45: 810-825.
40. Shapiro, B.A. and Zhang, K. (1990) Comparing multiple RNA secondary structures using tree comparisons. CABIOS 6: 309-318.
41. Simon, C., Frati, F., Beckenbach, A., Crespi, B., Liu, H. and Flook, P. (1994) Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Ann Entomol Soc Am 87: 651-701.
42. Stanizcek, A.H. (2000) The mandible of Silverfish (Insecta: Zygentoma) and Mayflies (Ephemeroptera): its morphology and phylogenetic significance. Zool Anz 239: 147-179.
43. Swofford, D.L. (2001) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4. Sinauer Associates, Sunderland, MA.
44. Thompson, J.D., Higgins, D.G. and Gibson, T.J, (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucl Acids Res 22: 4673-4680.
45. Tillyard, R.J. (1935) The Biology of Dragonflies (Odonata or Paraneuroptera). Cambridge University Press, Cambridge.
46. Titus, T.A. and Frost, D.R. (1996) Molecular homology assessment and phylogeny in the lizard family Opluridae (Squamata: Iguania). Mol Phyl Evol 6: 49-62.
47. Trueman, J.W.H. (1996) A preliminary cladistic analysis of odonate wing venation. Odonatologica 25: 59-72.
48. Wuyts, J., De Rijk, P., Van de Peer, Y., Winkelmans, T. and De Wachter, R. (2001) The European Large Subunit Ribosomal RNA database. Nucl Acids Res 29: 175-177.