18S rRNA alignments derived from different secondary structure models can produce alternative phylogenies

Journal of Zoological Systematics and Evolutionary Research

Volumn 34, Issue 3, 1996, Pages 135-143

  Winnepenninckx, B ^a   Backeljau, T ^a  

^a ROYAL BELGIAN INSTITUTE OF NATURAL SCIENCES   (Belgium)

Author keywords

18s rRNA; Alignment; Molecular phylogeny; Phylogeny estimation; Secondary structure

Indexed keywords

EID: 0000634022     PISSN: 09475745     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1439-0469.1996.tb00819.x     Document Type: Article

References (21)

1. Dams, E.; Hendriks, L.; Van de Peer, Y.; Neefs J. -M.; Smits, G.; Vandenbempt, I.; De Wachter, R., 1988: Compilation of small ribosomal subunit rRNA sequences. Nucl. Acids Res. 16, r87-r178.
2. De Rijk, P.; Neefs J. -M.; Van de Peer, Y.; De Wachter, R., 1992: Compilation of small ribosomal subunit rRNA sequences. Nucl. Acids Res. 20, 2075-2089.
3. _; De Wachter, R., 1993: DCSE, an interactive tool for sequence alignment and secondary structure research. Comput. Appl. Biosci. 9, 735-740.
4. Farris, J. S., 1989: Hennig86: a PC-DOS program for phylogenetic analysis. Cladistics 5, 163.
5. Felsenstein, J., 1981: A likelihood approach to character weighting and what it tells us about parsimony and compatibility. Biol. J. Linn. Soc. 16, 183-196.
6. _, 1993: PHYLIP: Phylogeny Inference Package, Version 3.5c. Seattle, WA: University of Washington,.
7. Gutell, R. R.; Weiser, B.; Woese, C. R.; Noller, H. F., 1985: Comparative anatomy of 16S-like ribosomal rRNA. Progr. Nucl. Acids Res. Mol. Biol. 32, 155-216.
8. Hendriks, L.; De Baere, R.; Van Broeckhoven, C.; De Wachter, R., 1988a: Primary and secondary structure of the 18S ribosomal rRNA of the insect species Tenebrio molitor. FEBS Letters 232, 115-120.
9. _; Van Broeckhoven, C.; Vandenberghe, A.; Van de Peer, Y.; De Wachter, R., 1988b: Primary and secondary structure of the 18S ribosomal rRNA of the bird spider Eurypelma californica and evolutionary relationships among eukaryotic phyla. Eur. J. Biochem. 177, 15-20.
10. Higgins, D. G.; Sharp, P. M., 1988: CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73, 237-244.
11. Hillis, D. M.; Bull, J. J., 1993: An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42, 182-192.
12. Holland, P. W.; Hacker, A. M.; Williams, N. A., 1991: A molecular analysis of the phylogenetic affinities of Saccoglossus cambrensis Bramhell and Cole (Hemichordata). Phil. Trans. Roy. Soc. London B 332, 185-189.
13. Jukes, T. H.; Cantor, C. R., 1969: Evolution of protein molecules. In: Munro, H. N. (ed.). Mammalian Protein Metabolism. New York: Academic Press, pp. 21-132.
14. Kjer, K. M., 1995: Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs. Mol. Phyl. Evol. 4, 314-330.
15. Lake, J. A., 1987: A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony. Mol. Biol. Evol. 4, 167-191.
16. Neefs, J. -M.; De Wachter, R., 1990: A proposal for the secondary structure of a variable area of eukaryotic small ribosomal subunit rRNA involving the existence of a pseudoknot. Nucl. Acids Res. 18, 5695-5704.
17. _; Van de Peer, Y.; De Rijk, P.; Goris, A.; De Wachter, R., 1991: Compilation of small ribosomal subunit rRNA sequences. Nucl. Acids Res. 19, 1987-2015.
18. _; _; De Rijk, P.; Chapelle, S.; De Wachter, R., 1993: Compilation of small ribosomal subunit rRNA structures. Nucl. Acids Res. 21, 3025-3049.
19. _; _; Hendriks, L.; De Wachter, R., 1990: Compilation of small ribosomal subunit rRNA sequences. Nucl. Acids Res. 18, 2237-2317.
20. Riutort, M.; Field, K. G.; Turbeville, J. M.; Raff, R. A.; Baguña, J., 1992: Enzyme electrophoresis, 18S rRNA sequences, and levels of phylogenetic resolution among several species of freshwater planarians (Platyhelminthes, Tricladida, Paludicola). Can. J. Zool. 70, 1425-1439.
21. Telford, M. J.; Holland, P. W. H., 1993: The phylogenetic affinities of the chaetognaths: a molecular analysis. Mol. Biol. Evol. 10, 660-676