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. 1993 Jun;134(2):597–608. doi: 10.1093/genetics/134.2.597

Rates and Patterns of Base Change in the Small Subunit Ribosomal RNA Gene

L Vawter 1, W M Brown 1
PMCID: PMC1205501  PMID: 8325490

Abstract

The small subunit ribosomal RNA gene (srDNA) has been used extensively for phylogenetic analyses. One common assumption in these analyses is that substitution rates are biased toward transitions. We have developed a simple method for estimating relative rates of base change that does not assume rate constancy and takes into account base composition biases in different structures and taxa. We have applied this method to srDNA sequences from taxa with a noncontroversial phylogeny to measure relative rates of evolution in various structural regions of srRNA and relative rates of the different transitions and transversions. We find that: (1) the long single-stranded regions of the RNA molecule evolve slowest, (2) biases in base composition associated with structure and phylogenetic position exist, and (3) the srDNAs studied lack a consistent transition/transversion bias. We have made suggestions based on these findings for refinement of phylogenetic analyses using srDNA data.

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Selected References

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  1. Bernardi G., Bernardi G. Codon usage and genome composition. J Mol Evol. 1985;22(4):363–365. doi: 10.1007/BF02115693. [DOI] [PubMed] [Google Scholar]
  2. Brown W. M., Prager E. M., Wang A., Wilson A. C. Mitochondrial DNA sequences of primates: tempo and mode of evolution. J Mol Evol. 1982;18(4):225–239. doi: 10.1007/BF01734101. [DOI] [PubMed] [Google Scholar]
  3. Chan Y. L., Gutell R., Noller H. F., Wool I. G. The nucleotide sequence of a rat 18 S ribosomal ribonucleic acid gene and a proposal for the secondary structure of 18 S ribosomal ribonucleic acid. J Biol Chem. 1984 Jan 10;259(1):224–230. [PubMed] [Google Scholar]
  4. Clary D. O., Wolstenholme D. R. The mitochondrial DNA molecular of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code. J Mol Evol. 1985;22(3):252–271. doi: 10.1007/BF02099755. [DOI] [PubMed] [Google Scholar]
  5. Ellis R. E., Sulston J. E., Coulson A. R. The rDNA of C. elegans: sequence and structure. Nucleic Acids Res. 1986 Mar 11;14(5):2345–2364. doi: 10.1093/nar/14.5.2345. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Fitch W. M., Markowitz E. An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem Genet. 1970 Oct;4(5):579–593. doi: 10.1007/BF00486096. [DOI] [PubMed] [Google Scholar]
  7. Freier S. M., Kierzek R., Jaeger J. A., Sugimoto N., Caruthers M. H., Neilson T., Turner D. H. Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci U S A. 1986 Dec;83(24):9373–9377. doi: 10.1073/pnas.83.24.9373. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Gutell R. R., Weiser B., Woese C. R., Noller H. F. Comparative anatomy of 16-S-like ribosomal RNA. Prog Nucleic Acid Res Mol Biol. 1985;32:155–216. doi: 10.1016/s0079-6603(08)60348-7. [DOI] [PubMed] [Google Scholar]
  9. Hixson J. E., Brown W. M. A comparison of the small ribosomal RNA genes from the mitochondrial DNA of the great apes and humans: sequence, structure, evolution, and phylogenetic implications. Mol Biol Evol. 1986 Jan;3(1):1–18. doi: 10.1093/oxfordjournals.molbev.a040379. [DOI] [PubMed] [Google Scholar]
  10. Jaeger J. A., Turner D. H., Zuker M. Predicting optimal and suboptimal secondary structure for RNA. Methods Enzymol. 1990;183:281–306. doi: 10.1016/0076-6879(90)83019-6. [DOI] [PubMed] [Google Scholar]
  11. Jukes T. H., Bhushan V. Silent nucleotide substitutions and G + C content of some mitochondrial and bacterial genes. J Mol Evol. 1986;24(1-2):39–44. doi: 10.1007/BF02099949. [DOI] [PubMed] [Google Scholar]
  12. Jukes T. H. Transitions, transversions, and the molecular evolutionary clock. J Mol Evol. 1987;26(1-2):87–98. doi: 10.1007/BF02111284. [DOI] [PubMed] [Google Scholar]
  13. Lake J. A. Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences. Nature. 1988 Jan 14;331(6152):184–186. doi: 10.1038/331184a0. [DOI] [PubMed] [Google Scholar]
  14. Lawrence C. B., Goldman D. A. Definition and identification of homology domains. Comput Appl Biosci. 1988 Mar;4(1):25–33. doi: 10.1093/bioinformatics/4.1.25. [DOI] [PubMed] [Google Scholar]
  15. Li W. H., Wu C. I., Luo C. C. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol. 1985 Mar;2(2):150–174. doi: 10.1093/oxfordjournals.molbev.a040343. [DOI] [PubMed] [Google Scholar]
  16. Mantel N. The detection of disease clustering and a generalized regression approach. Cancer Res. 1967 Feb;27(2):209–220. [PubMed] [Google Scholar]
  17. Marshall C. R. Substitution bias, weighted parsimony, and amniote phylogeny as inferred from 18S rRNA sequences. Mol Biol Evol. 1992 Mar;9(2):370–378. doi: 10.1093/oxfordjournals.molbev.a040726. [DOI] [PubMed] [Google Scholar]
  18. Nelles L., Fang B. L., Volckaert G., Vandenberghe A., De Wachter R. Nucleotide sequence of a crustacean 18S ribosomal RNA gene and secondary structure of eukaryotic small subunit ribosomal RNAs. Nucleic Acids Res. 1984 Dec 11;12(23):8749–8768. doi: 10.1093/nar/12.23.8749. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Ohta T. On the evolution of multigene families. Theor Popul Biol. 1983 Apr;23(2):216–240. doi: 10.1016/0040-5809(83)90015-1. [DOI] [PubMed] [Google Scholar]
  20. Raynal F., Michot B., Bachellerie J. P. Complete nucleotide sequence of mouse 18 S rRNA gene: comparison with other available homologs. FEBS Lett. 1984 Feb 27;167(2):263–268. doi: 10.1016/0014-5793(84)80139-8. [DOI] [PubMed] [Google Scholar]
  21. Salim M., Maden B. E. Nucleotide sequence of Xenopus laevis 18S ribosomal RNA inferred from gene sequence. Nature. 1981 May 21;291(5812):205–208. doi: 10.1038/291205a0. [DOI] [PubMed] [Google Scholar]
  22. Sogin M. L., Elwood H. J. Primary structure of the Paramecium tetraurelia small-subunit rRNA coding region: phylogenetic relationships within the Ciliophora. J Mol Evol. 1986;23(1):53–60. doi: 10.1007/BF02100998. [DOI] [PubMed] [Google Scholar]
  23. Torczynski R. M., Fuke M., Bollon A. P. Cloning and sequencing of a human 18S ribosomal RNA gene. DNA. 1985 Aug;4(4):283–291. doi: 10.1089/dna.1985.4.283. [DOI] [PubMed] [Google Scholar]
  24. Woese C. R., Gutell R., Gupta R., Noller H. F. Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. Microbiol Rev. 1983 Dec;47(4):621–669. doi: 10.1128/mr.47.4.621-669.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Zuker M. Computer prediction of RNA structure. Methods Enzymol. 1989;180:262–288. doi: 10.1016/0076-6879(89)80106-5. [DOI] [PubMed] [Google Scholar]

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