• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of geneticsGeneticsCurrent IssueInformation for AuthorsEditorial BoardSubscribeSubmit a Manuscript
Genetics. Apr 1998; 148(4): 1993–2002.
PMCID: PMC1460107

High apparent rate of simultaneous compensatory base-pair substitutions in ribosomal RNA.


We present a model for the evolution of paired bases in RNA sequences. The new model allows for the instantaneous rate of substitution of both members of a base pair in a compensatory substitution (e.g., A-U-->G-C) and expands our previous work by allowing for unpaired bases or noncanonical pairs. We implemented the model with distance and maximum likelihood methods to estimate the rates of simultaneous substitution of both bases, alphad, vs. rates of substitution of individual bases, alphas in rRNA. In the rapidly evolving D2 expansion segments of Drosophila large subunit rRNA, we estimate a low ratio of alphad/alphas, indicating that most compensatory substitutions involve a G-U intermediate. In contrast, we find a surprisingly high ratio of alphad/alphas in the core small subunit rRNA, indicating that the evolution of the slowly evolving rRNA sequences is modeled much more accurately if simultaneous substitution of both members of a base pair is allowed to occur approximately as often as substitution of individual bases. Using simulations, we have ruled out several potential sources of error in the estimation of alphad/alphas. We conclude that in the core rRNA sequences compensatory substitutions can be fixed so rapidly as to appear to be instantaneous.

Full Text

The Full Text of this article is available as a PDF (209K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Hillis DM, Dixon MT. Ribosomal DNA: molecular evolution and phylogenetic inference. Q Rev Biol. 1991 Dec;66(4):411–453. [PubMed]
  • Maidak BL, Olsen GJ, Larsen N, Overbeek R, McCaughey MJ, Woese CR. The Ribosomal Database Project (RDP). Nucleic Acids Res. 1996 Jan 1;24(1):82–85. [PMC free article] [PubMed]
  • Muse SV. Evolutionary analyses of DNA sequences subject to constraints of secondary structure. Genetics. 1995 Mar;139(3):1429–1439. [PMC free article] [PubMed]
  • Noller HF. Structure of ribosomal RNA. Annu Rev Biochem. 1984;53:119–162. [PubMed]
  • Olsen GJ, Woese CR. Ribosomal RNA: a key to phylogeny. FASEB J. 1993 Jan;7(1):113–123. [PubMed]
  • Rousset F, Pélandakis M, Solignac M. Evolution of compensatory substitutions through G.U intermediate state in Drosophila rRNA. Proc Natl Acad Sci U S A. 1991 Nov 15;88(22):10032–10036. [PMC free article] [PubMed]
  • Rzhetsky A. Estimating substitution rates in ribosomal RNA genes. Genetics. 1995 Oct;141(2):771–783. [PMC free article] [PubMed]
  • Schöniger M, von Haeseler A. A stochastic model for the evolution of autocorrelated DNA sequences. Mol Phylogenet Evol. 1994 Sep;3(3):240–247. [PubMed]
  • Dixon MT, Hillis DM. Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis. Mol Biol Evol. 1993 Jan;10(1):256–267. [PubMed]
  • Vawter L, Brown WM. Rates and patterns of base change in the small subunit ribosomal RNA gene. Genetics. 1993 Jun;134(2):597–608. [PMC free article] [PubMed]
  • Gutell RR. Collection of small subunit (16S- and 16S-like) ribosomal RNA structures: 1994. Nucleic Acids Res. 1994 Sep;22(17):3502–3507. [PMC free article] [PubMed]
  • Hasegawa M, Kishino H, Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 1985;22(2):160–174. [PubMed]

Articles from Genetics are provided here courtesy of Genetics Society of America


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...