Phylogeny of Organisms Investigated by the Base-Pair Changes in the Stem Regions of Small and Large Ribosomal Subunit RNAs |
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Authors: | Jinya Otsuka Goro Terai Takao Nakano |
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Institution: | (1) Department of Applied Biological Science, Faculty of Science and Technology, Science University of Tokyo, Noda 278, Japan, JP |
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Abstract: | In order to obtain the evolutionary distance data that are as purely additive as possible, we have developed a novel method
for evaluating the evolutionary distances from the base-pair changes in stem regions of ribosomal RNAs (rRNAs). The application
of this method to small-subunit (SSU) and large-subunit (LSU) rRNAs provides the distance data, with which both the unweighted
pair group method of analysis and the neighbor-joining method give almost the same tree topology of most organisms except
for some Protoctista, thermophilic bacteria, parasitic organisms, and endosymbionts. Although the evolutionary distances calculated
with LSU rRNAs are somewhat longer than those with SSU rRNAs, the difference, probably due to a slight difference in functional
constraint, is substantially decreased when the distances are converted into the divergence times of organisms by the measure
of the time scale estimated in each type of rRNAs. The divergence times of main branches agree fairly well with the geological
record of organisms, at least after the appearance of oxygen-releasing photosynthesis, although the divergence times of Eukaryota,
Archaebacteria, and Eubacteria are somewhat overestimated in comparison with the geological record of Earth formation. This
result is explained by considering that the mutation rate is determined by the accumulation of misrepairs for DNA damage caused
by radiation and that the effect of radiation had been stronger before the oxygen molecules became abundant in the atmosphere
of the Earth.
Received: 23 October 1997 / Accepted: 12 August 1998 |
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Keywords: | : Base pairs — Divergence time — Functional constraint — Molecular clock — Mutation rate — Phylogenetic tree — Ribosomal RNA |
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