The Lineage-Specific Base-Pair Contents in the Stem Regions of Ribosomal RNAs and Their Influence on the Estimation of Evolutionary Distances

The base-pair changes in the stem regions of ribosomal RNAs provide a useful measure for resolving the phylogeny of organisms. In the present study, how the biased base-pair content influences the estimation of evolutionary distances is theoretically investigated. By regarding the biased base-pair content as a result of the difference in selective strength between A:U and G:C base pairs, the evolutionary distance empirically obtained by enumerating base-pair changes is theoretically expressed in terms of selective strength, base-pair change rate, and divergence time. Its application to nuclear-coded large subunit ribosomal RNAs (LSU rRNAs) reveals the followings. LSU rRNAs from most organisms have moderate base-pair contents and the empirical evolutionary distances obtained by the comparison of these LSU rRNAs are approximately proportional to their divergence times. In the comparison of these moderate LSU rRNAs with the GC-rich LSU rRNAs such as those from Mycoplasma, Crenarchaeota, and Giardia, however, the empirically calculated distances are considerably smaller than the true evolutionary distances, while the comparison with AU-rich LSU rRNAs from Microsporidia overestimates their distances. With this result in mind, the relative base-pair change probabilities among three kingdoms are carefully estimated from the statistical distribution of base-pair change ratios enumerated for LSU rRNAs showing almost the same base-pair contents, leading to the result that prokaryotes and eukaryotes first diverged and that archaebacteria and eubacteria diverged on the line of prokaryotes slightly later, by about 0.3 billion years.