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PMID: 8647409 Published · ppublish English Comparative Study Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

Estimating substitution rates in ribosomal RNA genes.

Genetics ·Vol. 141 ·No. 2 ·1995-10-00 ·Pages 771-83

Rzhetsky A

Abstract

A model is introduced describing nucleotide substitution in ribosomal RNA (rRNA) genes. In this model, substitution in the stem and loop regions of rRNA is modeled with 16- and four-state continuous time Markov chains, respectively. The mean substitution rates at nucleotide sites are assumed to follow gamma distributions that are different for the two types of regions. The simplest formulation of the model allows for explicit expressions for transition probabilities of the Markov processes to be found. These expressions were used to analyze several 16S-like rRNA genes from higher eukaryotes with the maximum likelihood method. Although the observed proportion of invariable sites was only slightly higher in the stem regions, the estimated average substitution rates in the stem regions were almost two times as high as in the loop regions. Therefore, the degree of site heterogeneity of substitution rates in the stem regions seems to be higher than in the loop regions of animal 16S-like rRNAs due to presence of a few rapidly evolving sites. The model appears to be helpful in understanding the regularities of nucleotide substitution in rRNAs and probably minimizing errors in recovering phylogeny for distantly related taxa from these genes.

MeSH Terms
Animals Arthropods/genetics Base Composition Biological Evolution DNA, Ribosomal/genetics Hominidae/genetics Humans Mammals Markov Chains Mathematics Models, Genetic Nematoda/genetics Nucleic Acid Conformation Point Mutation RNA, Ribosomal/chemistry,genetics RNA, Ribosomal, 16S/chemistry,genetics Saccharomyces cerevisiae/genetics
Chemicals
DNA, Ribosomal RNA, Ribosomal RNA, Ribosomal, 16S
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
Rzhetsky A
Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802, USA.
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Article Info
Journal
Genetics
Abbr.
Genetics
ISSN
0016-6731
DOI
10.1093/genetics/141.2.771
Published
1995-10-00
Pages
771-83
Language
English
Region
United States
NLM ID
0374636
PMCID
PMC1206772
Subset
IM
External Links
PubMed source DOI: 10.1093/genetics/141.2.771 PMC Full Text View journal details
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