ArticleGenetics1995
Estimating substitution rates in ribosomal RNA genes.
Article in Genetics, 1995. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies.Microbiome · 2022Article
- Adenine·cytosine substitutions are an alternative pathway of compensatory mutation in angiosperm ITS2.RNA (New York, N.Y.) · 2020Article
- Widespread Historical Contingency in Influenza Viruses.Genetics · 2017Article
- Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon.Scientific reports · 2016Article
- Article
- Assessing the state of substitution models describing noncoding RNA evolution.Genome biology and evolution · 2014Article
- A phylogenetic model for the detection of epistatic interactions.Molecular biology and evolution · 2013Article
- Structural characterization of the internal transcribed spacer 2 (ITS2) of the ribosomal DNA (rDNA) cluster in Calyptratae (Diptera: Schizophora) and its implications for molecular phylogenetic analyses.Journal of molecular evolution · 2013Article
- Article
- Potential pitfalls of modelling ribosomal RNA data in phylogenetic tree reconstruction: evidence from case studies in the Metazoa.BMC evolutionary biology · 2011Article
- Accurate and efficient reconstruction of deep phylogenies from structured RNAs.Nucleic acids research · 2009Article
- Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA.Scientific and statistical database management : International Conference, SSDBM ... : proceedings. International Conference on Scientific and Statistical Database Management · 2009Article
- Identifying coevolving partners from paralogous gene families.Evolutionary bioinformatics online · 2008Article
- Why should we care about molecular coevolution?Evolutionary bioinformatics online · 2008Article
- TCR-MHC docking orientation: natural selection, or thymic selection?Immunologic research · 2008Review
- Detecting coevolution in and among protein domains.PLoS computational biology · 2007Article
- Phylogenetic analyses under secondary structure-specific substitution models outperform traditional approaches: case studies with diploblast LSU.Journal of molecular evolution · 2007Article
- Evolutionary rates vary among rRNA structural elements.Nucleic acids research · 2007Article
- Selection intensity against deleterious mutations in RNA secondary structures and rate of compensatory nucleotide substitutions.Genetics · 2001Article
- RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximum-likelihood methods.Genetics · 2001Article
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1 author.
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No grant is acknowledged in the PubMed record.
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.
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