ArticleGenetics2001
RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximum-likelihood methods.
Article in Genetics, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
- Developing and Applying RNA Empirical Models With Secondary Structure Insights for Orthoptera Phylogenetics.Ecology and evolution · 2025Article
- Principles ofJournal of the Royal Society, Interface · 2025Article
- GC heterogeneity reveals sequence-structures evolution of angiosperm ITS2.BMC plant biology · 2023Article
- Structure-Based GC Investigation Sheds New Light on ITS2 Evolution inInternational journal of molecular sciences · 2023Article
- Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies.Microbiome · 2022Article
- Compensatory Base Changes and Varying Phylogenetic Effects on Angiosperm ITS2 Genetic Distances.Plants (Basel, Switzerland) · 2022Article
- Stem Region of tRNA Genes Favors Transition Substitution Towards Keto Bases in Bacteria.Journal of molecular evolution · 2022Article
- The constraints between amino acids influence the unequal distribution of codons and protein sequence evolution.Royal Society open science · 2021Article
- Phylogenetic Utility of rRNA ITS2 Sequence-Structure under Functional Constraint.International journal of molecular sciences · 2020Review
- Adenine·cytosine substitutions are an alternative pathway of compensatory mutation in angiosperm ITS2.RNA (New York, N.Y.) · 2020Article
- Alternative analyses of compensatory base changes in an ITS2 phylogeny of Corydalis (Papaveraceae).Annals of botany · 2019Article
- The Effect of RNA Substitution Models on Viroid and RNA Virus Phylogenies.Genome biology and evolution · 2018Article
- Size-variable zone in V3 region of 16S rRNA.RNA biology · 2017Article
- An integrative systematic framework helps to reconstruct skeletal evolution of glass sponges (Porifera, Hexactinellida).Frontiers in zoology · 2017Article
- The evolutionary origins of the southern ocean Philobryid bivalves: hidden biodiversity, ancient persistence.PloS one · 2015Article
- Article
- Hidden state prediction: a modification of classic ancestral state reconstruction algorithms helps unravel complex symbioses.Frontiers in microbiology · 2014Article
- 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
- Phylogenomics of strongylocentrotid sea urchins.BMC evolutionary biology · 2013Article
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3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We test models for the evolution of helical regions of RNA sequences, where the base pairing constraint leads to correlated compensatory substitutions occurring on either side of the pair. These models are of three types: 6-state models include only the four Watson-Crick pairs plus GU and UG; 7-state models include a single mismatch state that combines all of the 10 possible mismatches; 16-state models treat all mismatch states separately. We analyzed a set of eubacterial ribosomal RNA sequences with a well-established phylogenetic tree structure. For each model, the maximum-likelihood values of the parameters were obtained. The models were compared using the Akaike information criterion, the likelihood-ratio test, and Cox's test. With a high significance level, models that permit a nonzero rate of double substitutions performed better than those that assume zero double substitution rate. Some models assume symmetry between GC and CG, between AU and UA, and between GU and UG. Models that relaxed this symmetry assumption performed slightly better, but the tests did not all agree on the significance level. The most general time-reversible model significantly outperformed any of the simplifications. We consider the relative merits of all these models for molecular phylogenetics.
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