ArticleMolecular biology and evolution2018
Unbiased Estimate of Synonymous and Nonsynonymous Substitution Rates with Nonstationary Base Composition.
Article in Molecular biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
27 citing papers in PubMed.
- The Use of dN/dS Ratios to Investigate Types of Selection in Related Sexual and Asexual Lineages.Genome biology and evolution · 2026Review
- The tiny germline chromosomes of Paramecium aurelia have an exceptionally high recombination rate and are capped by a new class of Helitrons.BMC biology · 2026Article
- Stochastic Character Mapping: An Under-Exploited Approach to the Study of Molecular Evolution.Journal of molecular evolution · 2025Article
- Article
- Relaxed Purifying Selection is Associated with an Accumulation of Transposable Elements in Flies.Molecular biology and evolution · 2025Article
- GTDrift: a resource for exploring the interplay between genetic drift, genomic and transcriptomic characteristics in eukaryotes.NAR genomics and bioinformatics · 2024Article
- GhiPLATZ17 and GhiPLATZ22, zinc-dependent DNA-binding transcription factors, promote salt tolerance in upland cotton.Plant cell reports · 2024Article
- Article
- Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis.Nature plants · 2023Article
- Base Composition, Codon Usage, and Patterns of Gene Sequence Evolution in Butterflies.Genome biology and evolution · 2023Article
- Defining the characteristics of interferon-alpha-stimulated human genes: insight from expression data and machine learning.GigaScience · 2022Article
- HSP70 Gene Family inCells · 2022Article
- An Improved Codon Modeling Approach for Accurate Estimation of the Mutation Bias.Molecular biology and evolution · 2022Article
- In silico prediction of HIV-1-host molecular interactions and their directionality.PLoS computational biology · 2022Article
- Identification of Raf-Like Kinases B Subfamily Genes inInternational journal of molecular sciences · 2021Article
- Protein-Coding Genes ofGenes · 2021Article
- Article
- DGINN, an automated and highly-flexible pipeline for the detection of genetic innovations on protein-coding genes.Nucleic acids research · 2020Article
- Amalgamated cross-species transcriptomes reveal organ-specific propensity in gene expression evolution.Nature communications · 2020Article
- Polymorphism Data Assist Estimation of the Nonsynonymous over Synonymous Fixation Rate Ratio ω for Closely Related Species.Molecular biology and evolution · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The measurement of synonymous and nonsynonymous substitution rates (dS and dN) is useful for assessing selection operating on protein sequences or for investigating mutational processes affecting genomes. In particular, the ratio dNdS is expected to be a good proxy for ω, the ratio of fixation probabilities of nonsynonymous mutations relative to that of neutral mutations. Standard methods for estimating dN, dS, or ω rely on the assumption that the base composition of sequences is at the equilibrium of the evolutionary process. In many clades, this assumption of stationarity is in fact incorrect, and we show here through simulations and analyses of empirical data that nonstationarity biases the estimate of dN, dS, and ω. We show that the bias in the estimate of ω can be fixed by explicitly taking into consideration nonstationarity in the modeling of codon evolution, in a maximum likelihood framework. Moreover, we propose an exact method for estimating dN and dS on branches, based on stochastic mapping, that can take into account nonstationarity. This method can be directly applied to any kind of codon evolution model, as long as neutrality is clearly parameterized.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.