ArticleGenetics2012
Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models.
Article in Genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed.
- Article
- Separating selection from mutation in antibody language models.bioRxiv : the preprint server for biology · 2025Article
- Accurate prediction of substitution rates at protein sites with a mutation-selection model.Scientific reports · 2025Article
- Estimating the proportion of beneficial mutations that are not adaptive in mammals.PLoS genetics · 2024Article
- Genomic Evidence for the Purging of Deleterious Genetic Variation in the Endangered North Atlantic Right Whale.Evolutionary applications · 2024Article
- PEMPS: a phylogenetic software tool to model the evolution of metabolic pathways.BMC bioinformatics · 2024Article
- Increased Positive Selection in Highly Recombining Genes Does not Necessarily Reflect an Evolutionary Advantage of Recombination.Molecular biology and evolution · 2024Article
- Next-generation development and application of codon model in evolution.Frontiers in genetics · 2023Review
- The relative fitness of the de novo variants in general Lithuanian population vs. in individuals with intellectual disability.European journal of human genetics : EJHG · 2022Article
- An Improved Codon Modeling Approach for Accurate Estimation of the Mutation Bias.Molecular biology and evolution · 2022Article
- A Mutation-Selection Model of Protein Evolution under Persistent Positive Selection.Molecular biology and evolution · 2022Article
- Inferring Long-Term Effective Population Size with Mutation-Selection Models.Molecular biology and evolution · 2021Article
- Inferring the number and position of changes in selective regime in a non-equilibrium mutation-selection framework.BMC ecology and evolution · 2021Article
- Contrast-FEL-A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches.Molecular biology and evolution · 2021Article
- Site-Specific Amino Acid Distributions Follow a Universal Shape.Journal of molecular evolution · 2020Article
- Efficient inference, potential, and limitations of site-specific substitution models.Virus evolution · 2020Article
- Relative Model Fit Does Not Predict Topological Accuracy in Single-Gene Protein Phylogenetics.Molecular biology and evolution · 2020Article
- Article
- Population Genetics Based Phylogenetics Under Stabilizing Selection for an Optimal Amino Acid Sequence: A Nested Modeling Approach.Molecular biology and evolution · 2019Article
- Detecting amino acid preference shifts with codon-level mutation-selection mixture models.BMC evolutionary biology · 2019Article
3 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
Estimation of the distribution of selection coefficients of mutations is a long-standing issue in molecular evolution. In addition to population-based methods, the distribution can be estimated from DNA sequence data by phylogenetic-based models. Previous models have generally found unimodal distributions where the probability mass is concentrated between mildly deleterious and nearly neutral mutations. Here we use a sitewise mutation-selection phylogenetic model to estimate the distribution of selection coefficients among novel and fixed mutations (substitutions) in a data set of 244 mammalian mitochondrial genomes and a set of 401 PB2 proteins from influenza. We find a bimodal distribution of selection coefficients for novel mutations in both the mitochondrial data set and for the influenza protein evolving in its natural reservoir, birds. Most of the mutations are strongly deleterious with the rest of the probability mass concentrated around mildly deleterious to neutral mutations. The distribution of the coefficients among substitutions is unimodal and symmetrical around nearly neutral substitutions for both data sets at adaptive equilibrium. About 0.5% of the nonsynonymous mutations and 14% of the nonsynonymous substitutions in the mitochondrial proteins are advantageous, with 0.5% and 24% observed for the influenza protein. Following a host shift of influenza from birds to humans, however, we find among novel mutations in PB2 a trimodal distribution with a small mode of advantageous mutations.
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