ArticleGenetics2014
A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data.
Article in Genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 66 citations in OpenAlex.
- 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
- Beginner's Guide on the Use of PAML to Detect Positive Selection.Molecular biology and evolution · 2023Article
- Phylogenetic inference of changes in amino acid propensities with single-position resolution.PLoS computational biology · 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
- A phylogenetic approach for weighting genetic sequences.BMC bioinformatics · 2021Article
- Inferring the number and position of changes in selective regime in a non-equilibrium mutation-selection framework.BMC ecology and evolution · 2021Article
- A Bayesian Mutation-Selection Framework for Detecting Site-Specific Adaptive Evolution in Protein-Coding Genes.Molecular biology and evolution · 2021Article
- Site-Specific Amino Acid Distributions Follow a Universal Shape.Journal of molecular evolution · 2020Article
- Hybrid of Restricted and Penalized Maximum Likelihood Method for Efficient Genome-Wide Association Study.Genes · 2020Article
- 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
- Review
- Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral sequence divergence.Virus evolution · 2018Article
- Protein evolution depends on multiple distinct population size parameters.BMC evolutionary biology · 2018Review
- A new parameter-rich structure-aware mechanistic model for amino acid substitution during evolution.Proteins · 2018Article
- Sequence entropy of folding and the absolute rate of amino acid substitutions.Nature ecology & evolution · 2017Article
- Detecting consistent patterns of directional adaptation using differential selection codon models.BMC evolutionary biology · 2017Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We develop a maximum penalized-likelihood (MPL) method to estimate the fitnesses of amino acids and the distribution of selection coefficients (S = 2Ns) in protein-coding genes from phylogenetic data. This improves on a previous maximum-likelihood method. Various penalty functions are used to penalize extreme estimates of the fitnesses, thus correcting overfitting by the previous method. Using a combination of computer simulation and real data analysis, we evaluate the effect of the various penalties on the estimation of the fitnesses and the distribution of S. We show the new method regularizes the estimates of the fitnesses for small, relatively uninformative data sets, but it can still recover the large proportion of deleterious mutations when present in simulated data. Computer simulations indicate that as the number of taxa in the phylogeny or the level of sequence divergence increases, the distribution of S can be more accurately estimated. Furthermore, the strength of the penalty can be varied to study how informative a particular data set is about the distribution of S. We analyze three protein-coding genes (the chloroplast rubisco protein, mammal mitochondrial proteins, and an influenza virus polymerase) and show the new method recovers a large proportion of deleterious mutations in these data, even under strong penalties, confirming the distribution of S is bimodal in these real data. We recommend the use of the new MPL approach for the estimation of the distribution of S in species phylogenies of protein-coding genes.
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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.