ArticleMolecular biology and evolution2017
Detecting Adaptation in Protein-Coding Genes Using a Bayesian Site-Heterogeneous Mutation-Selection Codon Substitution Model.
Article in Molecular biology and evolution, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 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
17 citing papers in PubMed.
- Estimating the proportion of beneficial mutations that are not adaptive in mammals.PLoS genetics · 2024Article
- Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Jump-Chain Simulation of Markov Substitution Processes Over Phylogenies.Journal of molecular evolution · 2022Review
- 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
- Shifts in amino acid preferences as proteins evolve: A synthesis of experimental and theoretical work.Protein science : a publication of the Protein Society · 2021Review
- Characterizing Amino Acid Substitution with Complete Linkage of Sites on a Lineage.Genome biology and evolution · 2021Article
- 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
- A Bayesian Mutation-Selection Framework for Detecting Site-Specific Adaptive Evolution in Protein-Coding Genes.Molecular biology and evolution · 2021Article
- Evolutionary Genomics of Niche-Specific Adaptation to the Cystic Fibrosis Lung in Pseudomonas aeruginosa.Molecular biology and evolution · 2021Article
- 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
- Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models.Biology direct · 2017Article
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
Codon substitution models have traditionally attempted to uncover signatures of adaptation within protein-coding genes by contrasting the rates of synonymous and non-synonymous substitutions. Another modeling approach, known as the mutation-selection framework, attempts to explicitly account for selective patterns at the amino acid level, with some approaches allowing for heterogeneity in these patterns across codon sites. Under such a model, substitutions at a given position occur at the neutral or nearly neutral rate when they are synonymous, or when they correspond to replacements between amino acids of similar fitness; substitutions from high to low (low to high) fitness amino acids have comparatively low (high) rates. Here, we study the use of such a mutation-selection framework as a null model for the detection of adaptation. Following previous works in this direction, we include a deviation parameter that has the effect of capturing the surplus, or deficit, in non-synonymous rates, relative to what would be expected under a mutation-selection modeling framework that includes a Dirichlet process approach to account for across-codon-site variation in amino acid fitness profiles. We use simulations, along with a few real data sets, to study the behavior of the approach, and find it to have good power with a low false-positive rate. Altogether, we emphasize the potential of recent mutation-selection models in the detection of adaptation, calling for further model refinements as well as large-scale applications.
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.