ReviewBiology letters2015
Changing preferences: deformation of single position amino acid fitness landscapes and evolution of proteins.
Review in Biology letters, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Estimating the proportion of beneficial mutations that are not adaptive in mammals.PLoS genetics · 2024Article
- Dynamic expedition of leading mutations in SARS-CoV-2 spike glycoproteins.Computational and structural biotechnology journal · 2024Article
- Phylogenetic inference of changes in amino acid propensities with single-position resolution.PLoS computational biology · 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
- Episodic evolution of coadapted sets of amino acid sites in mitochondrial proteins.PLoS genetics · 2021Article
- Senescence and entrenchment in evolution of amino acid sites.Nature communications · 2020Article
- Excessive Parallelism in Protein Evolution of Lake Baikal Amphipod Species Flock.Genome biology and evolution · 2020Article
- SELVa: Simulator of evolution with landscape variation.PloS one · 2020Article
- Allele-specific nonstationarity in evolution of influenza A virus surface proteins.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- mtProtEvol: the resource presenting molecular evolution analysis of proteins involved in the function of Vertebrate mitochondria.BMC evolutionary biology · 2019Article
- Detecting amino acid preference shifts with codon-level mutation-selection mixture models.BMC evolutionary biology · 2019Article
- Article
- Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral sequence divergence.Virus evolution · 2018Article
- Compensatory mutations and epistasis for protein function.Current opinion in structural biology · 2018Review
- Article
- Parallel Evolution of Metazoan Mitochondrial Proteins.Genome biology and evolution · 2017Article
- The Impact of Selection at the Amino Acid Level on the Usage of Synonymous Codons.G3 (Bethesda, Md.) · 2017Article
- Compensatory Evolution of Intrinsic Transcription Terminators in Bacillus Cereus.Genome biology and evolution · 2017Article
- Article
- Detecting Adaptation in Protein-Coding Genes Using a Bayesian Site-Heterogeneous Mutation-Selection Codon Substitution Model.Molecular biology and evolution · 2017Article
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Abstract
The fitness landscape-the function that relates genotypes to fitness-and its role in directing evolution are a central object of evolutionary biology. However, its huge dimensionality precludes understanding of even the basic aspects of its shape. One way to approach it is to ask a simpler question: what are the properties of a function that assigns fitness to each possible variant at just one particular site-a single position fitness landscape-and how does it change in the course of evolution? Analyses of genomic data from multiple species and multiple individuals within a species have proved beyond reasonable doubt that fitness functions of positions throughout the genome do themselves change with time, thus shaping protein evolution. Here, I will briefly review the literature that addresses these dynamics, focusing on recent genome-scale analyses of fitness functions of amino acid sites, i.e. vectors of fitnesses of 20 individual amino acid variants at a given position of a protein. The set of amino acids that confer high fitness at a particular position changes with time, and the rate of this change is comparable with the rate at which a position evolves, implying that this process plays a major role in evolutionary dynamics. However, the causes of these changes remain largely unclear.
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