ArticleMolecular biology and evolution2015
A model of substitution trajectories in sequence space and long-term protein evolution.
Article in Molecular biology and evolution, 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.
- Descent from a common ancestor restricts exploration of protein sequence space.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
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- Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm.Genetics and molecular 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
- 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
- Relative Efficiencies of Simple and Complex Substitution Models in Estimating Divergence Times in Phylogenomics.Molecular biology and evolution · 2020Article
- Unified rational protein engineering with sequence-based deep representation learning.Nature methods · 2019Article
- mtProtEvol: the resource presenting molecular evolution analysis of proteins involved in the function of Vertebrate mitochondria.BMC evolutionary biology · 2019Article
- The evolution of gene regulatory networks controlling Arabidopsis thaliana L. trichome development.BMC plant biology · 2019Article
- Compensatory mutations and epistasis for protein function.Current opinion in structural biology · 2018Review
- Protein evolution depends on multiple distinct population size parameters.BMC evolutionary biology · 2018Review
- Sequence entropy of folding and the absolute rate of amino acid substitutions.Nature ecology & evolution · 2017Article
- Parallel Evolution of Metazoan Mitochondrial Proteins.Genome biology and evolution · 2017Article
- Article
- Epistasis in protein evolution.Protein science : a publication of the Protein Society · 2016Review
- Article
- Article
- The complete local genotype-phenotype landscape for the alternative splicing of a human exon.Nature communications · 2016Article
- Causes of molecular convergence and parallelism in protein evolution.Nature reviews. Genetics · 2016Review
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Authors and funding
5 authors.
Funding
Abstract
The nature of factors governing the tempo and mode of protein evolution is a fundamental issue in evolutionary biology. Specifically, whether or not interactions between different sites, or epistasis, are important in directing the course of evolution became one of the central questions. Several recent reports have scrutinized patterns of long-term protein evolution claiming them to be compatible only with an epistatic fitness landscape. However, these claims have not yet been substantiated with a formal model of protein evolution. Here, we formulate a simple covarion-like model of protein evolution focusing on the rate at which the fitness impact of amino acids at a site changes with time. We then apply the model to the data on convergent and divergent protein evolution to test whether or not the incorporation of epistatic interactions is necessary to explain the data. We find that convergent evolution cannot be explained without the incorporation of epistasis and the rate at which an amino acid state switches from being acceptable at a site to being deleterious is faster than the rate of amino acid substitution. Specifically, for proteins that have persisted in modern prokaryotic organisms since the last universal common ancestor for one amino acid substitution approximately ten amino acid states switch from being accessible to being deleterious, or vice versa. Thus, molecular evolution can only be perceived in the context of rapid turnover of which amino acids are available for evolution.
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