ArticleScientific reports2019
A common root for coevolution and substitution rate variability in protein sequence evolution.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Epistasis plays a limited role in driving entrenchment during neutral protein evolution.Genome biology · 2026Article
- Identification of coevolving positions by ancestral reconstruction.Communications biology · 2025Article
- Analysis of lineage-specific protein family variability in prokaryotes combined with evolutionary reconstructions.Biology direct · 2022Article
- Epistasis Creates Invariant Sites and Modulates the Rate of Molecular Evolution.Molecular biology and evolution · 2022Article
- Protein Complexes Form a Basis for Complex Hybrid Incompatibility.Frontiers in genetics · 2021Review
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We introduce a simple model that describes the average occurrence of point variations in a generic protein sequence. This model is based on the idea that mutations are more likely to be fixed at sites in contact with others that have mutated in the recent past. Therefore, we extend the usual assumptions made in protein coevolution by introducing a time dumping on the effect of a substitution on its surrounding and makes correlated substitutions happen in avalanches localized in space and time. The model correctly predicts the average correlation of substitutions as a function of their distance along the sequence. At the same time, it predicts an among-site distribution of the number of substitutions per site highly compatible with a negative binomial, consistently with experimental data. The promising outcomes achieved with this model encourage the application of the same ideas in the field of pairwise and multiple sequence alignment.
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