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Published on: February 10, 2023
Frequent and widespread parallel evolution of protein sequences.
Antonis Rokas1, Sean B Carroll
1Department of Biological Sciences, Vanderbilt University, USA.
Molecular Biology and Evolution
|June 28, 2008
Summary
Molecular homoplasy, or independent evolution of amino acids, is common in eukaryotic proteins. This suggests selection plays a larger role in protein evolution than previously thought.
Area of Science:
- Evolutionary biology
- Molecular evolution
- Bioinformatics
Background:
- Understanding protein sequence evolution is key in evolutionary biology.
- The roles of selection and genetic drift in amino acid differences between species remain unclear.
- Molecular homoplasy is a potential marker of selection, but its prevalence in eukaryotes is understudied.
Purpose of the Study:
- To quantify the extent and types of molecular homoplasy in eukaryotic proteomes.
- To investigate the evolutionary forces driving amino acid substitutions.
Main Methods:
- Phylogenetic methods were used to analyze 8 genome-scale data matrices.
- Data spanned diverse eukaryotic clades of varying evolutionary depths.
- Analysis focused on identifying homoplastic amino acid substitutions at orthologous sites.
Main Results:
- Homoplastic amino acid substitutions were over 2-fold more frequent than predicted by neutral evolution models.
- Most homoplasies were parallel substitutions involving frequently exchanged amino acids with similar physicochemical properties.
- These substitutions were often achievable via single mutational steps.
Conclusions:
- Molecular homoplasy significantly shapes the protein evolutionary record.
- High homoplasy frequency may result from weak positive selection for specific substitutions.
- Purifying selection may also contribute by restricting substitutions to a limited set of functionally equivalent amino acids.
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