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Updated: Jun 10, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Phylogenetic substitution models for detecting heterotachy during plastid evolution.
Simon Whelan1, Benjamin P Blackburne, Matthew Spencer
1Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom. simon.whelan@manchester.ac.uk
Molecular Biology and Evolution
|August 21, 2010
Summary
Protein evolution shows rate variation (heterotachy), potentially driven by simultaneous changes (covarion shifts) affecting multiple sites. New models better capture these shifts, revealing their frequency in deep plastid gene evolution.
Area of Science:
- Evolutionary biology
- Molecular evolution
- Genomics
Background:
- Protein evolution exhibits lineage-specific rate variation (heterotachy).
- Changes in selective pressures can cause simultaneous rate shifts across multiple amino acid sites (covarion shifts).
- Existing models may not fully capture coordinated rate changes.
Purpose of the Study:
- To develop and apply novel models for detecting covarion shifts in protein evolution.
- To investigate the frequency and patterns of covarion shifts in plastid genes.
Main Methods:
- Development of phylogenetic models allowing variable substitution and switching rates across tree branches.
- Application of these models to genes from nonphotosynthetic bacteria, cyanobacteria, and algal plastids.
Main Results:
- Evidence of rate switching (heterotachy) was found in 4 out of 5 genes studied.
- Differential relative switching rates among taxonomic groups were observed in 3 out of 5 genes.
- Covarion shifts appear frequent in the deep evolutionary history of plastid genes.
Conclusions:
- Covarion shifts are likely common during the deep evolution of plastid genes.
- The new modeling approach provides a powerful tool for studying evolutionary rate shifts in various biological systems.
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