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Updated: Sep 5, 2025
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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
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A subfunctionalisation model of gene family evolution predicts balanced tree shapes
Jiahao Diao1, Małgorzata M O'Reilly2, Barbara Holland1
1Discipline of Mathematics, University of Tasmania, Australia; Australian Research Council Centre of Excellence for Plant Success, Australia.
Molecular Phylogenetics and Evolution
|July 10, 2022
Summary
This study models gene family evolution using a subfunctionalisation model. We found that gene duplication and loss rates influence gene tree shape, impacting balance and diversification rates.
Area of Science:
- Evolutionary biology
- Systems biology
- Bioinformatics
Background:
- Gene families evolve through duplication and loss.
- Subfunctionalisation is a key model for gene family evolution.
- Gene function is maintained by selection, ensuring essential functions persist.
Purpose of the Study:
- To analyze the long-term behavior of a subfunctionalisation model of gene family evolution.
- To determine conditions for gene tree growth versus stability.
- To link evolutionary rates to gene tree shape statistics.
Main Methods:
- Representing gene families as binary matrices (genes x functions).
- Modeling evolution using a continuous-time Markov chain (CTMC).
- Analyzing gene tree shapes using beta (balance) and gamma (diversification) statistics.
Main Results:
- Gene duplication and loss rates significantly alter gene tree shapes.
- High duplication rates lead to unstable processes and uniform ranked tree distributions.
- Stable processes predict balanced trees (positive beta) and early diversification (negative gamma).
Conclusions:
- The subfunctionalisation model's predictions for gene tree shape can be tested against empirical data.
- Tree shape statistics provide insights into evolutionary dynamics.
- Comparing model predictions to empirical gene trees can validate the subfunctionalisation model.
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