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Terraces in species tree inference from gene trees
Mursalin Habib1, Kowshic Roy1, Saem Hasan1
1Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, 1205, Bangladesh.
BMC Ecology and Evolution
|November 4, 2024
Summary
Species tree terraces, regions of equally optimal phylogenetic trees caused by missing data, are mathematically characterized. New "peak terraces" account for gene tree topology, potentially improving phylogenetic inference accuracy and branch support.
Area of Science:
- Phylogenetics
- Computational Biology
- Bioinformatics
Background:
- Phylogenetic tree estimation can result in multiple equally optimal trees due to missing data, forming 'terraces' in tree space.
- Previous work defined species tree terraces but did not fully account for gene tree heterogeneity or topological proximity.
Purpose of the Study:
- To mathematically characterize species tree terraces and their underlying conditions.
- To introduce and define 'peak terraces' that incorporate gene tree topology.
- To empirically investigate the implications of species tree terraces in phylogenetic inference.
Main Methods:
- Mathematical characterization of species tree terraces.
- Introduction and definition of 'peak terraces'.
- Empirical studies using simulated and real biological data.
Main Results:
- Species tree terraces are mathematically defined and shown to be agnostic to gene tree heterogeneity.
- A novel 'peak terrace' concept is introduced, considering gene tree topology.
- Terraces are prevalent, causing ambiguity in tree search algorithms, but their identification offers opportunities for improved accuracy and branch support.
Conclusions:
- Mathematical characterization clarifies species tree terrace properties.
- Peak terraces offer a more refined understanding by including gene tree topology.
- Identifying terraces can enhance phylogenetic summary methods and branch support accuracy.
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