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Updated: Jul 11, 2025
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
15.9K
Relative timing information and orthology in evolutionary scenarios
David Schaller1, Tom Hartmann1, Manuel Lafond2
1Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, Leipzig, 04107, Germany.
Algorithms for Molecular Biology : AMB
|November 8, 2023
Summary
This study introduces a polynomial-time algorithm for constructing gene family evolutionary scenarios using three graphs: equal-divergence-time (EDT), later-divergence-time (LDT), and prior-divergence-time (PDT). It characterizes these graphs and their relationships, aiding in understanding gene evolution and horizontal gene transfer (HGT).
Area of Science:
- Computational Biology
- Evolutionary Genetics
- Graph Theory
Background:
- Gene family evolution involves mapping gene trees to species trees.
- Relative divergence times of genes and species indicate horizontal gene transfer (HGT) and duplications.
- Three colored graphs (EDT, LDT, PDT) capture gene and species divergence timing.
Purpose of the Study:
- To provide a complete characterization of informative and forbidden triples for gene evolutionary graphs.
- To develop a polynomial-time algorithm for constructing evolutionary scenarios from these graphs.
- To analyze the properties of EDT, LDT, and PDT graphs, including their relationship to cographs and perfect graphs.
Main Methods:
- Characterization of informative and forbidden triples within EDT, LDT, and PDT graphs.
- Development of a polynomial-time algorithm for constructing evolutionary scenarios.
- Analysis of graph properties: cographs, perfect graphs, and polynomial-time recognition.
Main Results:
- A complete characterization of informative and forbidden triples is provided.
- A polynomial-time algorithm for constructing evolutionary scenarios is presented.
- EDT graphs are shown to be perfect; LDT and PDT graphs are cographs. Recognition of EDT graphs is NP-complete in general scenarios but polynomial in HGT-free cases. PDT graphs are polynomial-time recognizable.
Conclusions:
- The study provides a robust framework for analyzing gene family evolution using graph theory.
- The developed algorithm and characterizations offer significant advancements in understanding evolutionary scenarios, including HGT.
- The findings connect graph properties to orthology definitions in the presence of HGT.
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