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Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks

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Finding maximum common contractions between phylogenetic networks.

Bertrand Marchand¹, Nadia Tahiri², Shohreh Golpaigani Fard³

¹Departement d'Informatique, University of Sherbrooke, 2500 Boulevard de l'Universite, J1K2R1, Sherbrooke, QC, Canada. bertrand.marchand@usherbrooke.ca.

Algorithms for Molecular Biology : AMB

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Summary

This summary is machine-generated.

This study introduces an operational distance for comparing phylogenetic networks using edge contractions and expansions. It proves this distance is NP-hard to compute but offers a polynomial-time solution for weakly galled trees.

Keywords:

Algorithms Contractions Phylogenetic networks Weakly galled trees

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Area of Science:

Computational Biology
Phylogenetics
Graph Theory

Background:

Phylogenetic trees are foundational in evolutionary biology.
Comparing phylogenetic networks requires robust methodologies.
Existing methods for tree comparison, like Robinson-Foulds, need adaptation for networks.

Purpose of the Study:

To define and analyze an operational distance for phylogenetic networks.
To investigate the computational complexity of comparing phylogenetic networks.
To explore algorithmic solutions for specific network types.

Main Methods:

Defining phylogenetic network comparison using edge contractions and expansions.
Proving connectivity of the network space under these operations.
Analyzing the complexity of computing maximum common contractions.
Developing algorithms for specific network classes.

Main Results:

Edge contractions and expansions connect the space of phylogenetic networks.
An operational distance can be defined based on these edit operations.
Computing maximum common contractions is NP-hard, even with bounded parameters.
Lower bounds for the problem are established using the Exponential-Time Hypothesis.
A polynomial-time algorithm is presented for weakly galled trees.

Conclusions:

The proposed operational distance provides a novel way to compare phylogenetic networks.
The NP-hardness result highlights the computational challenges in network comparison.
The algorithm for weakly galled trees offers a practical solution for a relevant network class.
This work contributes to understanding evolutionary relationships through network analysis.