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A Practical Guide to Phylogenetics for Nonexperts

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PhyBin: binning trees by topology.

Ryan R Newton¹, Irene L G Newton

¹School of Informatics and Computing, Indiana University , Bloomington, IN , United States.

|October 30, 2013

Summary

This summary is machine-generated.

PhyBin software clusters gene trees to reveal evolutionary histories. This analysis highlights that while a dominant evolutionary path exists, many genes show alternative histories, suggesting complex evolutionary processes.

Keywords:

Evolutionary history Horizontal gene transfer Phylogenetics Robinson-Foulds Wolbachia

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Area of Science:

Evolutionary biology
Bioinformatics
Genomics

Background:

Determining an organism's true evolutionary history is a key goal in evolutionary analysis.
Genome-wide evolutionary perspectives are often limited by analyzing only a few genes.
Individual genes within a genome can exhibit distinct evolutionary trajectories.

Purpose of the Study:

To introduce PhyBin, a flexible program for clustering gene trees based on topological similarity.
To enable the analysis of numerous phylogenetic topologies within a genome-wide orthologous gene set.
To provide a tool for exploring discrepancies in gene-specific evolutionary histories.

Main Methods:

PhyBin clusters gene trees based on identical topologies or uses Robinson-Foulds distance for similar trees.
The program allows pre-processing of trees to manage noise by collapsing short branches or low bootstrap support nodes.
Tested using an orthologous gene set from 10 Wolbachia species across four supergroups (A-D).

Main Results:

PhyBin successfully categorized the complete set of phylogenetic topologies from the Wolbachia dataset.
A dominant topology confirmed the separation of Wolbachia supergroups.
A significant number of genes supported alternative evolutionary histories, indicating complex evolutionary dynamics.

Conclusions:

PhyBin facilitates the identification of genes with alternative evolutionary paths.
The software aids in investigating reasons for phylogenetic discrepancies, such as homoplasy or horizontal gene transfer.
This approach offers a more comprehensive understanding of genome-wide evolutionary processes.