A rooted net of life

Area of Science:

• Evolutionary Biology
• Genomics
• Bioinformatics

Background:

• Phylogenetic reconstruction using DNA and protein sequences is crucial for understanding evolutionary histories.
• Existing methods often analyze gene families and overall organismal phylogeny separately.

Purpose of the Study:

• To present a unified model, the Rooted Net of Life genome phylogeny, for reconstructing evolutionary histories.
• To incorporate discrete evolutionary units and acknowledge horizontal gene transfer events within a single framework.

Main Methods:

• Constructing a rooted tree scaffold from a supermatrix of combined ribosomal genes.
• Reconstructing unrooted phylogenies for gene families with four or more members.
• Superimposing gene family phylogenies onto the tree scaffold and identifying reticulations.

Main Results:

• The model successfully integrates genome-wide gene family phylogenies with a core ribosomal gene tree scaffold.
• Reticulations in the combined phylogeny highlight incongruities, potentially indicating horizontal genetic transfers or endosymbioses.
• Differentiating tree edges allows for the distinction between vertical inheritance and horizontal gene transfer events.

Conclusions:

• The Rooted Net of Life model offers a comprehensive approach to visualizing and understanding the complex evolutionary trajectories of genomes.
• This framework enhances the reconstruction of evolutionary histories by explicitly modeling horizontal gene transfer and endosymbiosis alongside vertical inheritance.