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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony.

Edwin Jacox¹, Cedric Chauve², Gergely J Szöllősi³

¹ISE-M, Université Montpellier, CNRS, IRD, EPHE, Montpellier, France.

Bioinformatics (Oxford, England)

|May 7, 2016

Summary

We introduce ecceTERA, a novel program for gene tree-species tree reconciliation. It accurately models gene family evolution, including duplication, loss, and transfer events, improving upon existing methods.

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Area of Science:

Computational Biology
Evolutionary Genomics

Background:

Gene tree-species tree reconciliation is crucial for understanding gene family evolution.
Existing methods often have limitations in modeling complex evolutionary events.

Purpose of the Study:

To present ecceTERA, a new program for gene tree-species tree reconciliation.
To implement a generic parsimony algorithm accounting for gene duplication, loss, and transfer (DTL) events.

Main Methods:

Developed a parsimony reconciliation algorithm within ecceTERA.
The algorithm handles DTL events and speciation across dated and undated species trees.
Incorporated amalgamation for species-tree aware gene tree estimation.

Main Results:

ecceTERA generalizes and improves upon existing DTL parsimony algorithms.
The program accurately estimates gene trees within species trees.
Demonstrated improved reconciliation for binary species and gene trees.

Conclusions:

ecceTERA offers a robust and versatile tool for gene tree-species tree reconciliation.
The program enhances the accuracy of evolutionary analyses by accounting for complex gene family dynamics.
Facilitates more precise reconstruction of gene and species evolutionary histories.