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Related Experiment Video

Updated: Jul 5, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Rooted triple consensus and anomalous gene trees.

Gregory B Ewing¹, Ingo Ebersberger, Heiko A Schmidt

¹Center for Integrative Bioinformatics Vienna, Max F, Perutz Laboratories, Dr, Bohr Gasse 9, A-1030 Vienna, Austria. gregory.ewing@univie.ac.at

BMC Evolutionary Biology

|April 29, 2008

Summary

This study introduces a rooted triple method to identify the correct species tree despite anomalous gene trees (AGTs). The new approach outperforms existing strategies and helps resolve phylogenetic relationships, even with lineage sorting.

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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

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Published on: August 16, 2017

Area of Science:

Phylogenetics
Computational Biology
Evolutionary Biology

Background:

Anomalous gene trees (AGTs) present topological differences from species trees and are more probable than congruent trees.
Reconstructing accurate species phylogenies is challenged by AGTs and potential errors in gene tree reconstruction.

Purpose of the Study:

To propose and evaluate a novel rooted triple approach for species tree reconstruction in the presence of AGTs.
To assess the performance of the new method against established strategies like extended majority rule consensus.

Main Methods:

Development of a rooted triple approach to infer species trees.
Simulation of data to compare the proposed method with the extended majority rule consensus strategy.
Application of both methods to a large metazoan gene data set (216 genes).

Main Results:

The proposed rooted triple method demonstrates superior performance compared to the extended majority rule consensus strategy.
The method successfully resolves the species tree, even when AGTs are present.
Analysis of the metazoan data set did not reveal significant interference from AGTs in phylogenetic reconstruction.

Conclusions:

Erroneously reconstructed gene trees, rather than AGTs, appear to be the primary challenge in current phylogenetic studies.
The developed rooted triple method effectively rules out erroneous reconstruction of deep or poorly resolved splits caused by lineage sorting.