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Updated: Jul 4, 2026

A Practical Guide to Phylogenetics for Nonexperts

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Published on: February 6, 2014

Do orthologous gene phylogenies really support tree-thinking?

E Bapteste¹, E Susko, J Leigh

¹GenomeAtlantic, 1721 Lower Water Street, Suite 401, Halifax, NS, B3J 1S5, Canada. eric.bapteste@dal.ca

BMC Evolutionary Biology

|May 26, 2005

Summary

Phylogenetic analyses challenge the traditional Tree of Life model. Results suggest gene congruence is limited, questioning the reliability of concatenating markers for evolutionary history reconstruction.

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Published on: August 14, 2018

Area of Science:

Evolutionary Biology
Phylogenetics
Genomics

Background:

Reconstructing the Tree of Life is a central goal in evolutionary biology, with tree-thinking as a key concept.
Traditional phylogenetic analyses face limitations with morphological characters at higher taxonomic levels.
Molecular sequences (genes, proteins, genomes) are increasingly relied upon for constructing universal phylogenies.

Purpose of the Study:

To investigate the congruence of orthologous genes across different domains of life.
To evaluate the suitability of using large numbers of molecular markers for phylogenetic reconstruction.
To assess the impact of lateral gene transfer on phylogenetic signal.

Main Methods:

Utilized heat map analyses to assess gene congruence in archaeal, bacterial, eukaryotic, and alpha-proteobacterial datasets.
Examined the history of orthologous genes within these diverse datasets.
Evaluated the presence and impact of lateral gene transfer.

Main Results:

A significant portion of genes could not be reliably determined to share a common evolutionary history.
None of the analyzed datasets were found to be entirely free from the influence of lateral gene transfer.
Phylogenetic congruence among orthologues was insufficient to support a universal tree model.

Conclusions:

Phylogenetic analyses do not support the concept of a singular Tree of Life.
The findings challenge the assumption that gene inheritance universally follows a tree-like model.
Alternative representations beyond a simple tree structure may be necessary for depicting evolutionary relationships due to potential misleading signals from concatenated markers.