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Updated: Jul 14, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Supertrees disentangle the chimerical origin of eukaryotic genomes
Davide Pisani1, James A Cotton, James O McInerney
1Department of Biology, The National University of Ireland, Maynooth, Maynooth, County Kildare, Ireland, UK.
Molecular Biology and Evolution
|May 17, 2007
Summary
Eukaryote origins trace back to symbiotic relationships, not Archaebacteria. Genomic analysis reveals strong eubacterial links, supporting endosymbiotic theories for mitochondria and plastids.
Area of Science:
- Genomics
- Evolutionary Biology
- Phylogenetics
Background:
- Eukaryotes are a major domain of life, traditionally sister to Archaebacteria.
- Eukaryotic genomes contain numerous genes of eubacterial origin, leading to many hypotheses about their origin.
- Over 20 conflicting hypotheses exist regarding eukaryote origins.
Purpose of the Study:
- To investigate the phylogenetic origins of eukaryotes using a novel computational method.
- To test existing hypotheses for eukaryote evolution by analyzing genomic data.
- To identify the symbiotic partners involved in eukaryote formation.
Main Methods:
- Phylogenetic signal-stripping using supertrees.
- Analysis of 5,741 single gene families across 185 genomes.
- Comparative genomics to identify prokaryotic homologs in eukaryotic genes.
Main Results:
- Three primary phylogenetic signals were identified in eukaryotic genomes.
- These signals link eukaryotes to Cyanobacteria (plastids), Proteobacteria (mitochondria), and Thermoplasmatales (host).
- Up to 83% of eukaryotic genes with prokaryotic homologs are eubacterial, not archaebacterial.
Conclusions:
- Eukaryotes are not the sister group to Archaebacteria.
- The findings support endosymbiotic theories involving specific bacterial partners for mitochondria and plastids.
- Only hypotheses involving sulfur-dependent or hydrogen-dependent syntrophy for mitochondrial origin remain plausible.
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