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Updated: May 27, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Rooting the eukaryotic tree with mitochondrial and bacterial proteins.
1Bioinformatics and Genomics Program, Centre for Genomic Regulation and Universitat Pompeu Fabra, Barcelona, Spain. romain.derelle@crg.es
Molecular Biology and Evolution
|December 3, 2011
Summary
Rooting the eukaryotic tree is challenging due to evolutionary distance. This study uses mitochondrial proteins to place the eukaryotic root between unikonts and bikonts, identifying new relationships.
Area of Science:
- Eukaryotic evolution and phylogenomics.
- Molecular evolution and bioinformatics.
Background:
- Phylogenomic studies offer insights into eukaryotic relationships but struggle to confidently place the eukaryotic root.
- The large evolutionary distance between eukaryotes and Archaea, coupled with phylogenetic artifacts like long-branch attraction, complicates rooting efforts.
Purpose of the Study:
- To establish a robust rooting of the eukaryotic tree using mitochondrial protein-coding genes.
- To investigate the phylogenetic position of Thecamonas trahens and reassess the affiliation of Malawimonas species within eukaryotes.
Main Methods:
- Identification and assembly of a dataset comprising 42 mitochondrial proteins, primarily encoded by the nuclear genome.
- Phylogenetic analyses using Bayesian and maximum likelihood methods with expanded taxon sampling, including Thecamonas trahens.
Main Results:
- The study successfully places the eukaryotic root between the monophyletic unikont and bikont clades.
- Thecamonas trahens is robustly supported as sister to Opisthokonta.
- The affiliation of Malawimonas species with the bikont or excavate lineages is questioned.
Conclusions:
- Mitochondrial protein data provide a valuable alternative approach for resolving deep eukaryotic evolutionary relationships.
- This dataset confirms previously observed eukaryotic supergroup relationships and offers new insights into basal eukaryotic divergences.
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