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08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Rooted phylogeny of the three superkingdoms
Ajith Harish1, Anders Tunlid, Charles G Kurland
1Microbial Ecology, Department of Biology, Lund University, Ecology Building, Sölvegatan 37, Lund, Sweden.
Biochimie
|May 15, 2013
Summary
Phylogenetic analysis using protein domains reveals archaea and bacteria as sister groups, diverging from a complex common ancestor, not bacteria. This re-roots the tree of life, suggesting a bottleneck survivor seeded modern lineages.
Area of Science:
- Genomics
- Evolutionary Biology
- Bioinformatics
Background:
- Traditional phylogenetic trees based on gene sequences conflict with genome content data.
- Previous models of the three superkingdoms (Archaea, Bacteria, Eukaryota) lack resolution.
Purpose of the Study:
- To reconstruct a robust rooted tree of life using genome content data.
- To investigate the nature and complexity of the most recent universal common ancestor (MRUCA).
Main Methods:
- Analysis of compact protein domains from the SCOP superfamily (SF) across sequenced genomes.
- Application of maximum parsimony to resolve phylogenetic relationships.
- Comparative proteomic analysis of extant superkingdoms.
Main Results:
- Genome content analysis resolves fully rooted trees, identifying Archaea and Bacteria (akaryotes) as sister clades.
- Eukaryotes form a separate sister clade, with both akaryote and eukaryote ancestors diverging from MRUCA.
- MRUCA was a complex entity, not a bacterium, possessing a large repertoire of protein domains, with subsequent reductive and cumulative evolution in descendant lineages.
Conclusions:
- The tree of life is re-rooted, challenging the traditional bacterial ancestor model.
- The MRUCA was highly complex, suggesting it was not the first cell lineage.
- A bottleneck event may have preceded the diversification of modern life forms.
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