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The deep(er) roots of Eukaryotes and Akaryotes
Ajith Harish1, David Morrison2
1Independent Researcher, Uppsala, 756 57, Sweden.
F1000Research
|July 22, 2020
Summary
Finding the root of the tree of life is challenging. Protein structural domains, not amino acids, provide more reliable phylogenetic reconstructions for deep evolutionary divergences, supporting a two-domain tree of life model.
Area of Science:
- Evolutionary Biology
- Phylogenetics
- Genomics
Background:
- The universal common ancestor (UCA) and the root of the tree of life (ToL) remain challenging to pinpoint due to evolutionary time depth.
- Two competing two-domain tree of life (2D-ToL) models exist: one with eukaryotes and akaryotes as sister clades, and another placing eukaryotes within archaea.
- A recent study favored eukaryotes as closest relatives to Asgard archaea, but this conclusion is contested due to poor archaeal resolution.
Purpose of the Study:
- To critically evaluate methods for phylogenetic reconstruction of deep evolutionary divergences.
- To determine whether protein domains or amino acids are more reliable for resolving the root of the tree of life.
- To clarify the evolutionary relationships between eukaryotes, akaryotes, and archaea.
Main Methods:
- Comparative analysis of phylogenetic signal from protein domains versus amino acid sequences.
- Phylogenetic character reconstructions focusing on the universal common ancestor (UCA) and early branching lineages.
- Re-evaluation of existing phylogenetic data and methods concerning the two-domain tree of life (2D-ToL) proposals.
Main Results:
- Protein structural domains offer more reliable phylogenetic reconstructions for deep-diverging clades compared to amino acid sequences.
- The analysis supports a two-domain tree of life (2D-ToL) where eukaryotes and akaryotes are distinct, well-supported clades.
- Critique of previous analyses highlights overlooked aspects of phylogenetic signal assessment and evolutionary relatedness estimation.
Conclusions:
- Protein structural domains are superior to amino acids for resolving deep evolutionary history and the root of the tree of life.
- The findings support a two-domain tree of life (2D-ToL) model with eukaryotes and akaryotes as sister clades.
- Accurate phylogenetic reconstruction at deep divergences relies on appropriate character type selection and robust analytical methods.
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