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Archaeal phylogeny based on ribosomal proteins.
Oriane Matte-Tailliez1, Céline Brochier, Patrick Forterre
1Institut de Génétique et Microbiologie, Université Paris-Sud, Orsay, France.
Molecular Biology and Evolution
|April 19, 2002
Summary
New archaeal phylogeny using ribosomal proteins confirms rRNA findings and reveals lateral gene transfer (LGT) mainly introduces noise, not altering the core evolutionary picture.
Area of Science:
- Microbiology
- Evolutionary Biology
- Bioinformatics
Background:
- Phylogenetic analyses of Archaea traditionally relied on ribosomal RNA (rRNA) sequences, establishing two main phyla: Euryarchaeota and Crenarchaeota.
- Recent advancements in whole-genome sequencing have enabled new approaches to archaeal phylogeny.
Purpose of the Study:
- To construct a robust archaeal phylogeny using a concatenated dataset of 53 ribosomal proteins.
- To assess the impact of lateral gene transfer (LGT) on phylogenetic reconstructions in Archaea.
Main Methods:
- Phylogenetic tree construction based on the combined sequences of 53 ribosomal proteins from sequenced archaeal genomes.
- Application of a novel method to detect and quantify the influence of lateral gene transfer (LGT) on specific genes.
Main Results:
- The ribosomal protein-based phylogeny showed strong congruence with the established rRNA phylogeny, reinforcing the understanding of archaeal domain evolution.
- A core set of 45 non-transferred ribosomal protein genes was identified as reliable for inferring archaeal phylogeny.
- Analysis indicated that LGT events, affecting 8 out of 53 proteins, primarily introduced random noise rather than significantly altering the overall phylogenetic structure.
Conclusions:
- Ribosomal protein phylogenies provide a reliable complement to rRNA-based analyses for Archaea.
- Lateral gene transfer in Archaea appears to be largely driven by environmental proximity rather than phylogenetic relatedness, with minimal impact on the core evolutionary tree.