Toward Automatic Reconstruction of a Highly Resolved Tree of Life

2006/03/02 by Francesca D. Ciccarelli, Tobias Doerks, Christian von Mering +3 · 35 citations
Biochemistry, Genetics and Molecular Biology · Environmental Science · #Genomics and Phylogenetic Studies #RNA and protein synthesis mechanisms #Microbial Community Ecology and Physiology

paper · doi:10.1126/science.1123061

openalex publication_date 2006/03/02 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/04

Abstract

We have developed an automatable procedure for reconstructing the tree of life with branch lengths comparable across all three domains. The tree has its basis in a concatenation of 31 orthologs occurring in 191 species with sequenced genomes. It revealed interdomain discrepancies in taxonomic classification. Systematic detection and subsequent exclusion of products of horizontal gene transfer increased phylogenetic resolution, allowing us to confirm accepted relationships and resolve disputed and preliminary classifications. For example, we place the phylum Acidobacteria as a sister group of delta-Proteobacteria, support a Gram-positive origin of Bacteria, and suggest a thermophilic last universal common ancestor.

Citations

• Cases in which Parsimony or Compatibility Methods will be Positively Misleading
• Reductive evolution of resident genomes
• The New View of Animal Phylogeny
• Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity

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• Domain (taxonomy) [wikipedia]
• Evolution [wikipedia]
• History of life [wikipedia]
• Introduction to evolution [wikipedia]
• Marine life [wikipedia]
• Most recent common ancestor [wikipedia]
• Pseudomonadota [wikipedia]