Toward Automatic Reconstruction of a Highly Resolved Tree of Life

TLDR

The method concatenates 31 orthologs from 191 sequenced genomes and removes horizontal gene transfer products to enhance phylogenetic resolution. The resulting tree of life has comparable branch lengths, uncovers interdomain taxonomic discrepancies, confirms accepted relationships, resolves disputed classifications, places Acidobacteria as sister to delta‑Proteobacteria, supports a Gram‑positive bacterial origin, and suggests a thermophilic last universal common ancestor.

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.