Genome trees constructed using five different approaches suggest new major bacterial clades

Area of Science:

• Genomics
• Evolutionary Biology
• Bioinformatics

Background:

• Increasing availability of complete genome sequences necessitates advanced phylogenetic methods.
• Comparative analysis of gene sets is crucial for understanding prokaryotic evolution, considering horizontal gene transfer and gene loss.

Purpose of the Study:

• To develop and apply novel phylogenetic approaches using genome-scale data.
• To investigate deep evolutionary relationships among prokaryotic lineages.

Main Methods:

• Five independent phylogenetic methods were used: gene presence-absence, conserved gene order, ortholog identity distribution, concatenated ribosomal proteins, and multiple protein families.
• Phylogenetic trees were constructed for bacterial and archaeal genomes.
• Statistical tests (Kishino-Hasegawa) and census of orthologous protein topologies were employed for validation.

Main Results:

• All methods supported the separation of bacteria and archaea, with some variations in terminal branches.
• Methods sensitive to gene loss and horizontal gene transfer (gene presence-absence, gene pairs) showed significant differences.
• Concatenated ribosomal protein sequences yielded a robust phylogenetic signal, identifying potential high-level bacterial clades (Chlamydia-Spirochetes, Thermotogales-Aquificales, Actinomycetes-Deinococcales-Cyanobacteria).
• Analysis questioned the sister-group relationship of Euryarchaeota and Crenarchaeota, suggesting Euryarchaeota may be paraphyletic.

Conclusions:

• Genome-scale phylogenetic analysis can uncover deep evolutionary relationships in prokaryotes, even with significant horizontal gene flow and gene loss.
• Concatenated ribosomal protein analysis offers a reliable method for inferring robust prokaryotic phylogenies.