Reconstructing evolutionary relationships from functional data: a consistent classification of organisms based on...

Area of Science:

• Evolutionary Biology
• Genomics
• Molecular Biology

Background:

• Reconstructing the Tree of Life is challenged by discrepancies between gene family phylogenies and single-gene trees, potentially due to horizontal gene transfer (HGT).
• Consensus tree reconstructions increasingly integrate molecular data with additional phylogenetic markers.
• Ribosomal RNA (rRNA) and ribosomal protein (r-protein) operons are highly conserved, rarely undergo HGT, and possess significant phylogenetic value.

Purpose of the Study:

• To reconstruct phylogenies using ribosomal function, specifically protein synthesis antibiotic sensitivity, as a novel phylogenetic marker.
• To investigate the role of ribosomal performance in resolving evolutionary relationships and addressing discrepancies in the Tree of Life.
• To affiliate archaea with eukarya based on information-processing systems.

Main Methods:

• Utilized a database of 33 ribosomal systems from three major cellular lineages, probed against 38 protein synthesis inhibitors.
• Explored different distance metrics between organism pairs.
• Adapted the bootstrap evaluation algorithm to assess the reliability of phylogenetic reconstructions.

Main Results:

• A consistent phylogeny was obtained, systematically affiliating archaea with eukarya.
• This result aligns with recent phylogenies derived from information-processing systems.
• The study demonstrates the utility of functional markers in phylogenetic analysis.

Conclusions:

• Ribosomal function, measured by antibiotic sensitivity, provides valuable phylogenetic information.
• Integrating functional markers like ribosomal performance can help achieve a consensus Tree of Life.
• The findings support the affiliation of archaea with eukarya, reinforcing current evolutionary models.