Including Viruses in the Tree of Life

1.Framing the Inclusion Argument (Intro + Definition of Life)

Goal: Set the lens and justify why inclusion is worth considering.

• Start with the purpose of biological classification:
• To represent evolutionary relationships, not just biological independence
• Acknowledge the core controversy:
• Viruses lack metabolism and depend on hosts
• Thesis:
• Viruses should be included in the tree of life if life is defined by evolutionary capacity rather than strict autonomy
• Briefly preview key evidence:
• Giant viruses
• Viral evolutionary arms races
• Open-ended evolution and gene exchange
• Signal relevance:
• Excluding viruses risks oversimplifying early evolutionary history and LUCA research

2.Giant Viruses, Virophages, and Viral Complexity

Goal: Use empirical evidence to challenge the simple parasite view.

• Introduce Acanthamoeba polyphaga mimivirus (APMV)
• Large genome size comparable to bacteria
• Genes involved in transcription, DNA repair, and translation
• Argue:
• These features blur the viruscell boundary
• Suggest viruses may have complex evolutionary origins
• Introduce virophages and MIMIVIRE
• Giant viruses can be infected and evolve defenses
• Key claim:
• These interactions demonstrate adaptation, selective pressure, and coevolution
• Conclusion:
• Viral complexity supports inclusion in evolutionary classification systems

3.Evolution, Autonomy, Polyphyly, and Horizontal Gene Transfer

Goal: Address the biggest theoretical objections head-on.

• Autonomy:
• Acknowledge viruses lack metabolism
• Introduce Ruiz-Mirazos open-ended evolution
• Argue autonomy exists on a continuum
• Polyphyly:
• Viral polyphyly complicates classification but does not invalidate it
• Many biological traits evolved multiple times
• Horizontal gene transfer:
• Viruses are major agents of gene exchange
• Shape host evolution and genetic innovation
• Key move:
• Viruses function as evolutionary actors, not passive byproducts

4. Implications for the Tree of Life (Conclusion for Inclusion Section)

Goal: Pull together your case and tee up synthesis.

• Summarize:
• Viruses evolve, adapt, and influence life across domains
• Clarify:
• Inclusion does not require redefining viruses as fully autonomous organisms
• Broader implication:
• The traditional tree model may need expansion toward network-based evolution
• Bridge to synthesis:
• Whether viruses belong on the tree depends less on what life is and more on how evolution is conceptualized