Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions

Area of Science:

• Evolutionary biology
• Phylogenetics
• Systematics

Background:

• Phylogenetic methods reconstruct evolutionary history using continuity, singularity, and memory axioms.
• Rooting phylogenies, particularly the "tree of life," often relies on narratives rather than empirical retrodictive exploration, especially with molecular sequence data.

Purpose of the Study:

• To review available phylogenetic rooting criteria and identify the most powerful approach.
• To propose a shift in focus from whole systems to parts of systems for more robust phylogenetic analysis.

Main Methods:

• Review of existing phylogenetic rooting criteria.
• Evaluation of the outgroup comparison method versus the generality criterion (Weston rule).
• Proposal for analyzing the evolution of system parts to address character independence.

Main Results:

• The generality criterion, embodying nesting and additive phylogenetic change (Weston rule), is identified as a powerful rooting approach.
• Minimizing ad hoc and auxiliary assumptions is crucial for reliable phylogenetic rooting.
• Focusing on the evolution of system parts can mitigate violations of character independence.

Conclusions:

• The Weston rule provides a robust method for rooting phylogenies by formalizing the generality criterion.
• Shifting focus to the evolution of system parts offers new avenues for phylogenetic research and addresses limitations of current methods.