Nothing to it: a reply to Wheeler's "much ado about nothing".

Area of Science:

• Evolutionary Biology
• Systematics
• Computational Biology

Background:

• Phylogenetic analysis aims to reconstruct evolutionary relationships.
• Inapplicable characters pose challenges in phylogenetic analysis.
• Wheeler's dynamic homology view proposes treating absences as insertion/deletion events.

Purpose of the Study:

• To evaluate Wheeler's dynamic homology framework for phylogenetic analysis.
• To identify and address limitations of the dynamic homology approach.
• To propose modifications for improved accuracy and biological realism.

Main Methods:

• Analysis of a four-taxon dataset with observed absences.
• Comparison of dynamic homology with classic algorithms for independent characters.
• Evaluation of character ordering assumptions and their impact on tree reconstruction.

Main Results:

• Wheeler's dynamic homology framework, with ordering assumptions, yields different results than classic methods.
• The framework can produce biologically impossible reconstructions.
• Removing character ordering resolves these issues and aligns with established methods like Maddison's and Goloboff et al.'s.

Conclusions:

• Character ordering assumptions in dynamic homology can lead to inaccurate phylogenetic inferences.
• Removing these assumptions improves the framework's robustness and biological plausibility.
• The modified framework integrates well with existing methods for handling complex and inapplicable characters.