Taxic Homology = Overall Similarity.

Area of Science:

• Systematic Botany
• Evolutionary Biology
• Phylogenetic Systematics

Background:

• Modified three-taxon analysis (m3ta) is presented as a model-free method for assessing group monophyly using nonadditive binary coding.
• The method utilizes the taxic concept of homology, which is itself a model.
• This approach has been advocated for its potential to simplify phylogenetic assessments.

Purpose of the Study:

• To critically evaluate the methodology and underlying assumptions of modified three-taxon analysis (m3ta).
• To determine if m3ta accurately assesses monophyly and aligns with evolutionary principles.
• To contrast m3ta with established phylogenetic systematics and phenetic methods.

Main Methods:

• Analysis of the theoretical framework of m3ta, focusing on its use of nonadditive binary coding.
• Comparison of m3ta's grouping criteria (all similarities) with principles of phylogenetic systematics (shared derived characters).
• Examination of the implications of m3ta's reliance on similarity for phylogenetic interpretation, including the necessity of a clock assumption for phylogenetic trees.

Main Results:

• The taxic concept underlying m3ta functions as a model that appears to contradict evolutionary theory.
• m3ta employs a grouping-by-all-similarities strategy, characteristic of phenetic methods.
• Phylogenetic interpretation of m3ta requires a clock assumption, and its groupings are fundamentally phenetic, not monophyletic.
• Definitions of phylogenetic systematics based solely on presence data, as favored by m3ta advocates, are inadequate as absences can be apomorphic.

Conclusions:

• Modified three-taxon analysis (m3ta) is a phenetic method that does not reliably assess monophyly.
• The method's reliance on all similarities and its underlying model are incompatible with evolutionary principles.
• Phenetic groupings generated by m3ta have limited relevance to true phylogenetic relationships, even when absences are not considered.