Towards an inclusive philosophy for phylogenetic inference

Area of Science:

• Philosophy of Science
• Evolutionary Biology
• Phylogenetics

Background:

• Current phylogenetic frameworks often rely on interpretations of Popperian philosophy, particularly falsificationism.
• Existing justifications for methods like cladistic parsimony have limitations in their philosophical underpinnings.
• There's a need for a more inclusive philosophical framework for phylogenetics that accommodates diverse methods.

Purpose of the Study:

• To defend and expand an inclusive philosophical framework for phylogenetics.
• To reinterpret Popperian corroboration independently of falsificationism for phylogenetic inference.
• To establish a basis for evaluating phylogenetic methods and learning from errors.

Main Methods:

• Interpreting Popperian corroboration as the improbability of evidence given the hypothesis and background knowledge (including chance).
• Analyzing goodness-of-fit values from phylogenetic inference methods as 'test statements' or 'evidence'.
• Applying corroboration assessments to likelihood methods and a novel form of parsimony.

Main Results:

• Phylogenetic methods provide 'evidence' based on goodness-of-fit, and corroboration assesses the severity of the test.
• Cladistic 'corroboration' reflects goodness-of-fit, not true corroboration or severity, and lacks philosophical status.
• The framework allows for combining evidence based on overall corroboration/severity, not just overall fit.

Conclusions:

• The proposed Popperian corroboration framework is method-neutral, justifying neither nor excluding specific phylogenetic methods.
• It provides a robust system for phylogenetics to learn from errors, where apparent good evidence is probable without the hypothesis.
• Progress in phylogenetics is advanced by adopting this inclusive framework and moving beyond restrictive cladistic philosophy.