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A Practical Guide to Phylogenetics for Nonexperts

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Probabilism and Phylogenetic Inference.

Mark E Siddall¹, Arnold G Kluge¹

¹Museum of Zoology, University of Michigan, Ann Arbor, Michigan, 48109, U.S.A.

Cladistics : the International Journal of the Willi Hennig Society

|December 16, 2021

Summary

Maximum likelihood methods are unsuitable for phylogenetic inference due to their reliance on frequency probability. Parsimony, grounded in logical probability, offers a more appropriate framework for historical sciences, emphasizing explanation over prediction.

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Area of Science:

Phylogenetics
Philosophy of Science
Statistical Inference

Background:

Phylogenetics seeks to infer evolutionary history.
Maximum likelihood (ML) and parsimony are two major phylogenetic methods.
ML relies on frequency probability, while parsimony uses logical probability.

Purpose of the Study:

To critically evaluate the epistemological foundations of maximum likelihood in phylogenetics.
To contrast ML with cladistic parsimony regarding historical inference.
To argue for a falsificationist approach in phylogenetic epistemology.

Main Methods:

Deconstruction of maximum likelihood estimation procedures.
Analysis of the theoretical underpinnings of frequency probability versus logical probability.
Examination of assumptions, including calculus independence (e.g., i.i.d.) in ML models.
Critique of deterministic models in ML compared to cladistics' background knowledge.

Main Results:

Frequency probability methods, central to ML, are deemed inappropriate for historical inferences.
ML models are shown to be problematic, deterministic, and violate calculus independence.
Parsimony's justification is external to ML's criticisms, and its assumptions are less problematic.
ML is susceptible to Wald's dilemma when realism is considered.

Conclusions:

Maximum likelihood estimation is fundamentally ill-suited for inferring phylogenetic history.
Cladistic parsimony offers a more rational epistemological foundation for historical sciences.
Phylogeneticists should adopt a sophisticated falsificationist approach over metaphysical appeals.