Dissolving the star-tree paradox

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Abstract

While Bayesian methods have become very popular in phylogenetic systematics, the foundations of this approach remain controversial. The star-tree paradox in Bayesian phylogenetics refers to the phenomenon that a particular binary phylogenetic tree sometimes has a very high posterior probability even though a star tree generates the data. I argue that this phenomenon reveals an unattractive feature of the Bayesian approach to scientific inference and discuss two proposals for how to address the star-tree paradox. In particular, I defend the polytomy prior as a solution (or rather dissolution) of the paradox and argue that it is preferable to a data-size dependent branch lengths prior from a methodological perspective. However, while this reply dissolves the star-tree paradox, the general challenge to Bayesian confirmation theory remains unmet.

Original languageEnglish
Pages (from-to)409-419
Number of pages11
JournalBiology and Philosophy
Volume31
Issue number3
DOIs
Publication statusPublished - 1 May 2016
Externally publishedYes

Keywords

  • Bayesian confirmation theory
  • Bayesian phylogenetics
  • Phylogenetic systematics
  • Polytomy prior
  • Prior probabilities
  • Star-tree paradox

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