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 language | English |
|---|---|
| Pages (from-to) | 409-419 |
| Number of pages | 11 |
| Journal | Biology and Philosophy |
| Volume | 31 |
| Issue number | 3 |
| DOIs | |
| Publication status | Published - 1 May 2016 |
| Externally published | Yes |
Keywords
- Bayesian confirmation theory
- Bayesian phylogenetics
- Phylogenetic systematics
- Polytomy prior
- Prior probabilities
- Star-tree paradox
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