Constraining prior probabilities of phylogenetic trees

Biology and Philosophy 26 (4):567-581 (2011)

Abstract
Although Bayesian methods are widely used in phylogenetic systematics today, the foundations of this methodology are still debated among both biologists and philosophers. The Bayesian approach to phylogenetic inference requires the assignment of prior probabilities to phylogenetic trees. As in other applications of Bayesian epistemology, the question of whether there is an objective way to assign these prior probabilities is a contested issue. This paper discusses the strategy of constraining the prior probabilities of phylogenetic trees by means of the Principal Principle. In particular, I discuss a proposal due to Velasco (Biol Philos 23:455–473, 2008) of assigning prior probabilities to tree topologies based on the Yule process. By invoking the Principal Principle I argue that prior probabilities of tree topologies should rather be assigned a weighted mixture of probability distributions based on Pinelis’ (P Roy Soc Lond B Bio 270:1425–1431, 2003) multi-rate branching process including both the Yule distribution and the uniform distribution. However, I argue that this solves the problem of the priors of phylogenetic trees only in a weak form
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DOI 10.1007/s10539-011-9253-7
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References found in this work BETA

Darwin's Dangerous Idea: Evolution and the Meanings of Life.David L. Hull - 1997 - British Journal for the Philosophy of Science 48 (3):435-438.
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Philosophy of Biology in the Twenty-First Century. [REVIEW]Trevor Pearce - 2012 - Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1):312-315.

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