Constraining prior probabilities of phylogenetic trees Authors Bengt Autzen Department of Philosophy, Logic and Scientific Method, London School of Economics and Political Science Article

First Online: 06 March 2011 Received: 02 July 2010 Accepted: 01 February 2011 DOI :
10.1007/s10539-011-9253-7

Cite this article as: Autzen, B. Biol Philos (2011) 26: 567. doi:10.1007/s10539-011-9253-7
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.

Keywords Bayesian epistemology Multi-rate branching process Phylogenetic trees Phylogenetics Principal Principle Prior probabilities Yule process

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