Constraining prior probabilities of phylogenetic trees

Biology and Philosophy 26 (4):567-581 (2011)
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 No keywords specified (fix it)
Categories (categorize this paper)
 Save to my reading list
Follow the author(s)
My bibliography
Export citation
Find it on Scholar
Edit this record
Mark as duplicate
Revision history Request removal from index
Download options
PhilPapers Archive

Upload a copy of this paper     Check publisher's policy on self-archival     Papers currently archived: 13,029
External links
Setup an account with your affiliations in order to access resources via your University's proxy server
Configure custom proxy (use this if your affiliation does not provide a proxy)
Through your library
References found in this work BETA

View all 9 references

Citations of this work BETA
Trevor Pearce (2012). Philosophy of Biology in the Twenty-First Century. Studies in History and Philosophy of Science Part C 43 (1):312-315.
Similar books and articles
Joel D. Velasco (2013). Phylogeny as Population History. Philosophy and Theory in Biology 5 (20130604).
R. D. Rosenkrantz (1973). Probability Magic Unmasked. Philosophy of Science 40 (2):227-233.
Jacob Feldman (2013). Tuning Your Priors to the World. Topics in Cognitive Science 5 (1):13-34.
Michael Huemer (2009). Explanationist Aid for the Theory of Inductive Logic. British Journal for the Philosophy of Science 60 (2):345-375.
Paul D. Thorn (2014). Defeasible Conditionalization. Journal of Philosophical Logic 43:283-302.

Monthly downloads

Added to index


Total downloads

21 ( #92,945 of 1,410,448 )

Recent downloads (6 months)

4 ( #57,804 of 1,410,448 )

How can I increase my downloads?

My notes
Sign in to use this feature

Start a new thread
There  are no threads in this forum
Nothing in this forum yet.