The prior probabilities of phylogenetic trees

Biology and Philosophy 23 (4):455-473 (2008)
Abstract
Bayesian methods have become among the most popular methods in phylogenetics, but theoretical opposition to this methodology remains. After providing an introduction to Bayesian theory in this context, I attempt to tackle the problem mentioned most often in the literature: the “problem of the priors”—how to assign prior probabilities to tree hypotheses. I first argue that a recent objection—that an appropriate assignment of priors is impossible—is based on a misunderstanding of what ignorance and bias are. I then consider different methods of assigning prior probabilities to trees. I argue that priors need to be derived from an understanding of how distinct taxa have evolved and that the appropriate evolutionary model is captured by the Yule birth–death process. This process leads to a well-known statistical distribution over trees. Though further modifications may be necessary to model more complex aspects of the branching process, they must be modifications to parameters in an underlying Yule model. Ignoring these Yule priors commits a fallacy leading to mistaken inferences both about the trees themselves and about macroevolutionary processes more generally.
Keywords No keywords specified (fix it)
Categories (categorize this paper)
Options
 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: 11,105
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

No references found.

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
Analytics

Monthly downloads

Added to index

2009-01-28

Total downloads

20 ( #85,199 of 1,101,681 )

Recent downloads (6 months)

3 ( #116,934 of 1,101,681 )

How can I increase my downloads?

My notes
Sign in to use this feature


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