The prior probabilities of phylogenetic trees

Biology and Philosophy 23 (4):455-473 (2008)
  Copy   BIBTEX

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.

Links

PhilArchive



    Upload a copy of this work     Papers currently archived: 94,726

External links

Setup an account with your affiliations in order to access resources via your University's proxy server

Through your library

Analytics

Added to PP
2009-01-28

Downloads
139 (#135,444)

6 months
28 (#132,516)

Historical graph of downloads
How can I increase my downloads?

Author's Profile

Joel D. Velasco
Texas Tech University

References found in this work

Scientific reasoning: the Bayesian approach.Peter Urbach & Colin Howson - 1993 - Chicago: Open Court. Edited by Peter Urbach.
How Degrees of Belief Reflect Evidence.James M. Joyce - 2005 - Philosophical Perspectives 19 (1):153-179.
Reconstructing the Past. [REVIEW]Peter Godfrey-Smith - 1993 - Philosophy and Phenomenological Research 53 (2):487-490.

Add more references