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.