Yule model bug

From BEAST Software

Prior to version 1.4.3, BEAST did not correctly implement the Yule model speciation prior.

Description of the problem

The normal specification of the Yule prior in former publications (e.g. Yang and Rannala 1997) ignores the waiting time of the last interval because the likelihood of the Yule process is written in terms of a condition on the root height rather than a condition on the number of tips.

Consequences

This bug can cause problems in divergence time estimation of the root of the tree, especially in combination with a relaxed molecular clock model and/or no calibration prior on the root. If, however, the analysis used a strict clock, or there was a node height calibration on the root of the tree, then this bug is unlikely to have caused any significant bias.

Solution

The solution is to obtain BEAST v1.4.3 and reanalyse BEAST XML files that used the Yule model as a prior on tree shape. The XML does not need to be changed.