Geoff Nicholls (Oxford)
A stochastic Dollo-model for phylogenetic inference from binary trait data: model elaboration and
checking.
Nicholls and Gray (2008) describe a phylogenetic model for binary trait data. They use their model to
estimate branching times on a Indo-European language tree from the lexical data of Ringe et al. (2002),
dropping seven languages with missing data. We summarise this work and report three further
developments. We give a model for rate heterogeneity in the trait evolution which adds a point process
of evolutionary bursts to the background birth-death process. We show how to compute the likelihood
when there are trait data missing at random. We fit the model to the full dataset, and check the fit using
Bayes factors to measure support for known constraints on the phylogenetic branch lengths and subtree structures. We reject three of thirty historically attested constraints. This is joint work with Robin J.
Ryder.