Incorporating continuous characters in joint estimation of dicynodont phylogeny

Continuous characters have received comparatively little attention in
Bayesian phylogenetic estimation. This is predominantly because they
cannot be modeled by a standard phylogenetic Q-matrix approach due to
their non-discrete nature. In this manuscript, we explore the use of
continuous traits under two Brownian Motion models to estimate a
phylogenetic tree for Dicynodontia, a well-studied group of early
synapsids (stem mammals) in which continuous characters have been
extensively used in parsimony-based tree reconstruction. We examine the
differences in phylogenetic signal between a continuous trait partition, a
discrete trait partition, and a joint analysis with both types of
characters. We find that continuous and discrete traits contribute
substantially different signals to the analysis, even when other parts of
the model (clock and tree) are held constant. Tree topologies
resulting from the new analyses differ strongly from the established
phylogeny for dicynodonts, highlighting continued difficulty in
incorporating truly continuous data in a Bayesian phylogenetic framework.