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 signal 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.