Beta regression (proportions) with phylogenetic comparative analysis? Is there a package in R that allows phylogenetic comparative analysis of proportion data (i.e. a beta distribution)?

You can do GLMMs including phylogeny as an error term in the package brms. See here for an example. The package also allows for beta distribution. The new version of glmmTMB also allows you to include several types of covariance structures and includes the beta distribution.
