Apologies, in the meantime I've realized my core problem isn't related to file type. Newick doesn't retain metadata like this. I'm trying to use my tree in an MCMCglmm() but my values of phylogenetic heritability (vp/(vp+vs) keep coming up as ~0.5 independent of treatment. I thought this had to do with support values being brought through the analysis, but as the previous (functional) analysis used a .nwk tree, this can't be why. Indeed, the code I'm using works with a different .nwk tree. But when I input my tree and build my MCMCglmm models, it fails to yield realistic results...
Any experts in MCMCglmm that could offer advice, much appreciated.