in the estimation, the lower bound could be too small (e.g. negative), making the phylogenetic variance covariance non-positive semidefinite singular. tru to use the bound option (bounds = list(a=c(X,> 0))), with X being the loest bound you are willing to accept. Also, check this thread... http://permalink.gmane.org/gmane.comp.lang.r.phylo/2376