- 1997). In the latter case, the specification of \code{phy} and
- \code{model} are actually ignored: it is instead given through a
- correlation structure with the option \code{corStruct}.
+ 1997, Cunningham et al. 1998). In the latter case, the specification
+ of \code{phy} and \code{model} are actually ignored: it is instead
+ given through a correlation structure with the option
+ \code{corStruct}.
+
+ In the default setting (i.e., \code{method = "ML"} and \code{model =
+ "BM"}) the maximum likelihood estimation is done simultaneously on
+ the ancestral values and the variance of the Brownian motion process;
+ these estimates are then used to compute the confidence intervals in
+ the standard way (see the package \pkg{geiger} for a different
+ implementation). If \code{method = "pic"} or \code{"GLS"}, the
+ confidence intervals are computed using the expected variances under
+ the model, so they depend only on the tree.