I am not sure whether you can do that in a straightforward fashion.

What I would do in your case is create a vector with the names of the species in the clade you want to analyze and use that to obtain a subtree that has been prunned down to just that clade of interest, which you can then feed into ltt.plot.

species

Maybe using the function: extract.clade(phy, root.edge = 0, interactive = TRUE) of the ape package to extract the clade of interest and place it into an object for subsequent analyses?

Cheers