Hi Alejandra,

it really depends on which "variance" are you talking about. Phylogenetic variance is, of course, the same for the two traits (there is one single tree, a single set of species). If you talk about trait variance as such, you shouldn't care, because contrasts work, in a sense, on different variances at the tree tips. Finally, there are methods for including intraspecific variance in phylogenetic analyses, by Ives, and by Revell.

Hope this helps,

Pas