Question

Do adaptive and non-adaptive variations differ in their usefulness for phylogenetic inference?

Answer 1

Yes. They Differ.

Adaptive variation means the the development of different functional structures from common ancestors.

For example, Adaptive variation gave rise to different marsupials in Australia. In Adaptive radiation,

On the other hand the Genetic drift and Mutation are the key process for Non adaptive variation,

The result of Adaptive variation is sympatric (occuring in overlapping geographical area which helps in interbreeding of the species) in nature. But the result for non adaptive variation is allopatric (occuring in non overlapping geographical area which restricts the interbreeding and creates selection pressure and different species from same clad evolve) in nature.