An ape phylogeny. The tree must be ultrametric and
this is enforced on entry.
data_species
A vector of species names for which we have
trait data. Species names in both the tree and in this vector
must be separated with underscores, not with spaces.
topology
A topological tree used to determine patterns of
relatedness among species in phy. The better resolved this
tree is and the better the overlap it has with phy and
data_species the more useful this will be. Branch length
information is not used.