New research on fruit fly's different species' genome has found some immunity related genes that have evolved quickly causing that hybridation among these two species often fails (the offspring die).
It seems that they evolve as response from viral threats as well as defense against the animals' own "malicious" genes (those that are not really of any use other than replicating themselves but that can condition the carrier species' evolution). In the long run this has caused that the two species, isolated from each other by some 3 million years, have not anymore compatible genomes.
After all, like with technology, this seems to be mostly a matter of compatibility and we all know that what works in Windows, seldom does in a Mac (and viceversa). .