Remember, species is an artificial term designated by men to describe different types of animals. If you put a herd of 100 stallions and 100 female donkeys on an island, and came back in 100 years, there wouldn't be any equidae at all there. Sounds like different speicies to me, by any reasonable definition.
You acknowledge they have a common ancestor. But now they can't produce fertile offspring.
If they're really the same 'kind', what did Noah save? Donkeys, horses, zebras, what? If they're different 'kinds', how can they have a common ancestor?
Probably some type of horse. Variation occurred within the species (micro evolution) and much like the breeding of dogs different kinds of horse came about. For some reason, genetically they have been damaged (lost information) so that some of them can no longer breed together or they breed offspring that are infertile. These same group of creatures will not have gained completely different genetic information to turn them into a different KIND.