I would say that some of those in the Northern Crater may well be. Many creatures in the world at large, though, don't appear as though they would serve any obvious benefit to their ecosystems. That may be an indication that they're not natural, or it just might be reading too much into it.

In any event, I'd say that some of the regular creatures encountered in the game may well be a result of JENOVA's mutation of the Cetra.