Oh, I misunderstood... Most of those skulls are absolutely from the prop department. The prominent ones, anyhow. Real skulls look nothing like that at all. Even the ones that look like ape skulls are obvious fakes. I do think the skull visible past the front of Nimoy's face in the pic Robert Comsol
linked to, probably is a real skull that has been painted white with black in the eye sockets. Probably a deer or a dog. The black-ish one on the shelf outside of the niche I'm not as sure about. That might be real, or else a prop. It's certainly a mix and match game.