I took it as evolution fast forwarded. The black stuff obviously was some alien organism. It got into the Dna of the doctor, who then fucked a baby into the female, who then produced an alien form. That allen form then impregnated the alien/humanoid and he birthed what we've all known as the traditional alien. I think this theory might be wrong tho. I thought what the movie ultimately was trying to say, was that the original alien that we know and love, was essentially part human.
Now, this could be wrong becausE, when they walk into the room with the mural on the ceiling, I remember seeing something silver plated that looked a lot like the queen alien.