In the room with the urns there was an alien in a crucifiction position.
Why?
obviously the aliens already exist - meaning the alien at the end isnt the first alien (also backed up that in AvP there are aliens on earth from thousands of years BC)
I think one earth the engineers made humans which i believe was at the beginning of the movie.
on another planet (which didnt have water but more acidic atmosphere) they created another life that resulted in aliens (humans are 80% water - aliens seem to be 80% acid)
Also there was the rock human head that the urns where scattered around?