Dr.Retarded
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The predators also used to capture queens and use them to seed a planet for a hunt in the comics as established in the very first AVP series. Think I still have all 5 of those, and the follow-up series.I too saw the murals in Prometheus, but they don't really make sense. The murals depict a xenomorph as we know it, that is from a facehugger impregnating a human and the resulting xenomorph from human stock. As far as we know in Prometheus, the Engineers only have the black goo and no access to human livestock to test it on, we see the black goo creating Hammerpedes which don't infest people with embryonic xenomorphs, and we see the black goo directly infecting humans and the result is either zombie-xeno (depending on deleted scene or not) or the infected person being able to sexually transmit an embryonic squid which then evolves into a huge parasite that then infects an Engineer to create a proto-xeno called a Deacon. None of this connects the dots to the actual xenomorphs we have known since Alien. There is really no perfect way to reconcile those two origin stories, especially if you also take in consideration the added lore from Aliens (queens, hives, etc) or Alien 3 assembly edition (royal facehugger)
As for the xenomorphs being a naturally-occuring species, that's developped in the comics and books too, they have a homeworld we call Xenomorph Prime (with an empress-type queen that can telephatically communicate with other distant queens, it gets a bit crazy). Maybe the Engineers captured some specimens, and modified them with their engineered black goo mutagen to allow them to spread in the galaxy as a bio-weapon that could adapt to any terrain or environment since it takes some of its host's DNA?
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