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Pokemon and Animals are two different beings. Pokemon happens to be mutated, genetically altered, Alien, or Artificial beings with a continuing mutating genome. This is what allows Pokemon to "Evolve" or metamorph when they reach a certain age or interact certain environments.
All evolution stones emit radiation. Sun Stone, Fire Stone, Water Stone, Thunder Stone, Moss Rock, etc.
Many artificial and natural constructions also emit radiation. Things like Mt.Coronet or the Trade Machine.
Another thing which may affect the transformation is the Pokemon's own mental state. It's emotions can also dictate how it's genes will alter as it ages.
Mega-Stones however are quite different, as unlike the mentioned stones and methods of evolution, the Mega-Stones effect Pokemon of a certain species, and the change is not ever complete. We could hypothesis that Mega-Stones merely "unlock" further potential, that a Pokemon already has; essentially being the key to a "hyper" body state which can be seen for abilities like Blaze or Torrent or when a Pokemon is in Shadow Corrupted mode as seen in the events of the Orre Region.
