PokéBase - Pokémon Q&A
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What exactly are you asking? Why the Pokemon are their specific colours or why they exist at all?

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In real life we all have animal species, and some of those species have very unique patterns. Shiny Pokémon may refer to some animals having a different skin/feathers/fur that are very rare (like a very unique cat pattern).

Also, some animals have changed pigments, such as the Black tiger or black panther's them having melanism(mostly a darker color). And albino (mostly a whiter color) badger's. GameFreak could be creative and made melanism and albinism other colors then they usually have. And these animals are pretty rare, shiny's are pretty rare.
Now, what about amorphous Pokémon. Rust, mold, (wait a sec.) radiation (water, grass, ground). And Electric (that is hot so fire too) can sometimes be Ultra Violet if created by men.

That's all.
SeeYaLater!

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Like white lion. Which is ultra rare.
Wut about location. In hawaii here is a black sand beach which influences Palossands shiny
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The different colourations of Shiny Pokemon is merely Game Freak Logic. From this source, you can see that Shiny Pokemon were called alternate coloration or rare coloration Pokemon, indicating that it used to represent a very rare specie within its species. The drastic different of the shiny Pokemon is essentially Game Freak's choice since we can't really relate it much to real life since not all Pokemon are animals, evident by Pokemon such as Rotom, Pallosand, or Klefki (hence the name Pokemon derived from "Pocket Monsters" )

Yes, it is logical that in terms of animals, that different textures of skins etc. of an animal represents a rarer specie, but then again, the only different in terms of physical appearance between a regular Pokemon and it's shiny-counterpart of the same gender is just the colour. Simply, it's just used to distinguish a rarer specie.

In newer games, a Pokemon is simply calculated to be shiny based of "Personality Values" and incorporates the original trainer's Trainer ID number and Secret ID number to do so. As of Gen III, the mathematical breakdown of a shiny Pokemon can be found here.

Hope I helped! :)

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