A lot of theories on how shifters came to be seem to appeal to a spiritual or mystical basis, which is fine, and can sync up with several belief systems. However, if you don't hold a spiritual view when it comes to shifting it may be hard to reason how any shapeshifting group came to be on this Earth. I think I have a plausible theory as to how shifters could have come to be, and why, without necessarily invoking spirituality.

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I think shifters evolved on this planet like every other organism in existence. How does one end up evolving a shapeshifting, genetic ability?

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I believe it starts off with tribes of humans living in isolated places, with animals that can and do pose a threat to themselves and others. However, as you know some animals are less likely to attack others- a wolf is less likely to attack a big cat, a big cat is less likely to attack a crocodile, a crocodile is less likely to attack a hippo. So there are tribes living alongside these animals, and sometimes they attack the humans. Now, let's say there's a mutation in a particular allele of a person's genome they were born with, that causes a person attacked by an animal to go through a physiological change when the flight or fight reflex is triggered. Their body starts to change ever so slightly, their mentality changes a little, and they become more animalistic and unpredictable, scaring off their attacker. Those who don't have this mutation aren't as lucky during fights.

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The person with this weird genetic mutation grows up, has children who also have a chance of having this same mutation, and they spread out, join new tribes, and this mutation begins to permeate the human population. The behavior and look of the people going through this physiological transformation is dictated by the environment. A person who begins to take on a more wolfish set of behaviors in an area populated by aggressive coyotes escapes with their life during a coyote attack, while a person who takes on the behavior of a fox fares very poorly and is less likely to survive. Who takes on what behavior is random, but depending on what situation they're in it can either help or hurt them. In this way each different tribe of humans has shifters that take on animal forms correlated with the animals that live around them.

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As generations of 'physiological shifters' go by, various other genetic mutations appear within that population that alter the behavior of the person as they go through their change, and increase how far the transformation goes. These changes become more and more extreme as a result of mutations within that particular allele, and arise out of a need to keep predators at bay. Over time the descendants of the first physiological shifters are more capable of a physical transformation, and can actually sustain fur growth, bone alteration, and more in order to look like animals and defend themselves against predators, while taking on a normal human form the rest of their life. This eventually leads to a person managing to perform a full animal transformation when threatened or in high-stress situations, taking on a near identical appearance to a physical animal.

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This is similar to the way other 'shapeshifting' animals may have evolved over time. Octopi and mutable rainfrogs can change their shape and skin texture back and forth, usually to avoid and evade predators. Both try to camouflage and blend in with objects in their environment; it is not hard to imagine another creature going a step further and actually shapeshifting to blend in with other living animals in order to survive.

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This would also explain the apparent "issues" when it comes to shifting, and why real shifters are limited in many ways: why you can only shift fully at a certain age, why any major bodily injury or changes risks keeping you in one form, and why it's so painful and hard to shift at all. Despite it being for protection, we're still working within natural, physical laws, and the most drastic the change, the more energy needs to be saved up. If it's a genetic mutation born out of a need for self-defense, it makes sense that as you mature and distance yourself from family the ability would get ready to kick in right around that time.

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Looking at it this way I can see how some would end up developing the ability to shift, and why. It may need tweaking here and there, but I think it can explain the existence of shifting well enough.