It’s just selective breeding.
Cats show up to eat rodents, and people let them because that’s good for us. We kill or run-off problem cats. Cats that are very intolerant of our presence don’t stick around. The comfortable-wit-people and well-behaved cats breed and create their own population, partially isolated. People find and adopt kittens, and kittens that grow up around people become tame. Those that don’t be tame and act nice get killed or kicked out, and the nice cats are allowed to live with us and breed.
Eventually, we end up with cats almost as physically capable of hunting and killing as wild populations, but with some behavioral and physiological changes that make living with, tolerating, and communicating with humans.
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