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Time, and careful selection of which animals that are allowed to breed.

Let's say you want a long-legged dog. You start by selecting the the most long-legged males you can find, and the most long-legged females you can find, then you let them breed.

Out of their offspring, you then select the most long-legged puppies, and when they're grown, you let them breed.

Keep this up for several generations, and soon you have really long legged dogs.

The same method is used for whatever other feature you want the dog to have.

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