Mutations of DNA can cause different characteristics to what you might consider "standard" for a particular species - This is genetics and it happens all the time. If the environment in which a particular species lives changes then a certain mutation may become beneficial. The organisms with this mutation then become better adapted to live in the new conditions than the other organisms. The unmutated organisms may then begin to die out while the mutated organisms survive. These mutated organisms, over time, become the majority through breeding and the passing on of this beneficial mutation of DNA. This is evolution.
What we now know as the Horse originally had cloven feet (sort of like a camel's foot but more hand like!) which was perfectly adapted to the boggy terrain on which they lived. As the Earth began to dry out, the terrain became less and less boggy. A mutation caused some of the "Horses" to have fewer extremities (their feet were slightly more hoof-like) and they were now better adapted to the surroundings and were able to travel much faster over the drier land and escape predators. This mutation then gets passed on through breeding as the cloven footed "Horses" began to die out. Successive mutations over thousands of years resulted in the hoof and the Horse that we recognise today.
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