The breaking apart of continents took animals/plants that were ancestrally the same to different continents. This continents are now apart and these animals/plants had to adapt to their new condition becoming different from their original group. We can take, for example, the penguin. The penguins from South Africa are different from the penguins in the Antarctica. They have the same ancestry but their different locations, because of the continents' breaking apart, pushed them to a different set of characteristics making of them different animals.