"It is believed that the penguins are derived from a type of bird that is able to fly." -http://www.penguins-world.com/penguins/
Fossil evidence from years ago provides us with details that penguins long ago were different from penguins today. Penguins long ago were much bigger, stronger and were adapted to different areas, such as New Zealand and Southern South America rather than Antarctica, the location of the most penguins in the world today.
How Penguins Changed by Mutations
There is a 1 in a 10,000 chance of a penguin mutation occurring. If a penguin mutation happens to occur, the penguin with the mutation will either adapt to its environment and live with the mutation or it will not live long because it is easily visible to predators or too exposed to freezing temperature. If the penguin with the mutation makes it to breed with another penguin, then their baby will gain their parents' traits. If the baby has a mutation, then the process will go on and the species of penguins will slowly change due to mutations and other differences as the cycle goes on. This is how penguins change.
Penguins today are more spread out along the Southern part of earth, smaller with an average height of 20 to 30 inches versus the five foot nine penguins back then, and 17 different breeds rather than the few that they started out with.