Pokemon origins project - Dragons

You could possibly fit Gyarados into this tree, as another offshoot from the Dratini ancestor. This might also explain the red Gyarados as being a genetic throwback.

For some reason, possibly a lack of food, some members of proto-Dratini venture out from the safety of their shallow bays deep into the ocean. Here they find themselves in a harsh, inhospitable environment which necessitates certain morphological changes.

The most obvious is their young, struggling to survive the waves with their soft, tadpole-like bodies. Their scales grow rigid and tough, restricting movement until they are less like animals and more like eggs, being buffeted by the waves until they evolve into their adult form. Many trainers will agree that the Magikarp, whilst having the appearance of a fish, is far more akin to a Metapod of the sea.

It's evolved form, Gyarados, shares its tough scales, restricting it from evolving the limbs of its Dragonair brethren, but not the ability to fly. Another sign of its evolutionary history can be seen in the tendrils they share, sprouting from Dragonair's forehead and Gyarados' chin.