It`s all about the radiation the people receive that determines the amount of melanine, and thus the pigmentation.

Since the people in northern europe commonly were heavily dressed in order to withstand the cold climate, and the people on southern europe wore lighther clothes in order to be more comfortable, or no clothes inthe upper torso at all, the amount of radiation received by those peoples was substantially different. Also there is the thing of the differences of the cloud cover in those areas and such.

That`s it. Pure logic.