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There's probably not just one gene for skin color, but a variety of genes for skin color. Physical features such as nose shape and eye color, along with skin color, probably evolved in response to selective pressures from environment - high/low levels of radiation, heat, cold, etcetera. This is why, for example, you get tall thin people in hot climates and short, stocky people in cold areas. These are adaptive responses to the environment.

In most cases we have some sense how dif...

I want to expand on Alan's comment about adaptation. The basis of the Darwinian theory, after all, is that if you have a particular feature or suite of features, those allow you to thrive or survive and reproduce with greater efficiency than people with alternative features. Those features will be disproportionately represented in succeeding generations, and thus, the average appearance of the population will change through time. That's what Darwin meant by natural selection. What that c...