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The Qur'an says that varieties among people (including colour and language) are part of the divine plan, as one of the signs of God (30:22). However, it does not specify the physical mechanism by which people developed into different appearances.

Even if Adam and Eve were the first parents of all people, there is no reason why all people forever should look identical.

Scientifically, the current explanations are mutation and natural selection over time. (For instance, pale skin is advantageous in northern Europe because it assists in absorbing Vitamin D.) 

However, there may be other scientific or metaphysical mechanisms for the development of variations among people that are not yet discovered or understood. Still, it is acceptable from an Islamic standpoint to refer this question to science. 

Allah knows best.