It’s due to the presence of melanin in the skin which determines the skin colour ,Due to natural selection, people who lived in areas of intense sunlight developed dark skin colouration to protect against ultraviolet (UV) light, mainly to protect their body from folate depletion. Evolutionary pigmentation of the skin was caused by ultraviolet radiation of the sun.
Mostly because in antiquity boat transport was by far faster and better way to get around. It was faster to get anywhere on the Mediterranean coast than to cross the Sahara desert.
Nile was navigable up to Aswan, with the rapids above that. So Egypt up to that point was connected to Mediterranean area, but Sudan further south was isolated, even though it’s not that far in absolute distance.
So as the result Egyptians mingled more with lighter skinned people around the sea, than with their southern neighbours.
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