Dark skinned people didn’t get enough vitamin D when they migrated to less sunny climates, so those with lighter skin were more likely to survive and have children. Other differences have similar explanations, like brown eyes being better at seeing in bright light but blue eyes being better in the dark.
In some cases it’s just random chance, things are bound to diverge when you’ve been apart for long enough. I doubt most of the differences in facial features (nose shape, etc) would have much of an effect on anything, except for the epicanthic folds Asian people have on their eyes.
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