Just a wild, random guess... possibly darker skin helped to protect our unabashed, naked caveman ancestors from potential sunburn on sensitive areas. Maybe it also worked as an insect repellent of sorts: some bugs "see" color much differently than we do.
We're probably seeing a gradual evolutionary trend away from this since prehistoric man's invention of the fig leaf, followed quickly by the loincloth, the Lycra-Spandex Speedo (TM), and the mesh jogging short. We can thank early cave-women for this: all the constant laughing and pointing when not busy grinding roots provided the impetus for the guys to give some thought to their flopping, dangling, prehistoric willies.
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