The thing is that the places where you’ll notice pruning (palms of the hands, soles of the feet along with the grasping surfaces of fingers/toes) have different, thicker skin. You may also notice these parts don’t have hair on them for a similar reason- you just plain don’t have hair follicles on them. These particular areas are unique in many ways, such as typically being of lighter pigment- people who have darker skin have a more noticable contrast between the pigment of the rest of their skin and the areas used for grasping. This particular feature of thicker skin on grasping surfaces is not unique to humans, you’ll actually observe it in many species.
As for why the skin prunes there *specifically*, the prevailing idea is that the skin folds in order to increase surface area and therefore the increase the ability to grasp things while wet. There’s also some speculation that this plays a role in retaining moisture, but that’s a little more complicated and has to do with pressure gradients. It might seem counterintuitive, but being in water does not make one immune to dehydration.
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