What would cause the peel of a lime to turn yellow?
Ethylene, most likely.
You've said that that lime was at the bottom of the bowl, mostly covered with other fruit. I'll bet it was very close to some kiwis.
Fruit -- particularly fruit like kiwi which ripens after being picked -- produces and releases ethylene. Ethylene serves a key role in fruit ripening. This is why you're advised to keep bananas in a closed paper bag to ripen them: the ethylene gas produced by the bananas builds up and ripens them faster. In open air, ethylene concentrations (in the fruit, not just around it) remain lower, and ripening is retarded.
In fact, citrus producers commonly use ethylene gas to artificially ripen (&quot;de-green&quot;) the rind of citrus fruit. This would normally be done for lemons and oranges, which are commonly picked when still slightly green.
While you didn't have a fully closed container, it sounds like the lime was deep enough in the bowl for some concentration of ethylene, produced largely by the kiwis, to build up around it, ripening at least the rind of the lime. (Yes, some limes are yellow when fully ripe -- limes at the store are picked unripe because consumers like the look of green ones.)
Congratulations on your accidental biochemistry experiment.