There are many reasons. Life re-uses structures, hormones, and proteins in different areas of the body for different functions. A mutation can make a structure more efficient in one area and have little effect in another... for now, but many mutations later that mutation can become a key enabler of a whole new class of features from the secondary structure.

It may also be that the gene doesn't confer any specific advantage but a population bottleneck or isolation event can spread it nonetheless.