Animals With The Eyes Of Different Colors

Pigmentation
The pigment molecules used in the eye are various, but can be used to define the evolutionary distance between different groups, and can also be an aid in determining which are closely related – although problems of convergence do exist.
Opsins are the pigments involved in photoreception. Other pigments, such as melanin, are used to shield the photoreceptor cells from light leaking in from the sides. The opsin protein group evolved long before the last common ancestor of animals, and has continued to diversify since.