Investigators, in their work on photoperiodism, accidentally discovered that the pineal also acts as a clock(at least in house sparrows). The initial discovery occurred when birds that had their pineals removed were placed in constant darkness(so there were no light cues to entrain the SCN), they became arrhythmic. Furthermore, if the same birds were given a transplanted pineal from another sparrow on a different L/D cycle, the birds resumed their activity but now conformed to the schedule that matched the donor sparrow. This experiment created a bit of skepticism, since the existence of photoreceptors outside of the retina was scoffed at by members of the field.
In an attempt to locate these photoreceptors outside of the retina, sparrows were put in a cage with a specific L/D cycle. If their eyes were the only means of photoreception, one would expect that the sparrows would quickly begin to free run in the absence of light cues to entrain them. However, this was not the case; the birds quickly entrained to the L/D cycle of the cage. How? Researchers then took free-running, blinded sparrows in dim light and plucked the feathers from the top of the skull. Amazingly enough the birds became entrained. It had already been well established by this point that among fish, amphibians, and reptiles, the pineal contained some sort of photoreceptors that were sensitive to levels of light. To further prove that sparrows possessed such receptors, researchers placed India ink under the skin on top of the skull. These birds resumed their free-running behavior, and presumably lost their sensitivity to light. Finally, the flap of skin and the ink were removed and again the bird was able to entrain to the L/D cycle.
Although the story appears to end here, there is yet one final twist: if a sparrow is blinded, pinealectomized(pineal removed), and put in a L/D cycle, it still has the ability to entrain. This led investigators to the additional discovery of other extra-retinal photoreceptors.
While a great deal of the anatomy is currently known, the relationships between the two clocks and their photoreceptors is still under investigation.