Who knows. However, I believe the origin lies in the Juubi, but for the Rinnegan to be activated the correct human has to experience near death first.
Nagato had no early memories about his eyes, because they didn't exist there, until he experienced his parents death and him close to the death. Same happened with Madara, it activated only when he was near death.
I don't think Kishi calls it the Samsara Eye without reason.