Where did the ninja clans other then Senju and Uchiha originate from?
Recall that the Sage of the Six Paths discovered the existence of chakra and used it to create jutsu. The direct descendants of him became Senju and Uchiha, where their powers were split between body and eye.

Other ninja clans were not descendents, however they were able to learn how to use chakra as well in different forms of jutsus. Of course there are some clans, like the Hyuuga where the series notions the possibility of them deriving from the Uchiha.

Clans like Sarutobi, Nara, and Inuzuka clans are not related to the Sage of Six Paths though. On the other hand, Uzumaki is blood related to Senju.