A bit of both, IIUC. The core Prothean race were Jarvik's race, but they assimilated other races into their empire thoroughly enough that they were generically called "Protheans" after 50k years of history muddied the waters sufficiently. That is to say, nobody was really sure wtf all that was about until they talked to Jarvik.
I've been debating since I finished the game ages ago, and I still can't decide whether to write up my thoughts on the ending. It's a topic of great interest to me, but I don't know that anything I have to say will really be all that useful in furthering the conversation. The horse looks pretty dead to me, and even if it's not, do I really want to wake up and smack around the poor beast during its last, tortured hours?