In Japanese, why are there different numbers for 4, 7, and 9?

4 can be yon or shi; 7 can be nana or shichi, and 9 is ku or kyu. Does one choice come from one dialect? If so, which is which? I understand there was a vanishing or struggling minority people who still live or lived until recently on either Hokkaido or the island just to the south of it. Innu? They were called Innu?