Probably because Africa is very hard to cross on foot. There is a desert up north and a very dense jungle in the middle surrounded by savannahs and rivers full of dangerous animals. Also probably hunter gatherers in Africa had it pretty good because of the abundant flora and fauna, so there was no need to trek far. So the only people that mixed with others were sea faring tribes or came in contact with sea faring traders. Like Madagascar people have Austronesian genes in their DNA and even their languages falls under the Austronesian family.