A paper published online this week in Science (http://scim.ag/MGLlorente) reveals the first prehistoric genome from Africa: that of Mota, a hunter-gatherer man who lived 4500 years ago in the highlands of Ethiopia. Named for the cave that held the remains, the Mota genome “is an impressive feat,” says Hodgson, who was not involved in the work. It “gives our first glimpse into what an African genome looked like prior to many of the recent population movements.” And when compared with the genomes of living Africans, it implies something startling. Africa is usually seen as a source of outward migrations, but the genomes suggest a major migration into Africa by farmers from the Middle East, possibly about 3500 years ago. These farmers' DNA reached deep into the continent, spreading even to groups considered isolated, such as the Khoisan of South Africa and the pygmies of the Congo.
By comparing 250,000 base pairs from Mota's genome with the same sites in individuals from 40 populations in Africa and 81 populations from Europe and Asia, the team found that Mota was most closely related to the Ari, an ethnic group that still lives nearby in the Ethiopian highlands. They zeroed in on the DNA that the Ari carry but Mota doesn't, which was presumably added during the past 4500 years. They found that Mota lacks about 4% to 7% of the DNA found in the Ari and all other Africans examined. This new DNA most closely matches that of modern Sardinians and a prehistoric farmer who lived in Germany. Hints of these early farmers' DNA previously had turned up in some living Africans, but Mota helped researchers zero in on the farmer's genetic signature in Africa, and to establish when it arrived.
Manica suggests that both the European farmers and living Africans inherited this DNA from the same source—a population in the Middle East, perhaps Anatolia or Mesopotamia. Some of these Middle Easterners headed into Europe and Asia starting 8000 years ago, and were the first farmers of Europe (Science, 20 February, p. 814). But other descendants of this population migrated into Africa, likely after Mota lived. This fits with traces of Middle Eastern grains found in Africa and dated to 3000 to 3500 years ago.
http://m.sciencemag.org/content/350/6257/149.fullBecause so many far-flung Africans still carry the farmers' DNA, the study suggests a “huge” migration, Manica says. Farming had already been established in Africa by this time, but the newcomers likely had some advantage that explains why their genes spread. “It must have been lots of people coming in or maybe they had new crops that were very successful,” Manica says.
And it's been revealed that "Mota" carried E1b1(Y-DNA ) and L3x2a (mtDNA)
This is the first ancient genetic sample from the Horn of Africa documented so far. 
That's an ape, not human.