The African story is complicated, and getting steadily more so. But some of the big picture – involving relatively recent events – is fairly simple.
The biggest African language family is Niger-Kordofanian, which was probably spoken by most people in west Africa at least 5,000 years ago – a mark of an early expansion. One subgroup near the border between Nigeria and Cameroons seems to have had a set of crops that was less specialized for high-rainfall areas like west Africa – probably including some cereals like millet, as well as wet-country yams and bananas. This allowed the Bantus to expand out into dryer areas of Africa, which at the time were occupied by various hunter-gatherer groups. You could think of the Bantu as a bit like marcher lords, but at first more advantaged by their crops than their military technology. From genomics, it looks as if the Bantu first moved south and only later expanded into East Africa. They didn’t have iron-working in the beginning, but picked it up perhaps 500 to 1,000 years later. Iron-working led to better tools and weapons, which made displacement of hunter-gatherers even easier.
A few of the hunter-gatherer peoples are still around, but most have been replaced. The replacement was in some cases near-total, while other encounters sometimes led to substantial admixture between the Bantu and the previous hunter-gatherers. For example the Xhosa, a major tribe in South Africa, have about 25% Bushman ancestry. Look at Mandela. A similar group, one that only persists as an admixture component, account for about 20% of the ancestry in Mozambique. On the other hand, there’s no sign of hunter-gather admixture in some populations, like Malawi.
The remaining hunter-gatherers also have had varying amounts of Bantu admixture. The Ju/’hoansi, the population that Henry Harpending studied, have the least (about 10%). Pygmies also have substantial amounts of Bantu ancestry. Interestingly, the more Bantu ancestry, the taller the Pygmy (on average).
The Bantu expansion was the largest in Africa, but there were others. The Nilotic people, tall cattle-herders, expanded into East Africa, leaving tribes like the Masai and Tutsi.
Farmers from the Middle East settled Egypt and North Africa a long time ago, which strongly suggest that the Afroasiatic languages (traditionally known as Hamito-Semitic) originated in the Near East. A following pulse in the Bronze Age brought a later version of Middle Eastern genes (with an added eastern component) into Ethiopia and Somalia, which likely explains the origin of the Cushitic branch.
A fourth branch, the Khoe-Kwadi languages of southern Africa, are spoken by people also called Hottentots. They appear to be the result of an admixture between cattle-herders from the north and local hunter-gather populations (similar to the Bushmen). Those cattle-herders derive from an ancient West Eurasian population – so you see some Middle Eastern alleles in the Hottentots, a surprisingly result due to Joe Pickrell.
One thing to remember: although some of the hunter-gatherer groups are very interesting and tell us things about really deep prehistory – Bushmen, for example, apparently split off from the rest of the human race about 300,000 years ago – they make up a very small fraction of Africa’s population today. There are roughly 50,000 Bushmen, 1,000 Hadza (descendants of East African hunter-gatherers) and perhaps a million Pygmies.
These small remnant populations can be informative. It looks as if some of the hunter-gatherer populations mixed with unknown archaics about 50,000 years ago. Maybe not that surprising, since skeletons with archaic features have been found (in Africa) that are relatively recent, as recent as 11,000 years ago. Or consider homo naledi, a very different population (many skeletons found in a cave in South Africa), something like humans but with a very small brain, that seems to have lived in South Africa 200,000 years ago. Or recent analysis that suggests West Africans carry significant admixture (~10%) from a pop that split off after Neanderthals [ 600 k years] , but well before the Bushmen.
Another question: how did the Bushmen ( and apparently other populations) manage to stay so genetically isolated over hundreds of thousands of years? We’ve recently learned a bit more about their history, from sequencing Bushmen skeletons found in South Africa – skeletons that are only a couple of thousand years old, but date from before the Bantu arrived. Ur-Bushmen – which showed us how different they were before Bantu admixture.
Reich mentions some work by Peter Ralph and Graham Coop on the multiple origins of the sickle-cell mutation in different parts of Africa, which suggests very low rates of gene flow, since otherwise such a favorable mutation would spread rapidly, without the required wait for multiple occurrences. Alas, it turns out that HbS really does have a single origin, probably in West Africa about 7000 years ago – a nearby recombination hotspot confused the Issue. Which is what some people expected a long time ago – multiple origins never squared with the fact that there is no sickle-cell at all in South East Asia or New Guinea, even though there’s plenty of malaria.. However the point – very low gene flow – is still valid, since we see several different mutations that cause lactase persistence in cattle-herding populations in Northeast Africa. That implies very low gene flow from the parts of Eurasia that had the common European lactase mutation, as well as low gene flow within Africa. Or, possibly, it may suggest that these different mutations have different effects, so that they work better in some environments than others…
In some ways, on some questions, learning more from genetics has left us less certain. At this point we really don’t know where anatomically humans originated. Greater genetic variety in sub-Saharan African has been traditionally considered a sign that AMH originated there, but it possible that we originated elsewhere, perhaps in North Africa or the Middle East, and gained extra genetic variation when we moved into sub-Saharan Africa and mixed with various archaic groups that already existed. One consideration is that finding recent archaic admixture in a population may well be a sign that modern humans didn’t arise in that region ( like language substrates) – which makes South Africa and West Africa look less likely. The long-continued existence of homo naledi in South Africa suggests that modern humans may not have been there for all that long – if we had co-existed with homo naledi, they probably wouldn’t lasted long. The oldest known skull that is (probably) AMh was recently found in Morocco, while modern humans remains, already known from about 100,000 years ago in Israel, have recently been found in northern Saudi Arabia.
While work by Nick Patterson suggests that modern humans were formed by a fusion between two long-isolated populations, a bit less than half a million years ago.
So: genomics had made recent history Africa pretty clear. Bantu agriculuralists expanded and replaced hunter-gatherers, farmers and herders from the Middle East settled North Africa, Egypt and northeaat Africa, while Nilotic herdsmen expanded south from the Sudan. There are traces of earlier patterns and peoples, but today, only traces. As for questions back further in time, such as the origins of modern humans – we thought we knew, and now we know we don’t. But that’s progress.