One of the major changes in our understanding of human genetic demographic patterning across the world over the last twenty years is that we no longer believe most of the extant patterns date to the Last Glacial Maximum ~20,000 years ago. If you do not think this was a view held a generation ago, read Stephen Oppenheimer’s The Real Eve: Modern Man’s Journey Out of Africa. In a broad sense, the current understanding is reflected in 2014’s Toward a new history and geography of human genes informed by ancient DNA. There has been a lot of change, and a lot of admixture.
One of the regions subject to this change has been Africa. The expansion of the Bantu-languages across much of the continent seems to have been accompanied by widespread genetic replacement. Groups like the Pygmies of the Congo rainforest, the Hadza of Tanzania, and the various Khoi and San people of southern Africa, reflect a broad underlying genetic diversity that was to a great extent erased. Though it is correct that African people as a whole exhibit more genetic diversity than all other people in the world, when looking at genetic variation across peoples (as opposed to within them), Bantu Kenyans and people in Malawai are quite similar.
The reason for this is straightforward. The differentiation of Bantu peoples dates to the last four to one thousand years. This is not a great deal of time for genetic drift to accumulate differences. Rather, a primary avenue for a variation to occur is through admixture with the local substrate, which as noted above did not occur in much of the range of the expansion.
All that being said, the landscape that the Bantus expanded into obviously wasn’t empty. And it wasn’t just hunter-gatherers. Ancient DNA and cultural anthropology make it obvious that Cushitic-origin pastoralists occupied large zones of East Africa. They interacted with the Khoi pastoralists of southern Africa at some point, transmitting pastoralism (and some genes!). But to the northeastern edge of the Bantu range, there were other people, who did not speak Afro-Asiatic languages. These are what we today call “Nilo-Saharan” populations.
As can be seen on any language map, the Nilo-Saharan people seem to be squeezed between two expanding cultural zones: the Afro-Asiatic and Bantu. But after the decline of Cushitic speakers in East Africa (due to absorption into expanding Bantus), Nilo-Saharan peoples like the Masai seem to have moved southward, and specialized in pastoralism. Nilo-Saharans are a diverse bunch, and I’m not sure how ethno-linguistically coherent they are. Some of them, like the Masai, seem to have assimilated Cushitic pastoralists. Others, such as the Dinka of Sudan, have almost no Eurasian ancestry.
A new paper in AJHG, High Levels of Genetic Diversity within Nilo-Saharan Populations: Implications for Human Adaptation, uses whole-genome sequencing to look at the relationships of these peoples to others in Africa. The abstract:
Africa contains more human genetic variation than any other continent, but the majority of the population-scale analyses of the African peoples have focused on just two of the four major linguistic groups, the Niger-Congo and Afro-Asiatic, leaving the Nilo-Saharan and Khoisan populations under-represented. In order to assess genetic variation and signatures of selection within a Nilo-Saharan population and between the Nilo-Saharan and Niger-Congo and Afro-Asiatic, we sequenced 50 genomes from the Nilo-Saharan Lugbara population of North-West Uganda and 250 genomes from 6 previously unsequenced Niger-Congo populations. We compared these data to data from a further 16 Eurasian and African populations including the Gumuz, another putative Nilo-Saharan population from Ethiopia. Of the 21 million variants identified in the Nilo-Saharan population, 3.57 million (17%) were not represented in dbSNP and included predicted non-synonymous mutations with possible phenotypic effects. We found greater genetic differentiation between the Nilo-Saharan Lugbara and Gumuz populations than between any two Afro-Asiatic or Niger-Congo populations. F3 tests showed that Gumuz contributed a genetic component to most Niger-Congo B populations whereas Lugabara did not. We scanned the genomes of the Lugbara for evidence of selective sweeps. We found selective sweeps at four loci (SLC24A5, SNX13, TYRP1, and UVRAG) associated with skin pigmentation, three of which already have been reported to be under selection. These selective sweeps point toward adaptations to the intense UV radiation of the Sahel.
There are few moving parts in this paper. The three primary ones involve genomics, phylogenetics, and evolutionary and population genetics. Basically, discovering new variation, genetic relationships, and the possibility of adaptation.
As noted in the paper these are under-sequenced populations. Using deep-sequencing they were able to discover variation particular to Nilo-Saharans, more than three million novel variants. This is unsurprising. As a stylized fact non-Africans diverged a bit over 50,000 years ago. If you look for new variants, you’ll find some, but there’s only so much new variation that could accumulate in 50,000 years. In contrast, African populations have lineages that are 100,000 to 300,000 years diverged. This means there is a lot of time for the variation to accumulate (also, less variation lost through bottlenecks due to larger effective population sizes).
Nilo-Saharans are particularly interesting because many people suspect that they are the closest Sub-Saharan Africans to the ancestors of the people who expanded outside of Africa 50-60,000 years ago. Part of this is geography, but there are suggestive signs in the genetics this is true (though perhaps the Hadza are the closet to non-Africans?). The main issue with these sorts of suppositions is that the real population history is always more complex than stylized models.
For example, the Bantu expansion is in some ways a “reflux” migration. That is, the people of West Africa seem to be derived mostly from an eastern population which mixed with deeply indigenous local lineages (termed “Basal Human” in some papers). Out of this synthesis emerged the “West African” populations, which eventually adopted an advantageous cultural toolkit 4,000 years ago, and migrated back eastward (the Bantu origins seem on the eastern edge of this western Africa zone).
This PCA panel illustrates the major phylogenetic trend. First, you can see the non-African to African cline. It is well known that some Ethiopian groups (usually Semitic language ones) have more West Eurasian than Somalis (Cushitic speakers). But all these Horn of Africa populations are on the cline.
Then there is the West Africa/Bantu vs. Nilo-Saharan cline. There is a strong correlation across East Africa in language and genes, though there has been admixture between various groups. This is why Zambian Bantus are Nilo-Saharan shifted. The migration southward resulted in the assimilation of Cushitic and Nilo-Saharan people.
The admixture plot recapitulates the same patterns. Note, as observed by Dienekes Pontikos over a decade ago, the populations of Horn of Africa are mixed between Sub-Saharan African and Eurasian, but their Sub-Saharan African donor population is not Bantu/West African. Rather, they seem close to Nilo-Saharan populations. The latest work out of Ethiopia I’ve seen suggests admixture between three and two thousand years ago, so that makes temporal sense in terms of the donor populations, as well as the fact that there seem to have been ecological limits to the Bantu cultural package in very arid regions.
The most interesting aspect of this paper though is in regard to adaptation. I’ll just quote:
Nilo-Saharans have some of the darkest skin tones in the world82 and the Lugbara generally have a darker skin compared to the Basoga.83 Skin reflectance is correlated with UV radiation84 and the dark skin tones of the Nilo-Saharans could be an adaptation to the open savannah conditions of the Sahel where there is limited tree and cloud cover and which is predicted by models to be one of the regions of the world with darkest skin pigmentation UVRAG may be an important contributor to the exceptionally dark skin tones of the Nilo-Saharans in conjunction with SNX13 and TYROBP in particular and possibly also IRF4, TYRP1, HERC2, SLC24A5, and OPRM1.
Nilotic peoples are famously very dark. You may remember some of these genes from other GWAS in regards to pigmentation. Crawford et al. also discussed the selection for darker skin in parts of East Africa due to the ecological pressures. The methods used in this particular paper, such as iHS and EHH, are indicative of relatively recent sweeps.
Humans have been in Africa for hundreds of thousands of years. Many have lived in the savanna. In fact, that’s supposedly our environment of evolutionary adaptiveness. How is it that Nilotic peoples weren’t already very dark? Did they live in the rainforest? In other words, I’m a bit confused as to why they moved into the savanna, and where the moved from. It’s not like they were not present on this continent during the Pleistocene. Did solar radiation increase?
The selection story is not what we think in some fundamental way I can’t put my finger on.
The real question is where most of the modern human ancestors of Subsaharans lived and with which people, possibly including archaic and even “super-archaic” Hominids they mixed. Because my current understanding is that there were at least the following layers:
– archaic Hominids in tropical and West African zone
– archaic Homo sapiens spread from North/East Africa
– modern Homo sapiens spread from North East Africa/Near East
– more clearly West Eurasians coming in, largely equivalent to Afro-Asiatic
This explains to a large degree why Subsaharan Africans are more diverse and it also answers your question, if the conclusion is right:
“How is it that Nilotic peoples weren’t already very dark? Did they live in the rainforest?”
Some archaic Homo sapiens are supposed to have lived there, while the tropical regions were most likely sparsely inhabited by more archaic Hominids, probably similar to the skulls found in Iwo Eleru.
A large portion of the modern Homo sapiens ancestry came in from further North and East, and these were pushed from the true source region of modern Homo sapiens, which might have been either the Nile region or the Near East in all likelihood.
With the retreat of the Green Sahara, the conditions are supposed to have worsen once more, with more pressure from different competing human groups and harder living conditions for humans.
Whenever I look at some of the most extreme living conditions in Africa, like the dense parts of the tropical rainforest, the very open, hot and UV-heavy regions of Southern Sudan, or the Kalahari, what comes up first is the people living there being not Afro-Asiatic, being not Niger-Congo (at least not originally), but people being pushed there.
If having the choice, you don’t live in a place like the Kalahari, thats a habitat you take and adapt to, if there is no other place to go for your people.
Especially in Africa the best places were along the rivers and fertile valleys. I think the population density map from the 1960’s is quite instructive:
https://na.unep.net/siouxfalls/globalpop/africa/Appendix_6.html
Nilo-Saharans were obviously more competitive in the face of the main expansive groups and part of the reason might have been exactly their early adaptation to that niche, withstanding high UV-radiation and extreme dry heat in otherwise fairly friendly habitats.
That Crawford-Tishkoff study suggests that “these ancestral hominins may have been moderately, rather than darkly, pigmented.” Perhaps a moderately brown skin color like present day Khoisan peoples? One would think the Kalahari bushmen would have also evolved darker skin tones due to the sunny climate. Their skin does often look a quite a bit more weathered when compared to Nilotic peoples, even those who also keep a rural, outdoors lifestyle.
My pet theory about the Khoisan is that the majority of their population was located in less sunny South Africa, south of the Tropic of Capricorn, where there was less selective pressure to develop dark skin. Areas further north were continuously populated from the south, a trend that continued into the 19th century with migrating Griqua, Nama, and Korana tribes. Perhaps it’s as you suggest and the Nilo-Saharans similarly had a different source area before the Sahel became their main population center.
The typical darkest skinned people live in fairly open lands with high UV radition, so close to the equator. Another aspect might have been living very close to the water, probably as fishers and divers.
Living as fishers makes you particularly vulnerable to high UV radiation. There are up to modern days e.g. Nilotic people which lived to a large degree from fishing:
https://en.wikipedia.org/wiki/Shilluk_people
Something similar can be observed in other places around the equator: People of the sea and fishermen are somewhat darker skinned than related people from further inland and with a different lifestyle. We know that the Nilotics became more competitive once they adopted pastoralism, but from what are they supposed to have live from before? The later modern human colonisation, from which they descend for the most part, came in much earlier and it is clear to me that in the zone they were living, fishing and living close to the water must have been highly important.
As divers and fishers, you are close to the water which reflects and increases the strength of the sun, your body is often wet and for the most time simple fishermen have little protection. So assuming they started that way of life even just 20-15.000 years ago, this surely had an effect. And places to live close to the water were even more widespread once the Sahara was Greener than is now and basically the majority of the ancestry of modern Subsaharans might have come from a people which lived, before the region dried out and Afro-Asians came in, in the Green Sahara.
Up to about 12.000 years minimum most of West Africa was still inhabited by archaic Hominids, and just North of them lived archaic sapiens, the newcomers of fully modern sapiens came from the Sahara which was a more hospitable place then:
“At Gobero in the Ténéré desert a cemetery has been found, which has been used to reconstruct the lifestyle of these former inhabitants of the Sahara,[8] and at Lake Ptolemy in Nubia humans settled close to the lake shore, using its resources and perhaps even engaging in leisure activities.[302] At that time, many humans appear to have depended on water-bound resources, seeing as many of the tools left by the early humans are associated with fishery; hence this culture is also known as “aqualithic””
https://en.wikipedia.org/wiki/African_humid_period
The quick adoption of pastoralism and the push South were just necessary for survival, because during the dry out, the grown human population could no longer survive from the habitat any more. This led to the extinction of archaic groups and the large scale replacement of early archaic Homo sapiens. The Bantu expansion was like the last part of this, at a later time and with even better tools at hand for the next wave rolling down.
Before agriculture, crops and pastoralism, fishing and aquatic resources were some of the prime food sources available in many regions. The only comparable resource was the megafauna, but the problem with this source was, that its far easier to overuse, resulting in the extinction of the megafauna in many places, especially if additional stress factors appear, like climate change. So the primary, long term, persistent resource supporting large scale populations with a half-sedentary lifestyle was fishing/aquatic resources.
And for Africans in the Greens Sahara, with likely no strong protection of the body by clothing, like up to modern times again, UV radiation was a real issue. That’s why they got darker and probably some admixture with already darker locals introduced alles in the modern population.
Razib: you wrote: “The differentiation of Bantu peoples dates to the last four to one thousand years.”
4,000 to 1,000?
Or some other interpretation?
The pay-off of very dark pigmentation is reduced vitamin D production and perhaps also increased heating? Fish in particular is high in vitamin D, the only other foods are mushrooms (more ineffective form) and egg yolks. So a dark pigmentation has to go together with a diet high in fish. Hair might have protected us once from the sun and other environmental influences, but we have lost this is seems. Major leftovers from hairy people are from the dry Mediterranean. Humans losing hair must be for a good reason considering it’s rather useful. Other mammals that have lost their hair are the aquatic ones, whales and the like.
Looking at Africa’s environments savanna and sub-tropical climates circling around the congo tropics seem to be dominant. It’s these climates that are reliant and carved by the intense rainy season. Mundo Park’s niger expedition book details that when the rainy season comes the moors move to the desert, even if it means surviving on camel milk for months. Mundo park himself got quite sick in that environment in which for months the savanna changes to swamps, muddy murky pools full of flies, emerging streams and voluptuous rivers with the huts of the natives often collapsing or flooding.
In a greener sahara of the past this might have been more extreme, and there might have been quite some fish paving the way for selection of the hairless humans and later very pigmented Africans to combat the sun. An adaptation quite useful in many of the now densely populated parts of the world.
Nilotes are not just among the darkest people of mankind, but they also are, together with Khoisan, among those with the shortest hair, which is especially noticeable in the Dinka. I think that’s related to their skin being enough protection and the fact that they had to withstand extreme heat. But it could also be related to their water oriented lifestyle, we don’t know for sure.
Typical for the Subsaharan people is the adaptation to Malaria and I guess that too started already in the Green Sahara, which made the expansion deep into the continent later much easier than for everybody coming in later and being not as well adapted to the endemic disease.
“the Bantu origins seem on the eastern edge of this western Africa zone”
I assume you mean the origins of Bantu admixture into Nilotic people. The origin of the Bantu people as a whole is fixed, on linguistic grounds, to an area about the size of a large U.S. county on the southern border of Nigeria on the western Atlantic coast of Africa.
Thus, the implication is that the Bantu infusion into Nilotic peoples was not of a direct unadmixed Bantu source population, but instead, of an Eastern Niger Congo population that underwent language shift and culture shift in an event with a significant source Bantu demic component.
Also, to quote Wikipedia:
“Genetic studies of Nilo-Saharan-speaking populations are in general agreement with archaeological evidence and linguistic studies that argue for a Nilo-Saharan homeland in eastern Sudan before 6000 BCE, with subsequent migration events northward to the eastern Sahara, westward to the Chad Basin, and southeastward into Kenya and Tanzania.[77]
Linguist Roger Blench has suggested that the Nilo-Saharan languages and the Niger–Congo languages may be branches of the same macro–language family.[78][79] Earlier proposals along this line were made by linguist Edgar Gregersen in 1972.[80] These proposals have not reached a linguistic consensus, however, and this connection presupposes that all of the Nilo-Saharan languages are actually related in a single family, which has not been definitively established.
Razib Khan, based on analysis of the autosomal genetics of the Tutsi ethnic group of Africa, suggests that “the Tutsi were in all likelihood once a Nilotic speaking population, who switched to the language of the Bantus amongst whom they settled.”[81][82]”
Adaption to an aquatic environment seems to be the most parsimonious explanation. It certainly holds true when I think of Oceania- coastal Andamanese and Melanesians vs New Guinea Highlanders for instance. This is relevant: https://www.jstor.org/stable/180989.
Interesting that the Afro-Asiatic pastoralists generally had a fish taboo. Maasai traditionally had a fish taboo, despite speaking a Nilotic language. On the other hand Kenyan Luo combined pastoralism with fishing. Makes sense since the Maasai I think have mostly Cushitic patrilineal markers while the Luo have far less.
The common Eastern Bantu term for a Hunter-gatherer is Twa. There are fishermen in Zambia called Twa who are dark-skinned and distinct from the Khoisan (who, except for the Khoikhoi, are also called AbaTwa)
The Green Sahara went along with an expanded tropical rainforest, didn’t it? It’s possible that the ancestors of Nilo-Saharans merely stayed in place as the rainforest gradually retreated, and adapted accordingly.
I wonder why you people talk all day about how the Bantu migration displaced the hunter gatherers but never ever talk about how the Bantus were pushed further south by incoming Levantine herders.
Cattle only entered Africa in 8,000 bc and that came with the Nilotics and Levantines. The ancestors of the Bantu were already living in the east.
Bantus themselves are a mix of Cro Magnon who carried the haplogroup CT and early Hadza people. This means Bantus were firmly derived from a eastern population, long before the Cushitic speakers even existed.
The arrival of pastoralists led to the ancestors of Bantus losing their original North Eastern homeland. They then migrated to West Africa where they mixed with super archaic and then migrated back toEast Africa.
So your analysis of Bantus is flawed. If you want to talk about the Bantu migration, tell us the full history of why their ancestors left North East Africa before telling us how the displaced hunter gatherers.
Also why do the Nuba nilotics speak a Niger Congo language?? Why do you people never talk about the genocide committed against the Nuba farmers of Sudan???
Nuba are the original people of North Africa. They carry the ancestral DNA of alll Niger Congo speakers. Everyone else came afterwards.
The Bantu were most likely pushed by fellow Niger-Congo kinsmen to the edge and got lucky with their strategy and toolkit, which was superiour to their Southern neighbours.
The core region of Niger-Kordofan groups in West Africa is much more densely populated and much harder terrain.
The Bantus which specialised and adapted to new habitats had half of the continent open to them, rather than fighting for every inch with their relatives.
In a way its a simple story to tell, because like usual, whats coming from a larger and highly competitive meta-population is superiour to thinned out fringe groups, low in numbers and isolated from the centres of development.
Iron Age full package agro-pastoralists, well adapted to the local habitat and endemic diseases, could just roll over the foragers in the forests and South.
Going North or West or even very East would have been a much harder challenge.
A large portion of Bantu speaking Africa was and in part still is rather sparsely inhabited. I know the exceptions though.
@Obs
Bantus were not pushed by Niger-Congo. Both Niger Congo and Bantus are cousins. Both groups derive from the same North eastern population.
Some migrated intoWest Africa, others went to southeastern Africa.
Both NigerCongo and Bantu were pushed by Levantine herders. Even still
To this day, farmers like the Dogon are being pushed by the herders.
This article explains it better
https://assets.publishing.service.gov.uk/media/57a08d5140f0b649740017b8/R6618a.pdf
@Sally: “Bantus were not pushed by Niger-Congo. Both Niger Congo and Bantus are cousins. Both groups derive from the same North eastern population.”
You might be right insofar, as more Northern people might have started a chain of events, but the Bantus were still pushed by “their cousins” if you like, because that were their neighbours. Being related didn’t stop tribes from pushing its others, like in Europe Germanic and Slavic tribes prove.
The Bantus were the Niger-Congo speakers at the fringe of their distribution, they adopted a toolkit which could expand beyond their usual habitat and used that for a big expansion. Most likely under pressure from their neighbours, but more crucial for my argument is that their path to the West, North and very East was blocked by minimum as advanced and competitive groups, whereas to the South was, at that time, “almost nothing” on a comparable level, like “virgin soil” for a colonisation with the exception of some Eastern regions.
Razib has written about the penetration of Indo-Aryans into South Asia and criticized the some of the politicized extremes of the narrative (https://www.gnxp.com/WordPress/2019/09/12/the-aryan-integration-theory-ait/). There was that article a while back about an ancient “race war” in the Sudan where the archaeologists discovered what looked like a massacre of probably Nilo-Saharan affiliated peoples committed by a probably West Eurasian affiliated group of peoples. But largely the narrative of one group completely supplanting another is an oversimplification. Rather there was a lot of cultural and genetic mixing. I think in most cases the hunter-gathers were forced to assimilate into a society where they would be initially low status and only acquire cultural capital after many generations. Among the Tswana even the pioneers who had mixed most with the Khoisan were seen as inferior to later arrivals. Hunter-gatherers who preferred freedom to the tyranny of chiefs departed to places less hospitable for agriculture or pastoralism- the Kalahari, the Ituri forest, the dry rifts around Lake Eyasi. There are still hunter-gatherers in the Boni forest of Kenya, speaking a Cushitic language interestingly enough. The Okiek were another hunter-gatherer group in a caste relationship with the Maasai.
There are lots of examples of mixing between very different societies in Africa. The Fulanis encroaching on the Dogon and attacking farmers in the Nigerian Middle Belt do have northern genetic affinities but speak a Niger-Congo language. While the Maasai have many features of the Cushitic cultural package, such as circumcision, they extract the bottom teeth like Nilotes and speak a Nilotic language. Tutsi people, who have Cushitic and Nilotic affinities, traditionally practiced neither Cushitic circumcision nor Nilotic tooth extraction. However their warriors collected a certain part of male anatomy as trophies from the fallen, as did the Cushitic Afar of Eritrea. Even groups who have little Cushitic ancestry like the Nguni (I think it’s been established that the Bantu went south first and then north https://www.pnas.org/content/112/43/13296) can have much of the Cushitic package including the fish taboo. The Swazis called their northern Mozambican neighbors by the derisive term ‘Mdlanyoka’ which means ‘snake eaters,’ as fish to a Swazi of the old days was just as repugnant a scaly creature as a snake. I wonder if the branch of Y haplogroup E found in Niger-Congo speaking males itself emerged from a west Eurasian population that entered the continent at an ancient date. Nilotes, Pygmies, and Khoisan who largely have the Y haplogroups A or B.
“What about the Khoisan genocide?” is a canard made by white South Africans and even a few Coloureds in response to the land issue in Southern Africa. I’ve seen plenty of Xhosa and Tswana people who look almost 100% Khoisan. There are lots of narratives of Boer and Griqua commandos extirpating the bushmen in their area (as well as mixing with their captives). Those Boer and Khoikhoi groups who massacred the bushmen constitute a big chunk of the Cape Coloured heritage. Because of the nature of historical documentation we have far less stories about Nguni and Sotho groups committing the same kinds of attacks. Swazi impis raided the bushmen of Lake Chrissie to capture them as slaves but they raided their northern neighbors a lot more.
Yes there isn’t much about state-sponsored violence against the peoples of Kordofan, which got less press than even Darfur. Nor does anyone outside of Burundi remember the Ikiza/Ubwicanyi, or the massacres of the Hutu population by the Tutsi-dominated army. The Rwandan genocide is remembered but few paid much attention to Paul Kagame’s campaigns of violence in the Congo, and I wonder if his arrest of the hero of Hotel Rwanda (https://www.washingtonpost.com/opinions/2020/09/01/rwanda-just-kidnapped-its-most-famous-activist-will-anyone-speak-out-against-regime/) will make a difference. We’ve completely forgotten about the Rohingya and will probably do so with the Uighurs.
Here’s a good link for anyone interested in the history of the South African bushmen: https://www.academia.edu/39959881/Sonqua_Southern_San_History_and_Art_after_Contact
There is actual stone art from San related people depicting big black Bantus which hunted smaller, reddish people, so themselves.
One of the main causes of conflict between farmers or pastoralists and hunters always was that the former occupied and changed land, while the later stole and robbed animals of the herd.
These conflicts could quickly escalate into gruesome, genocidal wars. That’s just natural without a higher order playing judge. Its about behaviours and interests which collide.
I’m not saying that Bantu and bushmen never got into scrapes. In fact, the last bushman chief in Lesotho was defeated at Sehonghong Cave by two Sotho chiefs who tired of his cattle raids. You can read more about it in the last link I posted. I just haven’t seen evidence of Bantu people having cetain genocidal policies, kill every bushman on sight, that were part of the Griqua and Trekboer ethos. Bushmen had a marginal role in Bantu societies supplying them with ivory and other wilderness products. Slave taking and marginalization is a bit different than genocide imo.
@Obs
You wrote”
“– archaic Hominids in tropical and West African zone
– archaic Homo sapiens spread from North/East Africa
– modern Homo sapiens spread from North East Africa/Near East”
The 50-60kya (or possibly 50-70kya) group/wave of modern Homo sapiens you allude to (likely from North East Africa, and/or, as you say, possibly also the Near East) do not seem to have been the first fully modern Homo sapiens. Anatomically fully modern homo sapiens (as opposed to more “archaic” or “early” homo sapiens like Irhoud) existed for instance perhaps at least from around 200kya (Omo I, Ethiopia) and 100kya (among the Aterian remains in North Africa), and possibly earlier.
Culturally/behaviorally, some evidence of modern behaviors begins to appear in some places (in Africa) at the time of the earliest Homo sapiens (ca 320-270kya – e.g. Gademotta, Olorgesailie), but evidence of a more full modern behavioral package appears more distinctly by around 150-75kya at several African sites, which include Sibudu in South Africa (e.g. arrows/evidence of the bow and a needle around 65kya), Katanda in Central Africa (several bone harpoons ca 90kya), Blombos in South Africa (including paint making ca 100kya and other indicators ca 75kya), Aduma in Ethiopia and the Aterian in North Aftica (including evidence of atlatls ca 80kya and 100kya respectively, and bone knives ca 90kya), Pinnacle Point in South Africa 164-70kya (heat treating of stone for flakeability, microliths, etc.) and a Kenyan site ca 75kya.
South African peoples likely ancestral to the Khoisan (the Khoisan rarely carry haplogroups E or L3 – which are linked with the aforementioned 50-60kya perhaps northeast African wave – , and did not originally carry those haplogroups at all until relatively recent admixture events of the last few thousand years) had the equivalent of the “Upper Paleolithic package” of technology (a local native African equivalent) by about 50kya (as attested at Border Cave, South Africa) before any admixture/contact with northeast Africans (let alone Eurasians). Khoisan peoples and Pygmies (who mostly descend from Homo sapiens groups more early-diverged than the 50-60kya wave) are certainly fully modern both anatomically and behaviorally (and archaeological evidence indicates that they have been for a long time (as are Nilotes, who tend to be dominated by Y-dna A and B). Fully modern sapiens seem to significantly predate the divergence of the population(s) associated with haplogroups E and L3, or even DE and CT (which was more likely only one of several branches of modern Homo sapiens – whose common ancestral origin may have been North and/or East Africa).
Edit: “…did not originally carry those haplogroups at all until relatively recent admixture events of the last few/several thousand years”
Edit to phrasing: “…but more distinct/clear evidence of modern behavior occurs/is known from by around 150-75kya…”
@Razib Khan
It seems possible that another candidate for the closest modern sub-Saharan African group to the OOA ancestors of Eurasians might be the Omotic peoples of southern Ethiopia (minus the roughly 13-15% Western Eurasian admixture Omotic peoples tend to have – which is nonetheless much less than the West Eurasian admixture present in most other Horn Africans, like Cushitics and Ethio-Semites): basically a Mota-like population (I believe Mota genetically resembled Omotics the most of all modern groups, but lacked the aforementioned West Eurasian component current Omotic peoples have, perhaps picked up by them from later admixture from/with Cushitic groups). I would think that this group (related to but quite distinct from both Nilotes/Nilo-Saharans and the Hadza) would also be the same as (or be very close to) the sub-Saharan donor population that makes up part of the ancestry of other Horn Africans (like Ethiopians or Somalis).
Also, Hadzas, as well as Omotic peoples (who both live in savannah-like areas), though some are very dark, tend to be a little lighter on average than Nilotes do (with a somewhat higher incidence of medium brownish skin shades – not unlike what is seen in many West African groups). Perhaps the ancestors of Nilotes were also closer to that range (with more variation), and later climatic changes involving more intense sunlight in the area could have lead to a somewhat more intense selection for deeper/darker skin shades than previously.