Revisiting the Out of Africa event with a novel Deep Learning approach:
Anatomically modern humans evolved around 300 thousand years ago in Africa. Modern humans started to appear in the fossil record outside of Africa about 100 thousand years ago though other hominins existed throughout Eurasia much earlier. Recently, several researchers argued in favour of a single out of Africa event for modern humans based on whole-genome sequences analyses. However, the single out of Africa model is in contrast with some of the findings from fossil records, which supports two out of Africa, and uniparental data, which proposes back to Africa movement. Here, we used a novel deep learning approach coupled with Approximate Bayesian Computation and Sequential Monte Carlo to revisit these hypotheses from the whole genome sequence perspective. Our results support the back to Africa model over other alternatives. We estimated that there are two successive splits between Africa and out of African populations happening around 60-80 thousand years ago and separated by 12-13 thousand years. One of the populations resulting from the more recent split has to a large extent replaced the older West African population while the other one has founded the out of Africa populations.
This is basically Dienekes Pontikos’ old Afrasian/Paleo-African Hypothesis. These models are not crazy. We have so much data there is room for them. The problem with “Deep Learning” is that we’re not too familiar with these methods, and who knows how to get a sense whether the results are just crazy artifacts? Even the authors say “it is still challenging to measure the significance of a prediction performed by NN, given that it is a black-box approach.”
Is there going to be a future where we just throw all the data into machine-learning approaches and let them converge to the best/most likely models? Perhaps. The problem seems to be that human population history a bit more complicated than we’d thought twenty years ago, requiring more complicated methods to figure out the details.
Without ancient DNA from Paleolithic Africa and South West Asia, there is no conclusive evidence. What about the new studies on Paleolithic Near Eastern DNA, did it work? Can we expect new results any time soon?
i heard just backed up cuz of covid19. but i don’t know details
It looks like the new paper is incompatible with claims that the split between the Khoisan and other modern humans goes back as far as 300,000 years. Has that idea been debunked, and if so what is the current thinking?
the estimates often presuppose particular models. so if the model is different/wrong then the values will be different.
in the ‘afrasian’ model the khoisan are just the most ‘paleoafrican’ enriched lineage. so all african populations can be thought of as mixes and the khoisan diverge the most cuz they have the most paleoafrican
Since I was the first person to suggest a Back to Africa theory, I’m glad to be vindicated once again.
Dienekes correctly predicted deep population structure, within Africa.
I’m curious that there rarely seems to be reference to glacial climate and associated sea level excursions during the last 200k years impacting human evolution/migration/survival. It’s acknowledged from time to time in a few papers, but not consistently. I anticipate both sea level variation and associated land ice build up from glaciation would be highly impactful on humans success or otherwise.
in all likelihood, the predicted massive, and massively replaced, “AA” population may have been a structured set of several small but genetically distinct semi-archaic populations. 2 or 3 separate small but related populations groups who shared ancestors tens thousand years earlier, may easily appear to mimic a much larger, but similarly diverse, unstructured population.
Then the conclusion may still be that a relatively small ancestral group swept (West) Africa less than 100,000 years ago. But not that they nearly-replaced a huge preexisting population. Maybe more like, they incorporated a few small, but diverse, semi-archaic groups as they expanded?
Dates seem somewhat compressed relative to prior modelling.
They note that Nean-Denisovan divergence somewhat compressed compared to previous modelling. E.g. Reich’s “Who We Are…” presents the estimated NeanderSovan divergence date at 470-380k (median 425k), while here only 200k (Figs from “Who We Are..” – https://imgur.com/a/CEKwamI).
Likewise EUR (HGDP French) and EAS (HGDP Han_N_China) divergence date here only 37.5k. Seems shallow, given models with Tianyuan and Ust Ishim suggest split prior to 45kya, and Basal Eurasian effect (real or statistical should push back divergence a bit), albeit there is potentially some signal of geneflow between EUR and EAS ancestors.
It also doesn’t seem like the model necessarily implies that split between AFR_main and EURASN_main had to have happened within Eurasia, necessarily, so I don’t know if “Back to Africa” is warranted.
Also worth noting that in their model I think they assume the 2.4% Neolithic edge from EUR to AFR (Yoruba), but also state that this is to incorporate a possible pulse of Neolithic migration into Africa and is not really necessary for the model (doesn’t really change fit much). It’s not “discovered” naturally by the modelling process as required to fit.
(I’d add the snarky bit about the graph showing time travel in main AMH lineage but not really necessary).
Could be useful to test with WGS from San, Papuans, North African populations, if possible, for the obvious reasons.
To add, obviously one reason to still not think that this was a “Back to Africa” scenario is the lack of Neanderthal pulse in the AFR_main group. There is a possible scenario where some Eurasian resident group that did not mix with Neanderthals migrated “Back to Africa” and then was wholly replaced in Eurasia by one that did, but it seems unlikely.
There was another preprint mentioning a very basal Eurasian backflow into sub Sahara Africa. Considering how early it was after the bottleneck and the lack of definitive Eurasian back flow such as Neanderthal ancestry, it could just be some population from North Africa moving to sub Saharan Africa. It could be ANA.
The authors caution that the B2A and OOA split didn’t necessarily have to take place outside of Africa. This study lends weight to deep population substructure in Africa (which has been staring us in the face for decades), but calling it “Back to Africa” seems misleading.
Their preferred model dates the “Back to Africa” and “Out of Africa” split to 60 kya, which is approximately 20 kyr older than the admixture event between Neanderthals and the ancestors of all non-Africans (i.e. OoA), which must have taken place in the Middle East or West Asia more broadly. The same model suggests that the B2A population absorbed an “Ancient African” or AA population, which we can assume occupied parts of equatorial West Africa in this case, in half that time at 48 kya.
The effective population size of B2A, absence of Neanderthal admixture in this population, and timing of the B2A-AA and OoA-Neanderthal admixture events all point to B2A and OoA splitting off in Northern or NE Africa, with B2A later spreading across the rest of the continent and OoA colonizing the rest of the world.
I also found this excerpt from the study particularly interesting, because of its implications for ancient AMH gene flow into Neanderthals. Perhaps were underestimating the extent of this gene flow?
“We cannot also reject a simpler model of no Neolithic migration55. Even if we assume the Neolithic migration affected Yoruba, the predicted total length of Neanderthal sequence in an average Yoruba genome would be less than 5 Mb compared to the 17 Mb identified by Chen et al55. This discrepancy also cannot be explained by the back to Africa model as introgression happened much later after the separation. This suggests that most of the Neanderthal signal in Yoruba should be explained by some other migration (for example from Human to Neaderthal28).“
If we’re speaking in terms of macro populations, I think we can broadly categorize these populations as “Basal African” (e.g. ancient Southern and Central African hunter-gatherers, secondary ancestry in West Africans, Mota, and most East Africans), Neo African (e.g. Ancient North Africans and the primary ancestry in West and East Africans including groups as distinct as Yoruba, Dinka, and Mota), and lastly non-Africans. The latter group is marked by the OoA bottleneck and Neanderthal introgression, which took place quite sometime after the Neo-African and OoA split. This seems to be corroborated by this study and countless other recent studies including Lipson et al. 2020.
I also found this excerpt from the study particularly interesting, because of its implications for ancient AMH gene flow into Neanderthals. Perhaps were underestimating the extent of this gene flow?
yeah. there is too much evidence of ‘modern’ populations from archaeology in SE and E asia before the OoA expansion. what happened to these ppl? i bet they were low density and so hard to pick up in assimilation, but they also probably mixed with other eurasian hominins
Razib,
Did you ever see this interesting response Lazaridis had to that Neanderthal Y replacement by AMH from a few months ago?
https://twitter.com/iosif_lazaridis/status/1309202796047073281
He brings up an interesting hypothesis that AMH and Neans are actually a clade to the exclusion of Denisovans, not only uniparentally but at an autosomal level as well. I would be very curious if some pursued this line of inquiry further.
A just updated version of this paper’s Figure 1 moves the 5% admixture edge from the XAFR population from AA to AFR: https://imgur.com/a/DnHZtTP
After accounting for diluation from AA, that would put 4.6% ancestry in AFR (Yoruba) from outside the clade of main ancestry from AMH. It seems a little odd that the model would give similar same total xAMH clade into AFR, EUR and ASN?
(If you have effectively an 5% edge into AFR that diverges 610k and an 8% edge that diverges 90k, then is that like a single edge of 13% that diverges 290k? And is that similar to some of those Basal Human divergence models?).
@Matt
When you mention gene flow between EAS and EUR you are referring to ANE right? I assume most of that signal would have come from there given, it seems mostly Paleolithic (pre 25kya) gene flow from East Eurasians to West Eurasians.
@James, well you know about the arguments for East Eurasian geneflow to West Eurasia right (argument that increased relatedness of late Upper Paleolithic Europeans to East Eurasians compared to early, and then argued that patterns of f-stats tend to make this fit better as East->West than through Basal Eurasian or West->East)? From Fu paper in 2016.
Could be via East Eurasian geneflow into “ANE” but it is not so clear if this is the only explanation (like how well correlated East Eurasian increase in relatedness is to increased relatedness to ANE/Native Americans).
@Matt
“Could be via East Eurasian geneflow into “ANE” but it is not so clear if this is the only explanation (like how well correlated East Eurasian increase in relatedness is to increased relatedness to ANE/Native Americans).”
What exactlty do you mean here? You’re saying the more related a population is to ANE/Natives, the more related they are to East Eurasians? Wouldn’t that just simply imply EE into ANE?
It’s not clear how well correlated the East Eurasian shift among Late European Upper Paleolithic is to ANE shift among same set. If they’re well correlated then it seems like it would be that they are mediated by the same phenomenon (e.g. East Eurasian shift is via ANE shift) while if they’re separable trends among samples then not really.
@ Matt
Do you have some stats or just some examples demonstrating this incongruity? I thought it was a fairly straightforward relationship – ANE is X% EE, WHG is X% ANE, ergo WHG is X% EE, or the magnitude of the demonstrated WHG-EE affinity is proportionate to the amount of EE baked into the ANE side of WHG, relative to a non-ANE admixed ancient West Eurasian. But you’re saying this correlation might not be so clear-cut?
Only from what I remember from Fu et al 2016. Have a look there and see how correlated the Native American and East Asian and Oceania stats among ancient samples look to you. There’s probably some more stuff since that which I’m not remembering – probably the other papers by Fu on Tianyuan might be worth looking at as well, as she seems to be the only person who has published on this topic.
There are probably different ANE groups with different ratios of ANE:East Eurasian about though, so it may not be as clear cut. If ANE is not X% EE but X-Y% EE depending on substructure it would be hard to estimate if X-Y was a significant range I guess.
It seems as if everything I’ve been saying is coming to light. The first farmers of West Africa migrated back from the Levant. Both the indigenous Levantines of pre-12,000 BC, as well as the Andaman Islanders were connected to modern day West African people.
The invasion of herding tribes from Central and West Asia split the genetic flow from West Africa to South West Asia.
West Africans didn’t just migrate into West Africa. They were pushed from the Levant into West Africa by Central Asian herders.
I am just waiting for Western genetic scientists and historians to finally admit that West African culture, spirituality, and farming birthed the civilized world. Ancient Egypt is much older than what they are claiming.
My article says it all.
https://amarachi-living.com/blog/black-ancient-egyptians-and-the-first-farmers
Continued…
The ancient archaic population (which the study claims that the migrants absorbed in equatorial West Africa) was actually living all over Africa. The ENTIRE African continent was equatorial at that time. So there was no ‘equatorial WEST Africa’, it was simply ‘equatorial Africa’.
In fact, the Levant was an extension of Africa.
The farmers (ancestors of Niger-Congo and Bantu) moved from the Levant into the grounds of the AA population, due to pressure from nomadic migrants coming in from Asia.
Also, farming is much older than what many of these historians are telling us. Much much older.
Further research will also prove that Bantus did not migrate from Central Africa. They came from the Levant.
We Africans have been saying this for decades. We only needed enough evidence to prove our theories are correct.
@Sally
The population that migrated deeper (and westward) into Africa was not necessarily from Eurasia (and if it was from Eurasia, south Arabia would be more likely than the Levant since it lacked Neanderthal admixture), and an origin for that population in north or east Africa (or northeast Africa) is just as likely (if not more likely) as Eurasia/the Near East, perhaps from an ANA-like group.
See the comments above by Gihanga Rwanda (and others)
And as much is expressed by the study itself.
From the study:
“We would like to caution that although we are naming the model “Back to Africa”, the OOA population did not need to be geographically out of Africa. Our estimates, particularly the effective population size of B2A (N_BC) and the time of Neanderthal introgression (T_NIntro), advocate that the split might have happened within Africa itself before the actual out of Africa event. In such a case, our results can be explained by the separation of West and East African population 80 kya (T_B) and then later the primary separation of OOA and East African population 67 kya (T_Sep) (assuming mutation rate of 1.25×10-8 per bp per generation58,59 and generation time of 29 years69). In this regard, our model is more akin to Lipson et al. 202036 model rather than what is suggested by Cole et al. 202035. If we assume model from Lipson et al. to be true, the most parsimonious explanation would be that our B2A population represents Basal West African population which separated from OOA populations 67 kya (T_Sep). Our AA represents Ghost modern36 which contributed to modern West African population around 10% which admixed around 60 kya from our prediction. On the other hand, if we assume true back to Africa, then most likely the OOA event took place less than 80 kya (T_B). This suggests that most of the older fossils (>80 kya) found outside Africa are unlikely to have contributed to OOA populations (assuming the ancestor of all modern human originated in Africa and never left Africa before OOA event). Geographical location where B2A separated from OOA is immensely important for this hypothesis but cannot be estimated from our approach. It will be especially fascinating to test this hypothesis using ancient genomes from those areas from that time point when they will be available.”
The study concluded that the so called “back to Africa” (B2A)” could have split from the OOA group in (north and/or east) Africa (then back-migrating deeper into Africa, with the OOA branch going to Eurasia).
Also, the putative back-migration (whether from east/north Africa or the Near East) would have ocurred (ca. 50-80 kya) several tens of thousands of years before the divergences of language families such as Niger-Congo (and long before any Central Asian herders existed). Also, the Andamanese are not retated to West Africans and they (like all existing non-Africans) belong to the same branch as most other Eurasians (including Austro-Melanesians) which split after the Neanderthal admixture exent (the carry Neanderthal admixture (they are part of the “Crown Eurasian” branch, less basal than BE/”Basal Eurasia” and certainly even less basal than ANA or the study’s “B2A” group). But it may indeed be true than early “Caucasian”/West Eurasian groups from northward replaced earlier (maybe vaguely/broadly Andamanese-like or Melanesian-like) peoples in the Near East descended from the earliesr OOA settlers, around the time you suggest (or earlier).
Edit”
“…Caucasian”/West Eurasian groups from northward (the northern Near East, Caucasus, or Central Asia) may have (mostly) replaced an earlier (maybe phenotypically broadly Andamanese-like, Melanesian-like, or AASI-like) population in the Near East descended from the earlier OOA settlers, around the time you suggest (or somewhat earlier).
Another edit to:
“But it may indeed be true than early “Caucasian”/West Eurasian groups…replaced a population in the Near East descended from the earlier OOA settlers [to that area], around the time you suggest (or earlier).”
It would have been significantly earlier than 12kya, since West Eurasian peoples were in the Levant before then (by ca 20-25kya, they had already back-migrated to the Magreb region of North Africa through/from the Levant and contributed to the formation of the Ibermaurusians). But some of the earlier populations may have survived longer in Arabia.
@Jm8
You said;
‘Also, the putative back-migration (whether from east/north Africa or the Near East) would have ocurred (ca. 50-80 kya) several tens of thousands of years before the divergences of language families such as Niger-Congo (and long before any Central Asian herders existed). “
Yes the migration happened thousands of years before, however, I won’t agree that the ENTIRE population migrated back 50-80kya. Many still remained in the Levant and back migrated around 12,000 BC.
Even recent West African history shows us that many South Sudanese migrated to Nigeria even as recent as 200 years ago.
This was during the Arab Slave Trade when they were fleeing from Sudan. The so called Arab slave trade actually was started by the Natufians 6,000 years ago. Arabs had nothing to do with slavery until 700 years ago.
So clearly, there were many different waves of back migration. There was no one single back migration.
Also, even the Bantus themselves only just arrived in South Africa 2,000 years ago. I doubt they came from Central Africa. As of yet, no evidence supports that claim. Most Bantus claim they came directly from North Africa. Some Xhosa and Zulus will even tell you it was Israel their ancestors migrated from.
My guess is that the ancestors of the Niger Congo were the ones who migrated to West Africa first. Whilst the Bantus were part of a much much later wave that went straight from North Africa and the Levant into South Africa.
Also You said;
“But it may indeed be true than early “Caucasian”/West Eurasian groups…replaced a population in the Near East descended from the earlier OOA settlers [to that area], around the time you suggest (or earlier).”
Well I’m glad we’re on the same page with that. Those ancient people of the Near East who disappeared after the Central Asians arrived are what West Africans are mixed with.
West Africans are the closest to what they looked like, more specifically West-Central Africans.
@JM8
You said;
“It would have been significantly earlier than 12kya, since West Eurasian peoples were in the Levant before then (by ca 20-25kya, they had already back-migrated to the Magreb region of North Africa through/from the Levant and contributed to the formation of the Ibermaurusians). But some of the earlier populations may have survived longer in Arabia.”
Can you please post sources that West Eurasians were on the Levant around 25yka?
Most sources say Iberomarusians reached the Levant around 12,000 BC. Yes they were in North Africa around 20yka but as of yet, I haven’t seen much evidence that they were in the Levant around that time you claimed.
@Sally
You wrote:
“Can you please post sources that West Eurasians were on the Levant around 25yka?
Most sources say Iberomarusians reached the Levant around 12,000 BC. Yes they were in North Africa around 20yka but as of yet, I haven’t seen much evidence that they were in the Levant around that time you claimed.”
I did not say that Iberomaurusians were in the Levant around 20kya. I said that the Iberomaurusians were descended partly from a paleolithic West Eurasian population that had migrated to North Africa from the Near East (from the Levant) – and partly from a native North African population (called “ANA” in Lazaridis’ 2018 paper on Dzudzuana). (West Eurasians had to have lived in the Levant by ca 20kya or earlier to have migrated to North Africa by around that time). 20-25 kya is the time the Iberomaurusian culture began to form (from that mixture) – it was preceeded by the indigenous North African Aterian culture (which began around 145kya and ended around 25kya – ending around the time the hybridized Iberomaurusian culture began, with the arrival of Western Eurasian back-migrants). (Later, ca. 11-12kya, according to Lazaridis, Iberomaurusian groups migrated to the Levant and intermixed with local peoples there, bringing the ANA admixture they carried).
There are two recent (2018 papers that discuss the makeup of the Iberomaurusians (from specimens dating to ca 17kya), one by Loosedrecht and one by Lazaridis. Both model them ( though differently) as a mixture of a (now-extinct) African (non-Eurasian) population unique to North Africa and a Western Eurasian population that migrated to North Africa from the Middle East (sometime around 25kya, with that mixture producing the Iberomaurusians).
Loosedrecht suggested a Natufian-like contribution in the Iberomaurusians (as the source of their West Eurasian ancestry). But, according to Lazaridis, the Iberomaurusians’ Eurasian admixture came from an earlier West Eurasian back-migration to North Africa from the Middle East from ca. 20ky or before (by people with affinities to peoples then living in the Caucasus). Lazaridis suggests that the Natufians were largely Western Eurasian but also carried a contribution from a group of the mixed Iberomaurusian-like peoples from North Africa who entered the Levant around 11kya (and through the Iberomaurusians, they inherited a native African ANA ancestral component).
Loosedrecht:
https://science.sciencemag.org/content/360/6388/548
Lazaridis:
https://www.biorxiv.org/content/10.1101/423079v1
You wrote:
“Also, even the Bantus themselves only just arrived in South Africa 2,000 years ago. I doubt they came from Central Africa. As of yet, no evidence supports that claim. Most Bantus claim they came directly from North Africa. Some Xhosa and Zulus will even tell you it was Israel their ancestors migrated from.
My guess is that the ancestors of the Niger Congo were the ones who migrated to West Africa first. Whilst the Bantus were part of a much much later wave that went straight from North Africa and the Levant into South Africa.”
Bantu is a branch of the Niger-Congo language family (and a relatively recent-branching one of only about 3-4 thousand years old). Niger-Congo (which has many old/deep branches in Africa significantly older than Bantu) may have originated in the West African Sahel/Savannah or alternately perhaps sahelian East Africa (central Sudan/Chad?), (possibly ca. 13-15kya or earlier, according to Roger Blench) spreading west and south, and may share a distant common ancestor with Nilo-Saharan. Niger-Congo, as mentioned, could have come from the Sahel (and/or southern Sahara) during around the Mesolithic – which is not too far from North Africa (but does not originate from a Levantine back-migration from 12kya.).
Bantu languages are considered to come from the so-called West Benue Congo branch of Niger-Congo. They likely diverged somewhere around the Cameroon/Gabon region (and some of the very southeasternmost corner of Nigeria), where a diversity Bantu-related/”semi-Bantu languages are still spoken), and gradually migrated east and southward (archaeology – a sequence of aerchaeological cultures – supports this). For example, Bantus were in the Great Lakes region of East Central Africa (Uganda, Rwanda, Burundi, etc) by about 600 BC, (where the are attested by the “Urewe culture” known from archaeology) and gradually migrated further south (and also some places east), bringing Urewe cultural variants, and eventually reaching parts of South Africa by about 2,000 years ago (as you mention). (The Urewe culture has even older roots in the western parts of Central Africa.)
I am not an expert on Bantu oral history, but the beginning of the Bantu migration was a fairly long tine ago (ca. 3,000-4,000 years ago), so precise memories of geographical origins are perhaps not to be expected. But a general memory (among some southern African Bantu groups) of coming from the north could easily refer to central Africa (or east central Africa, through which the ancestors of many southern Bantu groups passed). Claims of origins in Israel (if they ocurr) would seem unlikely to be/have been traditional but rather may reflect the influence of Abrahamic religions (except in rare cases like that of the Lemba tribe, who have actual recent Middle Eastern ancestry/admixture). This
effect is found, not only among some African groups, but many others throughout history that experienced the influence of Christianity or Islam – religions which, by their nature, often rather chauvinistically, cast the Middle East as the center of the universe, including of spiritual merit and prestige, and even creation itself).
@Jm8
You said:
”Bantu languages are considered to come from the so-called West Benue Congo branch of Niger-Congo. They likely diverged somewhere around the Cameroon/Gabon region (and some of the very southeasternmost corner of Nigeria), where a diversity Bantu-related/”semi-Bantu languages are still spoken), and gradually migrated east and southward (archaeology – a sequence of archaeological cultures – supports this)”.
Again, there is no evidence that Bantu’s migrated from Nigeria. NONE whatsoever. Languages are not proof of anything.
Ancient fossils prove more than languages. The fauna of the Levant was similar to that of Nigeria 12,000 years ago. Brace. C.L Nelson observed that the Natufian fossils lay between those of the Niger-Congo-speaking populations and the other samples.
https://www.pnas.org/content/103/1/242
So again, you are mistaken. In ancient times, the PRESENT DAY Niger congo area was not always limited to Nigeria. It encompassed the Levant and various parts of the Middle East.
The direction in which the Sahara has spread from Asia into Africa proves that a massive migration has taken place from Asia into Africa. The evidence lies in the ancient fossils of the Levant as well as the migration of the herding tribes from Asia into Africa. The original fauna of the Levant was similar to that of West Africa.
You also said;
”Niger-Congo, as mentioned, could have come from the Sahel (and/or southern Sahara) during around the Mesolithic – which is not too far from North Africa (but does not originate from a Levantine back-migration from 12kya.).”
This kind of information is up for debate. It’s all subjective. No real evidence to prove what you wrote. Like I said, whoever was in the Levant has a real distinct culture to West Africans. There was a distinct migration back into Africa from a group of people in the Levant pre-12,000 BC. The entire ancient African population had genetics similar to the Hadza. Niger-Congo and Bantu autosomal genetics (not language) were distinctly formed from another ancient group that migrated from the Levant and mixed with the older humans in Africa. There were various successive waves of migrants into Africa. The oldest will be somewhere in Congo.
Again, my article has sound evidence of this;
https://amarachi-living.com/blog/black-ancient-egyptians-and-the-first-farmers
@Jm8
Also, if the herders were able to migrate all the way from central Asia, what makes you think the farmers were not also back-migrating and being pushed southwards?
Fulanis carry R1b-V88 which is linked to the Central Asia herders and was found in the European mesolithic samples in Sardinia. So, you somehow agree that only the herders have been migrating but the farmers were static? That doesn’t make any sense whatsoever.
I stick to my claims that Niger-Congo and Bantu farmers have in fact migrated from the Levant. The fact is, more genetic studies need to be done in the Levant and Europe.
For those of us who actually live in Africa and understand the social and cultural dynamics, we are able to spot that there are way too many holes in your theory. Again, if herders back-migrated with V88, then farmers (who live next door to them) likely also back-migrated.
@Jm8
Also, you mentioned;
”Loosedrecht suggested a Natufian-like contribution in the Iberomaurusians (as the source of their West Eurasian ancestry). But, according to Lazaridis, the Iberomaurusians’ Eurasian admixture came from an earlier West Eurasian back-migration to North Africa from the Middle East from ca. 20ky or before (by people with affinities to peoples then living in the Caucasus). Lazaridis suggests that the Natufians were largely Western Eurasian but also carried a contribution from a group of the mixed Iberomaurusian-like peoples from North Africa who entered the Levant around 11kya (and through the Iberomaurusians, they inherited a native African ANA ancestral component).”
Did Lazaridis’ study prove that the West Eurasian component found on the Natufians/Iberomaurusians came from the Middle East? I thought his study only linked the West Eurasian component to the Dzudzuana caves? Did he actually confirm with real evidence that the West Eurasian component in the Iberomaurusians was from the Middle East? In my opinion, it traversed through Europe into North Africa not via the Middle East.
Please post the quote where he claims it was from the Middle East.
@Razib I think about that a lot myself. It’s an interesting story to imagine, all those early humans lost in jungles and savannas loaded with bizarre looking semi-humans.
@Sally
You wrote:
“Did he actually confirm with real evidence that the West Eurasian component in the Iberomaurusians was from the Middle East? In my opinion, it traversed through Europe into North Africa not via the Middle East.
Please post the quote where he claims it was from the Middle East.”
Both Loosdrech and Lazaridis seem to agree that the Western Eurasian component in the Iberomaurusians did not migrate to North Africa from Europe (that’s an old obsolete theory – it clearly did not arrive in North Africa from Iberia/Western Europe). The component instead showed affinities to the Dzudzuana people of the Caucasus, who had Middle Eastern affinities (not Europe, even less so Western Europe) and had likely come to the Caucasus from the Near East. Similar Dzudzuana-like peoples are suggested to have inhabited the Middle East at the time. The migration into North Africa was from the east (the Near East, not the immediate north or west), which would have come through the Levant and then westward to the Maghreb. The ancient Middle Eastern component Lazardis finds in the Iberomaurusians is pre-Neolithic (rather than Neolithic).
From Lazaridis:
“The CHG [Caucasus hunter-gatherers], geographically intermediate between Europe and the Near East resembled Near Eastern populations in the possession of Basal Eurasian ancestry5. The Dzudzuana population was not identical to the WHG [Western European hunter-gatherers], as it shared fewer alleles with both an early Upper Paleolithic Siberian (Ust’Ishim19) and an early Upper Paleolithic East Asian (Tianyuan20) (Extended Data Fig. 5c), thus, it too—like the PGNE populations—had Basal Eurasian ancestry6,9. The detection of this type of ancestry, twice as early as previously documented5,6 and at the northern edge of the Near East, lends weight to the hypothesis that it represents a deep Near Eastern lineage rather than a recent arrival from Africa6.”
https://www.biorxiv.org/content/10.1101/423079v1.full
In Lazaridis (see Figure 2) the Iberomaurusians (of Taforalt) descend from a native North African group (ANA) and a Dzudzuana-like group. The Natufians were largely of Dzudzuan-like ancestry but also with admixture from Iberomaurusian-like people (who migrated to the Levant later, ca. 11kya).
@Sally
You wrote:
“Again, there is no evidence that Bantu’s migrated from Nigeria. NONE whatsoever. Languages are not proof of anything.”
Bantu is a language family. And the Bantu family is clearly a branch of the much older Niger Congo family (this is univerally agreed upon by linguists). The greatest diversity of languages most similar to Bantu is in the Cameroon region. Bantu peooles also show evidence of largely West African-like genetic origins/derived from a branch of Niger-Congo people (sometimes along with other minor admixture picked up later depending on region, e.g. Pygmy, Cushitic, Nilotic, Khoisan, etc.)
You wrote:
“So again, you are mistaken. In ancient times, the PRESENT DAY Niger congo area was not always limited to Nigeria. It encompassed the Levant and various parts of the Middle East.”
I never said Niger-Congo was restricted to Nigeria. I specifically said it could have come from the West African Sahel/Savanah region (e.g
Mali, Niger) or Mesolithic southern Sahara or even East Africa (e.g. Sudan, Chad, South Ethiopia). There is no evidence that it came from the Levant or the Middle East, or that the Natufians were Niger-Congo (The Natufians show mostly West Eurasian genetic affinities, and the minor African affinities they show are native North African/ANA and/or East African). West Africans are clearly distinct from Natufians and Neolithic Levantines (autosomally and in maternal and paternal lineages). West Africans are dominated by Y-DNA E1b1a (and sometimes E1a), neither of which appear in Natufians or Iberomaurusians (who carried mostly E1b1b – which, according to Lazaridis, was most likely brought to the Natufians from North Africa by the Iberomaurusians, who may have in turn inherited it from their ANA ancestors.
E1b1a and E1b1b are thought to have split around 40-45 kya somewhere in Africa – maybe East Africa – (from their earlier ancestor, E-P2/E1b1, which also originated in Africa, also likely East Africa.
You wrote:
“The entire ancient African population had genetics similar to the Hadza.”
This is not in evidence. Africa is massive and African genetics are vastly diverse and show evidence of very deep splits (Homo sapiens having lived there the longest), with old populations very different from the Hadza in some regions. The most divergent genetics are found in the Khoisan and Pygmies (who derive from two of the oldest branches (likely of early Homo sapiens). The Hadza are a less basal branch native to a region of East Africa (and show certain affinities to Eurasians because, as East Africans, they may be among the closest Africans to the northest African population from which the OOA group came).
You wrote:
Niger-Congo and Bantu autosomal genetics (not language) were distinctly formed from another ancient group that migrated from the Levant and mixed with the older humans in Africa.”
Bantu is primarily a language family, which is nested within Niger-Congo (among many other branches). The “into Africa” component (which is also found in Nilotics/Nilo-Saharans) could easily have originated from North or East Africa (rather than the Middle East) and (wherever it came from) is extremely old (entering West Africa by ca. 60kya)
@Sally
Also, you wrote:
“I stick to my claims that Niger-Congo and Bantu farmers have in fact migrated from the Levant. The fact is, more genetic studies need to be done in the Levant and Europe.”
I’m afraid this would not make sense. The population that migrated to West Africa (either from North/East Africa or the southern Middle East) did so around 50-70 kya and did not carry Neandertal admixture (the Neanderthal admixture event happened later, around 40-55kya, most likely in the Levant, where Neanderthal lived). (And according to the recent study that is the subject if this blog post, the migrating population contributed ca. 90% genetically to modern West Africans, and the Cole et al. study estimated ca. 35%, also without Neanderthal DNA, but either way it could not have been from post-55kya Levantines). The migration of the ancestors of Niger-Congo peoples to West Africa ocurred long before farming (with their descendents developing farming afterward).
The peoples who lived in the Levant after ca. 40-50kya had Neanderthal admixture. And the peoples of the Levant by the time farming was developed there (and likely earlier) were mostly Western Eurasian. These were not the populations that contributed to West Africans. Also, the invention of West African agriculture (associated with ancient Niger-Congo peoples) is/was distinct and independent from that which developed/had developed in the Middle East. The two domestication events involved entirely different crops (indigenous to their respective regions of the world). (Just as independent domestication events ocurrent in various other regions: including China, Central America, and Papua New Guinea).
I do agree that more genetic studies need to be done.
You wrote:
“For those of us who actually live in Africa and understand the social and cultural dynamics, we are able to spot that there are way too many holes in your theory. Again, if herders back-migrated with V88, then farmers (who live next door to them) likely also back-migrated.”
It is not my theory but rather the opinion of the majority of mainstream scholarship on genetics, lingiuistics, and archaeology.
The branch of R1b-V88 found in Fulanis and Chadic peoples entered Africa during or just prior to the Neolithic. Other lineages found in West Africa (including as E1b1a and E1a, which are dominant there and are associated with Niger-Congo) are much older and are not the result of a Contemporary Mesolithic or Neolithic-era migration from Eurasia like the one that brought R1b-V88 (they are not found in Eurasia, barring recent introduction) and are in fact unique to Africa.
As mentioned, the people that lived in the Levant after 40-50kya (including whatever Levantine group was later replaced by West Eurasians) were not (they were quite different from) the population that migrated into West Africa (which may be more likely to have been from North and/or East Africa than from the Middle East, as the study explains, let alone the Levant). The people of the Levant by that time (and later) were part of the OOA branch and had received Neanderthal admixture (which is shared by all modern populations from outside Africa). The Neanderthal admixture event (which took place around 40-50kya) probably happened in the Levant (where Neanderthals are known to have lived). The group that migrated to West Africa (and according to this recent study, mostly replaced the locals) lacked Neanderthal admixture – they were very basal – (Cole et al. found that as well).
@Jm8
You said;
”Bantu is a language family. And the Bantu family is clearly a branch of the much older Niger Congo family (this is univerally agreed upon by linguists). The greatest diversity of languages most similar to Bantu is in the Cameroon region. Bantu peooles also show evidence of largely West African-like genetic origins/derived from a branch of Niger-Congo people (sometimes along with other minor admixture picked up later depending on region, e.g. Pygmy, Cushitic, Nilotic, Khoisan, etc.)”
Again, you are just repeating yourself. You have no proof of anything you’ve said. Language alone doesn’t determine the origin of a people. Ancient fossils prove more than languages. The fauna of the Levant was similar to that of Nigeria 12,000 years ago. Brace. C.L Nelson observed that the Natufian fossils lay between those of the Niger-Congo-speaking populations.
Read his study carefully;
https://www.pnas.org/content/103/1/242
You also said;
”The population that migrated to West Africa (either from North/East Africa or the southern Middle East) did so around 50-70 kya and did not carry Neandertal admixture (the Neanderthal admixture event happened later, around 40-55kya, most likely in the Levant, where Neanderthal lived). (And according to the recent study that is the subject if this blog post, the migrating population contributed ca. 90% genetically to modern West Africans, and the Cole et al. study estimated ca. 35%, also without Neanderthal DNA, but either way it could not have been from post-55kya Levantines). The migration of the ancestors of Niger-Congo peoples to West Africa ocurred long before farming (with their descendants developing farming afterward).”
My study has debunked everything you said about farming. Farming came with the SAME migrating population. There is a clear cultural continuation linked to farming all the way from Niger-Congo to the Levantine Natufian.
Cultural continuation refers to the fact that the same culture that was in the Levant prior to the Natufians’ replacement in 12,000 BC is found amongst the Niger-Congo. Genetics alone doesn’t cut it. So, Go and read my study (if you haven’t read it yet).
The same farming artifacts linked to West African farmers are identical to the Natufian ones.
What’s more, the dates in which they claim farming began is up for debate. It might even be as old as 40,000 years ago. Farming cultural artifacts are all over West Africa linked to hunter-gatherers even.
You also said;
”The branch of R1b-V88 found in Fulanis and Chadic peoples entered Africa during or just prior to the Neolithic.”
That’s beside the point. The fact is that the same Rib-V88 branch carried by the Fulani was detected in Sardinia. So, clearly, it was in Europe. So, again, you’re swaying from the facts. The ancestors of the Fulani were Central Asian herders who migrated into Africa. Their push into Africa pushed others that lived alongside them.
You also said;
”This is not in evidence. Africa is massive and African genetics are vastly diverse and show evidence of very deep splits (Homo sapiens having lived there the longest), with old populations very different from the Hadza in some regions. The most divergent genetics are found in the Khoisan and Pygmies (who derive from two of the oldest branches (likely of early Homo sapiens). The Hadza are a less basal branch native to a region of East Africa (and show certain affinities to Eurasians because, as East Africans, they may be among the closest Africans to the northest African population from which the OOA group came).”
Yes, I know Africa is massive and has older humans. If you’ve read my study, you’ll be aware I know a lot about Africa. Even the social and cultural dynamics which you have no clue about – which makes much of your statements (and those of certain others) lack substance for many of us Africans.
Again, studying genetics alone doesn’t cut it. Certain cultural and social dynamics in modern Africa do not add up to your statements or those of some other ‘genetic scholars’.
Clear recent migrations have taken place in Africa from the Levant.
Even the trail of the Sahara doesn’t lie.
@Jm8
More on evidence that farming was spread to Europe by the same people who spread it to West Africa.
” The assessment of prehistoric and recent human craniofacial dimensions supports the picture documented by genetics that the extension of Neolithic agriculture from the Near East westward to Europe and across North Africa was accomplished by a process of demic diffusion (11–15). If the Late Pleistocene Natufian sample from Israel is the source from which that Neolithic spread was derived, then there was clearly a SubSaharan African element present of almost equal importance as the Late Prehistoric Eurasian element. At the same time, the failure of the Neolithic and Bronze Age samples in central and northern Europe to tie to the modern inhabitants supports the suggestion that, while a farming mode of subsistence was spread westward and also north to Crimea and east to Mongolia by actual movement of communities of farmers, the indigenous foragers in each of those areas ultimately absorbed both the agricultural subsistence strategy and also the people who had brought it. The interbreeding of the incoming Neolithic people with the in situ foragers diluted the Sub-Saharan traces that may have come with the Neolithic spread so that no discoverable element of that remained. This picture of a mixture between the incoming farmers and the in situ foragers had originally been supported by the archaeological record alone (6, 9, 33, 34, 48, 49), but this view is now reinforced by the analysis of the skeletal morphology of the people of those areas where prehistoric and recent remains can be metrically compared.”
It will help if you actually read this study;
https://www.pnas.org/content/103/1/242
It confirms that the farmers who brought farming to Europe had clear links to Sub Saharan Africa but were heavily absorbed.
Again, debunking your claim that farming in the Middle East and Africa developed independently from separate populations. There was a common ancestor. That’s why there is a clear cultural continuation between the farming artifacts found in West Africa and that of the ancient Levant.
@Matt
“well you know about the arguments for East Eurasian geneflow to West Eurasia right (argument that increased relatedness of late Upper Paleolithic Europeans to East Eurasians compared to early, and then argued that patterns of f-stats tend to make this fit better as East->West than through Basal Eurasian or West->East)? From Fu paper in 2016.”
Yes I’ve heard of them, though you also had Goyet have some kind of affinity to East Asians that later samples don’t. Do you think there was continuous gene flow from East to West or more of a pulse admixture thing?
Have any other papers made that inference btw? It’s certainly an interesting scenario yet still you see deep “splits” with East and West Eurasians so I am assuming that gene flow must have been low overall.
Ydna haplogroup R after all is a downstream clade of Ydna haplogroup P of likely East Eurasian origin.
@Sally
The inference of African ancestry in Anatolian farmers is a very odd finding. Never seen it in genetic papers, just in Brace’s one.
One puzzling issue with this study that comes to mind seems possibly to conflict with the claim of a 90% genetic replacement in much of sub-Saharan Africa (including West Africa presumably) from East/North/Northeast African or Mid Eastern migrants. The migrants would likely be suppisedly associated with Y-dna E and Mt-dna L3, but a dominant to very significant Mt-dna lineage in West Africa (and some other places) is L2, which diverged before the proposed migration (possibly in west or central Africa) and would be associated with the pre-existing West Africans “AA” population supposedly mostly replaced (yet it exists in much of West Africa, and some other places in Africa like South Sudan, along with other non-L3 lineages, at frequencies seemingly too high for that to make sense).
Edit:
”
..but a dominant to very significant Mt-dna lineage in….
is L2, which diverged before the proposed migration….. and supposedly, according to some studies, also (ca. 80-100kya) just before the divergence of the population from which the migration came.”
@Jm8
It’s not just L2, non-L3 mtDNA lineages make up something like 50-60% of all non-Afroasiatic SSA mtDNA. Not to mention groups like Nilotes, pygmies, and San who have lots of old African y-DNA like A and B. These facts coupled with the absurdly recent dating of the Neanderthal introgression into Eurasians makes me not really read too much at all into this particular paper, though I appreciate that they’re trying to apply new machine learning methods to these types of questions.