Ancient DNA and deep population structure in sub-Saharan African foragers

[bicicleur 2]

https://www.nature.com/articles/s41586-022-04430-9

Multiple lines of genetic and archaeological evidence suggest that there were major demographic changes in the terminal Late Pleistocene epoch and early Holocene epoch of sub-Saharan Africa1,2,3,4. Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations3,5. Here we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the past approximately 18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase the data quality for 15 previously published ancient individuals and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, probably reflecting Pleistocene interactions around 80–20 thousand years ago, including deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of ancestry that occurs in highest proportion today in central African rainforest hunter-gatherers. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analyses but remain contested, suggesting increasing regionalization at the end of the Pleistocene epoch.

[kingjohn]

Uniparental markers
All four newly reported males are similar to most published ancient foragers from this region of Africa in carrying the widely distributed Y chromosome haplogroup B2 (Extended Data Table 1)


So E came later

[bicicleur 2]

Uniparental markers
All four newly reported males are similar to most published ancient foragers from this region of Africa in carrying the widely distributed Y chromosome haplogroup B2 (Extended Data Table 1)
So E came later

this paper deals with HG

Bantu and Cushite pastoralists were different clades of E

[Hawk]

Uniparental markers
All four newly reported males are similar to most published ancient foragers from this region of Africa in carrying the widely distributed Y chromosome haplogroup B2 (Extended Data Table 1)
So E came later

It looks like Y-DNA E became more prominent in Africa after the Bantu expansion. Y-DNA A and B were more common prior to that.

[Riverman]

Uniparental markers
All four newly reported males are similar to most published ancient foragers from this region of Africa in carrying the widely distributed Y chromosome haplogroup B2 (Extended Data Table 1)
So E came later

E spread with Basal Eurasian most likely and that was sitting in North East Africa and/or the Near East, especially the Southern Levante and Arabian peninsula, Yemen.

[bicicleur 2]

E spread with Basal Eurasian most likely and that was sitting in North East Africa and/or the Near East, especially the Southern Levante and Arabian peninsula, Yemen.

E1b1b1-M35 to be more specific.

[Riverman]

E1b1b1-M35 to be more specific.

That's for sure, but essentially, I think E as such came from the same source, the main modern Subsaharan African branches just departed earlier. Therefore there were several waves of E moderns from North East Africa and/or the Near East coming down to the Rest of Africa. Subsaharan Africa proper. Especially Western Africa, was reached extremely late, after the Green Sahara period most likely. For much of Africa, they are truly newcomers.

[Hawk]

E1b1b1-M35 to be more specific.

We have to wait in order to classify the dilemma between ANA (Ancient North Africans) and Basal Eurasian. But, i strongly believe Y-DNA E as a whole has more to do with ANA, people heavy on ANA had distinct look from both SSA and Eurasians.

[Riverman]

We have to wait in order to classify the dilemma between ANA (Ancient North Africans) and Basal Eurasian. But, i strongly believe Y-DNA E as a whole has more to do with ANA, people heavy on ANA had distinct look from both SSA and Eurasians.

In my opinion ANA and Basal Eurasian is the same, but unlike some, I think Basal Eurasian is the main branch, and ANA a side branch which went out earlier from the cradle region and mixed with local Africans. That's like Bell Beakers vs. Balto-Slavic. Similar main source, but different timings and admixtures. Same here: ANA is the earlier branching event, Basal Eurasian/E-M35 the later. It could be argued the other way around, but IBM is definitely the earlier branching event, since even if E's cradle was in Africa, it was in very North East Africa, not where the mixed IBM were found.
And then again, Natufians show a high degree of comtinuity, physically and culturally, from earlier inhabitants of the Near East. We just need to sample the pre-Natufians to see what they are. If they are all G and J, no E, from Palestine to Mesopotamia, from Kurdistan to Yemen, then its clear, it was a recent migration even from North East Africa. But who knows at this point, probably the Southern Levante and Yemen was full of E even before the Natufians.

[Hawk]

In my opinion ANA and Basal Eurasian is the same, but unlike some, I think Basal Eurasian is the main branch, and ANA a side branch which went out earlier from the cradle region and mixed with local Africans. That's like Bell Beakers vs. Balto-Slavic. Similar main source, but different timings and admixtures. Same here: ANA is the earlier branching event, Basal Eurasian/E-M35 the later. It could be argued the other way around, but IBM is definitely the earlier branching event, since even if E's cradle was in Africa, it was in very North East Africa, not where the mixed IBM were found.
And then again, Natufians show a high degree of comtinuity, physically and culturally, from earlier inhabitants of the Near East. We just need to sample the pre-Natufians to see what they are. If they are all G and J, no E, from Palestine to Mesopotamia, from Kurdistan to Yemen, then its clear, it was a recent migration even from North East Africa. But who knows at this point, probably the Southern Levante and Yemen was full of E even before the Natufians.

This is something we don't agree, i agree with Lazaridis tree, ANA split from the common ancestor of (Basal Eurasian + Crown Eurasians) and remained in Africa if not they were the ones who pushed the common ancestor of (Basal Eurasian + Crown Eurasians) into Eurasia (Y-DNA C, F, D). Probably ANA (Y-DNA E-M215 mostly) migrated from East Africa and pushed north into North Africa in Paleolithic times. Then, during Mesolithic a group of these ANA males migrated into Levant forming the Natufians. (though i admit things are a bit messy and we can get further surprised due to lack of data determining these very deep ancestries).

Iberomaurusians heavy on ANA looked quite different from heavy Basal Eurasian populations (one of the main contributors of Mediterranean race). ANA superficially looked similar to Paleolithic Europeans based on crania but probably the anthropologists didn't dig deep on comparisons, they just noted the similarity on robust skulls (in fact ANA were more robust than Paleolithic Europeans). It was likely a convergent evolution thing, since ANA genetically were very different from Paleolithic Europeans, on the opposite end of axis. They were also medium to dark skin tone (but more leaning to medium from genetiker analysis), probably brownish-redish.

[Riverman]

This is something we don't agree, i agree with Lazaridis tree, ANA split from the common ancestor of (Basal Eurasian + Crown Eurasians) and remained in Africa if not they were the ones who pushed the common ancestor of (Basal Eurasian + Crown Eurasians) into Eurasia (Y-DNA C, F, D). Probably ANA (Y-DNA E-M215 mostly) migrated from East Africa and pushed north into North Africa in Paleolithic times. Then, during Mesolithic a group of these ANA males migrated into Levant forming the Natufians.

Iberomaurusians heavy on ANA looked quite different from heavy Basal Eurasian populations (one of the main contributors of Mediterranean race). ANA superficially looked similar to Paleolithic Europeans based on crania but probably the anthropologists didn't dig deep on comparisons, they just noted the similarity on robust skulls (in fact ANA were more robust than Paleolithic Europeans).

I think its a viable option that ANA stayed in Africa, while Basal Eurasian did not. We don't know. As for ANA/IBM, they being African admixed specimen, they don't represent what ANA really might have looked like. Whether or not ANA from Africa came to form Natufians, and where they lived before, that's completely in the dark.

[Hawk]

I think its a viable option that ANA stayed in Africa, while Basal Eurasian did not. We don't know. As for ANA/IBM, they being African admixed specimen, they don't represent what ANA really might have looked like. Whether or not ANA from Africa came to form Natufians, and where they lived before, that's completely in the dark.

Africa was heterogenous, ANA-like/IBM-like could have contributed into forming of SSA admixture we know today, along with Shum-Laka (whose Y-DNA was even outside the current phylogenetic tree, A0 or A00 if i remember correctly).

[Riverman]

Africa was heterogenous, ANA-like/IBM-like could have contributed into forming of SSA admixture we know today, along with Shum-Laka (whose Y-DNA was even outside the current phylogenetic tree, A0 or A00 if i remember correctly).

ANA did, that's not could, it did. That's fixed imho since the Shum Laka finds. The modern Subsaharan Africans are a completely different population because of this, and E is like the signal for it.

[kingjohn]

P.S
we can see that in east africa the ancients were B
and in south africa they were A1B
only later after e-m2 bantu expansion west and e-m293 expansion south ( an e-z830 derived branch who moved south)
all of africa was in the hand of E

[Diictodon]

With more and more Data coming out, I think African Multiregionalism will be the dominant concensus amongst most Scientists

[Palermo Trapani]

Regarding this growing consensus towards a African Multiregionalism, I think this paper by Bergmann et al 2022 is evidence consistent with that hypothesis. I have read the paper and there are some very interesting conclusions that are drawn. The paper looks at Jebel Irhoud Skull Morphology and Skulls in North Africa that are after Jebel Irhoud (Circa 300K years ago) and before the Iberomaurusians . Based on the analysis, they conclude that there is a direct continuity between the early Homo Sapiens in North Africa (Jebel Irhoud, 300K years ago) to the Aterian period (150k years ago) and the Iberomaurusian Civilization which appeared around 25K BC and lasted to 11K BC. Of course, it would be great to get DNA from the Aterian samples and Jebel Irhoud, but DNA from the Iberomaurusians have been analyzed. Here is a quote from the paper that is interesting

"From a regional perspective, resemblances in mandibular shape (Supplementary Table S2, Figs. 6 and 7) and discrete features (Table 1) indicate that the Tighenif, Tomas Quarry and Kébibat hominins were part of the same evolving lineage as the Jebel Irhoud humans, Aterians, Iberomaurusians and recent North Africans. Absolute sizes of Aterian mandibles are in the range of early H. sapiens and Iberomaurusians"

The authors based on the the morphological link, then move into the Genetics and make some plausible scenarios

"Apart from regional continuity, Aterians and other ancient North Africans (Tighenif, Tomas Quarry I) resemble Natufans, sub-Saharans and Upper Paleolithic people (Supplementary Table S2), shedding some light on the nature of potential exchanges between North Africa and adjacent areas. Genetically, this fnding parallels a close relatedness of Iberomaurusians to Natufans, southern Europeans57, and—on a smaller scale—to sub-Saharan Africans59. To that end, late glacial back-to-Africa migrations via the Mediterranean63–67 and via the Near-East59,68 ofer explanatory scenarios. Such population movements depended either on low sea-levels during glacial periods54,69or on the periodic emergence of green corridors throughout the Sahara, Sinai, Negev and Nafud deserts70–73. Te latter also allowed for human exchanges between North Africa and the Sahelian zone, accounting for the exceptional skeletal variation and/or signs of gene fow74,75 in most fnds from the African humid period (Later Stone Age until mid-Holocene). Among our samples, especially the El Harhoura mandible matches substantially to the Jebel Sahaba series (Supplementary Table S2)."



https://www.nature.com/articles/s41598-022-12607-5

Olade et al 2019 "The genomic history of the Iberian Peninsula over the past 8000 years" Supplement Figure S.4

I posted this PCA because it clearly plots both the Natufians and Iberomaurusians (along with the ancient Iberian samples) relative to modern populations, including modern North Africans. Kefi et al 2016 "On the origin of the Iberomaurusians" documents that for the 23 ancient Iberomaurusians, all the mtdna Haplogroups were North African or Eurasian. Van de Loosdrecht et al 2018 were able to examine autosomal DNA for 7 of the Iberomaurusians showing 2/3 of the ancestry was similar to Natufian with 1/6 coming from an East African source and 1/6 from West African, which would be consistent with movement from South of the Sahara into North Africa during the Wet Sahara periods. Van de Loosdrecht speculate that Natufian type ancestry was likely widespread from North Africa to the Levant before 25K years ago. Of course, it would be good if those other 16 ancient North Africans could be fully analyzed and some DNA further back in North Africa could be analyzed.

Still, if Jebel Irhoud and Iberomurusians to Modern North Africans are in morphological continuity, is there likely some genetic connection going back to Jebel Irhoud? Could Jebel Irhoud early Homo Sapiens admixed with Neanderthals in Iberia way, way, way back. Mounier and Lahr 2019 proposed this, but they also said that the North African early Homo Sapiens did not impact later Homo Sapiens. This paper by Bregmann et al 2022 seems to be questioning that and actually suggest Jebel Irhoud is in direct, at least morphological continuity, with Iberomarusians and modern North Africans. Bregmann et al 2022 also stated that the South African early Homo Sapiens (i.e Florisbad vs others) have too much variation to be in morphological continuity (they did not best I can tell discuss the early East African Homo Sapiens like Omo II).

https://www.nature.com/articles/s41467-019-11213-w





Anyway, I found this Bregmann et al 2022 paper really interesting and I think it does support the broadening consensus that a single source population of Early Homo Sapiens explains modern humans alone. Now I don't think it refutes OOA broadly understood, just the version that was considered orthodox 10-15 years ago that suggested a Recent OOA population of Homo Sapiens 40K years ago replaced all other Humans and was source for all modern humans. Much more complicated than that in my opinion

[Riverman]

Regarding this growing consensus towards a African Multiregionalism, I think this paper by Bergmann et al 2022 is evidence consistent with that hypothesis. I have read the paper and there are some very interesting conclusions that are drawn. The paper looks at Jebel Irhoud Skull Morphology and Skulls in North Africa that are after Jebel Irhoud (Circa 300K years ago) and before the Iberomaurusians . Based on the analysis, they conclude that there is a direct continuity between the early Homo Sapiens in North Africa (Jebel Irhoud, 300K years ago) to the Aterian period (150k years ago) and the Iberomaurusian Civilization which appeared around 25K BC and lasted to 11K BC.

That's pretty much against the anatomical and genetic comparisons I remember. A very strange conclusion. Genetically its very clear that Iberomaurusians had a significant amount of West Eurasian recent ancestry and the Aterians are hard to pin down, but comparing them with other human variants from around the world, they could be ancestral to anyone, but rather Subsaharans than IBM or let alone West Eurasians.

[Palermo Trapani]

That's pretty much against the anatomical and genetic comparisons I remember. A very strange conclusion. Genetically its very clear that Iberomaurusians had a significant amount of West Eurasian recent ancestry and the Aterians are hard to pin down, but comparing them with other human variants from around the world, they could be ancestral to anyone, but rather Subsaharans than IBM or let alone West Eurasians.

Riverman: Like I said, I found the paper's conclusions interesting, but that is what they said, there is morphological continuity between Jebel Irhoud early Homo Sapiens (300K years ago), the Aterian Homo Sapiens (150K years ago) to the Iberomarusians (23K to 11K years ago) down to modern North Africans. Yes, the Marieke van de Loosdrecht et al 2018 paper I linked above documents the Iberomarusians were predominantly West Eurasian harboring about 2/3 of their ancestry from Natufian like source population. The Kefi et al 2016 paper analyzed all 23 ancient Iberomarusians and found all 23 mtdna Haplogroups being either North African or Eurasian. So yes, they are genetically close to West Eurasians.

With respect to being ancestral to anyone, I don't dispute that and agree. But there are review papers out there talking of multi-regionalism in Africa going back 4 or so years now.

Scerri et al 2019 (Abstract Only) talks of this

https://www.nature.com/articles/s41559-019-0992-1

Scerri et al 2019 is a comment, but a 2018 paper, which I have linked is proposing a more multiregional view in Africa as well

Scerri et al 2018 "Did Our Species Evolve in Subdivided Populations across Africa, and Why Does It Matter?"


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6092560/

So my take, the notion that a single source population from East Africa, which was the old model, is being questioned. Morphological discontinuity does not mean there is no genetic continuity. So the Bergmann et al 2022 paper that seems to be saying the Morphology of the early South African Homo Sapiens is to varied to be in continuity with modern humans does not mean that the early South African Homo Sapiens are ancestral genetically to some or all of modern humans at some level. I would think we agree that modern humans are not in morphological continuity with Neanderthals and Denisovans but there is some genetic continuity with those ancient Humans.

"While early H. sapiens from South Africa display a rather large variation22,23, the Jebel Irhoud and Aterian humans share a robust craniofacial/mandibular morphology with late Early/Middle Pleistocene hominins from North Africa24–26, in particular a small number of archaic features. Broad braincases and faces with well defined superstructures in the Jebel Irhoud, Contrebandiers and Dar-es-Soltane II 5 crania were reported as intermediate Figure 1. Kébibat and Aterian mandibular specimens between preceding (Tighenif, Kébibat) and subsequent groups (Iberomau-rusians)2"

So I think this paper is suggesting, maybe not directly, that the morphological continuity between Jebel Irhoud to Iberomarusians to Modern North Africans, suggest also that the notion that Jebel Irhoud was a genetic dead end might not be accurate (it still might be). For example, the Mounier and Lahr 2019 paper suggested that Jebel Irhoud type homo Sapiens were absorbed into the Southern European Neanderthal populations (likely in Iberia) with no genetic impact on modern humans. They said only the early South African and East African early Homo Sapiens did. I think this paper is questioning that narrative and is more in line with what Scerri et al 2018 and 2019 were proposing.

Again, nothing here I am saying is being stated with dogmatic certainty, but just looking at plausible scenarios.

Cheers, PT

[Palermo Trapani]

Riverman: The Aterian sites in North Africa date to around 150K years ago up to about 20K years ago, so no full genome DNA has been done, only Anthropological analysis best I can tell. It would be great to get DNA from earlier Aterian Fossils say from the same time frame as Upper Paleolithic Europeans (i.e Oase1, Kostinki14, the recent ones from Bulgaria, etc). Same time, those early Levant Homo Sapiens like Skhul and Qafzeh.

Maybe the Mods think this paper deserves its own thread. The Bergmann et al 2022 paper is making some interesting conclusions, as you state (my conclusions are more suggestions/questions based on the article). Again from the paper's abstract and I quote.

"The evidence we lay out for a long-term succession of hominins and humans emphasizes North Africa’s role as source area of the earliest H. sapiens."

[Riverman]

Riverman: The Aterian sites in North Africa date to around 150K years ago up to about 20K years ago, so no full genome DNA has been done, only Anthropological analysis best I can tell.

I know, but they are anatomically not closer to later IBM than let's say Paleolithic Europeans, not at all.

And we know from genetics that the IBM were much closer to West Eurasians and had significant West Eurasian direct ancestry.

[Palermo Trapani]

I know, but they are anatomically not closer to later IBM than let's say Paleolithic Europeans, not at all.

And we know from genetics that the IBM were much closer to West Eurasians and had significant West Eurasian direct ancestry.

Yes, I don't dispute the Ibermarusians were genetically close to West Eurasians. I cited 2 papers that clearly documented that fact and I am not disputing that fact.

And yes, you are correct, the Aterians are intermediate between Jebel Irhoud an, Iberomaurusians and Upper Paleolithic Europeans (latter 2 cluster together Morphologically) From the paper " Aterian remains have been described as less archaic than the earliest currently known H. sapiens from Jebel Irhoud, but not as modern as Iberomaurusian or European Upper Paleolithic groups." Although they do resemble them as the authors put it and are in terms of morphology, part of the link from Jebel Irhoud to Natufians, Iberomarusians, Upper Paleolithic Europeans, etc.

[Riverman]

Yes, I don't dispute the Ibermarusians were genetically close to West Eurasians. I cited 2 papers that clearly documented that fact and I am not disputing that fact.

And yes, you are correct, the Aterians are intermediate between Jebel Irhoud an, Iberomaurusians and Upper Paleolithic Europeans (latter 2 cluster together Morphologically) From the paper " Aterian remains have been described as less archaic than the earliest currently known H. sapiens from Jebel Irhoud, but not as modern as Iberomaurusian or European Upper Paleolithic groups." Although they do resemble them as the authors put it and are in terms of morphology, part of the link from Jebel Irhoud to Natufians, Iberomarusians, Upper Paleolithic Europeans, etc.

They have no intermediate position, but are just somewhat closer to Paleolithic Europeans. However, that doesn't mean they were the link, or there were no more modern, closer to UP Europeans and IBM, human beings around at the time of the Ateriens. Rather it just means they are somewhere close to some sort of transitional group which existed at some point in time. It doesn't prove they are the actual link. To prove that, there would be no other options - but there are, from the Near East for example, and we would need genetic evidence of some sort - even if its just a general ancient protein similarity.

[Palermo Trapani]

They have no intermediate position, but are just somewhat closer to Paleolithic Europeans. However, that doesn't mean they were the link, or there were no more modern, closer to UP Europeans and IBM, human beings around at the time of the Ateriens. Rather it just means they are somewhere close to some sort of transitional group which existed at some point in time. It doesn't prove they are the actual link. To prove that, there would be no other options - but there are, from the Near East for example, and we would need genetic evidence of some sort - even if its just a general ancient protein similarity.

Riverman: Maybe I am not being clear, the link being talked about in the paper is a morphological link. That is the one the authors are stating based on their analysis of the fossils. I agree, to establish a clear genetic link, there would have to be DNA from Jebel Irhoud to the Aterian fossils (Early to late ones), along with the Levant early Homo Sapiens (i.e. Qafzeh from 100K years ago) and then compare them to the Iberomarusians and Natufians.

Still I think the paper is making some interesting conclusions and again, I am going by what the authors are stating.

"Even though we have no proof of an in-situ population succession, Aterian morphology fts the human fossil gap between Jebel Figure 7. Superimpositions in Procrustes space of the original Irhoud 11 (pink), Tomas I Gh10717 (white), Dar-es-Soltane II 5 (green), El Harhoura (violet), Taforalt XVIII (turquoise), and a reconstructed version of Irhoud 11 (pink transparent). Irhoud 11 and Iberomaurusians, suggesting a greater time depth for regional continuity in Northern Africa than previously established"

[LIONFARM]

I sent a message to a geneticist about if E1B1* MOTA was actually NOT African BUT LEVANTINE !

This is his response highlight as follows...
2:33:00 (we spoke directly to him)
On Sun, May 22, 2022, 11:21 PM Peter Revesz wrote:
Hello Lion,

"You're RIGHT that it is NOT TRULY AFRICAN. However, not including it would have looked like we deliberately try to avoid any link with Africa. Therefore, our approach was to include as many samples as possible from all Old World cultures and worry about them more only if necessary, that is, they show a significant connection to the Minoans. If they do not, then nothing more needs to be said about them."

Best,
Peter Revesz