Basal Eurasians and Ancient North African explained with G25

[grabielx]

The concept of basal arise from the fact that some populations (mostly from the ancient middle east but also from India) appear to be closer to some African (but not all) compared to other non-Africans. A remnant population from before the split between SSA and Eurasians that got isolated in the middle east or North Africa and then admixed into crown Eurasians in the Upper Paleolithic could explain this phenomena.

Target: Levant_Natufian
Distance: 14.1443% / 0.14144347
40.4 WHG
32.2 Basal_TUR_Barcin_N_-56%_WHG
16.8 ANA_(simulated)
10.2 IRN_Ganj_Dareh_N
0.4 BRA_LapaDoSanto_9600BP

Target: TUR_Pinarbasi_HG
Distance: 3.5778% / 0.03577848
58.6 WHG
40.2 Basal_TUR_Barcin_N_-56%_WHG
0.8 Han
0.4 ANA_(simulated)


The concept of Ancient North African arise from the fact that ancient Moroccan (Taforalt) appears to be connected with SSA (genetically closer than Eurasians), but which way is the gene-flow is not clear. ANA would be a shared component, that is neither true SSA (South-African bushmen) nor crown Eurasian (Ust-ishim\Oase like).

Target: MAR_Taforalt
Distance: 1.8109% / 0.01810908
50.4 ANA_(simulated)
29.4 WHG
20.2 Basal_TUR_Barcin_N_-56%_WHG


Target: Yoruba
Distance: 39.0333% / 0.39033328
57.6 ZAF_2100BP (Ancient South African)
32.8 ANA_(simulated)
9.6 Basal_TUR_Barcin_N_-56%_WHG

According to these model Mota-like and HoA Africans could share both ANA, Basal and Crown Eurasian.

Target: KEN_Early_Pastoral_N
Distance: 19.7252% / 0.19725242
42.8 RUS_Ust_Ishim (Out of Africa)
20.0 ANA_(simulated)
19.0 ZAF_2100BP (Ancient South African)
18.2 Basal_TUR_Barcin_N_-56%_WHG


Some visualizations.
https://i.imgur.com/GzcW7B7.png
https://i.imgur.com/3xmgcgt.png
https://i.imgur.com/JuMFMtP.png
https://i.imgur.com/z4y2geH.png
https://i.imgur.com/63e7ncr.png



Ancient_North_African,-0.493537,-0.003656,-0.078366,-0.088502,-0.015511,-0.07028,-0.135319,0.034983,0.263345,-0.072639,0.035823,-0.072805,0.170841,-0.093308,0.184471,-0.068894,-0.033665,-0.129425,-0.292878,0.079238,-0.061516,-0.254403,0.149475,-0.018244,0.038534
Basal_Eurasian,0.108644,0.261368909,-0.227160545,-0.470805091,-0.0808105,-0.169071318,-0.026654727,-0.063189091,-0.0310245,0.160902773,0.037648364,0.047123773,-0.073550318,0.004919318,-0.163295409,-0.097243045,0.046586136,-0.016285182,0.042964182,-0.092906227,-0.152549227,-0.001123591,0.053765273,0.197543545,-0.031514136
SSA,-0.639686,0.058901,0.025644,0.041344,-0.00277,-0.002789,0.267912,-0.20653,0.011658,0.016766,0.002761,-0.06744,-0.01888,0.005092,0.026058,-0.013392,0.031944,0.289737,-0.092137,0.003752,-0.035188,-0.000495,0.002835,-0.000843,-0.00934
Crown_Eurasian,-0.050082,-0.11577,-0.090886,0.073644,0.027082,-0.018128,-0.00376,-0.004384,0.0452,0.010387,0.006008,-0.001798,0.000149,-0.003991,0.004614,-0.001724,-0.004955,0.004687,-0.005154,0.015382,0.006613,0.008532,-0.007641,-0.014942,0.007784
Oceania,-0.034716,-0.2620065,-0.19912,0.2094665,0.1641845,-0.340247,-0.0019975,0.0077305,-0.0197365,-0.0119365,0.002192,0.0048705,0.0038655,-0.00695,-0.0054285,0.000265,0.0015645,0.0015205,0.000503,0. 0010005,-0.0026205,-0.005317,-0.002403,-0.011387,-0.0154475


PS: G25 is not the right tool for this kind of analysis, and these models are highly incomplete and the relationship between Africa and Eurasians are likely very complex.

[grabielx]

I've done a lot of (probably far-fetched and pointless) experiments. Got a fancy calculator out of this, a very deep ancestry calc with basal, ANA + a simulated African ghost population. Imo, there were 5 main human groups in the OOA period: ANA,Basal,South Africa,West Africa and the main Eurasian. ANA and Basal have nothing to do with each other, they just happen to came together in Natufians and Taforalt. Basal is maybe the least African component, it just doesn't have Neanderthal. ANA, South and West Africa are all African lineages, mixed a lot in today's Africa, but they are not that related to each other really. I think that there are other clines in Africa too, like Biaka, Mbuti have they own drift, and Mota and Horn of Africa don't fit well in this picture, so it's complicated. My simulated Neo_African component could also have significant admixture for an Archaic source. Also what I believe that basically ancient middle eastern and also ancient South Asians\Indians had some form of ANA admixture, that maybe wasn't really ANA but something like it. Also some if not all Africans have some kind of back-migration signal mostly from a population similar to modern Jarawas, Onge populations, that could explain the D-E problem. Also some Africans have west Eurasian, think about the R1b in Africa, so we see that signal too. It's pretty obvious why and how they got it, it's post neolithic, some ancient samples didn't have it.



ANA_(Ancient_North_West_African)_(Taforalt_Barcin) ,-0.493537,-0.003656,-0.078366,-0.088502,-0.015511,-0.07028,-0.135319,0.034983,0.263345,-0.072639,0.035823,-0.072805,0.170841,-0.093308,0.184471,-0.068894,-0.033665,-0.129425,-0.292878,0.079238,-0.061516,-0.254403,0.149475,-0.018244,0.038534
Basal_Eurasian(Pinarbasi_Crown_WHG),0.108644,0.261 368909,-0.227160545,-0.470805091,-0.0808105,-0.169071318,-0.026654727,-0.063189091,-0.0310245,0.160902773,0.037648364,0.047123773,-0.073550318,0.004919318,-0.163295409,-0.097243045,0.046586136,-0.016285182,0.042964182,-0.092906227,-0.152549227,-0.001123591,0.053765273,0.197543545,-0.031514136
Main_Out_Of_Africa(+Neanderthal+Altai_Archaic?_RUS _Ust_Ishim),-0.050082,-0.11577,-0.090886,0.073644,0.027082,-0.018128,-0.00376,-0.004384,0.0452,0.010387,0.006008,-0.001798,0.000149,-0.003991,0.004614,-0.001724,-0.004955,0.004687,-0.005154,0.015382,0.006613,0.008532,-0.007641,-0.014942,0.007784
Paleo_African(Lateral_Click:Ju_hoan_North:B_Ju_hoa n_North-4),-0.619198,0.062963,0.023759,0.027455,0.000615,-0.002789,0.274022,-0.217376,0.022089,0.010387,0.007795,-0.08977,-0.034043,0.016652,0.03393,-0.045346,0.066365,0.58036,-0.194958,0.010005,-0.077738,-0.005564,0.025512,-0.000482,0.003353
Oceania_Cline(+Archaic_Denisovan:VUT_2500BP),-0.034716,-0.2620065,-0.19912,0.2094665,0.1641845,-0.340247,-0.0019975,0.0077305,-0.0197365,-0.0119365,0.002192,0.0048705,0.0038655,-0.00695,-0.0054285,0.000265,0.0015645,0.0015205,0.000503,0. 0010005,-0.0026205,-0.005317,-0.002403,-0.011387,-0.0154475
Neo_African(+Archaic?),-0.647824,0.069107,0.025286,0.008156,-0.008971,0.033202,-0.337182,0.292015,-0.12612,0.062161,0.013275,0.069433,0.072227,-0.002133,-0.003692,0.01314,-0.032661,-0.40363,0.148537,-0.010943,0.056382,0.007734,-0.014069,0.00397,-0.004754
West_Eurasian(Crown?_RUS_Kostenki14),0.035285,0.01 5233,-0.010182,0.063954,0.017849,-0.00251,-0.004465,-0.007846,0.032519,0.007654,0.006658,-0.005545,0.004014,-0.016239,0.013436,0.024794,0.01004,-0.003421,-0.00729,0.015132,0.020713,0.000371,-0.005916,-0.051212,-0.004071
East_Eurasian(Crown2?_CHN_Tianyuan),-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
Beringian_Drift(USA_WA_Kennewick),0.046667,-0.307705,0.109742,0.08721,-0.100634,-0.019801,-0.220675,-0.261681,-0.01268,-0.017677,0.001949,0.000599,0.001784,0.012524,-0.010043,0.010209,0.007302,0.005701,0.01345,0.0050 02,0.000499,-0.008532,-0.002342,0.001566,-0.001676

[Petalpusher]

I've done a lot of (probably far-fetched and pointless) experiments. Got a fancy calculator out of this, a very deep ancestry calc with basal, ANA + a simulated African ghost population. Imo, there were 5 main human groups in the OOA period: ANA,Basal,South Africa,West Africa and the main Eurasian. ANA and Basal have nothing to do with each other, they just happen to came together in Natufians and Taforalt. Basal is maybe the least African component, it just doesn't have Neanderthal.

This is the current most likely hypothesis, no/less Neanderthal/Denisovans in the early split between basal Eurasian and main Eurasians. Some papers have tried to substract the SSA of Mota as well but didn't came back with convincing results.

Still stuck around these estimations

https://1.bp.blogspot.com/-He8KH5HoUL4/V2SipopvDiI/AAAAAAAAFBY/KiqCB6AK6NIjQXFVoQ18ADphFo2N-PzjQCKgB/s1600/BE.png

[MechtoidAfalouHG]

The ancestral North African component is deeper than basal so it split off from the rest inside Africa most likely(probably around Egypt). Gene flow of this component was west to east (North Africa to levant). Before this migration of ANA rich and haplo E rich North Africans into the levant, the Levant was basically mostly basal and very closely related to Dzuzuana.

[Hamilcar]

I've done a lot of (probably far-fetched and pointless) experiments. Got a fancy calculator out of this, a very deep ancestry calc with basal, ANA + a simulated African ghost population. Imo, there were 5 main human groups in the OOA period: ANA,Basal,South Africa,West Africa and the main Eurasian. ANA and Basal have nothing to do with each other, they just happen to came together in Natufians and Taforalt. Basal is maybe the least African component, it just doesn't have Neanderthal. ANA, South and West Africa are all African lineages, mixed a lot in today's Africa, but they are not that related to each other really. I think that there are other clines in Africa too, like Biaka, Mbuti have they own drift, and Mota and Horn of Africa don't fit well in this picture, so it's complicated. My simulated Neo_African component could also have significant admixture for an Archaic source. Also what I believe that basically ancient middle eastern and also ancient South Asians\Indians had some form of ANA admixture, that maybe wasn't really ANA but something like it. Also some if not all Africans have some kind of back-migration signal mostly from a population similar to modern Jarawas, Onge populations, that could explain the D-E problem. Also some Africans have west Eurasian, think about the R1b in Africa, so we see that signal too. It's pretty obvious why and how they got it, it's post neolithic, some ancient samples didn't have it.

What's your opinion on this then ? :


Definitely, the Iberomaurusian specimens are the ones bearing a very high level of basal Eurasian lineage, which could have been contributed by the sub-Saharan African input added by the southwest Asian founder group, which moved to North Africa 20 ka bearing a high basal Eurasian component. It is interesting that the current-day southwest Asian populations that show more genetic sharing with Iberomaurusians are the east AP populations. We tried to disentangle between an ancient link and a bias due to recent sub-Saharan input in this signature by performing the haplotype-based clustering, and confirmed a still high proportion of the basal Eurasian lineage/Iberomaurusian founding effect in clusters D (east AP and Iran) and F (west AP). Probably, the Iberomaurusian specimens are currently the best proxy for the basal Eurasian population group.

https://www.biorxiv.org/content/10.1101/2021.02.24.432678v1.full


Also can modern khoisans be modeled with this simulated ANA ? There is some elements that pushed many to believe ANA/aterians are ancestors of khoisans.

[MechtoidAfalouHG]

What's your opinion on this then ? :


https://www.biorxiv.org/content/10.1101/2021.02.24.432678v1.full


Also can modern khoisans be modeled with this simulated ANA ? There is some elements that pushed many to believe ANA/aterians are ancestors of khoisans.


Don’t Yoruba have more genetic relation to ANA than Khoisan?

[grabielx]

The ancestral North African component is deeper than basal so it split off from the rest inside Africa most likely(probably around Egypt). Gene flow of this component was west to east (North Africa to levant). Before this migration of ANA rich and haplo E rich North Africans into the levant, the Levant was basically mostly basal and very closely related to Dzuzuana.

I mostly agree, I just think that DE has nothing to do with Basal or ANA directly. It's too hard to explain how DE end up in South-East Asia. It was probably a OOA y-dna lost early on in most Eurasians. Then it had more success in ANA and Basal compared to OOA. The problem is also that Basal in many models appears to be very non-African, Africans don't have Basal but rather Onge or Ust-Ishim. I think that DE is solidly Eurasian.

[Hamilcar]

Don’t Yoruba have more genetic relation to ANA than Khoisan?

I don't know that's why I'm asking if he can model them with it

[grabielx]

What's your opinion on this then ? :


https://www.biorxiv.org/content/10.1101/2021.02.24.432678v1.full


Also can modern khoisans be modeled with this simulated ANA ? There is some elements that pushed many to believe ANA/aterians are ancestors of khoisans.

First point you make:
It's possible for sure. But I think they are wrong. Becuase Mesolithic Caucasian Hunter Gatherers and Pinarbasi have massive amount of basal and yet don't have a clear African pull, it's a massive contradiction that it's been adknowledge many times, also that would imply that Ust-Ishim and Onge have some kind of African\Ana pull + maybe a Basal pull. I resolve this issue by separating Basal and ANA. It's only a guess. And works really well with G25 where the basal pull is very non-African. You just subtract Basal from Pinabarsi and you have the least African component in the world, even when it's still connected to West Eurasia. Suggesting that WHG has some minor Basal also. Minor SSA gene flows in the Middle east and Iran via ANA could explain the pull better IMO, rather than imagining a connection between ANA and Basal that is only possible in some samples (Taforalt and Natufian) but not in other (Mesolithic Caucasian Hunter Gatherers and Pinarbasi). Also I have the suspect that some Africans have a signal that is Onge like, it's connected to DE and was present in Mota. But that's far-fetched admittedly.


Second point you make:
There is a massive difference between Khoisans and other Africans, also some Ju-Juhan outliers are even more distant, suggesting that bushmen have some Neo-African admixture. The problem that ANA in g25 appears to be very distant from Khoisan. In some papers Khoisan and ANA were opposite splits. But again, g25 it's not the right tool so it could be an artifact. But Khoisan are not disproportionally distant compared to other Eurasians. That makes me think that there is a deeper component in Africa that defines Yoruba-like groups. That component has some relationship with ANA.

[grabielx]

https://i.imgur.com/l8Kcxl5.png

[grabielx]

I don't know that's why I'm asking if he can model them with it

Target: Yoruba
Distance: 4.5319% / 0.04531883
54.8 Neo_African(+Archaic?)
42.4 Paleo_African(Lateral_Click)(Ju_hoan_North)
1.2 East_Eurasian(Crown2?_CHN_Tianyuan)
0.8 ANA_(Ancient_North_West_African)_(Taforalt_Barcin)
0.8 West_Eurasian(Crown?_RUS_Kostenki14)

If you remove that Neo African component (that was made from Nigerians subtracting ANA and Khoisan), then you see a pull towards Eurasians (best is Onge,Jarawas) rather than Basal. I don't know how to explain this without thinking that Basal didn't back migrate into Africa until the neolithic and Mota.

Target: Yoruba
Distance: 45.2539% / 0.45253929
37.2 ANA_(Ancient_North_West_African)_(Taforalt_Barcin)
33.4 Paleo_African(Lateral_Click
24.8 East_Eurasian(Crown2?_CHN_Tianyuan)
4.6 Basal_Eurasian(Pinarbasi_Crown_WHG)

Target: ETH_4500BP
Distance: 32.4220% / 0.32422047
35.6 Paleo_African(Lateral_Click_Ju_hoan_North
30.2 ANA_(Ancient_North_West_African)_(Taforalt_Barcin)
28.6 Onge
5.6 Basal_Eurasian(Pinarbasi_Crown_WHG)

Even with Barcin N I still see a Eurasians signal indipendent from Basal or Levant (could be Onge - could be West Eurasians -could be East Eurasians - could be Ust-Ishim\OOA related - it could be shared drift IDK - but it's something)

Target: ETH_4500BP
Distance: 20.1058% / 0.20105758
40.0 Paleo_African(Lateral_Click
30.4 Neo_African(+Archaic?)
11.0 Jarawa
9.8 ANA_(Ancient_North_West_African)_(Taforalt_Barcin)
8.2 TUR_Barcin_N
0.6 Beringian_Drift(USA_WA_Kennewick)

[grabielx]

What's your opinion on this then ? :


https://www.biorxiv.org/content/10.1101/2021.02.24.432678v1.full


Also can modern khoisans be modeled with this simulated ANA ? There is some elements that pushed many to believe ANA/aterians are ancestors of khoisans.

https://www.biorxiv.org/content/biorxiv/early/2018/09/20/423079/F2.large.jpg
Also here in the tree from the Dzudzuana paper Yoruba(Neo_African) is in between Khoisan and ANA. So no clear relationship between Khoisan and ANA.

[MechtoidAfalouHG]

https://www.biorxiv.org/content/biorxiv/early/2018/09/20/423079/F2.large.jpg
Also here in the tree from the Dzudzuana paper Yoruba(Neo_African) is in between Khoisan and ANA. So no clear relationship between Khoisan and ANA.

I agree with everything you’re saying but I believe ANA is linked exclusively to Y-DNA E. It just makes sense because all the ancient ANA rich populations, for example Iberomaursians were EXCLUSIVELY haplo E. ANA-like groups spread their ancestry throughout Africa eliminating the native men and their haplogroups. These natives were probably more Khoisan like.

There is even evidence of a massive genocide event around southern Egypt I believe. The conquering people were mechtoid like in phenotype and closely related to the Iberomaursians metrically.

https://www.smithsonianmag.com/science-nature/ancient-brutal-massacre-may-be-earliest-evidence-war-180957884/

The skulls of the killed are very Khoisan like

[grabielx]

I agree with everything you’re saying but I believe ANA is linked exclusively to Y-DNA E. It just makes sense because all the ancient ANA rich populations, for example Iberomaursians were EXCLUSIVELY haplo E. ANA-like groups spread their ancestry throughout Africa eliminating the native men and their haplogroups. These natives were probably more Khoisan like.

There is even evidence of a massive genocide event around southern Egypt I believe. The conquering people were mechtoid like in phenotype and closely related to the Iberomaursians metrically. I need to find the link.

I think that ANA was AB and not DE, I don't disagree that E has something to do with Iberomaurusians though. But Taforalt had also basal and West Eurasians. And Taforalt is not pure ANA either. Also Khoisan-click languages have very little E. So it makes me think that E is not that old in Africa (some 0%).

[Hamilcar]

that's weird because craniometrically the people who predates Iberomaurusians show strong affinities with both bushmen and Taforalt maybe Aterians were not these "ANA" but that seems quite unlikely or maybe it's just similar phenotypes without shared genetics. It would also explain why epicanthic folds are more present among berbers rich in IBM admixture but I'm only speculating here.

[MechtoidAfalouHG]

I think that ANA was AB and not DE, I don't disagree that E has something to do with Iberomaurusians though. But Taforalt had also basal and West Eurasians. And Taforalt is not pure ANA either. Also Khoisan-click languages have very little E. So it makes me think that E is not that old in Africa (some 0%).

If ANA was AB then why is there not a single AB among Iberomaursians? That’s kind of weird because through who would this ANA ancestry survive in Iberomaursians? Iberomaursian mtDNA was Eurasian(U6) which explains their Eurasian admixture but all of their Y-DNA is E. it’s still possible but it doesn’t seem like it would be the case

[grabielx]

If ANA was AB then why is there not a single AB among Iberomaursians? That’s kind of weird because through who would this ANA ancestry survive in Iberomaursians? Iberomaursian mtDNA was Eurasian(U6) which explains their Eurasian admixture but all of their Y-DNA is E. it’s still possible but it doesn’t seem like it would be the case

It's possible. I just can't explain DE in Yomon in Japan for example. What I'm saying that E was ANA or Basal or both. But DE was already in OOA and Eurasian. So I can explain why both ANA and Basal had it, because ANA also had OOA admixture. That's my grand theory. I think it makes sense at least as an alternative explanation. It doesn't make sense that OOA people disappeared in Africa IMO. Also Mota has E but Mota has little to do with ANA. Also DE is far older than OOA. So some population that wasn't African or Eurasian must have had it.

I think that ANA has OOA admixture because of this: Ust_Ishim is much closer to ANA than to Neo_African and Khoisan. (even closer than Basal)

Distance to: Ust_Ishim

0.15067019 East_Eurasian
0.18586655 West_Eurasian
0.42490102 Oceania_Cline
0.47150757 Beringian_Drift
0.52387718 ETH_4500BP
0.77365229 ANA_(Ancient_North_West_African)_(Taforalt_Barcin)
0.82978748 Basal_Eurasian(Pinarbasi_Crown_WHG)
0.92179242 Neo_African(+Archaic?)
0.94254740 Paleo_African_Ju_hoan_North

[MechtoidAfalouHG]

It's possible. I just can't explain DE in Yomon in Japan for example. What I'm saying that E was ANA or Basal or both. But DE was already in OOA and Eurasian. So I can explain why both ANA and Basal had it, because ANA also had OOA admixture. That's my grand theory. I think it makes sense at least as an alternative explanation. It doesn't make sense that OOA people disappeared in Africa IMO. Also Mota has E but Mota has little to do with ANA. Also DE is far older than OOA. So some population that wasn't African or Eurasian must have had it.

I think that ANA has OOA admixture because of this: Ust_Ishim is much closer to ANA than to Neo_African and Khoisan. (even closer than Basal)

Distance to: Ust_Ishim

0.15067019 East_Eurasian
0.18586655 West_Eurasian
0.42490102 Oceania_Cline
0.47150757 Beringian_Drift
0.52387718 ETH_4500BP
0.77365229 ANA_(Ancient_North_West_African)_(Taforalt_Barcin)
0.82978748 Basal_Eurasian(Pinarbasi_Crown_WHG)
0.92179242 Neo_African(+Archaic?)
0.94254740 Paleo_African_Ju_hoan_North

“2003 study by Weale et al., of the DNA of over 8,000 males worldwide, found that five out of 1,247 Nigerian males belonged to DE*“

I think it’s safe to say that DE both left Africa and stayed in Africa.

Ust Ishim is closer to ANA not because of admixture but because ANA is simply closer to Ust Ishim than to other African groups. Just because ANA stayed in Africa doesn’t mean it is closely related to other African groups. It has enough genetic drift to be a group all on its own. If that makes sense.