Scientists discover genomic ancestry of Stone Age North Africans from Morocco

[bicicleur 2]

What do you think of this opinion from Maciamo https://www.eupedia.com/genetics/funnelbeaker_culture.shtml



There are some outdated concepts but intriguing none the less.

the oldest megalithic structures are in mesolithic Algarve, southern Portugal
view its location, some SSA admixture is possible
but note that early Funnelbeaker was not megalithic, all megalithic structures are late Funnelbeaker

 

[Angela]

I wanted to know whether the Levant PPNB also lacked SSA.

I'm not familiar with Treemix, but this is what Davidski commented in Eurogenes :

One of the biggest surprises in the new Lazaridis et al. preprint is that the Natufians don't show any Sub-Saharan African admixture when poked and prodded directly with formal statistics. However, TreeMix, which runs on formal statistics, doesn't have much trouble finding Sub-Saharan or related ancestry in both the Natufians and Neolithic farmers from the Levant. So what's going on?

see : http://eurogenes.blogspot.be/2016/06/the-natufian-puzzle.html

Also have a look at this, I think it is interesting :

Natufian, Levant N and Iran N cluster together, but they are not at the extreme right of Eurasians.
And what about Mota? It looks like some intermediate position to me.
All older African samples are at the right hand side of the line Yoruba - South Africa, even the old Malawi 8-6.1 ka.

I still haven't totally gone over the supplement, but do you (or anyone else) remember the strange news that anancient sample had been found in North Africa that was part Eurasian and part South African?

Doesn't it remind you of this? This would have been San, Bushmen, Khoisan type people carrying A and B. Their y lines would have been wiped out when Natufian like people arrived from the east.

It doesn't speak to the emergence of E-M78, however.

I still think it's possible it emerged in Egypt somewhere, as was often speculated, and then moved in two directions.

It doesn't answer the question of why formal stats don't find "African" in Natufians.

I wonder if using different "Africans" for the modeling would change things, i.e. San?

As time goes on, there is a bit of SSA showing up in the Levant, and I think that's because of continuing movement north from the Nile area. It wasn't always about movement from the Levant south, although that was by far the more important and substantial, imo.

 

[bicicleur 2]

I haven't heard yet about that part South African, part Eurasian North African individual.
But I agree with you. Probably most DNA radiated out of the Levant into Africa, but sometimes some DNA must have come the other way.
There is even some Y-DNA that seems to have come out of Africa after LGM but in precolonial times :
https://www.yfull.com/tree/A-M13/
https://www.yfull.com/tree/A-Y37658/

Eurasia
Haplogroup A has been observed as A1 in European men in England. As A3b2, it has been observed with low frequency in Asia Minor, the Middle East, and some Mediterranean islands, among Aegean Turks, Sardinians, Palestinians, Jordanians, Yemenites, and Omanis. Without testing for any subclade, haplogroup A has been observed in a sample of Greeks from Mitilini on the Aegean island of Lesvos[26] and in samples of Portuguese from southern Portugal, central Portugal, and Madeira.[27] The authors of one study have reported finding what appears to be haplogroup A in 3.1% (2/65) of a sample of Cypriots,[28] though they have not definitively excluded the possibility that either of these individuals may belong to haplogroup B or haplogroup C.

 

[Angela]

Finally...

It hasn't been published yet I guess. This was from a list of papers to be presented. The lead authors are from Uppala, which is where I think Pontus Skogland came from. Their latest published work is:
https://www.biorxiv.org/content/early/2017/07/17/164400

They may have been wrong in thinking it was a result of the slave trade. Fascinating if some of these people were still around in Medieval times. That may be a long shot, though.

The genomic enigma of two Medieval North Africans

Torsten Günther, Cristina Valdiosera, Juan Carlos Vera-Rodríguez, Ricardo Rodriguez-Varela, Emma Svensson, Rafael M Martínez Sánchez, Rafael Carmona Ávila, Leonor Peña Chocarro, Guillem Pérez Jordà, Youssef Bokbot, Eneko Iriarte, Colin Smith, Mattias Jakobsson

The trans-Saharan gold and salt trade as well as the trans-Saharan slave trade played an important role in population movements connecting sub-Saharan and Mediterranean economies during the Middle Ages. The slave trade alone is said to have transported more than 9 million slave soldiers and domestic servants along the trans-Saharan route. In this study, we present the genomic analysis of two human individuals from a cave site in the area of present-day Morocco which were directly dated to the Medieval period. The samples were processed in a designated ancient DNA lab and the genomic data obtained shows standard patterns of authentic ancient DNA with low levels of contamination. Both individuals – which represent the first ancient genome sequence data from North Africa – do not exhibit particular genetic affinities to modern North Africans or any other present-day population in published genotype data sets despite relatively extensive data has been produced from many areas of Africa. In fact, the most parsimonious way to model them genetically is as two-source admixture between Mediterranean Europeans and Southern Africans. The lack of archaeological context of the two individuals opens up various alternatives to explain their genomic pattern. Both individuals could represent a Medieval African population without population continuity to modern-day populations. Alternatively, both Mediterranean Europe and Southern Africa are known source regions in the Arab slave trade, thus they could potentially represent the offspring of slaves of different origin. The Arab slave trade extended over a longer period and may have involved more slaves than its transatlantic counterpart and our data might provide the first genetic insight into this historical process and the people who suffered in it. Our results highlight how archaeogenetic research can shed lights into historical events and long-distance population movements while opening new questions for the interpretation of the data.

 

[bicicleur 2]

as for lack of SSA in Natufians : it is lack of Yoruba, Mbuti or Ju hoan North

yet the new paper says the SSA in Tarofalt matches neither of the present SSA populations, it is a mixture of Hadza and West African that no longer exists

could that be why Laziridis didn't uncover any SSA ?

 

[Angela]

as for lack of SSA in Natufians : it is lack of Yoruba, Mbuti or Ju hoan North

yet the new paper says the SSA in Tarofalt matches neither of the present SSA populations, it is a mixture of Hadza and West African that no longer exists

Yes, it's why I suggested perhaps it would show up if they used another kind of African sample in the modeling.

However, you'd think if it's at least part West African like it would appear.

Here we go again: we need more ancient dna from Africa.

 

[bicicleur 2]

Finally...
It hasn't been published yet I guess. This was from a list of papers to be presented. The lead authors are from Uppala, which is where I think Pontus Skogland came from. Their latest published work is:
https://www.biorxiv.org/content/early/2017/07/17/164400
They may have been wrong in thinking it was a result of the slave trade. Fascinating if some of these people were still around in Medieval times. That may be a long shot, though.
The genomic enigma of two Medieval North Africans
Torsten Günther, Cristina Valdiosera, Juan Carlos Vera-Rodríguez, Ricardo Rodriguez-Varela, Emma Svensson, Rafael M Martínez Sánchez, Rafael Carmona Ávila, Leonor Peña Chocarro, Guillem Pérez Jordà, Youssef Bokbot, Eneko Iriarte, Colin Smith, Mattias Jakobsson
The trans-Saharan gold and salt trade as well as the trans-Saharan slave trade played an important role in population movements connecting sub-Saharan and Mediterranean economies during the Middle Ages. The slave trade alone is said to have transported more than 9 million slave soldiers and domestic servants along the trans-Saharan route. In this study, we present the genomic analysis of two human individuals from a cave site in the area of present-day Morocco which were directly dated to the Medieval period. The samples were processed in a designated ancient DNA lab and the genomic data obtained shows standard patterns of authentic ancient DNA with low levels of contamination. Both individuals – which represent the first ancient genome sequence data from North Africa – do not exhibit particular genetic affinities to modern North Africans or any other present-day population in published genotype data sets despite relatively extensive data has been produced from many areas of Africa. In fact, the most parsimonious way to model them genetically is as two-source admixture between Mediterranean Europeans and Southern Africans. The lack of archaeological context of the two individuals opens up various alternatives to explain their genomic pattern. Both individuals could represent a Medieval African population without population continuity to modern-day populations. Alternatively, both Mediterranean Europe and Southern Africa are known source regions in the Arab slave trade, thus they could potentially represent the offspring of slaves of different origin. The Arab slave trade extended over a longer period and may have involved more slaves than its transatlantic counterpart and our data might provide the first genetic insight into this historical process and the people who suffered in it. Our results highlight how archaeogenetic research can shed lights into historical events and long-distance population movements while opening new questions for the interpretation of the data.

I've recently seen a documentary on the salt and gold trade route. The guide was a Morrocan woman whose grandparents were still slaves in Morroco.
Slavery in Northern Africa has been abolished very recently.
The trade route isn't open any more either. To many conflicts in the Western Sahara. And Timboctoe, it has been pillaged by Fundamentalist Muslims.
If it was like that in Medieval times, I can imagine many ethnicities going extinct.

 

[bicicleur 2]

Yes, it's why I suggested perhaps it would show up if they used another kind of African sample in the modeling.

However, you'd think if it's at least part West African like it would appear.

Here we go again: we need more ancient dna from Africa.

I think the Yoruba is holocene in origin, maybe it still didn't exist 14.5 ka, the date of the Tarofalt samples.

 

[Angela]

I've recently seen a documentary on the salt and gold trade route. The guide was a Morrocan woman whose grandparents were still slaves in Morroco.
Slavery in Northern Africa has been abolished very recently.
The trade route isn't open any more either. To many conflicts in the Western Sahara. And Timboctoe, it has been pillaged by Fundamentalist Muslims.
If it was like that in Medieval times, I can imagine many ethnicities going extinct.

These are all facts which Arab/Muslim apologists in the west conveniently forget. Not that anyone should be held liable for atrocities committed in the distant past by their ancestors, but slavery still exists today in the Muslim world. It's the elephant in the room which people won't discuss.

Yes, indeed, I can imagine that they might have existed in pockets and been decimated in the Middle Ages.

 

[bicicleur 2]

testing SSA in Tarofalt, supplements S6 :

We also calculated f3(Ust’-Ishim; Taforalt, X) to explore the affinity of Taforalt with African
403 populations. Ust’-Ishim is an Upper Paleolithic Siberian individual, dated to 45,000 years before
404 present (yBP), whose ancestry is symmetrically related to prehistoric European hunter-gatherers
405 and present-day East Asians (77). In this case, North African populations, such as Saharawi and
406 Mozabite, show the highest frequencies of allele sharing with Taforalt, suggesting similarity in
407 their genetic profiles (Fig. S14). This matches well with their close positions in the PCA plot
11
408 (Fig. 2A). Following this, West African populations show high outgroup-f3 values (Fig. S14). We
409 found strong evidence visualizing the sub-Saharan African affinity of Taforalt by comparing this
410 outgroup-f3 with that of Natufian: f3(Ust’-Ishim; Natufian, X) (Fig. S15). While Eurasian
411 populations tightly fall on a line, all African populations clearly deviate from this line. This
412 suggests that sub-Saharan Africans, most notably West Africans, share ancestry with Taforalt
413 beyond what can be explained by their Natufian-like ancestry.
414
415 Next, we formally tested if the Taforalt individuals have sub-Saharan African ancestry by
416 calculating f4(Chimpanzee, X; Natufian, Taforalt). As expected, we observed significant positive
417 f4 values for all sub-Saharan Africans and significant negative values for all Eurasian populations
418 (Fig. S16). A reduced level of Neanderthal ancestry cannot be the sole explanation for this,
419 because we find that f4(Chimpanzee, Altai Neanderthal; Natufian, Taforalt) is non-significant and
420 positive (Z = -1.089 SE). Our results clearly support a dual ancestry of our Taforalt individuals,
421 genetically related to both early Holocene Near Easterners and present-day sub-Saharan Africans.
422
423 Finally, we tried to detect additional signatures of admixture between the Eurasian and sub424
Saharan African gene pools, using f3 statistics with Taforalt as the target and a linkage
425 disequilibrium (LD) decay-based method implemented in the ALDER v1.3 program (78). We
426 could not find any Eurasian and sub-Saharan African population pairs with negative f3(Taforalt;
427 Eurasian, sub-Saharan African), suggesting a strong post-admixture genetic drift in our Taforalt
428 individuals (Z > 44.320 SE). Neither could we detect a decay of admixture LD in our Taforalt
429 individuals, suggesting that the admixture may not be a recent event (Fig. S17).

If I understand well, it means that Tarofalt has more SSA and less Eurasian then Natufian, while Laziridis says Natufian has no more Yoruba, Mbuti or Ju hoan North than any other Eurasian anciant population.

 

[bicicleur 2]

Neanderthal ancestry in Tarafalt and Basal Eurasian :
471 Considering the dual ancestry of the Taforalt individuals, we can explain the Altai affinity in
472 Taforalt as a dilution of its Natufian-related ancestry with its significant proportion (~36.5%) of
473 sub-Saharan African ancestry. Interestingly, the Neanderthal ancestry in Taforalt is higher than in
474 early Neolithic Iran (Iran_N, f4 = 0.000628, Z = 1.934). We can therefore deduce that the Taforalt
475 individuals are not genetically closer to the hypothetical Basal Eurasian population than the early
476 Holocene populations from Iran.

so some Neanderthal imported through the Levant, and Northern Africa is not the source of Basal Eurasian

 

[Angela]

I agree that Basal Eurasian wasn't hiding in North Africa.

I've been thinking about it, though, and going through the Supplement, and I think the movement had to be from east to west. There's too much West African like admixture in these people for it to just disappear in the Natufians as it would have to do if the movement was from west to east.

E-M78 might have specifically formed somewhere near Egypt, or more likely it happened in Arabia or the Levant. In fact, I think all of E-M35 might be a back migration from Eurasia to Africa.

I think the increase in "African" alleles progressively in Arabia and the Levant is most likely female mediated. Look at the percentages in Arabia, for example, but it's almost all J1. I think it was the same in antiquity.

Men think if they keep other men away they'll insure the "purity" of their people, but their "people" are often changed by the women with whom they mate.

 

[bicicleur 2]

I think before LGM, the Nile valley was populated by Hap E, and E-M35 was in the Nile delta. Their subsistence was quite diverse, with meat, fish and plant food (Khormusan industry).
During LGM they got microlith technology, probably also bow and arrow, Basal Eurasian and mtDNA U6 and M1, all from Hap H2 in the Levant. They didn't get SSA, as the whole Nilevalley was Hap E. With their new technology, from the Nile delta they radiated into the Levant (Natufian), along the North African coast (Iberomaurisian) and upstream the Nile (Halfan and later Qadan), and maybe Berber (E-M81) stayed in the Nile delta for a while (maybe they were Capsian industry which appeared ca 12 ka).

I checked the Y-calls for Tarofalt from Genetiker. https://genetiker.wordpress.com/2018/03/18/y-snp-calls-from-the-iberomaurusian-culture/
I estimate TAF009 split from the main E-M78 branch ca 18.5 ka, and TAF010-015 split from the M78 branch ca 15 - 15.1 ka.
TAF010-015 are dated ca 14.55 ka, so they split from M78 some 500 years before their burial in the Grotte des Pigeons.
My guess is they arrived from the east, maybe Tamar Hat or Haua Fteah in Cyrenaica after their split from E-M78, without SSA, and they got SSA maybe in Tarofalt.
Then there would have been a backmigration of the main E-M78 branch from Tamar Hat or Haua Fteah to the Levant, before the TMRCA of E-M78 which is 13.4 ka.

I realise this is a rather complicated story, but it is still the simplest story I can figure out.
So I intend to stick to that story till new elements appear.

As for the Nile Valley and the Nile delta it got filled up with thick layers of sediment (50 meters and more) between LGM and the youngest dryas.
It will be hard to find anything there, but Qadan culture was found in the adjacent wadis.

 

[Angela]

I think before LGM, the Nile valley was populated by Hap E, and E-M35 was in the Nile delta. Their subsistence was quite diverse, with meat, fish and plant food (Khormusan industry).
During LGM they got microlith technology, probably also bow and arrow, Basal Eurasian and mtDNA U6 and M1, all from Hap H2 in the Levant. They didn't get SSA, as the whole Nilevalley was Hap E. With their new technology, from the Nile delta they radiated into the Levant (Natufian), along the North African coast (Iberomaurisian) and upstream the Nile (Halfan and later Qadan), and maybe Berber (E-M81) stayed in the Nile delta for a while (maybe they were Capsian industry which appeared ca 12 ka).

I checked the Y-calls for Tarofalt from Genetiker. https://genetiker.wordpress.com/2018/03/18/y-snp-calls-from-the-iberomaurusian-culture/
I estimate TAF009 split from the main E-M78 branch ca 18.5 ka, and TAF010-015 split from the M78 branch ca 15 - 15.1 ka.
TAF010-015 are dated ca 14.55 ka, so they split from M78 some 500 years before their burial in the Grotte des Pigeons.
My guess is they arrived from the east, maybe Tamar Hat or Haua Fteah in Cyrenaica after their split from E-M78, without SSA, and they got SSA maybe in Tarofalt.
Then there would have been a backmigration of the main E-M78 branch from Tamar Hat or Haua Fteah to the Levant, before the TMRCA of E-M78 which is 13.4 ka.

I realise this is a rather complicated story, but it is still the simplest story I can figure out.
So I intend to stick to that story till new elements appear.

As for the Nile Valley and the Nile delta it got filled up with thick layers of sediment (50 meters and more) between LGM and the youngest dryas.
It will be hard to find anything there, but Qadan culture was found in the adjacent wadis.

So, was y dna "E" as a whole a back migration from Eurasia into Africa in your theory? Or was it just E-M35.

I can see getting the Basal Eurasian from women from the Levant or Arabia, but what was their other component, Bicicleur? How could there be no SSA in these people living in the Nile Delta or anywhere in the Nile Valley, given that the Nile is such an easy mode of access from the heart of Africa? And again, if some of these E clades back migrated from western North Africa to the Levant, why didn't they bring any SSA with them.

Don't be shy about telling me I'm missing something obvious here.

 

[bicicleur 2]

So, was y dna "E" as a whole a back migration from Eurasia into Africa in your theory? Or was it just E-M35.
I can see getting the Basal Eurasian from women from the Levant or Arabia, but what was their other component, Bicicleur? How could there be no SSA in these people living in the Nile Delta or anywhere in the Nile Valley, given that the Nile is such an easy mode of access from the heart of Africa? And again, if some of these E clades back migrated from western North Africa to the Levant, why didn't they bring any SSA with them.
Don't be shy about telling me I'm missing something obvious here.

I think hap BT arrived in Arabia with Nubian Complex 106 ka or earlier.
https://www.yfull.com/tree/BT/
The Nubian Complex in Dhofar is dated 106 ka, but many sites in Arabia remain undated.
I think hap B came back to the Nile Valley from SW Asia some 85-88 ka.
I think hap E came back to the Nile Valley from SW Asia some 55-60 ka. They had no Neanderthal admixture.
The Nubian Complex existed in Arabia and NE Africa, but in the Nile Valley there is old and new Nubian Complex and there is a hiatus in between. That is why there was no SSA in the Nile Valley. A skeleton with mixed morphology has been dated 55 ka near Taramsa Hill, Upper Egypt. https://mathildasanthropologyblog.w...rial-of-a-modern-human-at-taramsa-hill-egypt/
Also I think in North Africa there was no SSA. North Africa was Aterian, these were the descendants of the Irhoud whose skulls were found in the Atlas Mts and dated 315 ka and 160 ka. They would have gone extinct prior to Iberomaurisian, or maybe because of the Iberomaurisian expansion.
Oh, and there was also Dabban, dated 40 ka in Cyrenaica, also going extinct before or during Iberomaurisian expansion. Dabban complex is remeniscent of paleolithical Levantine complexes.
These are all my speculations ...
Maybe SSA entered the Atlas Mts from the African westcoast, while Iberomaurusian entered from the African northcoast.

 

[bicicleur 2]

I would think that the main common DNA component of Natufian and Iberomaurusian developped in the Nile Delta by mixing E-M35 with mtDNA U6 and M1.

 

[Angela]

I think hap BT arrived in Arabia with Nubian Complex 106 ka or earlier.
https://www.yfull.com/tree/BT/
The Nubian Complex in Dhofar is dated 106 ka, but many sites in Arabia remain undated.
I think hap B came back to the Nile Valley from SW Asia some 85-88 ka.
I think hap E came back to the Nile Valley from SW Asia some 55-60 ka. They had no Neanderthal admixture.
The Nubian Complex existed in Arabia and NE Africa, but in the Nile Valley there is old and new Nubian Complex and there is a hiatus in between. That is why there was no SSA in the Nile Valley. A skeleton with mixed morphology has been dated 55 ka near Taramsa Hill, Upper Egypt. https://mathildasanthropologyblog.w...rial-of-a-modern-human-at-taramsa-hill-egypt/
Also I think in North Africa there was no SSA. North Africa was Aterian, these were the descendants of the Irhoud whose skulls were found in the Atlas Mts and dated 315 ka and 160 ka. They would have gone extinct prior to Iberomaurisian, or maybe because of the Iberomaurisian expansion.
Oh, and there was also Dabban, dated 40 ka in Cyrenaica, also going extinct before or during Iberomaurisian expansion. Dabban complex is remeniscent of paleolithical Levantine complexes.
These are all my speculations ...
Maybe SSA entered the Atlas Mts from the African westcoast, while Iberomaurusian entered from the African northcoast.

Excellent. You've persuaded me, Bicicleur.

 

[Maciamo]

Given that they had less of it than the Natufians and Iran_N, then we can dismiss North Africa as a possible "Urheimat" for Basal Eurasians. The Arabo-Persian Gulf region seems the most likely source in my opinion.

We can exclude Northwest Africa as the source of Basal Eurasians, but not necessarily Egypt or even the Horn of Africa, which have the highest diversity of E1b1b clades today, including very old ones not found anywhere else.

 

[bicicleur 2]

Excellent. You've persuaded me, Bicicleur.

my first story was wrong, you pointed that out by mentioning the SSA admixture

 

[Angela]

my first story was wrong, you pointed that out by mentioning the SSA admixture

I know.

I'm persuaded by this better narrative.