# Population Genetics > Paleogenetics > Paleolithic & Mesolithic >  Scientists discover genomic ancestry of Stone Age North Africans from Morocco

## Cato

An international team of researchers, led by Johannes Krause and Choongwon Jeong from the Max Planck Institute for the Science of Human History (Jena, Germany), and Abdeljalil Bouzouggar from the Institut National des Sciences de l'Archéologie et du Patrimoine (Rabat, Morocco) and including scientists from the Mohammed V University in Rabat, the Natural History Museum in London, University of Oxford, Université Mohammed Premier in Oujda and the Max Planck Institute for Evolutionary Anthropology in Leipzig, have sequenced DNA from individuals from Morocco dating to approximately 15,000 years ago, as published in Science. This is the oldest nuclear DNA from Africa ever successfully analyzed. The individuals, dating to the Late Stone Age, had a genetic heritage that was in part similar to Near Eastern populations and in part related to sub-Saharan African populations.

North Africa is an important area in the history of the evolution of our species. The geography of North Africa also makes it an interesting area for studying how humans expanded out of Africa. It is part of the African continent, but the Sahara desert presents a substantial barrier to travel to and from southern regions. Similarly, it is part of the Mediterranean region, but in the past the sea could have presented a barrier to interaction with others as well. "A better understanding of the history of North Africa is critical to understanding the history of our species," explains co-author Saaïd Amzazi of Mohammed V University in Rabat, Morocco.

In order to address this, the team looked at a burial site in Grotte des Pigeons, near Taforalt in Morocco, associated with the Later Stone Age Iberomaurusian culture. The Iberomaurusians are believed to be the first in the area to produce finer stone tools known as microliths. "Grotte des Pigeons is a crucial site to understanding the human history of north-western Africa, since modern humans frequently inhabited this cave intensively during prolonged periods throughout the Middle and Later Stone Age," explains co-author Louise Humphrey of the Natural History Museum in London. "Around 15,000 years ago there is evidence for more intensive use of the site and the Iberomaurusians started to bury their dead at the back of the cave."

15,000-year-old nuclear DNA is the oldest recovered in Africa

The researchers analyzed DNA from nine individuals from Taforalt using advanced sequencing and analytical methods. They were able to recover mitochondrial data from seven of the individuals and genome-wide nuclear data from five of the individuals. Because of the age of the samples, at approximately 15,000 years old, and the poor preservation characteristic of the area, this is an unprecedented achievement. "This is the first and the oldest Pleistocene DNA of our species recovered in Africa," explains co-senior author Abdeljalil Bouzouggar. "Due to challenging conditions for DNA preservation, relatively few ancient genomes have been recovered from Africa and none of them so far predate the introduction of agriculture in North Africa," explains first author Marieke van de Loosdrecht of the Max Planck Institute for the Science of Human History. "Successful genome reconstruction was possible by using specialized laboratory methods to retrieve highly degraded DNA, and relatively new analysis methods to characterize the genetic profiles of these individuals."

The researchers found two major components to the genetic heritage of the individuals. About two-thirds of their heritage is related to contemporaneous populations from the Levant and about one-third is most similar to modern sub-Saharan Africans, in particular West Africans.
Scientists discover genomic ancestry of Stone Age North Africans from Morocco
Archaeological excavations at Grotte des Pigeons at Taforalt. Credit: Abdeljalil Bouzouggar

As early as the Stone Age, human populations had links that stretched across continents

The high proportion of Near Eastern ancestry shows that the connection between North Africa and the Near East began much earlier than many previously thought. Although the connections between these regions have been shown in previous studies for more recent time periods, it was not generally believed that humans were interacting across these distances during the Stone Age. "Our analysis shows that North Africa and the Near East, even at this early time, were part of one region without much of a genetic barrier," explains co-senior author Choongwon Jeong.

Although the Sahara did present a physical barrier, there was also clearly interaction happening at this time. The strong connection between the Taforalt individuals and sub-Saharan populations shows that interactions across this vast desert were occurring much earlier than was previously thought. In fact, the proportion of sub-Saharan ancestry of the Taforalt individuals, one-third, is a higher percentage than found in modern populations in Morocco and many other North African populations.
Scientists discover genomic ancestry of Stone Age North Africans from Morocco
Co-author Marieke van de Loosdrecht retrieves ancient DNA in the clean room at the MPI-SHH. Credit: Vanessa Villalba

Sub-Saharan heritage from a previously unknown ancient population

Though the scientists found clear markers linking the heritage in question to sub-Saharan Africa, no previously identified population has the precise combination of genetic markers that the Taforalt individuals had. While some aspects match modern Hadza hunter-gatherers from East Africa and others match modern West Africans, neither of these groups has the same combination of characteristics as the Taforalt individuals. Consequently, the researchers cannot be sure exactly where this heritage comes from. One possibility is that this heritage may come from a population that no longer exists. However, this question would need further investigation.

"Clearly, human populations were interacting much more with groups from other, more distant areas than was previously assumed," states co-senior author Johannes Krause, director of the Department of Archaeogenetics at the Max Planck Institute for the Science of Human History. "This illustrates the ability of ancient genetics to add to our understanding of human history." Further studies in this region could help to clarify more about when and how these different populations interacted and where they came from.

More information: DOI: 10.1126/science.aar8380 M. van de Loosdrecht el al., "Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations," Science (2018). http://science.sciencemag.org/cgi/do...cience.aar8380

https://m.phys.org/news/2018-03-scie...stone-age.html

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## Angela

Very exciting, Cato. I'm very interested to read it. :)

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## Angela

Clearly, this is the big news:

*Even before the spread of agriculture*, "The researchers found two major components to the genetic heritage of the individuals. About *two-thirds of their heritage is related to contemporaneous populations from the Levant and about one-third is most similar to modern sub-Saharan Africans, in particular West Africans."*

The *contemporaneous population in the Levant is the Natufians. So, 2/3 Natufian and 1/3 SSA defined as West African. 
*
""Our analysis shows that* North Africa and the Near East, even at this early time, were part of one region without much of a genetic barrier,"* explains co-senior author Choongwon Jeong."

"Although the Sahara did present a physical barrier, there was also clearly interaction happening at this time. The strong connection between the Taforalt individuals and sub-Saharan populations shows that *interactions across this vast desert were occurring much earlier than was previously thought. In fact, the proportion of sub-Saharan ancestry of the Taforalt individuals, one-third, is a higher percentage than found in modern populations in Morocco and many other North African populations."
*
"*Abstract*

North Africa is a key region for understanding human history, but the genetic history of its people is largely unknown. We present genomic data from *seven 15,000-year-old modern humans from Morocco, attributed to the Iberomaurusian culture.* We find a *genetic affinity with early Holocene Near Easterners, best represented by Levantine Natufians*, suggesting a pre-agricultural connection between Africa and the Near East. We do not find evidence for gene flow from Paleolithic Europeans into Late Pleistocene North Africans. The Taforalt individuals derive one third of their ancestry from s*ub-Saharan Africans, best approximated by a mixture of genetic components preserved in present-day West and East Africans.* Thus, we provide direct evidence for genetic interactions between modern humans across Africa and Eurasia in the Pleistocene."

The second part is that they carried ydna "E", and lineages of "E" that were assumed to be about 3,000 years younger.

"Consistently, we find that all males with sufficient nuclear DNA preservation carry Y haplogroup E1b1b1a1 (M-78; table S16). This haplogroup occurs most frequently in present-day North and East African populations (_18_). The closely related E1b1b1b (M-123) haplogroup has been reported for Epipaleolithic Natufians and Pre-Pottery Neolithic Levantines (“Levant_N”) (_16_). Unsupervised genetic clustering also suggests a connection of Taforalt to the Near East. The three major components that comprise the Taforalt genomes are maximized in early Holocene Levantines, East African hunter-gatherer Hadza from north-central Tanzania, and West Africans (K = 10; Fig. 2B). In contrast, present-day North Africans have smaller sub-Saharan African components with minimal Hadza-related contribution (Fig. 2B)."

[IMG][/IMG]

 A two-way admixture model, comprising Natufian and a sub-Saharan African population, does not significantly deviate from our data (_χ2 p_ ≥ 0.128) with 63.5% Natufian and 36.5% sub-Saharan African ancestry on average (table S8). Adding Paleolithic European lineages as a third source only marginally increased the model fit (_χ2 p_ = 0.019 to 0.128; table S9). Consistently, using qpGraph (_21_) we find that a mixture of Natufian and Yoruba reasonably fits the Taforalt gene pool (|Z| ≤ 3.7; fig. S19 and table S10). Adding gene flow from Paleolithic Europeans does not improve the model fit and provides an ancestry contribution estimate of 0% (fig. S19). We thus find no evidence of gene flow from Paleolithic Europeans into Taforalt within the resolution of our data."

"We speculate that the Natufian-related ancestral population may have been widespread across North Africa and the Near East, associated with microlithic backed bladelet technologies that started to spread out in this area by at least 25,000 yBP ((_10_) and references therein). However, given the absence of ancient genome data from a similar time frame for this broader area, the epicenter of expansion, if there was any, for this ancestral population remains unknown."

Although the oldest Iberomaurusian microlithic bladelet technologies are found earlier in the Maghreb than their equivalents in northeastern Africa (Cyrenaica) and the earliest Natufian in the Levant, the complex sub-Saharan ancestry in Taforalt makes our individuals an unlikely proxy for the ancestral population of later Natufians who do not harbor sub-Saharan ancestry. An epicenter in the Maghreb is plausible only if the sub-Saharan African admixture into Taforalt either post-dated the expansion into the Levant or was a locally confined phenomenon. Alternatively, placing the epicenter in Cyrenaica or the Levant requires an additional explanation for the observed archaeological chronology.

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## Angela

Here's a very interesting bit from the Supplement:
"North Africa is a strong candidate for the place having kept Basal Eurasians because it is well connected to Eurasia. From this point of view, the Upper Paleolithic individuals from Taforalt are likely candidates as being direct descendants of, or closely derived from, the Basal Eurasian population."

"Table S16. Y-haplogroup assignment for six Taforalt males. All individuals could be assigned to haplogroup E1b1b, and five of them more 1274 specifically to E1b1b1a1 (M-78)."

[IMG][/IMG]

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## Ygorcs

Amazing results. If 15,000 years ago a people with 2/3 of Near Eastern affinity and carrying E-M78 lineages already lived in Morocco, then it seems like - compared to other regions, in relative terms - North Africa has had a strikingly high degree of population continuity. Imagine how utterly unrecognizable the genetic makeup of most parts of Europe were 15,000 years ago compared to the modern populations in them.

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## FIREYWOTAN

The hour glass sands seems to be rewarding us with another tide of knowledge. Filling the pools that once seemed so dry. Thank you for opening up this incredible find. I'll try to catch up and add something of value soon. The fact that so many notions are becoming there own dynamic moment is beyond the wildest imaginations.

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## bicicleur

> Amazing results. If 15,000 years ago a people with 2/3 of Near Eastern affinity and carrying E-M78 lineages already lived in Morocco, then it seems like - compared to other regions, in relative terms - North Africa has had a strikingly high degree of population continuity. Imagine how utterly unrecognizable the genetic makeup of most parts of Europe were 15,000 years ago compared to the modern populations in them.


on the other hand there was a very severe bottleneck some 2.3 ka, as the big majority is E-M81 with TRMCA only 2.3 ka
https://www.yfull.com/tree/E-M81/

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## IronSide

> North Africa is a strong candidate for the place having kept Basal Eurasians because it is well connected to Eurasia. From this point of view, the Upper Paleolithic individuals from Taforalt are likely candidates as being direct descendants of, or closely derived from, the Basal Eurasian population.


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. Interesting study, Natufians moved long distances even before agriculture.

Sub-Saharan ancestry decreased in North Africa, probably with the incoming farmers, is the medieval slave trade even necessary to explain West African ancestry in modern populations?

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## LeBrok

A vary interesting development indeed. I didn't expect Natufians to spread so soon to North West Africa. Though they were already partial farmers, knowing how to harvest wheat and bake bread.I was always wondering if North Africa was one of ice age refugium for WHG. Now we know it was not.

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## Cato

I think that they predate Natufians, maybe these Moroccan UP were Kebarians?

https://en.m.wikipedia.org/wiki/Kebaran

Utilizzando Tapatalk

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## IronSide

> I think that they predate Natufians, maybe these Moroccan UP were Kebarians?
> 
> https://en.m.wikipedia.org/wiki/Kebaran
> 
> Utilizzando Tapatalk


You're right, that would mean Kebarans have Basal Eurasian ancestry.

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## Angela

This seems to confirm my problems with the dating of programs like Globetrotter used by the Hellenthal-Busby group. 

It's difficult to know precisely what happened with regard to the SSA ancestry in North Africans. One could speculate that succeeding waves from the Middle East decreased it. Did they totally or almost totally remove it, however, only for it to increase again in the Middle Ages? Or, did they remove part of it, and so the impact of the Arab slave trade isn't as great as has been assumed?

We also have to consider, I think, that this SSA ancestry is closest to West African but it's not precisely that population. Would that influence the modeling?

One thing I do know is that contrary to what the Hellenthal-Busby group proposed, it is highly unlikely that the SSA in North Africans today is the result solely of the admixture in the early Middle Ages because of the Arab Slave trade. 

What we need to resolve this issue is come genomes from various spots, not just coastal, in North Africa, from intermediate periods. 

Amazing, isn't it, how ancient dna blows up so many prior certainties, but still leaves us with unanswered questions?

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## bicicleur

another contemporary backed bladelet technology appears in the Halfan culture

Halfan and Iberomaurisian may coincide with the spread of mtDNA M1 and U6

http://dienekes.blogspot.be/2012/12/...-of-mtdna.html

E1b1b1-M35 with TMRCA 24.1 ka may well have spread from the Nile delta

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## Angela

> another contemporary backed bladelet technology appears in the Halfan culture
> Halfan and Iberomaurisian may coincide with the spread of mtDNA M1 and U6
> http://dienekes.blogspot.be/2012/12/...-of-mtdna.html
> E1b1b1-M35 with TMRCA 24.1 ka may well have spread from the Nile delta


Yes, that makes sense. 

What of E-M81, though, which is very young? Where did that originate, do you think, and how did it spread, with what culture? 

Also, what y Dna did the farmers from the Levant bring then? Or was it a relatively small footprint? The "J" lines present are obviously from later on. 

The source of the "Basal Eurasian" is still a mystery, though. Perhaps, as we've speculated here, from somewhere near Mesopotamia, having spread from near India?

The WHG link is still a bit of a mystery to me too. Given that the authors model Natufians as 1/3 WHG like, I guess the WHG like ancestry in North Africans could come from them. However, what of the mtDna link with the SAMI?

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## IronSide

> Yes, that makes sense. 
> 
> What of E-M81, though, which is very young? Where did that originate, do you think, and how did it spread, with what culture? 
> 
> Also, what y Dna did the farmers from the Levant bring then? Or was it a relatively small footprint? The "J" lines present are obviously from later on. 
> 
> The source of the "Basal Eurasian" is still a mystery, though. Perhaps, as we've speculated here, from somewhere near Mesopotamia, having spread from near India?
> 
> The WHG link is still a bit of a mystery to me too. Given that the authors model Natufians as 1/3 WHG like, I guess the WHG like ancestry in North Africans could come from them. However, what of the mtDna link with the SAMI?


Natufians share ancestry with the WHG, but its not technically WHG, an "unknown" hunter-gatherer group, UHG.

here its n1n3

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## Angela

^^I know, that's why I said "WHG *LIKE*".

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## bicicleur

Natufians and Levant PPNB are E-L539 and E-Z830, these Iberomaurisians are E-M78, derived from E-L539, but they probably went extinct because they are 14.5 ka old, while TMRCA of E-L539 is only 13.4 ka.
And indeed, the 7.3 ka Morrocans in the Fregal 2017 study are on the E-M183 branch, the same as the pre-Columbian Guanche on the Canary Islands. This branch is not derived from E-L539.

A lot of travelling and replacements by different E1b1b1 subclades must have gone on.
These replacements could also explain the decrease in SSA.

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## bicicleur

> Natufians share ancestry with the WHG, but its not technically WHG, an "unknown" hunter-gatherer group, UHG.
> here its n1n3


the common ancestor is n1n1, it looks like some eastern European paleolithical branch, the Kostenki area?

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## bicicleur

also note that untill 30 ka Northern African west of the Nile was inhabited by Aterians, who are derived from the Irhoud samples, 315 ka.
those Aterians went extinct 30 ka when the Sahara expanded ahead of LGM.
the Iberomaurisians, and probably also some SSA tribes entered and filled up an empty territory.

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## bicicleur

> Here's a very interesting bit from the Supplement:
> "North Africa is a strong candidate for the place having kept Basal Eurasians because it is well connected to Eurasia. From this point of view, the Upper Paleolithic individuals from Taforalt are likely candidates as being direct descendants of, or closely derived from, the Basal Eurasian population."


So the only argument is geography?
I doubt it.
Yes, I stick with the theory of BA coming from Gujarat, India or the Indus delta into SW Asia during LGM, along with HG G and H2.

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## Angela

> So the only argument is geography?
> I doubt it.
> Yes, I stick with the theory of BA coming from Gujarat, India or the Indus delta into SW Asia during LGM, along with HG G and H2.


Me too. I don't think the authors are saying that BE comes from North Africa. They're just saying they're also BE derived, but I think the implication is that it came from the Near East.

The question is how did it get there. I still think likely from near India by way of Mesopotamia.

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## Ygorcs

> on the other hand there was a very severe bottleneck some 2.3 ka, as the big majority is E-M81 with TRMCA only 2.3 ka
> https://www.yfull.com/tree/E-M81/


Yes, there were certainly lots of events of partial population replacement since then, but what I meant is that it was apparently mostly between related groups of people, so that the transformations didn't cause a wholesale change of the genetic makeup that would be totally unrecognizable earlier. Also, in the case of the wide expansion of the E-M81 subclades in the last milennia, I think that does not necessarily imply a big genetic bottleneck or some kind of significant population replacement. It could've come without an equally transformative change in the autosomal DNA of the population, like, for example, Basques still being closely related to Neolithic Iberians even though they came to have an overwhelming majority of R1b. If I had to guess, the expansion of E-M81 involved people who were autosomally similar to other North Africans, so it was again a situation of internal dynamics, one wave replacing the other within the same broad group of genetic structures.

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## bicicleur

> Me too. I don't think the authors are saying that BE comes from North Africa. They're just saying they're also BE derived, but I think the implication is that it came from the Near East.
> The question is how did it get there. I still think likely from near India by way of Mesopotamia.


yes, and I would say that BE went further from the Zagros Mts or Mesopoamia into the Levant and the Nile delta
and that E1b1b1-M35 expanded further from there, carrying some BE
but that is of course, speculating even further

is there any mention how much BE these Ibero-Maurisians had?

did 4.5 ka Ethiopian highland Mota HG carry BE?

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## bicicleur

> Yes, there were certainly lots of events of partial population replacement since then, but what I meant is that it was apparently mostly between related groups of people, so that the transformations didn't cause a wholesale change of the genetic makeup that would be totally unrecognizable earlier. Also, in the case of the wide expansion of the E-M81 subclades in the last milennia, I think that does not necessarily imply a big genetic bottleneck or some kind of significant population replacement. It could've come without an equally transformative change in the autosomal DNA of the population, like, for example, Basques still being closely related to Neolithic Iberians even though they came to have an overwhelming majority of R1b. If I had to guess, the expansion of E-M81 involved people who were autosomally similar to other North Africans, so it was again a situation of internal dynamics, one wave replacing the other within the same broad group of genetic structures.


some claim Berber people live in the Atlas since at least 10 ka, but I doubt that
some of the Sea Peoples invading the Nile delta 3.2 ka would have been Berber, but coming from Cyrenaica
maybe E-L19-M81 stayed in Cyrenaica all that time till they appeared in Morroco 7.3 ka

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## Angela

> Yes, there were certainly lots of events of partial population replacement since then, but what I meant is that it was apparently mostly between related groups of people, so that the transformations didn't cause a wholesale change of the genetic makeup that would be totally unrecognizable earlier. Also, in the case of the wide expansion of the E-M81 subclades in the last milennia, I think that does not necessarily imply a big genetic bottleneck or some kind of significant population replacement. It could've come without an equally transformative change in the autosomal DNA of the population, like, for example, Basques still being closely related to Neolithic Iberians even though they came to have an overwhelming majority of R1b. If I had to guess, the expansion of E-M81 involved people who were autosomally similar to other North Africans, so it was again a situation of internal dynamics, one wave replacing the other within the same broad group of genetic structures.


I think we're finding out that populations weren't static since the Bronze Age and there were changes, just that, as you say it was caused by movements of people who weren't drastically different, like WHG versus the farmers, or the steppe people versus MN Europeans. 

That's true in Britain as well, where you have migration of Anglo-Saxons and Danes in the Middle Ages, and also a more "southern" shift as well, although I'm not sure how it happened. Perhaps it was hundreds of years of migrations from France starting with the Norman conquest? 

So, the same thing was going on in North Africa.

@Bicicleur,
There's a lot of discussion about Mota etc. in the Supplement, but I haven't come to grips with it yet.

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## IronSide

> is there any mention how much BE these Ibero-Maurisians had?





> A two-way admixture model, comprising Natufian and a sub-Saharan African population, does not significantly deviate from our data (χ2 p ≥ 0.128) with *63.5% Natufian* and 36.5% sub-Saharan African ancestry on average (table S8).


44.8% of Natufian ancestry is BE, so Ibero-Maurisians have 63.5 * 0.448 = 28.448% BE.

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## FIREYWOTAN

The opportunity to add a piece of research that seems to be pertinent to the ongoing discussions was today's focus since around 2:30 A.M. eastern standard time. I hope this can open up further dialogues. Thanks for sharing the greatest discovery's and point's of entry.
_On the origin of Iberomaurusian: new data based on ancient mitochondrial DNA and phylogenetic analysis of Afalou and Taforalt populations
_
The Western North African population was characterized by the genetic structure of TAF and AFA specimens contains only North African and Eurasian maternal lineages. These finding demonstrate the presence of these haplotypes in North Africa from at least 20,000 YBP. The very low contribution of a Sub-Saharan African haplotype in the Iberomaurusian samples is confirmed. We also highlighted the existence of genetic flows between Southern and Northern coast of the Mediterranean.presence of Iberomaurusian civilization at the Epipaleolithic period (around 20,000 years before present (YBP) to 10,000 YBP). The origin of this population is still not clear: they may come from Europe, Near East, sub-Saharan Africa or they could have evolved in situ in North Africa.

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## bicicleur

this is what Ted Kendall says :

https://www.facebook.com/groups/yful...8200650209778/

detailed SNPs show that these Tarofalt samples are not an extinct bracnh, but they are ancestral to todays subclades of E-M78

there is this sample, probably E-L618
Epicardial	Spain	Avellaner cave, Catalonia [Ave 07]	M	5000 BC	E1b1b1a1b1a	M35.1, V13, Ei in STR table	U5	Lacan 2011b
his ancestors could have gotten from Tarofalt to Iberia and mixed with incoming Cardial Ware people

but there are also these samples :

Impresso pottery	Croatia	Zemunica Cave [I3948]	M	5600-5470 BCE	E1b1b1a1b1 (E-L618) N1a1	Mathieson 2017	769991

Sopot (proto Lengyel)	Hungary	Bicske-Galagonyás [BICS 4] 5000-4800 BC	E1b1b1a1	M78	H39	Szécsényi-Nagy 2015 thesis

how could they have gotten there?

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## bicicleur

https://en.wikipedia.org/wiki/Berbers#Origins

Uniparental DNA analysis has established ties between Berbers and other Afroasiatic speakers in Africa. Most of these populations belong to the E1b1b paternal haplogroup, with Berber speakers having among the highest frequencies of this lineage.[54] Additionally, genomic analysis has found that Berber and other Maghreb communities are defined by a shared ancestral component. This Maghrebi element peaks among Tunisian Berbers.[55] It is related to the Coptic/Ethio-Somali, having diverged from these and other West Eurasian-affiliated components prior to the Holocene.[56]

about Ethio-Somali :

http://journals.plos.org/plosgenetic...type=printable

Early Back-to-Africa Migration into the Horn of Africa

Genetic studies have identified substantial non-African admixture in the Horn of Africa (HOA). In the most recent genomic
studies, this non-African ancestry has been attributed to admixture with Middle Eastern populations during the last few
thousand years. However, mitochondrial and Y chromosome data are suggestive of earlier episodes of admixture. To
investigate this further, we generated new genome-wide SNP data for a Yemeni population sample and merged these new
data with published genome-wide genetic data from the HOA and a broad selection of surrounding populations. We used
multidimensional scaling and ADMIXTURE methods in an exploratory data analysis to develop hypotheses on admixture
and population structure in HOA populations. These analyses suggested that there might be distinct, differentiated African
and non-African ancestries in the HOA. After partitioning the SNP data into African and non-African origin chromosome
segments, we found support for a distinct African (Ethiopic) ancestry and a distinct non-African (Ethio-Somali) ancestry in
HOA populations. The African Ethiopic ancestry is tightly restricted to HOA populations and likely represents an
autochthonous HOA population. The non-African ancestry in the HOA, which is primarily attributed to a novel Ethio-Somali
inferred ancestry component, is significantly differentiated from all neighboring non-African ancestries in North Africa, the
Levant, and Arabia. The Ethio-Somali ancestry is found in all admixed HOA ethnic groups, shows little inter-individual
variance within these ethnic groups, is estimated to have diverged from all other non-African ancestries by at least 23 ka,
and does not carry the unique Arabian lactase persistence allele that arose about 4 ka. Taking into account published
mitochondrial, Y chromosome, paleoclimate, and archaeological data, we find that the time of the Ethio-Somali back-toAfrica
migration is most likely pre-agricultural.

so there would have been a large late paleolithical dispersal of Natufian-like E1b1b1 all over North Africa of which Berber is a remnant

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## Angela

> this is what Ted Kendall says :
> 
> https://www.facebook.com/groups/yful...8200650209778/
> 
> detailed SNPs show that these Tarofalt samples are not an extinct bracnh, but they are ancestral to todays subclades of E-M78
> 
> there is this sample, probably E-L618
> Epicardial Spain Avellaner cave, Catalonia [Ave 07] M 5000 BC E1b1b1a1b1a M35.1, V13, Ei in STR table U5 Lacan 2011b
> his ancestors could have gotten from Tarofalt to Iberia and mixed with incoming Cardial Ware people
> ...


According to the latest paper on the Iberian Neolithic there's no trace of them autosomally or uniparentally in the far southern area, at least not yet. 

I find it a little hard to believe it made it from northwest Africa through Gibraltar and all the way to Croatia. 

The other possibility is that it went from somewhere in the Levant in both directions along the Med.




> "so there would have been a large late paleolithical dispersal of Natufian-like E1b1b1 all over North Africa of which Berber is a remnant".


Yes, that makes sense to me.

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## bicicleur

> According to the latest paper on the Iberian Neolithic there's no trace of them autosomally or uniparentally in the far southern area, at least not yet. 
> I find it a little hard to believe it made it from northwest Africa through Gibraltar and all the way to Croatia. 
> The other possibility is that it went from somewhere in the Levant in both directions along the Med.
> Yes, that makes sense to me.


Indeed, a split up of E-M78 into the Levant and into the Atlas Mts is another option.
And it is a little bit less hard to believe then Iberomaurisians getting all the way upto Cardial ware Croatia.
But it is quite a coincidence that the age estimated on Y-DNA SNP mutations almost exactly matches the calibrated carbon date age of these samples.
It has to be explained one way or another.

Whatever, these E1b1b1 must have wandered along a lot, in contrast to those who are supposed to have stayed in the Levant for so long (14.5 ka Natufians till 8 ka when farmers and herders started to move into Northern Africa)

Also don't forget the PPNB Levant sample :

I1710 Levant PPNB E1b1b1a1-CTS675  calls PPNB	Jordan	Ain Ghazal [I1710 / AG 83_6]	M	7733-7526 calBCE (8580±60 BP)	E1b1b1 (xE1b1b1b1a1, E1b1b1a1b1, E1b1b1a1b2, E1b1b1b2a1c)	M5041+ (CTS5819-, L618-, CTS5479-, V23-)	T1a2	129614	Lazaridis 2016

According to Genetiker, 3 SNPs were identified as E-M78, and he was positive for 2 of them and negative for the 3rd.

https://genetiker.wordpress.com/y-snp-calls-for-i1710/

----------


## bicicleur

> Also don't forget the PPNB Levant sample :
> I1710 Levant PPNB E1b1b1a1-CTS675 calls PPNB	Jordan	Ain Ghazal [I1710 / AG 83_6]	M	7733-7526 calBCE (8580±60 BP)	E1b1b1 (xE1b1b1b1a1, E1b1b1a1b1, E1b1b1a1b2, E1b1b1b2a1c)	M5041+ (CTS5819-, L618-, CTS5479-, V23-)	T1a2	129614	Lazaridis 2016
> According to Genetiker, 3 SNPs were identified as E-M78, and he was positive for 2 of them and negative for the 3rd.
> https://genetiker.wordpress.com/y-snp-calls-for-i1710/


Iberomausians were allready in Tarofalt since 22.5 ka

'Taforalt (or Grotte des Pigeons) is a cave in northern Oujda, Morocco, and the oldest known cemetery in the world. It contained at least 35 Iberomaurusian human skeletons dated to the Epipaleolithic between 15,100 and 14,000 years ago. There is archaeological evidence for Iberomaurusian occupation at the site between 22,500 and 12,500 years ago, as well as evidence for Aterian occupation as old as 85,000 years.[1][2]'

According to YFull, that was after the split of E-M35, but before E-L539 split, so the earliest Iberomaurisians were likely E-L539, while it's brotherclade, E-Z827 -> Z830 has been identified in Natufian Raqefet Cave.

It is still a complicated story, but most parsimonious seems to me that the PPNB Levant (Ain Ghazal) 9.5 ka E-M78 sample would be a backmigration of an Iberomaurisian into the Levant.

----------


## Angela

> Iberomausians were allready in Tarofalt since 22.5 ka
> 
> 'Taforalt (or Grotte des Pigeons) is a cave in northern Oujda, Morocco, and the oldest known cemetery in the world. It contained at least 35 Iberomaurusian human skeletons dated to the Epipaleolithic between 15,100 and 14,000 years ago. There is archaeological evidence for Iberomaurusian occupation at the site between 22,500 and 12,500 years ago, as well as evidence for Aterian occupation as old as 85,000 years.[1][2]'
> 
> According to YFull, that was after the split of E-M35, but before E-L539 split, so the earliest Iberomaurisians were likely E-L539, while it's brotherclade, E-Z827 -> Z830 has been identified in Natufian Raqefet Cave.
> 
> It is still a complicated story, but most parsimonious seems to me that the PPNB Levant (Ain Ghazal) 9.5 ka E-M78 sample would be a backmigration of an Iberomaurisian into the Levant.


Would it then have traveled from there into Europe with the Neolithic?

Isn't there some feeling that the age _estimations_ can be from 10-20% off?

----------


## bicicleur

> Would it then have traveled from there into Europe with the Neolithic?
> Isn't there some feeling that the age _estimations_ can be from 10-20% off?



that looks like neolithic Levant in origin, doesn't it?

in my experience YFull TMRCA estimates are quite accurate
TMRCA for E-M78 is 13.4 ka, maybe that is when the backmigration arrived in the Levant

there is a brotherclade of E-M78, it is E-V1039
anything known about this clade?

https://www.yfull.com/tree/E-L539/

----------


## Angela

> that looks like neolithic Levant in origin, doesn't it?
> 
> in my experience YFull TMRCA estimates are quite accurate
> TMRCA for E-M78 is 13.4 ka, maybe that is when the backmigration arrived in the Levant
> 
> there is a brotherclade of E-M78, it is E-V1039
> anything known about this clade?
> 
> https://www.yfull.com/tree/E-L539/


If E-M78 had a source in the Maghreb or western North Africa somewhere and then headed to the Levant, you would think it would have brought some SSA with it, since that was up to 1/3 of its ancestry. Yet, formal stats etc. find no SSA in the Natufians.

----------


## IronSide

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




> The Dodecad K12 calculator revealed a considerable amount of African admixture, which came as a big surprise since no African admixture is found in Scandinavia today. The two Funnelbeaker samples from Sweden tested below, display about 6% and 11% of African admixture respectively. How it got there is still a matter for debate, but the most likely explanation is that it came with Megalithic people from Iberia, who in turn inherited North African admixture from South Levantine Neolithic farmers who reached Iberia via North Africa. Remnants of this African DNA were found in every prehistoric sample in Scandinavia from the Chalcolithic until the Late Iron Age, as well as among the Anglo-Saxons.
> 
> The Funnelbeaker culture indeed marks the arrival of Megalithic structures in Scandinavia from western Europe. Megaliths seem to have originated in the Near East. The oldest ones in Europe were found in Sicily and southern Portugal and date from c. 7000 BCE. The Atlantic Megalithic culture really started with the advent of farming and would have spread from Iberia to France, the British Isles and the Low Countries before reaching Scandinavia. Considering the high Northwest African admixture in Funnelbeaker, there is a good chance that Iberian Megalithic people inherited genes from Northwest Africans, probably from the North African Neolithic route that brought R1b-V88, E-M78, J1 and T1a to Iberia. R1b-V88 and E-M78 (V13) have both been found in Early Neolithic Iberia, and are both found throughout western Europe today. The two samples below also carried about 3% of Southwest Asian admixture, which is perfectly consistent with a Neolithic dispersal from the southern Levant across North Africa until Iberia.


There are some outdated concepts but intriguing none the less.

----------


## bicicleur

> If E-M78 had a source in the Maghreb or western North Africa somewhere and then headed to the Levant, you would think it would have brought some SSA with it, since that was up to 1/3 of its ancestry. Yet, formal stats etc. find no SSA in the Natufians.


and how about the Levant PPNB samples?

----------


## Angela

> and how about the Levant PPNB samples?


Sorry, could you explain what you mean?

----------


## bicicleur

> If E-M78 had a source in the Maghreb or western North Africa somewhere and then headed to the Levant, you would think it would have brought some SSA with it, since that was up to 1/3 of its ancestry. Yet, formal stats etc. find no SSA in the Natufians.


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...an-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.

----------


## bicicleur

and watch this : 

is E-V1515 African or Natufian in origin?
E-Z830 has 2 subclades with TMRCA 19.2 ka : E-V1515 and PF1962
are both Natufian or only PF1962 ?

the Ethio-Somali is supposed to be pre-agricultural, even late paleolithic :

----------


## bicicleur

> What do you think of this opinion from Maciamo https://www.eupedia.com/genetics/fun..._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...an-puzzle.html
> 
> Also have a look at this, I think it is interesting : 
> ...


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

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

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

> 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

> 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

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

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

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...usian-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...usian-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.
> 
> ...


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

> 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.wo...sa-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

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.wo...sa-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.

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## bicicleur

> Excellent. You've persuaded me, Bicicleur. :)


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

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## Angela

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


I know. 

I'm persuaded by this better narrative. :)

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## IronSide

> 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.


I don't think Basal Eurasians are exclusively associated with E1b1b after all Iran Neolithic and hunter-gatherers had higher levels of Basal but no E1b1b.

----------


## Maciamo

> I don't think Basal Eurasians are exclusively associated with E1b1b after all Iran Neolithic and hunter-gatherers had higher levels of Basal but no E1b1b.


I didn't say that. Anyway the paternal side often hides a variety of maternal lineages. Basal Eurasian surely includes:

- N1a : most common in the Arabian peninsula and Mesopotamia. Very common among Early European Neolithic farmers and therefore associated with Y-haplogroup G2a.

- N1b : peaking in the Middle East and found among the Natufians.

- N2a : a rare clade found in the Middle East and Europe.

- W (aka mtDNA N2b) : quite common in the Caucasus, Iran and Mesopotamia, probably more linked to Y-haplogroup J1 and J2. 

- X : closely linked to Y-haplogroup G2a, both peaking in Anatolia and the Caucasus.

----------


## IronSide

In Lazaridis, Natufians didn't have Yoruba, Mbuti, Ju-Huan-North, or *Mota* individual from East Africa, so it seems Natufians didn't share anything with Africa except the Y-haplogroup E, which should have originated in Africa because of basal complexity of its subclades, and it should have brought some admixture with it to the Levant, Mota also carried E.

But Lazaridis didn't test for Hadza? you can see Natufians, Levant_N, and Anatolia_N also carry Hadza ancestry, it looks like real admixture:




the Hadza do have a strange position in this PCA.

----------


## Angela

A little late, but Razib Khan opines:
https://www.gnxp.com/WordPress/2018/...medium=twitter

He doesn't get into the ydna discussion.

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## FIREYWOTAN

Thank you for sharing this imformation. There's always so many different ideas but he sources that are available continues to expand. Open Access is more than a word it's impact continues to add creditibility to the shifting of notions and ideas. This article helps to demonstarte the pool of light no matter how dark it may have started.

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## ratchet_fan

> Here's a very interesting bit from the Supplement:
> "North Africa is a strong candidate for the place having kept Basal Eurasians because it is well connected to Eurasia. From this point of view, the Upper Paleolithic individuals from Taforalt are likely candidates as being direct descendants of, or closely derived from, the Basal Eurasian population."
> 
> "Table S16. Y-haplogroup assignment for six Taforalt males. All individuals could be assigned to haplogroup E1b1b, and five of them more 1274 specifically to E1b1b1a1 (M-78)."
> 
> [IMG][/IMG]


Guess my theory of y E being related to basal Eurasian has some support.

----------


## ratchet_fan

> Natufians and Levant PPNB are E-L539 and E-Z830, these Iberomaurisians are E-M78, derived from E-L539, but they probably went extinct because they are 14.5 ka old, while TMRCA of E-L539 is only 13.4 ka.
> And indeed, the 7.3 ka Morrocans in the Fregal 2017 study are on the E-M183 branch, the same as the pre-Columbian Guanche on the Canary Islands. This branch is not derived from E-L539.
> A lot of travelling and replacements by different E1b1b1 subclades must have gone on.
> These replacements could also explain the decrease in SSA.


Was the replacement internal within North Africa or from the east or south?

----------


## ratchet_fan

> also note that untill 30 ka Northern African west of the Nile was inhabited by Aterians, who are derived from the Irhoud samples, 315 ka.
> those Aterians went extinct 30 ka when the Sahara expanded ahead of LGM.
> the Iberomaurisians, and probably also some SSA tribes entered and filled up an empty territory.


Still confused on what Iberomasurians. Aren't they a mix of SSA and something basal?




> So the only argument is geography?





> I doubt it.
> Yes, I stick with the theory of BA coming from Gujarat, India or the Indus delta into SW Asia during LGM, along with HG G and H2.


Do you still believe this?




> 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.




This could be recent though no?

----------


## Salento

TAF09 TAF010 TAF011 TAF012 TAF013 TAF014 TAF015

Dodecad K12b and Dodecad Globe 13 coordinates




```
TAF009_Dod_K12b,0.00,3.54,60.38,2.05,0.00,0.00,2.48,18.95,8.83,0.00,0.00,3.78
TAF010_Dod_K12b,0.00,0.55,63.90,3.27,0.00,0.17,1.39,18.70,5.98,0.00,0.00,6.05
TAF011_Dod_K12b,0.00,1.28,64.11,2.45,0.00,0.07,0.70,18.22,5.74,0.18,0.00,7.24
TAF012_Dod_K12b,0.00,1.79,63.81,0.80,0.44,0.00,3.27,16.18,5.76,0.59,0.00,7.35
TAF013_Dod_K12b,0.00,1.07,61.84,2.72,0.00,0.02,1.89,18.58,6.99,0.00,0.00,6.89
TAF014_Dod_K12b,0.00,0.74,62.76,2.95,0.00,0.00,2.12,18.14,5.34,0.00,0.00,7.95
TAF015_Dod_K12b,0.00,0.00,62.82,1.87,0.00,0.90,0.00,15.76,6.67,3.45,0.00,8.52
```




```
TAF009_Dod_Globe13,3.36,0.73,9.60,0.00,33.75,1.10,21.08,0.01,0.65,0.00,0.00,3.82,25.90
TAF010_Dod_Globe13,0.33,0.38,11.52,0.00,35.15,2.09,18.07,0.89,0.52,0.00,0.00,3.78,27.26
TAF011_Dod_Globe13,1.07,0.72,13.03,0.00,35.94,1.51,17.38,1.16,0.47,0.00,0.00,2.00,26.73
TAF012_Dod_Globe13,3.46,0.76,12.00,0.00,34.31,0.00,20.31,1.79,0.00,0.00,0.00,1.89,25.48
TAF013_Dod_Globe13,0.32,1.18,12.17,0.00,35.23,1.20,17.84,1.47,0.42,0.00,0.00,3.25,26.93
TAF014_Dod_Globe13,0.69,1.47,12.77,0.00,33.73,1.45,18.36,1.22,0.50,0.00,0.00,2.56,27.25
TAF015_Dod_Globe13,0.79,0.12,12.92,0.00,35.18,4.03,15.06,3.08,0.00,0.00,0.97,2.45,25.39
```

----------


## Salento

TAF09 TAF010 TAF011 TAF012 TAF013 TAF014 TAF015

Dodecad K12b and Dodecad Globe 13 coordinates




```
TAF009_Dod_K12b,0.00,3.54,60.38,2.05,0.00,0.00,2.48,18.95,8.83,0.00,0.00,3.78
TAF010_Dod_K12b,0.00,0.55,63.90,3.27,0.00,0.17,1.39,18.70,5.98,0.00,0.00,6.05
TAF011_Dod_K12b,0.00,1.28,64.11,2.45,0.00,0.07,0.70,18.22,5.74,0.18,0.00,7.24
TAF012_Dod_K12b,0.00,1.79,63.81,0.80,0.44,0.00,3.27,16.18,5.76,0.59,0.00,7.35
TAF013_Dod_K12b,0.00,1.07,61.84,2.72,0.00,0.02,1.89,18.58,6.99,0.00,0.00,6.89
TAF014_Dod_K12b,0.00,0.74,62.76,2.95,0.00,0.00,2.12,18.14,5.34,0.00,0.00,7.95
TAF015_Dod_K12b,0.00,0.00,62.82,1.87,0.00,0.90,0.00,15.76,6.67,3.45,0.00,8.52
```




```
TAF009_Dod_Globe13,3.36,0.73,9.60,0.00,33.75,1.10,21.08,0.01,0.65,0.00,0.00,3.82,25.90
TAF010_Dod_Globe13,0.33,0.38,11.52,0.00,35.15,2.09,18.07,0.89,0.52,0.00,0.00,3.78,27.26
TAF011_Dod_Globe13,1.07,0.72,13.03,0.00,35.94,1.51,17.38,1.16,0.47,0.00,0.00,2.00,26.73
TAF012_Dod_Globe13,3.46,0.76,12.00,0.00,34.31,0.00,20.31,1.79,0.00,0.00,0.00,1.89,25.48
TAF013_Dod_Globe13,0.32,1.18,12.17,0.00,35.23,1.20,17.84,1.47,0.42,0.00,0.00,3.25,26.93
TAF014_Dod_Globe13,0.69,1.47,12.77,0.00,33.73,1.45,18.36,1.22,0.50,0.00,0.00,2.56,27.25
TAF015_Dod_Globe13,0.79,0.12,12.92,0.00,35.18,4.03,15.06,3.08,0.00,0.00,0.97,2.45,25.39
```

----------

