Scientists discover genomic ancestry of Stone Age North Africans from Morocco

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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/doi/10.1126/science.aar8380

https://m.phys.org/news/2018-03-scientists-genomic-ancestry-stone-age.html
 
Very exciting, Cato. I'm very interested to read it. :)
 
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 sub-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)."

MvVAo3y.png
[/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.
 
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)."

FmS2H2g.png
[/IMG]
 
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.
 
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.
 
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/
 
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?
 
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.
 
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?
 
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/disentangling-histories-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?
 
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
14avas9.jpg
 
^^I know, that's why I said "WHG LIKE".
 
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.
 
Natufians share ancestry with the WHG, but its not technically WHG, an "unknown" hunter-gatherer group, UHG.
here its n1n3
14avas9.jpg

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