Upcoming paper on medieval North African dna

Angela

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This is the preliminary abstract. I don't know when the full paper will be published.

http://smbe-2016.p.asnevents.com.au/days/2016-07-06/abstract/35210

"[FONT=&quot]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."

Speaking of confusing....:)

What I find confusing is their statement that they can be modeled genetically as a two source admixture between Mediterranean Europeans and Southern Africans. Couldn't all North Africans be modeled as an admixture between Mediterraneans and SSA or perhaps East African? Isn't the only reason they plot so far from other Mediterraneans because SSA ancestry is so divergent that approximately 20% of it is enough to pull them away on PCAs?[/FONT]
 
I hope not only for Y and mt but also for an autosomal analysis. At least we can know if Arabian, SSA, Turks and Europeans had significant impact among local North African gene-pool. Even if I think a pre-Phoenician Berber DNA would be better.
 
I hope not only for Y and mt but also for an autosomal analysis. At least we can know if Arabian, SSA, Turks and Europeans had significant impact among local North African gene-pool. Even if I think a pre-Phoenician Berber DNA would be better.

Let's hope there's a lot more detail in the paper itself. What's confusing to me is that they're saying that these people are not all that related to modern North Africans. If they're really just a unique blend of slaves from different parts of the world it's not going to tell us much about the population genetics of modern North Africans.
 
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.


That's certainly interesting.
The "medieval African population without continuity" would be far more intriguing than the "offspring of different slaves," IMO, even if the latter is more likely.
 
Let's hope there's a lot more detail in the paper itself. What's confusing to me is that they're saying that these people are not all that related to modern North Africans. If they're really just a unique blend of slaves from different parts of the world it's not going to tell us much about the population genetics of modern North Africans.
It would be useless in this sense.
 
Intriguing. Can't wait for more.
 
@Angela

What I find confusing is their statement that they can be modeled genetically as a two source admixture between Mediterranean Europeans and Southern Africans.

I was thinking they might mean Khoisan-like - which could potentially make this quite a thing.

If so it might mean Khoisan-like populations extended all the way to north Africa before the Bantu expansion and some survived in north Africa at least to the middle ages.

There's a tribe called 'worm eaters' (Dawada or Dawwada) in the Libyan desert which one source described as Khoisan-like.
 
@Angela



I was thinking they might mean Khoisan-like - which could potentially make this quite a thing.

If so it might mean Khoisan-like populations extended all the way to north Africa before the Bantu expansion and some survived in north Africa at least to the middle ages.

There's a tribe called 'worm eaters' (Dawada or Dawwada) in the Libyan desert which one source described as Khoisan-like.

Interesting. That would still leave the "Mediterranean" part to be explained, though. Still, as I said above, the West Eurasian majority part of the ancestry of modern North Africans could be broadly labelled "Mediterranean", so perhaps it could be some isolated group instead of the mating of slaves from widely scattered parts of the globe.

Supporting that is the fact that while obviously the slaves who were brought north might have contained some part of southern African ancestry, I find it hard to believe that the Arab slave traders got very many slaves who could be totally described as "southern" African.
 
Don't tell me they were EEF+African. I'm getting tired of all the Sardinian-like ancient DNA papers. The EEf race was really kicked around and beaten all over the place. They used to rule all the land from Turkey to Ireland, and North Africa?
 
Don't tell me they were EEF+African. I'm getting tired of all the Sardinian-like ancient DNA papers. The EEf race was really kicked around and beaten all over the place. They used to rule all the land from Turkey to Ireland, and North Africa?
Don't forget that they came and ruled all the Europe too. A very successful race, wouldn't you say?
 
Don't forget that they came and ruled all the Europe too. A very successful race, wouldn't you say?
I am trying to keep up with all of the new developments, but often with limited success.

Does EEF mean Early European Farmer?
Is this group the people who are labeled Old Europe on Maciamo's maps?
Is this group synonymous with Neolithic Greeks who have recently shown to be the same as Neolithic Anatolians, and who may be called Aegean?

Thanks.
 
Don't tell me they were EEF+African. I'm getting tired of all the Sardinian-like ancient DNA papers. The EEf race was really kicked around and beaten all over the place. They used to rule all the land from Turkey to Ireland, and North Africa?

Well, of course they did, in the sense that roughly similar people spread to all those areas, and all over Europe too as LeBrok pointed out, and not just Turkey but the whole Middle East, and they went south into Africa to create people like the Ethiopians and the Horners, and spread down into India too, to some extent, although perhaps mixed with a slightly different Near Eastern "farmer" group . Where have you been? The same thing happened in East Asia with their Neolithic migrations. Hunter-gatherers just can't compete with farmers.

I'm sorry to say that the fact that you're "tired" of seeing all the papers that prove this is irrelevant. Researchers should not reveal the facts about this aspect of ancient history and what percentage these ancient people contribute to modern people because they're not your "favorite" group? That's interesting in itself, by the way, given that you're probably at least 50% EEF.

Oh, and the steppe "Indo-Europeans" who came later and formed an elite in many countries had some specifically EEF ancestry by the time they reached central Europe, and the East, and in addition had a chunk of the Basal Eurasian that was also a part of EEF ancestry through their roughly 50% CHG. Not to mention that in my opinion everything other than the domestication of the horse they learned from heavily or at least significantly EEF like people.

Lest we forget, too, many Europeans can be modeled as 70-80% EEF, and the majority, if you weight results like this for all the European countries by population numbers, are at least 40-50% EEF.
http://2.bp.blogspot.com/-h2ktbF4-z7o/VZNUAIL72iI/AAAAAAAAC48/CWB4aR8R57Q/s1600/Untitled3.png

You might also want to remember that many of the ancient, great civilizations of the Near East to whom we owe so much in terms of metallurgy, urbanization, literacy, and on and on, including religion since you're religiously minded, were all developed by populations with significant EEF ancestry. We can add the Greek and Roman civilizations to that.

So, yes, I'd say they were a highly successful "race".
 
Apropos of all our discussions on the topic of the spread of the Neolithic through the movement of actual farmers, Razib Khan has a thread up on the subject called "It All Began At Eden".

http://www.unz.com/gnxp/it-all-began-at-eden/

He echoes things we've said repeatedly on this site. He also makes the obvious point that Dienekes predicted much of this long ago, in 2011, with his concept of "The Womb of Nations", and all without any of this ancient dna.
http://dienekes.blogspot.com/2011/12/womb-of-nations-how-west-eurasians-came.html

Unlike Razib Khan I always thought he was right, although Khan was always civil about his disagreement, in so far as I can remember, but oh, the irony of seeing people who excoriated him and the idea now acting as if they knew it all along. :)
 
Well, of course they did, in the sense that roughly similar people spread to all those areas, and all over Europe too as LeBrok pointed out, and not just Turkey but the whole Middle East, and they went south into Africa to create people like the Ethiopians and the Horners, and spread down into India too, to some extent, although perhaps mixed with a slightly different Near Eastern "farmer" group . Where have you been? The same thing happened in East Asia with their Neolithic migrations. Hunter-gatherers just can't compete with farmers.

we show that the eastern part of the Ancient Near East was inhabited by a population genetically most similar to hunter-gatherers from the Caucasus but distinct from the Neolithic Anatolian people who later brought food production into Europe

we only know that the farmers who came to Europe were EEF, we don't know anything about the others
 
we show that the eastern part of the Ancient Near East was inhabited by a population genetically most similar to hunter-gatherers from the Caucasus but distinct from the Neolithic Anatolian people who later brought food production into Europe

we only know that the farmers who came to Europe were EEF, we don't know anything about the others

I'll wait to see what more ancient dna turns up, of course, especially of people like the Mesopotamian farmers, and also what the authors of this paper proffer as evidence that the EEF and these CHG admixed farmers were all that distinct, but even so, distinct doesn't mean dissimilar.

From the abstract:
http://smbe-2016.p.asnevents.com.au/days/2016-07-07/abstract/35146
"Their high frequency of short runs of homozygosity, comparable to other early Neolithic farmers, suggests that they overwintered the Last Glacial Maximum in a climatically favourable area, where they may have received a genetic contribution from a population basal to modern Eurasians."

How much Basal Eurasian was modeled in Stuttgart, who had picked up an additional 5-7% Loschbour/Villabruna like ancestry in Europe? Wasn't it around 44%? So, what do the models show for the Anatolian Neolithic farmers? It should be more than 44%, yes? We'll see what the authors propose for the Basal Eurasian percentage in the woman from this isolated population. CHG may not be 100% Basal Eurasian as one recent paper suggested, but if it's anywhere near 50%, how dissimilar were these two populations? Even so, I did say that the population that moved into India might have been of a slightly different ancestry. I also excepted the steppe "Indo-Europeans" except for the specifically EEF ancestry they picked up.

That leaves East Africa, which has already been modeled in papers as "Sardinian like" plus SSA, and North Africa, which will also, I think, turn out to be "Sardinian like" plus SSA (perhaps a different kind of SSA), with some additional WHG. So, they had an impact genetically and certainly culturally from Britain to the borders of the steppe in Europe, North Africa, and East Africa. Now, the people who went down toward Africa (Egyptians have an awful lot of EEF according to all the models I've seen) had to come from the Levant. They didn't fly over it from Anatolia, so they probably had a presence there.

This raises another point: when did "CHG" related "eastern" farmer ancestry, if we can call it that, spread out from it's "isolated" region? Just because modern Near Eastern populations are not now as EEF like as Europeans doesn't mean that was always the case. If Hofmanova is right, which I think they are, a CHG like component started filtering west very early, early enough, in fact, to get into Europe rather early, but the incursion grew much stronger over time. There's a lot of papers showing that a big chunk of the mtDna in the Levant and Anatolia is still very EEF like, although some of the papers then called it "European" like, if I remember it correctly. (One of the papers was on Crete). I think that probably the CHG was brought by J2, and possibly also J1. Then, a drifted, more Arabian like population with a portion of SSA also moved north. I even think we'll see some South Asian inflow, as a recent paper did indeed find.

This is speculation, I know, but not unwarranted, I think.

We'll see when the details start to get filled in.

I have to run, but if anyone doesn't remember some of the papers to which I refer, I can hunt down the citations tomorrow.

The point Dienekes was making is indeed broader than the EEF.

"
The Neolithic of West Eurasia started, by most accounts, c. 12 thousand years ago. Its origin was in the area framed by the Armenian Plateau in the north, the Anatolian Plateau in the west, the Zagros Range in the east, and the lowlands of southern Mesopotamia and the Levant in the south. Intriguingly, the prehistoric site of Göbekli Tepe sits right at the center of this important area, in eastern Anatolia/northern Mesopotamia. "

If there is a candidate for where the ur-population that became the modern Six lived, the early Neolithic of the Near East is surely it. This hypothesis makes the most sense chronologically, archaeologically, genetically, and geographically."

His discussion of the fst numbers between the "Six" is also interesting, as is the following:

"Migrants out of the core area would have spread their genes in all directions, becoming differentiated by a combination of drift, admixture, and the selection pressures they faced in different natural and cultural environments; some of them would acquire lighter pigmentation, others lactase persistence, malaria resistence, the ability to process the dry desert air or to survive the long winter nights of the arctic. These spreads were sometimes gradual, sometimes dramatic: they took place over thousands of years and from a multitude of secondary and tertiary staging points.


In Arabia, the migrants would have met aboriginal Arabians, similar to their next door-neighbors in East Africa,undergoing a subtle African shift (Southwest_Asians). In North Africa, they would have encountered denser populations during the favorable conditions of MIS 1, and by absorbing them they would became the Berbers (Northwest_Africans). Their migrations to the southeast brought them into the realm of Indian-leaning people, in the rich agricultural fields of the Mehrgarh and the now deserted oases of Bactria and Margiana. Across the Mediterranean and along the Atlantic facade of Europe, they would have encountered the Mesolithic populations of Europe, and through their blending became the early Neolithic inhabitants of the Mediterranean and Atlantic coasts of Europe (Mediterraneans). And, to the north, from either the Balkans, the Caucasus, or the trans-Caspian region, they would have met the last remaining Proto-Europeoid hunters of the continental zone, becoming the Northern Europeoids who once stretched all the way to the interior of Asia."
I think the only place where he went wrong is in thinking a remnant of those early farmers remained in the Caucasus, but then he didn't have any ancient dna.Really extraordinarily prescient, since he was proposing all these things before 2010 and absent any ancient dna.

Goodness, I miss his input, which always showed not just a mastery of statistics, but a mastery of logic and language.
 
Interesting. That would still leave the "Mediterranean" part to be explained, though. Still, as I said above, the West Eurasian majority part of the ancestry of modern North Africans could be broadly labelled "Mediterranean", so perhaps it could be some isolated group instead of the mating of slaves from widely scattered parts of the globe.

Supporting that is the fact that while obviously the slaves who were brought north might have contained some part of southern African ancestry, I find it hard to believe that the Arab slave traders got very many slaves who could be totally described as "southern" African.

There were (are?) Khoisan-like people in Namibia IIRC so one possibility is slaves taken from there combined with slaves taken from Europe.

Another is some isolated group of Khoisan-like people hidden in the desert somewhere taken as slaves and combined with slaves raided from Europe.

I don't know which is more likely but the second is potentially more interesting.
 
I am trying to keep up with all of the new developments, but often with limited success.

Does EEF mean Early European Farmer?
Is this group the people who are labeled Old Europe on Maciamo's maps?
Is this group synonymous with Neolithic Greeks who have recently shown to be the same as Neolithic Anatolians, and who may be called Aegean?

Thanks.

It's got quite confusing recently but I think the current state of play is:

EEF does mean that however currently it appears there may have been more than one source of farmers and what were originally thought of as the singular EEF are now more often referred to as ENF (for near eastern) and centered around the Aegean (Greece and NW Anatolia).

These getting partially displaced later in SE Europe by another group of farmers who may or may not have come from the direction of the Caucasus.

So most of Europe would be: Aegean farmers + steppe pastoralists + native HGs with SE Europe getting an extra dose of CHG-like farmers later.

Either way I think two farmer waves is accepted now but I wouldn't swear I got the details right.

(and still leaves ydna E to figure out)
 
Apropos of all our discussions on the topic of the spread of the Neolithic through the movement of actual farmers, Razib Khan has a thread up on the subject called "It All Began At Eden".

http://www.unz.com/gnxp/it-all-began-at-eden/

He echoes things we've said repeatedly on this site. He also makes the obvious point that Dienekes predicted much of this long ago, in 2011, with his concept of "The Womb of Nations", and all without any of this ancient dna.
http://dienekes.blogspot.com/2011/12/womb-of-nations-how-west-eurasians-came.html

Unlike Razib Khan I always thought he was right, although Khan was always civil about his disagreement, in so far as I can remember, but oh, the irony of seeing people who excoriated him and the idea now acting as if they knew it all along. :)
I'm glad to learn that more smart people take under consideration genetic importance in farming and farming lifestyle. It is a rather new radical idea and for most hard to stomach. However these are the consequences of new genetic research, either in population genetics, human genome projects and genetic anthropology. This is where new genetic knowledge is pointing us to. To our genes dictating aspects of our behaviour, culture, food liking, traits of character, music creation, political affiliations, beliefs in supernatural, discipline, love, strong will, addictions, or sense of justice.
 
Apropos of all our discussions on the topic of the spread of the Neolithic through the movement of actual farmers, Razib Khan has a thread up on the subject called "It All Began At Eden".

http://www.unz.com/gnxp/it-all-began-at-eden/

He echoes things we've said repeatedly on this site. He also makes the obvious point that Dienekes predicted much of this long ago, in 2011, with his concept of "The Womb of Nations", and all without any of this ancient dna.
http://dienekes.blogspot.com/2011/12/womb-of-nations-how-west-eurasians-came.html

Dienikes was correct Stone age Middle Easterners contributed a lot of ancestry to a lot of modern Eurasians. However he was wrong in thinking the common West Asian ancestor was a farmer. We now know Neolithic people in the Zagros mountains and Aegean were very differnt, and the ones from the Zagros mountains were similar to previous hunter gatherer populations in the Caucasus mountains. Farming spread with genes to Europe but it may not have in some parts of the Middle East.

The common Stone age Middle Eastern ancestor I'm referring to were hunter gatherers. They're the common ancestors of EEF and CHG. EEF and CHG were very differnt but clearly had a lot of shared ancestry that Paleo Europeans did not have. It's amazing Dienkes was able to determine all West Eurasians have lots of recent common ancestry and their common ancestors lived in the Middle East, but he was wrong that they were the first farmers. The first farmers from Levant or whereever they lived might not have contributed a lot of ancestry to a lot of modern people.

Also, I don't buy the idea Neolithic farmers laid the foundation of modern ethnicities or cultures. Everything in our way of life doesn't have to do with farming. Neolithic West Asia was not a womb of nations.
 
Dienikes was correct Stone age Middle Easterners contributed a lot of ancestry to a lot of modern Eurasians. However he was wrong in thinking the common West Asian ancestor was a farmer. We now know Neolithic people in the Zagros mountains and Aegean were very differnt, and the ones from the Zagros mountains were similar to previous hunter gatherer populations in the Caucasus mountains. Farming spread with genes to Europe but it may not have in some parts of the Middle East.

The common Stone age Middle Eastern ancestor I'm referring to were hunter gatherers. They're the common ancestors of EEF and CHG. EEF and CHG were very differnt but clearly had a lot of shared ancestry that Paleo Europeans did not have. It's amazing Dienkes was able to determine all West Eurasians have lots of recent common ancestry and their common ancestors lived in the Middle East, but he was wrong that they were the first farmers. The first farmers from Levant or whereever they lived might not have contributed a lot of ancestry to a lot of modern people.

Also, I don't buy the idea Neolithic farmers laid the foundation of modern ethnicities or cultures. Everything in our way of life doesn't have to do with farming. Neolithic West Asia was not a womb of nations.

I agree with this.
 

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