Neolithic North African Paper

[Azzurro]

This is the preprint, there is Y and Mt information in the supplementary notes.

Abstract

One of the greatest transitions in the human story was the change from hunter-gatherer to farmer. How farming traditions expanded from their birthplace in the Fertile Crescent has always been a matter of contention. Two models were proposed, one involving the movement of people and the other based on the transmission of ideas. Over the last decade, paleogenomics has been instrumental in settling long-disputed archaeological questions, including those surrounding the Neolithic revolution. Compared to the extensive genetic work done on Europe and the Near East, the Neolithic transition in North Africa, including the Maghreb, remains largely uncharacterized. Archaeological evidence suggests this process may have happened through an in situ development from Epipaleolithic communities, or by demic diffusion from the Eastern Mediterranean shores or Iberia. In fact, Neolithic pottery in North Africa strongly resembles that of European cultures like Cardial and Andalusian Early Neolithic, the southern-most early farmer culture from Iberia. Here, we present the first analysis of individuals' genome sequences from early and late Neolithic sites in Morocco, as well as Andalusian Early Neolithic individuals. We show that Early Neolithic Moroccans are distinct from any other reported ancient individuals and possess an endemic element retained in present-day Maghrebi populations, indicating long-term genetic continuity in the region. Among ancient populations, early Neolithic Moroccans share affinities with Levantine Natufian hunter-gatherers (~9,000 BCE) and Pre-Pottery Neolithic farmers (~6,500 BCE). Late Neolithic (~3,000 BCE) Moroccan remains, in comparison, share an Iberian component of a prominent European-wide demic expansion, supporting theories of trans-Gibraltar gene flow. Finally, the Andalusian Early Neolithic samples share the same genetic composition as the Cardial Mediterranean Neolithic culture that reached Iberia ~5,500 BCE. The cultural and genetic similarities of the Iberian Neolithic cultures with that of North African Neolithic sites further reinforce the model of an Iberian intrusion into the Maghreb.

https://www.biorxiv.org/content/early/2017/09/21/191569

[Azzurro]

The Mtdna:

IAM.3: M1b1
IAM4: U6a1b
IAM5: U6a1b
IAM6: U6a7
IAM7: U6a3
KEB1: X2b
KEB3: K1a1b1
KEB4: K1a1b1
KEB6: K1a4a1
KEB7: T2b3
KEB8: X2b
TOR1: T2c1d
TOR5: J2b1a
TOR6: T2b3
TOR7: T2b3
TOR8: K1a1
TOR11: K1a2a
TOR12: J2b1a
BOT1: K1a4a1

The Y dna:

IAM4: E-L19
IAM5: E-L19
KEB6: T-Y6671 (matches a TSI NA20520 in description)
TOR5: G-Z39334 (G-P303)

[Pax Augusta]

"KEB (3780-3650 BCE)

KEB.6. The Y chromosome from KEB belongs to the T-M184 haplogroup; though scarce and broadly distributed today, this haplogroup has been already observed in European Neolitich individuals.

KEB.6. The only 1KG sample on the three matching that description is a Tuscan individual (NA20520) and it is classified as T-L208* (T1a1a). However it is worth mentioning that the 1KG database lacks samples from North Africa. In fact Haplogroup T-M70 (T1a) accounts for 1.16%-6.22% of NA Y-chromosome lineages.

The presence of Haplogroup T in KEB in agreement with the results observed for the mtDNA indicating a tight relationship of this people with Near Eastern/European populations. Haplogroup T has been observed in Neolitich samples from Germany, as well as, Neolitich samples from Jordan.

KEB.6 belongs to mtDNA K1a4a1 and is considered a typical European Neolitich lineage and it has been thoroughly observed in Neolithic population with a frequency of 10%."


Did KEB.6 carry an Iberian component autosomally? He is younger than T-M184 found in Germany.

[zanipolo]

"KEB (3780-3650 BCE)

KEB.6. The Y chromosome from KEB belongs to the T-M184 haplogroup; though scarce and broadly distributed today, this haplogroup has been already observed in European Neolitich individuals.

KEB.6. The only 1KG sample on the three matching that description is a Tuscan individual (NA20520) and it is classified as T-L208* (T1a1a). However it is worth mentioning that the 1KG database lacks samples from North Africa. In fact Haplogroup T-M70 (T1a) accounts for 1.16%-6.22% of NA Y-chromosome lineages.

The presence of Haplogroup T in KEB in agreement with the results observed for the mtDNA indicating a tight relationship of this people with Near Eastern/European populations. Haplogroup T has been observed in Neolitich samples from Germany, as well as, Neolitich samples from Jordan.

KEB.6 belongs to mtDNA K1a4a1 and is considered a typical European Neolitich lineage and it has been thoroughly observed in Neolithic population with a frequency of 10%."


Did KEB.6 carry an Iberian component autosomally? He is younger than T-M184 found in Germany.

And 2 samples of Neolithic T-M184 in Bulgaria ( Malek on the Danube river)

[Alpenjager]

"KEB6: T-Y6671 (matches a TSI NA20520 in description)"

Azzurro, TSI NA20520 belongs to T-Y6671 but KEB6 only is positive for "Branch 284" which belongs to a unique and unmentioned Y-SNP downstream T-M184 "Within the T clade, KEB.6 is only derived for branch 284". There isnt any Y-tree attached to the paper with equivalences, rather cryptic.

But they mention that "The only 1kG sample on the tree matching that description is a Tuscan individual (NA20520)" So, perhaps by discard we can figure out which is the positive SNP

[Alpenjager]

We have these in YFULL:

T1a2a1a1-CTS54 (id:NA20758TSI) No match LT=339+, T=285+, 284+ and 282- (284 sister).
T1a1a1b-Y6671* (id:NA20520TSI) Best Match
T1a1a1a1a1a1a1a1c-CTS6280* (id:NA19655MXL) No match LT=339+, T=285+, 284+ and 282- (284 sister).
T1a1a1a1a1a1a1a1a1a-Y4981* (id:NA20527TSI) No match LT=339+, T=285+, 284+ and 282- (284 sister).

http://loca.fudan.edu.cn/coca/Y_tree/img/T_mltree2.gif

Then KEB6 = T1a1a-L208 (xT1a1a1a1a1a1a-P77) / 4940ybp

T1a
T1a-M70 / I0797 / North European Plain-Karsdorf / 7100ybp
T1a1-CTS880 / I0795 / North European Plain-Karsdorf / 7100ybp
T1a1-PF5658 / I1108 / Danube-Malak Preslavets / 7600ybp
T1a1a-CTS4916 / I0700 / Danube-Malak Preslavets / 7600ybp

T1b
T1-PF5610 (xT1a) / I1707 / PPNB Ain Ghazal / 9573ybp

[Azzurro]

"KEB6: T-Y6671 (matches a TSI NA20520 in description)"

Azzurro, TSI NA20520 belongs to T-Y6671 but KEB6 only is positive for "Branch 284" which belongs to a unique and unmentioned Y-SNP downstream T-M184 "Within the T clade, KEB.6 is only derived for branch 284". There isnt any Y-tree attached to the paper with equivalences, rather cryptic.

But they mention that "The only 1kG sample on the tree matching that description is a Tuscan individual (NA20520)" So, perhaps by discard we can figure out which is the positive SNP

Exactly that is why I say KEB.6 is T-Y6671* because NA20520 is T-Y6671* and it makes sense too if we look at the T-Y6671 on Yfull downstreams include a sample from Libya and another from Morocco thus matching KEB.6, this is a very important find, this paper is proving to be crucial to understanding Neolithic movements. If we look at the brother clade T-Y13384 we see a Yemeni-Saudi dispersal, now the big question did T-Y6671 arrive in Morocco from the Sinai peninsula or the Straights of Gibraltar? Arguments can be made for both, but the very interesting thing about this find is now we have our 4th T-L208 ancient sample from the neolithic, meaning this line was very busy during the Neolithic, as I wrote at Anthrogenica, for me it seems and I believe that initially T-L208 was an Anatolian Farmer line that spread both to Europe and the Levant, where in the Levant it got integrated in AA dispersals and found itself in waves of migration into Africa and the Arabian peninsula.

[Angela]

I don't see Pax Augusta's question answered anywhere?

"Did KEB.6 carry an Iberian component autosomally? He is younger than T-M184 found in Germany."

If so, then the y may have come from Andalucia, yes or no?

Anyone have any figures on the levels of the T up the tree from this in Andalucia or Spain and Portugal in general?

Just generally, I think it's been likely to many that a big chunk of North African ancestry came from the Near East, yes? As I've said many times, there was a two pronged movement of the Neolithic, one traveling along the northern Mediterranean, and one along the southern Mediterranean.

The surprise for some is that there was some movement from Iberia into at least Morocco at that time.

One of the interesting things for the future is that this may impact how we model other groups, particularly, I would think, Egyptians.

[Alpenjager]

Azzurro. They dont have results, nor positive nor negative, for Y6671. As I explained before, KEB6 is closest to NA20520 than to any other 1000G because KEB6 is L208+ xP77. nothing more nothing less, just it.

[Maciamo]

What is interesting is that Y-haplogroup E-L19 (the precursor of M81) was already present in Morocco by 5000 BCE. All these early sample from Ifri n'Amr o'Moussa belong to this Y-DNA haplogroup and to typically North African mtDNA lineages (M1 and U6a).

Contemporary samples from El Toro in southern Spain display very different haplogroups, all of which fit perfectly in the Neolithic European landscape, namely G2a-P303 on the paternal side and maternal haplogroups J2b1a, K1a1, K1a2a, T2b3 and T2c1d.

The most recent site of Kehf el Baroud in northern Morocco has maternal lineages found mostly in western Europe today (K1a1b1, K1a4a1, T2b3 and X2b) and all found in Neolithic European samples. So the accompanying T-Y6671 most likely came from Neolithic Europeans. This branch of T1a1a is now found in Italy, Iberia, North Africa and the Arabian peninsula. However it seems to have spread from Southwest Europe to Northwest Africa then made its way back to the Middle East, where the deepest clades are now found.

[Alpenjager]

Maciamo, Y6671 is not mentioned anywhere. "Closest to NA20520" is not equal to "belonging to the same terminal SNP".

[bicicleur]

As I've said many times, there was a two pronged movement of the Neolithic, one traveling along the northern Mediterranean, and one along the southern Mediterranean.

yes, but also with 2 different starting points, the 1st in Anatolia, the 2nd in the Levant

[bicicleur]

What is interesting is that Y-haplogroup E-L19 (the precursor of M81) was already present in Morocco by 5000 BCE. All these early sample from Ifri n'Amr o'Moussa belong to this Y-DNA haplogroup and to typically North African mtDNA lineages (M1 and U6a).

so it looks like E-M81 expanded from within the Maghreb, replacing many of his own brothers

the IAM Y-DNA seems to be neolithic Levantine, while the mtDNA seems to be the result of a backmigration which happened > 20 ka

[Angela]

yes, but also with 2 different starting points, the 1st in Anatolia, the 2nd in the Levant

Still the Neolithic, and in terms of genetics, Anatolian Neolithic people had Levant Neolithic in them and vice versa.

The Neolithic movement into India was heavily Iran Neo, but that also had a bit of Anatolian Neolithic in it from the latest figures I've seen.

The mixing had started by the time it moved out of the Middle East, although the Iran Neo did not yet have a significant presence in Anatolia or the Levant until later.

[bicicleur]

Still the Neolithic, and in terms of genetics, Anatolian Neolithic people had Levant Neolithic in them and vice versa.

The Neolithic movement into India was heavily Iran Neo, but that also had a bit of Anatolian Neolithic in it from the latest figures I've seen.

The mixing had started by the time it moved out of the Middle East, although the Iran Neo did not yet have a significant presence in Anatolia or the Levant until later.

yes, and there were 3 SW Asian neolithic populations, not 2, Anatolian being the 3rd
during PPNA there was no mixing, but it started during PPNB when domesticated animals arrived in the Levant, and with it haplogroup T
the domestication of cereals happened in the Levant, the domestication of animals in the Zagros Mts
soon after, in Anatolia local HG adopted both through contacts with both groups through obsidian trading which had started already 16 ka

[Sile]

Exactly that is why I say KEB.6 is T-Y6671* because NA20520 is T-Y6671* and it makes sense too if we look at the T-Y6671 on Yfull downstreams include a sample from Libya and another from Morocco thus matching KEB.6, this is a very important find, this paper is proving to be crucial to understanding Neolithic movements. If we look at the brother clade T-Y13384 we see a Yemeni-Saudi dispersal, now the big question did T-Y6671 arrive in Morocco from the Sinai peninsula or the Straights of Gibraltar? Arguments can be made for both, but the very interesting thing about this find is now we have our 4th T-L208 ancient sample from the neolithic, meaning this line was very busy during the Neolithic, as I wrote at Anthrogenica, for me it seems and I believe that initially T-L208 was an Anatolian Farmer line that spread both to Europe and the Levant, where in the Levant it got integrated in AA dispersals and found itself in waves of migration into Africa and the Arabian peninsula.

The paper also states that with KEB.6 which is T-Y6671 he had K1a4a1 and this is Iberian

In our phylogenetic tree, we can see how K1a4a1 sublineages are
restricted to Europe, although we observed K1a4a1* lineages in the Near East and North
Africa, clustering with the two samples from KEB and TOR (Figure S4.10). The same K1a4a1
haplogroup has been detected in other Neolithic sample from Spain (Cova de la Sarsa, 5,321−5,227 BC)

[Sile]

interesting

https://twitter.com/iosif_lazaridis/...46340116541440

[Angela]

It would seem that it decreased because, at least in part, of Iberian Neolithic entering the genome.

In Egypt there was a rise by the time of the first millennium BC from the prior paper, but then much more of a rise with the Islamic slave trade. I think I recall that in Egypt proportionally more of the slave input was from East African women, whereas in Morocco it was higher in SSA from West Africa.

The Sahara was quite a barrier when desert like conditions prevailed.

[Maciamo]

Maciamo, Y6671 is not mentioned anywhere. "Closest to NA20520" is not equal to "belonging to the same terminal SNP".

Thanks for pointing this out. I only checked the info in this thread. However it could still be Y6671 as this clade is present in Tuscany, Iberia and Morocco today.

[Maciamo]

the IAM Y-DNA seems to be neolithic Levantine, while the mtDNA seems to be the result of a backmigration which happened > 20 ka

E-L19 is over 20k years old too, so it could have been present all over North Africa and the southern Levant. I think that these Y-DNA (E-L19) and mtDNA (M1 and U6a) could well represent indigenous Late Palaeolithic Northwest Africans.

[bicicleur]

E-L19 is over 20k years old too, so it could have been present all over North Africa and the southern Levant. I think that these Y-DNA (E-L19) and mtDNA (M1 and U6a) could well represent indigenous Late Palaeolithic Northwest Africans.

yes that could be, allthough in the neolithic context one would expect some influx from SW Asia too
in the PCA chart however there is some distance between IAM and Natufian/Levant Neo, so if there was an influx from there it was not a replacement, but admixture of Levantine with local North Africans

[Alpenjager]

Yes Maciamo. there is a chance. You can find several Amazighs belonging to PF7444 but this is rather unlikely because it is splitted only 2600 ybp from their European cousins of this same subclade.

[Pax Augusta]

Yes Maciamo. there is a chance. You can find several Amazighs belonging to PF7444 but this is rather unlikely because it is splitted only 2600 ybp from their European cousins of this same subclade.

PF7444 is found also in Sardinia?

https://www.yfull.com/tree/T-PF7444/

[Alpenjager]

Yes. This is shown in my work:

https://upload.wikimedia.org/wikiped...-M184_tree.png

[Alpenjager]

I have taken a look into the KEB6 genome from Neolithic Kelif el Boroud.
He belong to P77 branch.
M70+, L162+, L208+, Y4119+, CTS2214+, Z709+, Z710+, L906+, Y4984+, P77+
According to the authors, the Neolithic ancient KEB6 individual, belonged to a group that crossed the strait of Gibraltar from Iberian Peninsula to North Africa. Also they point his origin to the Early Neolithic Europe.

This is so curious because the KEB site is dated to 5665 yBP (5730-5600 yBP) and P77 is dated to 5500 yBP (6500-4500 yBP).

KEB6 belongs to P77 close to their Birthdate. So it looks like this P77 Late Neolithic population had a extreme movility through Europe until crossing Gibraltar.

I got this IRISPLEX results with the available genome data for KEB6:

Predicted phenotype
p-value--------------AUC-----------Loss
blue eye-------------0.99--------------0
intermediate eye--0.01--------------0
brown eye------------0-----------------0
blond hair-------------0----------------0.028
brown hair------------0-----------------0.015
red hair----------------1----------------0.097
black hair-------------0-----------------0.014
light hair---------------1-----------------0.007
dark hair---------------0-----------------0.007