EgyptSearch Forums: "Northwest African Neolithic initiated by migrants from Iberia and Levant"

This is topic "Northwest African Neolithic initiated by migrants from Iberia and Levant" in forum Egyptology at EgyptSearch Forums.

To visit this topic, use this URL:
http://www.egyptsearch.com/forums/ultimatebb.cgi?ubb=get_topic;f=8;t=010838

Posted by BrandonP (Member # 3735) on :

Northwest African Neolithic initiated by migrants from Iberia and Levant

quote:
In northwestern Africa, lifestyle transitioned from foraging to food production around 7,400 years ago but what sparked that change remains unclear. Archaeological data support conflicting views: (1) that migrant European Neolithic farmers brought the new way of life to North Africa1,2,3 or (2) that local hunter-gatherers adopted technological innovations4,5. The latter view is also supported by archaeogenetic data6. Here we fill key chronological and archaeogenetic gaps for the Maghreb, from Epipalaeolithic to Middle Neolithic, by sequencing the genomes of nine individuals (to between 45.8- and 0.2-fold genome coverage). Notably, we trace 8,000 years of population continuity and isolation from the Upper Palaeolithic, via the Epipaleolithic, to some Maghrebi Neolithic farming groups. However, remains from the earliest Neolithic contexts showed mostly European Neolithic ancestry. We suggest that farming was introduced by European migrants and was then rapidly adopted by local groups. During the Middle Neolithic a new ancestry from the Levant appears in the Maghreb, coinciding with the arrival of pastoralism in the region, and all three ancestries blend together during the Late Neolithic. Our results show ancestry shifts in the Neolithization of northwestern Africa that probably mirrored a heterogeneous economic and cultural landscape, in a more multifaceted process than observed in other regions.

They identify the influx of "Levantine ancestry" with Afroasiatic-speaking pastoralists arriving from the east.

quote:
Because this Neolithic Levantine ancestry has not been observed on the European side of the Mediterranean during the Neolithic, it probably represents an independent expansion of people from the Levant into North Africa. Migrations from the Levant to eastern Africa have been identified for Neolithic pastoralist individuals around 4,000 years ago, who are presumed descendants of unsampled northeastern African populations associated with the spread of Saharan pastoralism. Both in SKH and eastern African Neolithic pastoralists, Levantine ancestry is admixed with local ancestries (Fig. 1d, Supplementary Information 8 and Supplementary Data 12). The arrival of this Levantine ancestry coincides with the appearance of a new ceramic tradition in northern Morocco, often characterized by cord-impressed motifs (‘roulette’ or wavy line), like the grave goods at Skhirat belonging to Ashakar Ware pottery. In parallel, cattle pastoralism was expanding in the current Sahara territory and Afro-Asiatic language groups spread throughout the whole of North Africa.

UPDATE: Also of interest:

Signs of Genetic Substructure in Epipaleolithic North Africa? from Revoiye

Posted by Askia_The_Great (Member # 22000) on :

So all in all it was African pastoralist from Northeast Africa that bought Levantine ancestry to the Maghreb? Just want to confirm before I go on.

Posted by -Just Call Me Jari- (Member # 14451) on :

^^^^This seems to be more and more the case, seems these "Eurasian" "Levantine" people have an Afro-asiatic connection/cluster that spread Afroasiatic and Pastorialism across Africa

Posted by the lioness, (Member # 17353) on :

https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-023-06166-6/MediaObjects/41586_2023_6166_MOESM1_ESM.pdf

Posted by Elmaestro (Member # 22566) on :

quote:
The best admixture graph results with three migration events fits SKH as a mixture between a majority of a basal Levantine
ancestry an ancestral African ancestry, with a long private branch, in addition to the two migration events previously described.
The fit of basal lineages into SKH and the long branch probably try to account for this population’s unique genetic composition
with ancestry from different groups. Possible scenarios are that the genetic variation of SKH is rooted in (possibly several)
different and not yet sampled sources, not represented in this model. Previous efforts to search for a possible source of the
West Eurasian ancestry detected in East Africans have revealed no consensus regarding which sequenced ancient Levantine
population serves as the best fitting source of this ancestry75, 80. Similarly, here we observe that Levant Neolithic or Chalcolithic
are likely not proximal sources of the Levantine ancestry in SKH. A possible scenario is that the admixture between such
Levantine component and a North African component took place to the East of North Africa, either in an event common to that
giving rise to East African pastoralist populations or not. None of the currently sampled ancient populations is the best single
proxy for the source population of the North African related ancestry in these admixed groups. Future studies in northeastern
Africa (e.g. present-day Egypt) will hopefully help unravel this process and provide a better understanding of the proximal
sources involved in this admixture event

They beat me to it.

Fun fact. they're the closest proxies for the Eurasian ancestry in Chadic populations like the Toubou for example.

code:

test  = Chad_Toubou, chi^2 8.08, p valu = 4.26e-,     Skhirat_skh002 = 0.211     Chad_Maba = 0.742   Taforalt = 0.0475

Even then some non-zero amounts of Taforalt is required.

Posted by BrandonP (Member # 3735) on :

^ Good to see they're aware that the Levantine(-like) ancestry in SKH would have arrived indirectly.

Posted by Elmaestro (Member # 22566) on :

Not only that they're also suggesting that the Iberomaurasian-(like) ancestry they carry was not form North-west Africa.

Posted by Doug M (Member # 7650) on :

Without samples from the same time frame across coastal North Africa and the Nile Delta and other sites further South it will always be a hit or miss approach. Not to mention they don't include other contemporary sites of Neolithic activity across the Sahara and Sahel.

Because the evidence of early neolithic activity and pottery across the Sahara, Sahel and Upper Nile is far older than that in North West Africa.

https://www.sciencedirect.com/science/article/abs/pii/S1040618221000574

But yes this is basically the same conclusion that the another Taforalt paper came to, which is that there was another ancestral African population that was the parent of both Levantine and ancient North West Africans.

https://www.science.org/doi/10.1126/science.aar8380

Posted by Djehuti (Member # 6698) on :

quote:
Originally posted by Elmaestro:

quote:
The best admixture graph results with three migration events fits SKH as a mixture between a majority of a basal Levantine ancestry an ancestral African ancestry, with a long private branch, in addition to the two migration events previously described. The fit of basal lineages into SKH and the long branch probably try to account for this population’s unique genetic composition with ancestry from different groups. Possible scenarios are that the genetic variation of SKH is rooted in (possibly several) different and not yet sampled sources, not represented in this model. Previous efforts to search for a possible source of the West Eurasian ancestry detected in East Africans have revealed no consensus regarding which sequenced ancient Levantine population serves as the best fitting source of this ancestry75, 80. Similarly, here we observe that Levant Neolithic or Chalcolithic are likely not proximal sources of the Levantine ancestry in SKH. A possible scenario is that the admixture between such Levantine component and a North African component took place to the East of North Africa, either in an event common to that giving rise to East African pastoralist populations or not. None of the currently sampled ancient populations is the best single proxy for the source population of the North African related ancestry in these admixed groups. Future studies in northeastern Africa (e.g. present-day Egypt) will hopefully help unravel this process and provide a better understanding of the proximal sources involved in this admixture event

They beat me to it.

Fun fact. they're the closest proxies for the Eurasian ancestry in Chadic populations like the Toubou for example.
code:
test = Chad_Toubou, chi^2 8.08, p valu = 4.26e-, Skhirat_skh002 = 0.211 Chad_Maba = 0.742 Taforalt = 0.0475
Even then some non-zero amounts of Taforalt is required.

Right. And the Toubu are not even Afroasiatic speakers but Nilo-Saharan speakers! So is this ancestry even "Levantine" to begin with?

Posted by BrandonP (Member # 3735) on :

Phenotypic data from the supplementary files:

Posted by Elmaestro (Member # 22566) on :

Phenotypic data is the least important thing from this study. Which is surprisingly one of the better African aDNA studies if not the most comprehensive. I suggest people read it.

Posted by BrandonP (Member # 3735) on :

quote:
Originally posted by Elmaestro:
Phenotypic data is the least important thing from this study. Which is surprisingly one of the better African aDNA studies if not the most comprehensive. I suggest people read it.

It may not interest you that much, but the phenotype data does stand out to me as a hidden gem, especially considering status-quo narratives about North African people's history. Furthermore, it does stand out to me that even the European-shifted sample (KTG004) that was tested is predicted to have been dark-skinned. Not even I would have expected that!

Anything else of interest in the paper and supplements that you and others haven't pointed out before?

Posted by Elmaestro (Member # 22566) on :

quote:
Originally posted by BrandonP:

quote:
Originally posted by Elmaestro:
Phenotypic data is the least important thing from this study. Which is surprisingly one of the better African aDNA studies if not the most comprehensive. I suggest people read it.
It may not interest you that much, but the phenotype data does stand out to me as a hidden gem, especially considering status-quo narratives about North African people's history. Furthermore, it does stand out to me that even the European-shifted sample (KTG004) that was tested is predicted to have been dark-skinned. Not even I would have expected that!

Anything else of interest in the paper and supplements that you and others haven't pointed out before?

I recently joined in on critiquing the forum for not doing their own due diligence. There is quite a bit to point out but I'm not gonna initiate the conversation. People have been complaining about the lack of aDNA on Africa, yet now we have more and no one's talking about it.

Posted by BrandonP (Member # 3735) on :

quote:
Originally posted by Elmaestro:

quote:
Originally posted by BrandonP:

quote:
Originally posted by Elmaestro:
Phenotypic data is the least important thing from this study. Which is surprisingly one of the better African aDNA studies if not the most comprehensive. I suggest people read it.
It may not interest you that much, but the phenotype data does stand out to me as a hidden gem, especially considering status-quo narratives about North African people's history. Furthermore, it does stand out to me that even the European-shifted sample (KTG004) that was tested is predicted to have been dark-skinned. Not even I would have expected that!

Anything else of interest in the paper and supplements that you and others haven't pointed out before?
I recently joined in on critiquing the forum for not doing their own due diligence. There is quite a bit to point out but I'm not gonna initiate the conversation. People have been complaining about the lack of aDNA on Africa, yet now we have more and no one's talking about it.

I'm sorry, but I don't really know what we're supposed to be looking for (other than stuff you've already pointed out). Could you at least please point us in a direction that interests you?

Posted by Djehuti (Member # 6698) on :

^ I think I may know where you're going if we take into account Revoiye's findings.

https://i.postimg.cc/htF5Ch9z/admixturegraph-Kadruka.png

https://revoiye.com/signs-of-genetic-substructure-in-epipaleolithic-north-africa

At K7 the data really begins to diverge. A seemingly Arabian/Northeast African component which peaks in an individual from Chad forms its own cluster in the chart which included Taforalt in the initial run. And a Somalian/Cushitic cluster forms itself in simulation B. In both instances, the Iberomaurasian component was reduced in almost every non-North African, indicating overlapping variants in the three components. Moreover, the Cushitic component appears to be more relegated to East African populations, reaching high estimates in the horn of Africa and near negligible amounts in some North Africans and Middle eastern populations. However, the North East African/Arabian component (in red), reaches as far west as Chad and maintains moderate estimates in the Near East and North Africa. At K8 a component which peaks in the Mbuti, a population referred to as Pygmies of Central Africa forms in simulation B. For simulation A, The previously established component in red splits into a Chadic component (red) and a North East African/Arab component (aquablue), peaking in the Maba of Chad and the Batahin of East Sudan respectively. Notably, at K9, not only does simulation A have the Mbuti forming their own cluster, the earlier established (since K4) West African component, splits into a yellow component that follows mostly Bantu speakers and a lime green component which peaks in Sahelian/Westernmost Africans. As a result of Chadic populations being simulated to have more of the latter component, the previous NorthAfrican/Arabian component returns. Though at K9 it peaks in the horn of Africa. Simulation B simply has Bayira forming his own isolated component.

As expected, all runs produced a negative Z score signifying that these North Africans have more deep and or African ancestry than the Eurasians tested. Furthermore, western Africans once again seem to have the most positive score. Remarkably, the Laka appears to be the best fit overall for the African related ancestry in these samples. However, the Taforalt samples shows the most variance sometimes suggesting the Yoruba or the Maba to have the best fit. IAM and Oub02 seems to show more similarities with each other than either of the two with Taforalt, which can suggest that IAM could have been a more direct descendant of Oub02’s population. Her diploid and psuedo-haploid profile shows minor differences in which the latter is more shifted toward African populations overall. However, the pattern in relatedness remains somewhat identical. Bayira/Mota on the other hand might have a greater discrepancies between samples. This is indicated by the high variance in relatedness to these North African samples.

With the minor variance in mind I proceeded to look for more differences with more simple f4 stats. This time targeting a handful of various relevant populations from mostly Africa, the Near East and Europe. With the problem of f4(test, reference; Oub02/Taforalt, Chimp) I can use the relationship of the test population and the reference population to examine how many unique alleles the test population shares with either Taforalt or Oub02. And then with both problems ran, I can use arithmetic to see the difference in possibly unique alleles shared. f4((test, reference; Taforalt, Chimp) – (test, reference; Oub02, Chimp)), where a more negative value will result in relatedness to Oub02 and a more positive value will be relatedness to Taforalt. I explored these differences with four outgroups, Mbuti pygmies, Ballito Bay20⁠ (southern African huntergatheres similar to the individuals of Faroaskop Rockshelter), A Chinese Paleolithic sample referred to as Tian Yuan Man21⁠ (田园人) and Ust Ishim. The two African samples are often used as outgroups due to having more basal ancestry12,22⁠ and the two Eurasian samples represent Out of Africa populations not known to have contributed any geneflow to either the test samples or the North African samples.

Interestingly, when diploid samples are used as reference populations, the test samples are shifted more towards Oub02 though their sample selection might attribute that to coincidence. Some consistent outcomes to note is that IAM is always heavily shifted towards Oub02 which is a characteristic noticeable in the ADMIXTURE runs. Also, African populations with less Eurasian ancestry, Pastoral Neolithic populations of East Africa, and Near Eastern populations such as the Pre-pottery Neolithic samples of Jordan are relatively more shifted towards Taforalt.

Also, what do you make of the lacunae in autosomal data vs. available samples could be missing links.

https://qph.cf2.quoracdn.net/main-qimg-c8a49d0d33571bc7e28693705cf60b77

Posted by -Just Call Me Jari- (Member # 14451) on :

I think it might be the fact that despite the introduction of the Neolithic from European immigrants, the African population did not mix with them but adopted the technology, further the later "Levantine" Eurasian ancestry was introduced from the Rift Valley East African pastoralists...

Seems to me the population history of "Eurasian" North Africa is way more complex than the Biodiversity google scholars are trying to make it...esp. if one segment of the Eurasian ancestry....came from Rift Valley populations...IDK

quote:
Originally posted by BrandonP:

quote:
Originally posted by Elmaestro:

quote:
Originally posted by BrandonP:

quote:
Originally posted by Elmaestro:
Phenotypic data is the least important thing from this study. Which is surprisingly one of the better African aDNA studies if not the most comprehensive. I suggest people read it.
It may not interest you that much, but the phenotype data does stand out to me as a hidden gem, especially considering status-quo narratives about North African people's history. Furthermore, it does stand out to me that even the European-shifted sample (KTG004) that was tested is predicted to have been dark-skinned. Not even I would have expected that!

Anything else of interest in the paper and supplements that you and others haven't pointed out before?
I recently joined in on critiquing the forum for not doing their own due diligence. There is quite a bit to point out but I'm not gonna initiate the conversation. People have been complaining about the lack of aDNA on Africa, yet now we have more and no one's talking about it.
I'm sorry, but I don't really know what we're supposed to be looking for (other than stuff you've already pointed out). Could you at least please point us in a direction that interests you?

Posted by BrandonP (Member # 3735) on :

quote:
Originally posted by -Just Call Me Jari-:
I think it might be the fact that despite the introduction of the Neolithic from European immigrants, the African population did not mix with them but adopted the technology, further the later "Levantine" Eurasian ancestry was introduced from the Rift Valley East African pastoralists...

Yes, I did see the part where they claim the “Levantine” ancestry in East African pastoralists may be related to what they observe in the SKH samples.

Also, looking at the admixture graphs in the supplementary.pdf, I noticed that the “Levantine” ancestry thought to have contributed to SKH is relatively basal instead of coming from Neolithic or Chalcolithic Levantines. That might be consistent with a large chunk of that ancestry actually being eastern Saharan.

Posted by -Just Call Me Jari- (Member # 14451) on :

Its interesting is it not? From what I gather the Levantine Ancestry was introduced and the populations mixed for a while before spreading through the Sahara bringing pastorialism with them...

The article referenced says this about this group...

quote:
We propose a four-stage model that fits the data. First, admixture in northeastern Africa created groups with approximately equal proportions of ancestry related to present-day Sudanese Nilotic speakers and groups from northern Africa and the Levant. Second, descendants of these northeastern Africans mixed with foragers in eastern Africa. Third, an additional component of Sudan-related ancestry contributed to Iron Age pastoralist groups. Fourth, western African–related ancestry, similar to that found in present-day Bantu speakers, appeared with the spread of farming.

https://www.science.org/doi/10.1126/science.aaw6275
^^^^There's a lot more interesting stuff in that article..

quote:
Originally posted by BrandonP:

quote:
Originally posted by -Just Call Me Jari-:
I think it might be the fact that despite the introduction of the Neolithic from European immigrants, the African population did not mix with them but adopted the technology, further the later "Levantine" Eurasian ancestry was introduced from the Rift Valley East African pastoralists...
Yes, I did see the part where they claim the “Levantine” ancestry in East African pastoralists may be related to what they observe in the SKH samples.

Posted by -Just Call Me Jari- (Member # 14451) on :

^^^Of course this group probably spread to the Sahara and N/W Africa before acquiring the 3rd and 4th admixture documented in the study I linked but the original population that spread during the Neolithic was a mix of Nilotic/Levantine and Eastern African foragers..

Am I reading that correctly?

Posted by -Just Call Me Jari- (Member # 14451) on :

You know what, years ago Robert Bouval made the "Black Genesis" book, which IMO gave one of the first and few "scholarly" voices in support of the theory that is labeled as "afrocentric", this from a man who is clearly not an Afrocentric, and his core argument was that the Tibbu were a good modern example of the ancestral population that gave rise to Ancient Egypt, while it made waves at the time I still think it went largely ignored, esp. his thoery about the Tibbu/Toubou...

Maybe he was onto something though, seems that maybe the population of "Eurasians"/Levantines" who spread Pastoralism to the Sahara and are the ancestors of the Tibbu also spread Afro-Asiatic and had a part in the creation of the ancestral A. Egyptian population.

quote:
Originally posted by Djehuti:
quote:
Originally posted by Elmaestro:

quote:
The best admixture graph results with three migration events fits SKH as a mixture between a majority of a basal Levantine ancestry an ancestral African ancestry, with a long private branch, in addition to the two migration events previously described. The fit of basal lineages into SKH and the long branch probably try to account for this population’s unique genetic composition with ancestry from different groups. Possible scenarios are that the genetic variation of SKH is rooted in (possibly several) different and not yet sampled sources, not represented in this model. Previous efforts to search for a possible source of the West Eurasian ancestry detected in East Africans have revealed no consensus regarding which sequenced ancient Levantine population serves as the best fitting source of this ancestry75, 80. Similarly, here we observe that Levant Neolithic or Chalcolithic are likely not proximal sources of the Levantine ancestry in SKH. A possible scenario is that the admixture between such Levantine component and a North African component took place to the East of North Africa, either in an event common to that giving rise to East African pastoralist populations or not. None of the currently sampled ancient populations is the best single proxy for the source population of the North African related ancestry in these admixed groups. Future studies in northeastern Africa (e.g. present-day Egypt) will hopefully help unravel this process and provide a better understanding of the proximal sources involved in this admixture event

They beat me to it.

Fun fact. they're the closest proxies for the Eurasian ancestry in Chadic populations like the Toubou for example.
code:
test = Chad_Toubou, chi^2 8.08, p valu = 4.26e-, Skhirat_skh002 = 0.211 Chad_Maba = 0.742 Taforalt = 0.0475
Even then some non-zero amounts of Taforalt is required.
Right. And the Toubu are not even Afroasiatic speakers but Nilo-Saharan speakers! So is this ancestry even "Levantine" to begin with?

Posted by Djehuti (Member # 6698) on :

^ Yes, Jari! I do find it richly ironic that Bauval's theory does seem to have some if not a lot of truth to it. Although to be fair, there are many Egyptologists who hold the theory of Central Saharan origins for the Egyptians, specifically the Badarians.

quote:
Originally posted by BrandonP:

Yes, I did see the part where they claim the “Levantine” ancestry in East African pastoralists may be related to what they observe in the SKH samples.

Also, looking at the admixture graphs in the supplementary.pdf, I noticed that the “Levantine” ancestry thought to have contributed to SKH is relatively basal instead of coming from Neolithic or Chalcolithic Levantines. That might be consistent with a large chunk of that ancestry actually being eastern Saharan.

This is exactly what I was thinking!

Posted by Doug M (Member # 7650) on :

I just find it funny how all these European scholars consistently label African ancient populations as Eurasian and get little no push back whether in DNA or skeletal remains. Yet Africans are supposed to be careful about calling these same populations Africans for fear of being called "Afrocentric" when literally it is the most accurate.

But honestly most of these games specifically associated with the spread of farming is more to obfuscate the big role the Sahara had in human behavioral evolution that laid the foundations of the neolithic revolution. The evolution of survival strategies in and around the Sahara included experiments in domestication of various wild crops and various wild species which wouldn't bear fruit until applied to crops and species in the Levant. One example of how they play this game is the fact that the paper on the spread of the Neolithic in Europe deliberately filtered out any African genetic samples to focus purely on "Eurasian" ones which led to the whole fiasco of EEF and Basal Eurasians. Which is basically an echo of those ancient African influences even after the deliberate filtering out of African DNA.

Posted by Djehuti (Member # 6698) on :

^ LOL @ "filtering" African DNA. I think it's not only that but as Swenet says, the filtering of certain skeletal samples, with those researchers only picking out skeletal remains that look the 'least' African.