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Thread: 6.5 ka Levantine chalcolithic DNA

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    6.5 ka Levantine chalcolithic DNA

    https://www.jpost.com/Israel-News/DN...culture-565293

    One of the largest studies of ancient DNA ever conducted in Israel has shed light on the origins of the Chalcolithic culture in the Levant, approximately 6500 years ago, Tel Aviv University announced Monday.

    “It showed that the Peqi’in people had substantial ancestry from northerners – similar to those living in Iran and Turkey – that was not present in earlier Levantine farmers.”

    Does any one know more about this study?

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    Excerpts from the study:

    https://www.nature.com/articles/s41467-018-05649-9

    "(...) The material culture of the Late Chalcolithic period in the southern Levant (4500–3900/3800 BCE) is qualitatively distinct from previous and subsequent periods. Here, to test the hypothesis that the advent and decline of this culture was influenced by movements of people, we generated genome-wide ancient DNA from 22 individuals from Peqi’in Cave, Israel. These individuals were part of a homogeneous population that can be modeled as deriving ~57% of its ancestry from groups related to those of the local Levant Neolithic, ~17% from groups related to those of the Iran Chalcolithic, and ~26% from groups related to those of the Anatolian Neolithic. The Peqi’in population also appears to have contributed differently to later Bronze Age groups, one of which we show cannot plausibly have descended from the same population as that of Peqi’in Cave. These results provide an example of how population movements propelled cultural changes in the deep past.


    "Based on this uniquely fitting qpAdm model we infer the ancestry of Levant_ChL to be the result of a three-way admixture of populations related to Levant_N (57%), Iran_ChL (17%), and Anatolia_N (26%).


    It was striking to us that previously published Bronze Age Levantine samples from the sites of 'Ain Ghazal in present-day Jordan (Levant_BA_South) and Sidon in present-day Lebanon (Levant_BA_North) can be modeled as two-way admixtures, without the Anatolia_N contribution that is required to model the Levant_ChL population24,26. This suggests that the Levant_ChL population may not be directly ancestral to these later Bronze Age Levantine populations, because if it were, we would also expect to detect an Anatolia_N component of ancestry.

    In what follows, we treat Levant_BA_South and Levant_BA_North as separate populations for analysis, since the symmetry statistic f4(Levant_BA_North, Levant_BA_South; A, Chimp) is significant for a number test populations A (|Z| ≥ 3) (Supplementary Data 5), consistent with the different estimated proportions of Levant_N and Iran_ChL ancestry reported in24,26.


    (...)


    We observe a qualitatively different pattern in the Levant_BA_North samples from Sidon, Lebanon, where models including Levant_ChL paired with either Iran_N, Iran_LN, or Iran_HotuIIIb populations appear to be a significantly better fit than those including Levant_N + Iran_ChL. We largely confirm this result using the “Right” population outgroups defined in26. (abb. Haber: Ust_Ishim, Kostenki14, MA1, Han, Papuan, Ami, Chuckhi, Karitiana, Mbuti, Switzerland_HG, EHG, WHG, and CHG), although we find that the specific model involving Iran_HotuIIIb no longer works with this “Right” set of populations. Investigating this further, we find that the addition of Anatolia_N in the “Right” outgroup set excludes the model of Levant_N + Iran_ChL favored by26. These results imply that a population that harbored ancestry more closely related to Levant_ChL than to Levant_N contributed to the Levant_BA_North population, even if it did not contribute detectably to the Levant_BA_South population.


    We obtained additional insight by running qpAdm with Levant_BA_South as a target of two-way admixture between Levant_N and Iran_ChL, but now adding Levant_ChL and Anatolia_N to the basic 09NW “Right” set of 11 outgroups. The addition of the Levant_ChL causes the model to fail, indicating that Levant_BA_South and Levant_ChL share ancestry following the separation of both of them from the ancestors of Levant_N and Iran_ChL. Thus, in the past there existed an unsampled population that contributed both to Levant_ChL and to Levant_BA_South, even though Levant_ChL cannot be the direct ancestor of Levant_BA_South because, as described above, it harbors Anatolia_N-related ancestry not present in Levant_BA_South.


    (...)


    Our finding that the Levant_ChL population can be well-modeled as a three-way admixture between Levant_N (57%), Anatolia_N (26%), and Iran_ChL (17%), while the Levant_BA_South can be modeled as a mixture of Levant_N (58%) and Iran_ChL (42%), but has little if any additional Anatolia_N-related ancestry, can only be explained by multiple episodes of population movement. The presence of Iran_ChL-related ancestry in both populations – but not in the earlier Levant_N – suggests a history of spread into the Levant of peoples related to Iranian agriculturalists, which must have occurred at least by the time of the Chalcolithic. The Anatolian_N component present in the Levant_ChL but not in the Levant_BA_South sample suggests that there was also a separate spread of Anatolian-related people into the region. The Levant_BA_South population may thus represent a remnant of a population that formed after an initial spread of Iran_ChL-related ancestry into the Levant that was not affected by the spread of an Anatolia_N-related population, or perhaps a reintroduction of a population without Anatolia_N-related ancestry to the region. We additionally find that the Levant_ChL population does not serve as a likely source of the Levantine-related ancestry in present-day East African populations (see Supplementary Note 4)24.


    These genetic results have striking correlates to material culture changes in the archaeological record. The archaeological finds at Peqi’in Cave share distinctive characteristics with other Chalcolithic sites, both to the north and south, including secondary burial in ossuaries with iconographic and geometric designs. It has been suggested that some Late Chalcolithic burial customs, artifacts and motifs may have had their origin in earlier Neolithic traditions in Anatolia and northern Mesopotamia8,13,47. Some of the artistic expressions have been related to finds and ideas and to later religious concepts such as the gods Inanna and Dumuzi from these more northern regions6,8,47,48,49,50. The knowledge and resources required to produce metallurgical artifacts in the Levant have also been hypothesized to come from the north11,51.


    Our finding of genetic discontinuity between the Chalcolithic and Early Bronze Age periods also resonates with aspects of the archeological record marked by dramatic changes in settlement patterns43, large-scale abandonment of sites52,53,54,55, many fewer items with symbolic meaning, and shifts in burial practices, including the disappearance of secondary burial in ossuaries56,57,58,59. This supports the view that profound cultural upheaval, leading to the extinction of populations, was associated with the collapse of the Chalcolithic culture in this region18,60,61,62,63,64. (...)"

    PCA graph:


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    I don't understand the admixture graph, if authors believe that Levant_Ch is composed by Levant_N, Anatolia farmer and Iranian farmer... the bars lack the WHG that it might carry proportionaly the second one.
    "What I've seen so far after my entire career chasing Indoeuropeans is that our solutions look tissue thin and our problems still look monumental" J.P.Mallory

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    Yet again reinforcing my impressions that the "truly" Semitic Levant (Proto-Semitic was assumed to have been spoken in ~3850 BCE in a linguistic paper some years ago) came from the north of Levant and Mesopotamia during the Late Neolithic/Early Chalcolithic, possibly from the region immediately to the south of the Anatolian highlands in what is now Southern Turkey, Northern Syria and Northwestern Iraq. I have a hunch that the South Levant (Israel/Palestine) could've been more Egyptian-like before that northern influx, maybe the missing link in the continuum from the Egyptian to the Semitic AA language families. Of course it's all just a personal "feeling", not hard science, but most of the data I've read about that region subtly point that out to me. I do not think the movement that reshaped the Middle East came directly from Anatolia/Caucasus/Iran (northern West Asia), but via a northern Mesopotamia/Syria heavily influenced by those northern populations in relation to the southern populations nearer to the Arabian Peninsula.

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    As I said at least 3 years ago
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    The ydna and mtdna from the paper
    None of the T are from my branch T1a2
    .

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    0 out of 1 members found this post helpful.
    wait! nobody is suggesting that T and the Iranian farmer is the responsible of the introduction of Indoeuropean into Israel? wait... no IE there? what a fun we can have with genetics uh?

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    Quote Originally Posted by berun View Post
    I don't understand the admixture graph, if authors believe that Levant_Ch is composed by Levant_N, Anatolia farmer and Iranian farmer... the bars lack the WHG that it might carry proportionaly the second one.
    I was asking the exact same thing. I don't see any pink besides that one little blot on one of the samples. I'm confused
    mmmmmmmmm dooouuughhhnuuuutz

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    1 out of 1 members found this post helpful.
    Quote Originally Posted by Ygorcs View Post
    Yet again reinforcing my impressions that the "truly" Semitic Levant (Proto-Semitic was assumed to have been spoken in ~3850 BCE in a linguistic paper some years ago) came from the north of Levant and Mesopotamia during the Late Neolithic/Early Chalcolithic, possibly from the region immediately to the south of the Anatolian highlands in what is now Southern Turkey, Northern Syria and Northwestern Iraq. I have a hunch that the South Levant (Israel/Palestine) could've been more Egyptian-like before that northern influx, maybe the missing link in the continuum from the Egyptian to the Semitic AA language families. Of course it's all just a personal "feeling", not hard science, but most of the data I've read about that region subtly point that out to me. I do not think the movement that reshaped the Middle East came directly from Anatolia/Caucasus/Iran (northern West Asia), but via a northern Mesopotamia/Syria heavily influenced by those northern populations in relation to the southern populations nearer to the Arabian Peninsula.
    That's how I've always felt as well. There will be heart burn among some "experts", real or imagined, at this news.


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    2 out of 2 members found this post helpful.
    As for the Admixture results, it works the way it always does.

    Everything depends on the chosen "reference" sample or sample, which is just one way the samples could be modeled. Within that chosen reference are all sorts of other "hidden" ancestry, just as there is with modern components. Does anyone still think that "Northern European" like components don't already have EEF like ancestry in them? Within Levant Neolithic we know there was already "Anatolian" Neolithic, which contained some UHG related to WHG. They're just looking at the groups at that specific point in time and trying to show the admixtures going on at that time.

    The new paper I just posted on the pitfalls and misinterpretations of Admixture and Structure would be helpful in understanding what's going on.

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    ^^ thanks. also Levant Neolithic doesn't seem that far off from Anatolian, it's mostly the same thing without that extra whg but with a little more Iran like ancestry in a few cases. They're both very Natufian in the grand scheme.

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    Quote Originally Posted by berun View Post
    I don't understand the admixture graph, if authors believe that Levant_Ch is composed by Levant_N, Anatolia farmer and Iranian farmer... the bars lack the WHG that it might carry proportionaly the second one.
    I think it may be because WHG or a source much closer to WHG than to any other of the admixtures they used as proxies may have already been present in one or even all the other admixtures (Levant_Neolithic and Anatolia_Neolithic already had some WHG-like UHG), so it's not a component that is sufficiently different to distinguish the admixtures between themselves (except if the excess WHG was really large to make it really different), and that minor WHG may go unnoticed because it was already included within some other admixture. I think these graphs cannot be read too literally.

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    1 out of 1 members found this post helpful.
    ^^Prior to this paper Anatolian Neolithic was modeled with both more "UHG" and more northern Near East ancestry. It may depend on the exact samples chosen for the runs in each paper.

    As I keep emphasizing, one shouldn't over-interpret Admixture. There's no sign in the results, for example, of the facts as shown through other methods:
    " These individuals were part of a homogeneous population that can be modeled as deriving ~57% of its ancestry from groups related to those of the local Levant Neolithic, ~17% from groups related to those of the Iran Chalcolithic, and ~26% from groups related to those of the Anatolian Neolithic."

    The PCA shows more clearly that pull toward Anatolia Neolithic as well as the difference between Anatolia Neolithic and the Natufians, although of course that's only the two major components. Nor would you guess from Admixture that Levant Bronze Age North (Sidon) and Levant Bronze Age (South) are quite so different from one another, yet that's the case.

    I do think their analysis probably shows that the Levant Chl didn't directly impact the Bronze Age samples from Sidon and Jordan. The fact that nearly all the samples are "T" is further evidence and also evidence that the paternal line may have been perhaps more "Anatolian". However, I think it's early days to say that they didn't impact any other populations in the Levant.

    Interesting how many depigmentation snps the Levant Chl had.

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    Interesting the presence of mtdna U6d. Also mtdna H4 was never found in ancient samples from near-east until now, it was found in neolithic spain and is found in modern basque and sardinian people.

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    1 out of 1 members found this post helpful.
    Quote Originally Posted by Angela View Post
    That's how I've always felt as well. There will be heart burn among some "experts", real or imagined, at this news.
    This continued insistence that Semitic arose far in the south, in the face of all this migration from the north makes no sense to me. That would imply that the migrants who imposed their y dna to the almost eradication of the local male lineages somehow changed their language for that of the absorbed.

    Also interesting in terms of the West Eurasian component in East African populations is the following:

    "We find that the Levant_N and Levant_BA_South populations are both plausible sources for all but two of the East African populations (Oromo and Jew_Ethiopian). Levant_ChL is a plausible source population for all but three East African populations (Oromo, Jew_Ethiopian, and Masai).These results confirm that the West Eurasian ancestry observed in East Africa may be Levantine in origin, but suggest that the Levant_ChL population is not the best available source population to use to model this ancestry. Levant_N or Levant_BA_South are at least as good proxies for this ancestry, and possibly somewhat better."

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    1 out of 1 members found this post helpful.
    Quote Originally Posted by Angela View Post
    ^^Prior to this paper Anatolian Neolithic was modeled with both more "UHG" and more northern Near East ancestry. It may depend on the exact samples chosen for the runs in each paper.

    As I keep emphasizing, one shouldn't over-interpret Admixture. There's no sign in the results, for example, of the facts as shown through other methods:
    " These individuals were part of a homogeneous population that can be modeled as deriving ~57% of its ancestry from groups related to those of the local Levant Neolithic, ~17% from groups related to those of the Iran Chalcolithic, and ~26% from groups related to those of the Anatolian Neolithic."

    The PCA shows more clearly that pull toward Anatolia Neolithic as well as the difference between Anatolia Neolithic and the Natufians, although of course that's only the two major components. Nor would you guess from Admixture that Levant Bronze Age North (Sidon) and Levant Bronze Age (South) are quite so different from one another, yet that's the case.

    I do think their analysis probably shows that the Levant Chl didn't directly impact the Bronze Age samples from Sidon and Jordan. The fact that nearly all the samples are "T" is further evidence and also evidence that the paternal line may have been perhaps more "Anatolian". However, I think it's early days to say that they didn't impact any other populations in the Levant.

    Interesting how many depigmentation snps the Levant Chl had.
    From Iosif Lazaridis:

    "A huge surprise of the new @EadaoinSays et al. paper on Chalcolithic Levant is that the OCA2/s12913832 "blue eye" allele frequency is ~1/2, i.e., Chalcolithic Levantines were probably more blue-eyed than Bronze Age people from Russia, a complete inversion of what is now observed."


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    Quote Originally Posted by Angela View Post
    This continued insistence that Semitic arose far in the south, in the face of all this migration from the north makes no sense to me. That would imply that the migrants who imposed their y dna to the almost eradication of the local male lineages somehow changed their language for that of the absorbed.
    I find it quite possible, even likely that the Afro-Asiatic linguistic component was originally absorbed by (or imposed onto) the Anatolian & Iranian ("northern") population that probably merged with Levant_Neolithic ones, hypothetically because they were highland immigrants in a more technologically advanced region or something like that. But that would've happened before the consolidation of a Proto-Semitic language and culture, before its expansion to other areas, probably still during the Late Neolithic,, and during that "gestation period" it's possible that the foreign elements eventually became dominant even before Proto-Semitic was spread elsewhere in the Fertile Crescent. I say that because I find it hard to believe that Afro-Asiatic came originally from too much north or east of the Levant, considering the distribution of the rest of the family (all other branches in Africa, some of them with possible older links to Southwest Asia, like Cushitic) and the heavy Natufian affinities in other heavily AA regions like North Africa and Egypt.

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    Quote Originally Posted by Angela View Post
    From Iosif Lazaridis:

    "A huge surprise of the new @EadaoinSays et al. paper on Chalcolithic Levant is that the OCA2/s12913832 "blue eye" allele frequency is ~1/2, i.e., Chalcolithic Levantines were probably more blue-eyed than Bronze Age people from Russia, a complete inversion of what is now observed."

    1/2 is the frequency? Really? Now that is a really surprising finding. :-O Were the genetic changes from the Chalcolithic to the Bronze Age so profound and comparatively fast? (I mean, by ~2000 BCE there is already good evidence that the Levant was mainly Semitic, and Semitic presence there is totally proven at least since 2900 BCE) Or was it a matter of selection and evolutionary pressure on a path totally contrary to what happened in Europe?

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    2 out of 2 members found this post helpful.
    Quote Originally Posted by davef View Post
    I was asking the exact same thing. I don't see any pink besides that one little blot on one of the samples. I'm confused
    That's because "pink" is hidden within Anatolia_N, that's the source of WHG. It looks like an intrusion of a population from Anatolia_N to the south for a very short period of time, only to be superceded by Levant_BA which carried far more Iran/Mesopotamian ancestry. T1a (at minimum) seems to correspond to EEF like ancestry, which was also observed in a fairly recent central African study where some tribes of nomads rich in T1 and R1b-V88 carried rs1426654(A) alleles as well.

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    0 out of 1 members found this post helpful.
    For once, I'm going to read the entire paper before I go through this thread and have my mind poisoned by you bastards.

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    from other articles
    Finally, the anthropologists found no obvious signs of war or violence on the bones themselves. Though the researchers caution that a specific study on the pathologies and causes of death in Peki’in has not been done yet, when a war has taken place, the bodies tend to tell the tale.
    Drama and extinction
    The DNA analysis also offers clues to the ultimate fate of this population. Samples from Lebanon and Jordan dated to the early Bronze Age, the period immediately after the late Chalcolithic, show very little contribution from the DNA of the Peki’in people.
    In other words, at some point around 3,900 B.C.E., this group of Chalcolithic Galileans went almost completely extinct.

    .
    So what language did the people already in the levant and south levant speak when these northerners arrived ?
    .
    And these northerers had already moved emigrated as in left the levant by the early bronze-age.........how can they have taught any language from the north

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    Quote Originally Posted by Sile View Post
    from other articles
    Finally, the anthropologists found no obvious signs of war or violence on the bones themselves. Though the researchers caution that a specific study on the pathologies and causes of death in Peki’in has not been done yet, when a war has taken place, the bodies tend to tell the tale.
    Drama and extinction
    The DNA analysis also offers clues to the ultimate fate of this population. Samples from Lebanon and Jordan dated to the early Bronze Age, the period immediately after the late Chalcolithic, show very little contribution from the DNA of the Peki’in people.
    In other words, at some point around 3,900 B.C.E., this group of Chalcolithic Galileans went almost completely extinct.

    .
    So what language did the people already in the levant and south levant speak when these northerners arrived ?
    .
    And these northerers had already moved emigrated as in left the levant by the early bronze-age.........how can they have taught any language from the north
    The classic view already proposed by Heinrich Zimmern a hundred years ago which also Ehret and others adhere to is that the Semites moved in after the Ghassulian culture (which those samples in the paper seem to be associated with) declined. From a newer publication by Edward Lipinski:

    The collapse of the Ghassulian culture in Palestinearound 3300 B.C. and the Egyptian finds in southern Palestine from theEarly Bronze period I (ca. 3300-3050 B.C.) may testify to the arrival ofthese new population groups. The Palestinian tumuli, belonging to theculture of semi-nomadic groups during much of the fourth and third millennia B.C., seem to confirm this hypothesis, since a very similartype of sepulture characterizes pre-historic North Africa, especiallyAlgeria, and it is a typical feature of the old Libyco-Berber tradition.
    The objection against a development of Semitic in the Levant usually is that early Semitic toponymy is difficult to derive from Proto-Semitic. Place names tend to be Hurrian or of unknown origin across large parts of the Levant.

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    Ok so I read with an unadulterated mind and I'll post my hot takes, then see what you guys decided to argue about. This will be interesting.


    We begin to see appreciable Iran_N/Chl expansion in Levant_Chl, which appears to be admixture of Iran_N/Chl + Levant_N+Anatolian_N.

    The Levant_BA_South sample doesn't have Anatolian_N, so the Movement of Iran_N/Chl into the Levant could have occured before Anatolian_N expansion into the Northern regions of the Levant, OR some other mechanism where Iran_N/Chl+Levant_N ends up in Levant_BA_South.

    The Y-HG, aside from one E1b1b1ba, are all T1a1a with one T. The authors say that T "diversified in the Middle East", so that this makes sense.

    Levant_Chl is not in East Africans

    All of this is in alignment with the Archaeology that much of the material culture and art came from the North

    As Lazaridis pointed out in his tweet, there is a high frequency of the OCA2 allele for blue eyes at 1/2.

    This is in opposition to the increasingly proposed notion of gradual diffusion of everything, where neighbors are simply have sex with each other and sharing ideas while hitting the bongo drums. There were significant population movements that significantly changed things and the genetics continues to reinforce the earlier archaeological evidence supporting this idea.


    My Hot take:

    Looking just at the admixture myself it actually looks like Levant_N or Anatolian_N is expanding first, because you see it in Iran_LN and CHG while you don't really see Iran_N in Natufian and Levant_N, maybe a tad. This is in alignment with the archaeological evidence that Farming started with the Natufians, from which you would expect earlier expansion. Then you have Iranian_Chl/_N radiating in all directions from what could be Mesopotamia or the mountainous regions to the North, which I think ultimately is the genetic effect of the growing power of Mesopotamia through this period.

    Wouldn't T1a1a in this period likely be males from Anatolia or Europe?

    In spite of Lazaridis' virtue signalling tweet to show his excitement to the world that blue eyes were in the middle east 7000 years ago, the blue eyed alleles aren't surprising given all the new admixture into the region.


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    Quote Originally Posted by Ygorcs View Post
    Yet again reinforcing my impressions that the "truly" Semitic Levant (Proto-Semitic was assumed to have been spoken in ~3850 BCE in a linguistic paper some years ago) came from the north of Levant and Mesopotamia during the Late Neolithic/Early Chalcolithic, possibly from the region immediately to the south of the Anatolian highlands in what is now Southern Turkey, Northern Syria and Northwestern Iraq. I have a hunch that the South Levant (Israel/Palestine) could've been more Egyptian-like before that northern influx, maybe the missing link in the continuum from the Egyptian to the Semitic AA language families. Of course it's all just a personal "feeling", not hard science, but most of the data I've read about that region subtly point that out to me. I do not think the movement that reshaped the Middle East came directly from Anatolia/Caucasus/Iran (northern West Asia), but via a northern Mesopotamia/Syria heavily influenced by those northern populations in relation to the southern populations nearer to the Arabian Peninsula.
    Agreed


    ........................

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    and also


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