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Thread: A genomic snapshot of Upper Mesopotamia during during the Neolithic Transition.

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    A genomic snapshot of Upper Mesopotamia during during the Neolithic Transition.

    A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition




    Abstract


    Upper Mesopotamia played a key role in the Neolithic Transition in Southwest Asia through marked innovations in symbolism, technology, and diet. We present 13 ancient genomes (c. 8500 to 7500 cal BCE) from Pre-Pottery Neolithic Çayönü in the Tigris basin together with bioarchaeological and material culture data. Our findings reveal that Çayönü was a genetically diverse population, carrying mixed ancestry from western and eastern Fertile Crescent, and that the community received immigrants. Our results further suggest that the community was organized along biological family lines. We document bodily interventions such as head shaping and cauterization among the individuals examined, reflecting Çayönü’s cultural ingenuity. Last, we identify Upper Mesopotamia as the likely source of eastern gene flow into Neolithic Anatolia, in line with material culture evidence. We hypothesize that Upper Mesopotamia’s cultural dynamism during the Neolithic Transition was the product not only of its fertile lands but also of its interregional demographic connections.



    RESULTS AND DISCUSSION

    We studied the skeletal remains of 33 individuals from Çayönü (Fig. 1, A and B, and table S3). These were mainly found as subfloor burials located inside or within the proximity of six Pre-Pottery Neolithic B (PPNB) buildings (table S1). We screened 33 aDNA libraries by shotgun sequencing, which revealed endogenous DNA proportions varying between 0.04 and 5% (median = 0.2%; fig. S1). This was lower than aDNA preservation in a contemporaneous Central Anatolian settlement, Aşıklı (median = 1.4%, Wilcoxon rank sum test, P < 0.05), but comparable to another Central Anatolian site of a similar date, Boncuklu (median = 0.1%, Wilcoxon rank sum test, P > 0.05; fig. S2).
    Libraries from 14 individuals were chosen for deeper sequencing (Materials and Methods), from which we generated shotgun genomes with depths ranging from 0.016× to 0.49×. (fig. S1 and table S3). High rates of postmortem damage accumulation at read ends, short average fragment sizes [49 to 60 base pairs (bp), median = 51.4 bp], and mitochondrial haplotype-based estimates suggested the authenticity of all 14 libraries (Materials and Methods) (table S3). With these data, we first estimated genetic kinship among all individual pairs (Materials and Methods). Two samples, both identified as female infants (cay018 and cay020), were genetically inferred either to belong to the same individual or to be identical twins. Skeletal analyses also suggested that both petrous bones could belong to the same individual. We therefore merged their genomic data and treated these merged data as representing a single individual, reducing our sample size to 13 (6 adult females, 2 adult males, 3 subadult females, and 2 subadult males). We further identified four related pairs of first to third degree (see below) and removed all but one individual among sets of closely related individuals in population genetic analyses (Materials and Methods).
    The east-west genetic structure of Neolithic Southwest Asia

    To obtain an overview of genetic affinities among human populations in Neolithic Southwest Asia, we compared the 13 Çayönü genomes with published ancient genomes dating to c. 15,000 to 5500 BCE from the Fertile Crescent and neighboring regions (table S4) (79, 12, 13, 2225) using multidimensional scaling (MDS) of pairwise f3 results, D-statistics, and qpAdm analyses (26). These led to a number of observations. In the MDS analysis, the Çayönü group occupied a distinct and intermediate position within the space of Southwest Asian genetic diversity bordered by early Holocene South Levant, Central Zagros and South Caucasus, and Central Anatolia (Fig. 1D and fig. S3). Our sample of Çayönü genomes was internally homogeneous within this space, with the exception of an “outlier” individual, cay008, who appeared relatively closer to Zagros/Caucasus individuals. D-statistics likewise showed that the Çayönü group was genetically closer to western Southwest Asia, and particularly to early Holocene Central Anatolia, than to eastern Southwest Asia (Central Zagros) (Fig. 2A and table S5). At the same time, Central Zagros genomes showed higher genetic affinity to our Çayönü sample than to Central Anatolia or South Levant (Fig. 2B). Last, we found that cay008 harbors higher Zagros contribution than other Çayönü individuals (Figs. 1D and 2C, figs. S4 to S6, and table S6)..........



    An early Neolithic demographic shift in the “Fertile Crescent”

    Our dataset further allowed us to revisit a previous observation on the demographic impact of the Neolithic Transition. It had been earlier reported that the Central Anatolian PPN populations Aşıklı and Boncuklu had low levels of genetic diversity, similar to Upper Paleolithic and Mesolithic Europeans and Caucasians (9, 13). In comparison, Central Anatolian PN populations Tepecik-Çiftlik and Çatalhöyük, as well as West Anatolian and European Neolithic populations, carried higher genetic diversity levels. This temporal increase in genetic diversity was attributed to the transition to farming and associated intensification of population movements and admixture [(9); also see (12)].
    Here, we asked whether PPN populations in the Fertile Crescent, which comprises the main domestication centers of animals and plants in Southwest Asia, also had low genetic diversity levels similar to the Central Anatolian PPN groups. Measuring genetic diversity using outgroup f3 values in genetic samples from Upper Mesopotamia (Çayönü), South Levant (Ain Ghazal), and Central Zagros (Ganj Dareh), we found that genetic samples from all three Fertile Crescent PPN settlements had higher diversity levels than those of the Central Anatolia PPN and are on a par with those of later-coming PN communities of Central and Western Anatolia (Fig. 5A and table S7). We note, however, that this relatively high within-population diversity does not seem to involve visible interindividual differences in ancestry proportions (e.g., variable Zagros ancestry) within the Çayönü sample but may be attributed to heterozygosity within the group (figs. S5 to S7 and note S4)....

    https://www.science.org/doi/10.1126/...zoOlFM.twitter
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    2 members found this post helpful.
    Many thanks. Finally, Mesopotamia.

    So, just going by the posted quotes, Caucasus ancestry, via the Zagros, may have passed this way into Anatolia, and by implication, I would say, into European Neolithic.

    Also, no structure in the population, but variation in the genomes, so, the admixture had been taking place for long enough that the individual sources were well mixed, making the population homogeneous. Rather like Ashkenazim in that way.


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    Because of missing data among informative SNPs, we could determine only the basal branch “CT” for two individuals (cay012 and cay033). While cay011 was placed onto the haplogroup G branch (supported by 10 derived variants above the branch and 2 derived variants at the assigned branch), the cay007 individual was assigned J2a1a
    Not too surprising, just unfortunate deeper classification could not be made.
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    1 members found this post helpful.
    Real Expert: Thanks for the link to this paper, I concur with Angela, more Mesopotamian DNA is great. So this paper and the Southern Arc samples from Mesopotamia are at least going to give us some idea about ancient Mesopotamia and hopefully we can get some DNA from the Sumerians!

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    2 members found this post helpful.
    Upper Mesopotamia - Dodecad K12b:

    … edit the labels if you like
    :)

    Code:
    cay004,0,1.31,2.96,0.79,16.15,2.47,0,0,25.7,0,48.49,2.14
    cay007,1.76,0.92,4.68,1.24,20.66,0,0,0.32,20.36,0,47.87,2.17
    cay008,13.13,0,1.51,3.27,9.11,0,0,1.76,15.16,0.13,53.64,2.29
    cay011,4.16,0,0,4.3,7.86,0,0,1.86,18.24,0.86,61.47,1.25
    cay012,0,0,0,0,23.45,0,0,0,20.98,0,51.23,4.34
    cay013,0,0,5.06,0,17.91,1.01,0,1.65,18.74,0,54.12,1.51
    cay014,0,0,0,3.36,16.91,0,0,0,21.31,0,53,5.41
    cay016,2.36,0.55,4.66,0,31.53,1.72,2.97,2.99,11.02,0,42.2,0
    cay022,0,0,3.79,0.04,20,0,0,5.22,18.45,0,52.3,0.2
    cay1820,0,0.44,4.38,0,19.86,0,0,0,12.5,0,58.82,4
    cay015_lc,0,0,9.75,0,10.58,1.51,0,0,19.5,0,58.66,0
    cay027_lc,2.32,1.23,6.7,0,28.44,0,0,2.82,25.39,0,28.92,4.18
    cay033_lc,0,0,1.94,0.98,23.1,0,0,0,32.53,0,41.45,0
    🕷️

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    1 members found this post helpful.
    there are 4 ancient males in this paper:

    cay012- CT

    cay033-CT

    cay011-G

    cay007-J2a1a

    the G and J2 ancients were uploaded to theytree

    https://www.theytree.com/sample/56399484080fdef46b0be82ca3b5d2d9.html


    https://www.theytree.com/usersample/...5f5c92468.html
    Last edited by kingjohn; 05-11-22 at 16:13.
    Direct paternal line : mizrahi from damascus
    e-fgc7391
    https://www.yfull.com/tree/E-FGC7391/

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    Quote Originally Posted by kingjohn View Post
    there are 4 ancient males in this paper:

    cay012- CT

    cay033-CT

    cay011-G

    cay007-J2a1a

    the G and J2 ancients were uploaded to theytree

    https://www.theytree.com/sample/56399484080fdef46b0be82ca3b5d2d9.html


    https://www.theytree.com/usersample/...5f5c92468.html
    Thanks for the links.

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    Quote Originally Posted by Angela View Post
    Many thanks. Finally, Mesopotamia.

    So, just going by the posted quotes, Caucasus ancestry, via the Zagros, may have passed this way into Anatolia, and by implication, I would say, into European Neolithic.

    Also, no structure in the population, but variation in the genomes, so, the admixture had been taking place for long enough that the individual sources were well mixed, making the population homogeneous. Rather like Ashkenazim in that way.
    That's a good point.

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    Quote Originally Posted by Palermo Trapani View Post
    Real Expert: Thanks for the link to this paper, I concur with Angela, more Mesopotamian DNA is great. So this paper and the Southern Arc samples from Mesopotamia are at least going to give us some idea about ancient Mesopotamia and hopefully we can get some DNA from the Sumerians!

    That's so true. We were so close to having Sumerian samples from the Southern Arc paper. But unfortunately, the DNA sequencing for the Sumerians failed since they were buried in very aggressive soil that destroyed any DNA.



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    Quote Originally Posted by Palermo Trapani View Post
    Real Expert: Thanks for the link to this paper, I concur with Angela, more Mesopotamian DNA is great. So this paper and the Southern Arc samples from Mesopotamia are at least going to give us some idea about ancient Mesopotamia and hopefully we can get some DNA from the Sumerians!
    Sumer is still a long way from upper mesopotamia.

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    Quote Originally Posted by real expert View Post
    That's so true. We were so close to having Sumerian samples from the Southern Arc paper. But unfortunately, the DNA sequencing for the Sumerians failed since they were buried in very aggressive soil that destroyed any DNA.


    because of the thick sediment layers it will be very hard to get Sumerian DNA

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    Quote Originally Posted by kingjohn View Post
    there are 4 ancient males in this paper:

    cay012- CT

    cay033-CT

    cay011-G

    cay007-J2a1a

    the G and J2 ancients were uploaded to theytree

    https://www.theytree.com/sample/56399484080fdef46b0be82ca3b5d2d9.html


    https://www.theytree.com/usersample/...5f5c92468.html

    https://www.theytree.com/usersample/...6db7c6032.html


    cay012 - C1a

    it looks like his paternal ancestors came from Anatolia

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    Quote Originally Posted by bicicleur 2 View Post
    https://www.theytree.com/usersample/...6db7c6032.html


    cay012 - C1a

    it looks like his paternal ancestors came from Anatolia
    I mean from the Boncuklu-Pinarbasi area.

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    Haplogroup CT is still informative.

    It tells us that E haplogroup was in Morocco and Israel(if some other site from this time has it, please tell me).

    While it doesn't seem to be up north at this point.
    It isn't in Anatolia, it isn't in the Caucasus, neither seems to be in N. Mesopotamia... Or in Europe.

    Do we know if there's relevant Basal Eurasian in this site? Because if haplo E and BE are related(and I think so), we could solve this puzzle.

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