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Thread: New Holocene SW Asia and East Meditterranean Paper in Current Biology

  1. #1
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    New Holocene SW Asia and East Meditterranean Paper in Current Biology

    New paper in Current Biology "Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the Eastern Mediterranean" in Current Biology 8 December 2022 by Kopetink et al. A quick reading of the paper suggest some new samples not yet published. The paper already has cited the Southern Arc papers so I would think the results have been reconciled to those findings, maybe adding a little more information to what those papers documented (35 new samples) . I didn't see the paper already linked so if it has been, please delete or combine thread.

    https://www.sciencedirect.com/scienc...60982222018243

    Summary

    We present a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, a broad region that experienced the earliest Neolithic transition and the emergence of complex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 ancient and 23 present-day published genomes, we found that genetic diversity within each region steadily increased through the Holocene. We further observed that the inferred sources of gene flow shifted in time. In the first half of the Holocene, Southwest Asian and the East Mediterranean populations homogenized among themselves. Starting with the Bronze Age, however, regional populations diverged from each other, most likely driven by gene flow from external sources, which we term “the expanding mobility model.” Interestingly, this increase in inter-regional divergence can be captured by outgroup-f3-based genetic distances, but not by the commonly used FST statistic, due to the sensitivity of FST, but not outgroup-f3, to within-population diversity. Finally, we report a temporal trend of increasing male bias in admixture events through the Holocene.



    Keywords

    Southwest Asia
    East Mediterranean
    ancient DNA
    human mobility
    sex bias
    admixture

    Last edited by Palermo Trapani; 09-12-22 at 00:40. Reason: editing

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    It is not the same paper as by Anfanger (Reich and al study)?

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    1 members found this post helpful.
    Quote Originally Posted by MOESAN View Post
    It is not the same paper as by Anfanger (Reich and al study)?
    No, this is not related to the 3 Southern Arc papers, Lazaridis et al 2022 (which Reich's Harvard ADNA lab was part of). Different paper. The 3 Reich team Southern Arc papers were published in Science Advances

  4. #4
    Regular Member kingjohn's Avatar
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    1 members found this post helpful.
    by pribislav

    BOG020
    ; 130-190 AD; Boğazköy, Turkey;
    https://www.yfull.com/tree/J-PF5366/

    mus006; 7180-7039 BC; Musular, Turkey;
    https://www.yfull.com/tree/H-Y19966/

    G23; 2335-2140 BC; Theopetra, Greece;
    https://www.yfull.com/tree/I-Y5606/

    G31; 2700-2200 BC; Perachora, Greece;
    https://www.yfull.com/tree/J-ZS50/

    G62; 2700-2200 BC; Perachora, Greece;
    https://www.yfull.com/live/tree/G-Z39332/

    geo005; 1258-1049 BC; Didnauri, Georgia;
    https://www.yfull.com/tree/R-Y13369/

    geo015; 3016-2886 BC; Doghlauri, Georgia;
    https://www.yfull.com/tree/J-BY44581*/

    geo029; 1220-1016 BC; Didnauri, Georgia;
    https://www.yfull.com/tree/R-Y13369/

    zrj003; 206-347 AD; Shamakhi, Azerbaijan;
    https://www.yfull.com/tree/J-Y4423*/

    sha004; 3487-3101 BC; Shahtepe, Iran;
    https://www.yfull.com/tree/J-ZS50/

    sha012; 3200-3100 BC; Shahtepe, Iran;
    https://www.yfull.com/tree/J-Z1828/

    sha014; 3200-3100 BC; Shahtepe, Iran;
    https://www.yfull.com/tree/T-Y44858/

    BOG019; 100-350 AD; Boğazköy, Turkey https://www.yfull.com/tree/T-Z710/

    BOG024; 130-190 AD; Boğazköy, Turkey; https://www.yfull.com/tree/J-M2728/

    GOR001; 333-0 BC; Gordion, Turkey; https://www.yfull.com/tree/J-Z43668/

    G37; 2325-2300 BC; Sarakenos, Greece; https://www.yfull.com/tree/J-Y113289/

    gur017; 1500-1000 BC; Nazarlebi, Georgia; https://www.yfull.com/tree/I-Z26403/

    geo006; 1041-837 BC; Didnauri, Georgia; R1b1a2-M269

    p.s
    interesting to see y haplogroup j1 that ancient presence in greece
    Last edited by kingjohn; 17-12-22 at 15:25.
    Direct paternal line : mizrahi from damascus
    e-fgc7391
    https://www.yfull.com/tree/E-FGC7391/

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    1 members found this post helpful.
    Quote Originally Posted by kingjohn View Post
    by pribislav

    BOG020
    ; 130-190 AD; Boğazköy, Turkey;
    https://www.yfull.com/tree/J-PF5366/

    mus006; 7180-7039 BC; Musular, Turkey;
    https://www.yfull.com/tree/H-Y19966/

    G23; 2335-2140 BC; Theopetra, Greece;
    https://www.yfull.com/tree/I-Y5606/

    G31; 2700-2200 BC; Perachora, Greece;
    https://www.yfull.com/tree/J-ZS50/

    G62; 2700-2200 BC; Perachora, Greece;
    https://www.yfull.com/live/tree/G-Z39332/

    geo005; 1258-1049 BC; Didnauri, Georgia;
    https://www.yfull.com/tree/R-Y13369/

    geo015; 3016-2886 BC; Doghlauri, Georgia;
    https://www.yfull.com/tree/J-BY44581*/

    geo029; 1220-1016 BC; Didnauri, Georgia;
    https://www.yfull.com/tree/R-Y13369/

    zrj003; 206-347 AD; Shamakhi, Azerbaijan;
    https://www.yfull.com/tree/J-Y4423*/

    sha004; 3487-3101 BC; Shahtepe, Iran;
    https://www.yfull.com/tree/J-ZS50/

    sha012; 3200-3100 BC; Shahtepe, Iran;
    https://www.yfull.com/tree/J-Z1828/

    sha014; 3200-3100 BC; Shahtepe, Iran;
    https://www.yfull.com/tree/T-Y44858/


    p.s
    interesting to see y haplogroup j1 that ancient presence in greece

    The T ydna ....belongs to T1a3 branch

    https://www.researchgate.net/project...Y11151-FGC1350

    the oldest find for this branch IIRC was either South-Kazaks or North-Caucasus
    Fathers mtdna ...... T2b17
    Grandfather paternal mtdna ... T1a1e
    Sons mtdna ...... K1a4p
    Mothers line ..... R1b-S8172
    Grandmother paternal side ... I1-CTS6397
    Wife paternal line ..... R1a-PF6155

    "Fear profits man, nothing"

  6. #6
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    2 members found this post helpful.
    Some interesting insights in the paper.

    "The new genomes from Musular (n = 2; ca. 9,100 BP) of Central Anatolia can be modeled as earlier Aceramic Neolithic Central Anatolian genomes with additional southern (Levant-related) and eastern (Zagros/Caucasus-related) ancestry components (Figures 3 and S1; Tables S3 and S4). This profile closely resembles that of ca. 8,500 BP Çatalhöyük, which suggests that putative eastern/southern gene flow into Central Anatolia14,17,22,35 had taken place already by the late 10th millennium BP, before the Ceramic Neolithic."

    This is the very helpful chart based on qpAdm:


    "In the post-Neolithic period, we present new genomes from Ulucak (n = 1) and Çine-Tepecik (n = 1) of BA West Anatolia, from Gordion (n = 2) of Central Anatolia in the IA/Hellenistic period, and from Boğazköy in Central Anatolia dating to the Roman (n = 3) and Ottoman (n = 1) periods. Interestingly, all 8 genomes can be modeled as admixtures between Ceramic Neolithic/early Chalcolithic Anatolia (ca. 70%–80%) and Zagros/Caucasus-related ancestry sources (ca. 20%–30%) (Figure 3). This is highly similar to published BA Central and West Anatolian genomes, which were earlier described as being admixed between local Neolithic and eastern sources.18,20,37 The observation that ancestry components in Anatolia changed little from the BA to the Roman or even Ottoman periods suggests the apparent stability of the gene pool through four millennia, also observed in a recent study.38

    Exceptions include a published Kalehöyük IA genome carrying European ancestry (not observed in later-coming genomes), and Kalehöyük Ottoman genomes carrying Baikal Neolithic-related ancestry, likely representing Turkic admixture in the 1st millennium BP. Meanwhile, our Boğazköy Ottoman genome hints at the heterogeneity of this Baikal-related admixture in Anatolia; this heterogeneity can still be observed in modern-day Turkish genomes39 (Figures 3 and S1).

    Accordingly, we could model our new genomes from Perachora cave (n = 5), Sarakenos cave (n = 1), and Theopetra cave (n = 1) in mainland Greece via two- or three-way mixture models of Aegean Neolithic-related populations (60%–83%), Caucasus/Zagros-related populations (12%–20%), and EHG-related populations (0%–25%) (Figures 3 and S2). This confirms the earlier observation of a gradual and partial diffusion of EHG-related ancestry in present-day Greece.13,18

    Amazing how high CHG was in the Kura Araxes culture.

    "Our new genomes from Doghlauri, Georgia, belonging to the Early BA Kura Araxes culture (n = 1; ca. 4,900 BP)43 and to the Late BA (n = 1; ca. 3,200 BP) can likewise be modeled as two-way admixtures of local CHG (62%–57%) and Anatolian Chalcolithic populations (38%–43%) (Figures 3 and S4)."



    Amazing also how there's almost an even split in most of the South Caucasus samples between CHG and Anatolian Chalcolithic, and the same in the Levant. In fact, I'm surprised how little Levant Neo there is in some of the Levant samples. Take a look at Alalakh.

    Temporal changes in ancestry components in the Levant during the Holocene have been investigated in detail, and post-Neolithic Levant genomes could be modeled as two- or three-way admixtures of local Levant Neolithic populations and post-Neolithic populations from Iran and/or Anatolian Neolithic populations, with variable degrees.8,11,15,20,24,44 Our modeling of published data confirmed this general description (Figure 3; Table S4). We note that alternative models using external sources such as EHG have also been proposed16,44 and that two specific ancient genome samples, those from BA and IA Ashkelon26 and those representing Medieval Crusaders,44 both carrying high degrees of West European ancestry, appear not to have left permanent signatures in the local gene pool (STAR Methods)."


    The isotope paper on a bunch of Alalakh samples was discussed, and Jovialis' analysis showed they are closest to the Druze, at about a distance of 3. Perhaps I haven't read this paper deeply enough, but I think it may contradict the paper specifically on the Alalakh samples, which implied there was no gene flow from other areas. Or perhaps, those samples happened to come in a period of stasis where there was homogenization.


    https://www.eupedia.com/forum/thread...hlight=Alalakh


    "These observations suggest two sequential processes. The first involves intense mobility within Southwest Asia and the East Mediterranean after the Neolithic transition, in the early half of the Holocene. This is also evident in the qpAdm results (Figure 3): for instance, up until 6,000–4,000 BP, Anatolian and Aegean populations received intense gene flow from South Caucasus/Iran-related populations, while groups from Caucasus and Iran received gene flow from Anatolian-related populations. Similar patterns have also been reported in a recent analysis of the demographic history of the region.38 These putative admixture events could explain a reduction in genetic distance supported both by FST and (1 − f3) values, and may also be inferred in the PCA (Figure III in Document Z1; Methods S1D). The second inferred process involves external gene flow. After the 6,000–4,000 BP period, populations in all five regions likely received different degrees of gene flow from regions outside of Southwest Asia and the East Mediterranean. Examples include EHG/Steppe-related ancestry in the Aegean, South Caucasus, and Levant13,16; EHG- and Central-Asian-related ancestry in Anatolian IA and later genomes12; Western hunter-gatherer (WHG)-, South-Asian-, and Central-Asian-related ancestries in Levant Medieval populations16,44; and West-Siberian-related and South-Asian-related ancestry in Iran19 (Figures 3 and S1–S4). As a consequence of these inferred long-distance mobility events, inter-regional genetic differentiation in Southwest Asia, calculated as (1 − f3), rebounds over time (while FST remains low due to increasing intra-regional diversity). We call this “the expanding-mobility model.”"
    Last edited by Angela; 20-12-22 at 01:48.


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    Sorry, forgot to include the graphic:

    [IMG][/IMG]

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