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Thread: The genomic history of the Middle East

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    The genomic history of the Middle East

    The genomic history of the Middle East
    Mohamed A. Almarri, Marc Haber, Reem A. Loota, Pille Hallast, Saeed Al Turki, Hilary C. Martin, Yali Xue, Chris Tyler-Smith
    Open Access. Published:August 04, 2021. DOI: https://doi.org/10.1016/j.cell.2021.07.013

    Highlights
    Middle Easterners do not have ancestry from an early out-of-Africa expansion
    Basal Eurasian and African ancestry in Arabians deplete their Neanderthal ancestry
    Populations experienced bottlenecks overlapping aridification events
    Identification of recent single and polygenic signals of selection in Arabia

    Summary
    The Middle East region is important to understand human evolution and migrations but is underrepresented in genomic studies. Here, we generated 137 high-coverage physically phased genome sequences from eight Middle Eastern populations using linked-read sequencing. We found no genetic traces of early expansions out-of-Africa in present-day populations but found Arabians have elevated Basal Eurasian ancestry that dilutes their Neanderthal ancestry. Population sizes within the region started diverging 1520 kya, when Levantines expanded while Arabians maintained smaller populations that derived ancestry from local hunter-gatherers. Arabians suffered a population bottleneck around the aridification of Arabia 6 kya, while Levantines had a distinct bottleneck overlapping the 4.2 kya aridification event. We found an association between movement and admixture of populations in the region and the spread of Semitic languages. Finally, we identify variants that show evidence of selection, including polygenic selection. Our results provide detailed insights into the genomic and selective histories of the Middle East.
    https://www.cell.com/cell/fulltext/S...674(21)00839-4

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    Insights into the genomic histories of diverse human populations using whole-genome sequencing analysis.
    Mohamed A. A. M. Almarri (lead author of the Cell paper).
    Wellcome Sanger Institute
    Darwin College
    University of Cambridge
    This thesis is submitted for the degree of Doctor of Philosophy
    January 2021

    Abstract
    Despite the progress in sampling many populations, human genomics research is still not fully
    reflective of the diversity found globally. Understudied populations limit our knowledge of genetic
    variation and population history, and their inclusion is needed to ensure they benefit from future
    developments in genomic medicine. In this thesis, I describe extending our understanding of
    global genetic diversity and population history by two main projects. The first is focused on
    structural variation in a diverse set of 54 human populations which are part of the Human
    Genome Diversity Project (HGDP-CEPH) panel. Using whole-genome sequences previously
    produced at the Wellcome Sanger Institute, I generated a comprehensive catalogue of structural
    variation identifying a total of 126,018 variants, of which 78% are novel. Some reach high
    frequency and are private to continental groups or even individual populations, including
    regionally-restricted runaway duplications and putatively introgressed variants from archaic
    hominins. By de novo assembly of 25 genomes using linked-read sequencing, I discovered
    1643 breakpoint-resolved unique insertions, in aggregate accounting for 1.9 Mb of sequence
    absent from the GRCh38 reference genome, highlighting the limitation of a single human
    reference genome. In the second project I collected and analysed a dataset of 137 highcoverage
    physically-phased genome sequences from eight Middle Eastern populations using
    linked-read sequencing. Focusing on the population history using single nucleotide variants, I
    found no genetic traces of archeologically documented early expansions out-of-Africa in
    present-day populations in the region. I show that Arabian populations have the lowest
    Neanderthal ancestry of all non-African populations tested, which is explained by them having
    elevated Basal Eurasian ancestry. By comparing Levantines and Arabian historical population
    sizes, I find a divergence that starts before the Neolithic era, when Levantines expanded while
    Arabians maintained small populations that could have derived ancestry from local epipaleolithic
    hunter-gatherers. All populations suffered a bottleneck overlapping the archaeologicallydocumented
    aridification events, with Arabians decreasing in size with the onset of the desert
    climate in Arabia ~6 kya while the Levantine bottleneck overlaps the 4.2 kiloyear aridification
    event. I also identify an ancestry that is associated with the spread of Semitic languages across
    the region during the Bronze Age. Finally, I identify novel variants that show evidence of
    selection, including signals of polygenic selection. This thesis fills an important gap in the study
    of diverse human populations, although further work is needed to sequence and characterize
    additional genetically underrepresented groups
    YFull: YF14620 (Dante Labs 2018)

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    Good.

    In addition to the local ancestry from Epipaleolithic/Neolithic people, we found an ancestry related to ancient Iranians that is ubiquitous today in all Middle Easterners (orange component in Figure 1B; Table 1). Previous studies showed that this ancestry was not present in the Levant during the Neolithic period but appeared in the Bronze Age where ∼50% of the local ancestry was replaced by a population carrying ancient Iran-related ancestry (Lazaridis et al., 2016). We explored whether this ancestry penetrated both the Levant and Arabia at the same time and found that admixture dates mostly followed a North to South cline, with the oldest admixture occurring in the Levant region between 3,300 and 5,900 ya (Table S2), followed by admixture in Arabia (2,0003,500 ya) and East Africa (2,1003,300 ya). These times overlap with the dates for the Bronze Age origin and spread of Semitic languages in the Middle East and East Africa estimated from lexical data (Kitchen et al., 2009; Figure 2). This population potentially introduced the Y chromosome haplogroup J1 into the region (Chiaroni et al., 2010; Lazaridis et al., 2016). The majority of the J1 haplogroup chromosomes in our dataset coalesce around ∼5.6 (95% CI, 4.86.5) kya, agreeing with a potential Bronze Age expansion; however, we did find rarer earlier diverged lineages coalescing ∼17 kya (Figure S2). The haplogroup common in Natufians, E1b1b, is also frequent in our dataset, with most lineages coalescing ∼8.3 (79.7) kya, though we also found a rare deeply divergent Y chromosome, which coalesces 39 kya (Figure S2).
    The ancient Iranian population who bred and born Iranian J1-L620 on the land. They don't have or don't know the L620>FGC6064 and the L620>PF4816>ZS6599 basal Iranian branches/samples that we have. The Iranian=Indo-European X Semitic=Afro-Asiatic frontier close to the Zagros Mountain range Iraq/Iran border.
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    Well this one is interesting! Even if J2 seems almost absent (so far did see only J1, E-M25 and L/T) and I admit I did not read much of the admixture and ancient DNA papers of the last years, some assumptions others and me had on the Pre-Bronze "general migration path" and Pre-Chalcolithic origin of most of J2 or in particular J2a-L26 subclades seems to overlap with this findings from the Arabian Peninsula and the Fertile Crescent:
    Populations from the Levant and Iraq (Lebanese, Syrians, Jordanians, Druze, BedouinA, and Iraqi-Arabs) clustered together, while Iraqi-Kurds clustered with Central Iranian populations. Arabian populations (EmiratiA, Saudis, Yemenis, and Omanis) clustered with BedouinB from the HGDP. Within the Emirati population, we identified subpopulations with excess Iranian and South Asian ancestries (EmiratiB and EmiratiC; Figure 1.
    Principal component analysis (Figures 1D and S1) shows that present-day Middle Easterners are positioned between ancient Levantine hunter-gatherers (Natufians), Neolithic Levantines (Levant_N), Bronze Age Europeans, and ancient Iranians. Arabians and Bedouins are positioned close to ancient Levantines, while present-day Levantines are drawn toward Bronze Age Europeans. Iraqi-Arabs, Iraqi-Kurds, and Assyrians appear relatively closer to ancient Iranians. We found that most present-day Middle Easterners can be modeled as deriving their ancestry from four ancient populations (Table 1): Levant_N, Neolithic Iranians (GanjDareh_N), Eastern Hunter Gatherers (EHG), and an ∼4,500-year-old East African (Mota). We observed a contrast between the Levant and Arabia: Levantines have excess EHG ancestry (Figure 1E), which we showed previously had arrived in the Levant after the Bronze Age along with people carrying ancient south-east European and Anatolian ancestry (Haber et al., 2017, Haber et al., 2020).
    gr2.jpg

    So while they use CHG and it is tied firmly with ancient J2a-Z6046,Z6049 at least J1 and probably also a lot of J2a-L26 in the Arabian Peninsula and also the Fertile Crescent had a different more "southern" migration from the Iran area. J2a2-PF5008,PF5050 seems to have remained longer in the Iranian area (ancient and modern diversity in Central Asia). So I wonder if this could mean a main migration South of the Zagros (ancient Elam) or maybe even trough the Northern/Central Zagros (seems less likely?) to the Northern Fertile Crescent?
    The ancient J-Y-DNA seems to favor the migration along the South Caspian - South Caucasus - South Black Sea axis: https://haplotree.info/maps/ancient_...bp=500000,5000
    Also intriguing the Levantines with excess EHG: is this from the Late Bronze Age collapse (Aegean centered) ancestry? Which could be the main Y-Haplogroups in the Western part of the Fertile Crescent from the three "northern" ancient populations?
    Just trying :
    Levant_N: E, G, T, H (L)
    Neolithic Iranians (GanjDareh_N): J2a-L26, J1, R2a (L, R1b-V1636)
    Eastern Hunter Gatherers (EHG) from Aegean LBA: J2b-L283 (maybe explaining the few Jewish subbranches), E1b-V13, Some R1b like Z2103, Some I2 and maybe even some J2a?

    Interested in your comments...
    Last edited by ChrisR; 08-05-2021 at 09:55 AM. Reason: Hg Update
    Particularly interested in: DNA/Admixture from Historical Tyrol, Central Alps and related/connected populations; Y-DNA J2a-M67-L210, J2a-PF5197-PF5169, R1a-M17, R1b-U106-Z372; mtDNA J1b1b, J1c1d2-A11884G, U5a2b2-G10685A, U5b1b1-b-T16192C! Projects: Hidden Content , Hidden Content , J2a-PF5197, ISOGG Wiki, GenWiki (german)

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    Quote Originally Posted by ChrisR View Post
    ...
    Levant_N: E, G, T, (L)
    Neolithic Iranians (GanjDareh_N): J2a1a-L26, J1, (L, R1b-V1636)
    Eastern Hunter Gatherers (EHG): J2b-L283 (maybe explaining the few Jewish subbranches), E1b-V13

    Interested in your comments...
    Y-H2?

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    Quote Originally Posted by parasar View Post
    Y-H2?
    Thx. Looked it up and there is the 7300-6750 BC Motza Levantine Pre-Pottery Neolithic B sample. Seems this one is not in https://haplotree.info/maps/ancient_...bp=500000,5000
    In ancient and modern times H2 seems to be sparse and never dominating in any area - see phylogeographer heatmap in Levant under 3% modern presence
    H phylogeographer.com scripts heatmap.php.png
    Last edited by ChrisR; 08-05-2021 at 08:10 AM. Reason: Map
    Particularly interested in: DNA/Admixture from Historical Tyrol, Central Alps and related/connected populations; Y-DNA J2a-M67-L210, J2a-PF5197-PF5169, R1a-M17, R1b-U106-Z372; mtDNA J1b1b, J1c1d2-A11884G, U5a2b2-G10685A, U5b1b1-b-T16192C! Projects: Hidden Content , Hidden Content , J2a-PF5197, ISOGG Wiki, GenWiki (german)

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    Quote Originally Posted by ChrisR View Post
    Just trying :
    Levant_N: E, G, T, (L)
    Neolithic Iranians (GanjDareh_N): J2a-L26, J1, (L, R1b-V1636)
    Eastern Hunter Gatherers (EHG) from Aegean LBA: J2b-L283 (maybe explaining the few Jewish subbranches), E1b-V13, Some R1b like Z2103, Some I2 and maybe even some J2a?

    Interested in your comments...
    All male samples found in Neolithic Ganj Dareh by Narasimhan et al. 2019 come under R2a-M124, so that's another subclade to include for Ganj_Dareh_N.
    YFull: YF72440 (FTDNA - IN41220)

    Ancestral Haplos (Punjabi Jatt):
    * Father: R2-M479 > M124 > V1180 > SK2142 > Y1379 > Y1383 > Y154920* (xZ6135) - M5a1a-G9064A (185G)
    * Maternal Uncle: R1b-M343 > M269 > Z2103 > Z2109 > Y14416 > Y35099 > Y84821 - U7a3a-A9852G > G6150A > C15433T
    * MGMs MGF: R1a-M420 > M198 > Z93 > L657 > Y7 - ?

    Hidden Content

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    I looked more into Iran GanjDareh N:
    Neolithic settlement in western Iran. It is located in the Harsin County in east of Kermanshah Province, in the central Zagros Mountains.
    The genetic structure of the world’s first farmers 2016 Supplementary Information:
    five identified levels (A to E), with the lowest level E being the oldest. ... Current evidence places the occupation of the site at approximately 8000-7700 calBCE11. None of the human remains have been directly dated. The human remains are highly fragmentary. ... six Ganj Dareh individuals (all petrous bone samples) are included in this study. None has a direct radiocarbon date:
    GD13A (I1290): 30-50 year-old male from level C
    GD14B (I1944): 3-4 year-old child from level B1.
    GD16 (I1945): 5.5-7.5 year-old child from level D.
    GD37 (I1949): 30-50 year-old male from levels D/E.
    GD39 (I1951): 1.5-2.5 year-old child from level D crypt.
    Some Iran GanjDareh N admixture analysis seems to use I1944
    The genetics of an early Neolithic pastoralist from the Zagros, Iran 2016 Gallego-Llorente et al uses 13A (referred to as GD13a)

    In Almarri et al 2021 they use weights from ancient GanjDareh_N , so without digging I assume from all of the above samples.
    Given the location this individual seems more a "Neolithic Eastern Mesopotamian / Western Iranian" proxy to Fertile Crescent and Arabia, then representing the IMO very interesting Northeastern Iran Neolithic.

    Not sure if autosomal SNP coverage is satisfying but would this sample not be more appropriate, even a singleton?
    I2312 - Alborz Mountains, near Behshahr, Belt Cave, J2a2-PF5050
    Mean Age (ybp): 11950 ~ 9930 BC

    Unfortunately no Pre-Chalcolithic individual from the modern Turkmenistan/Uzbekistan area seems to exist, also nothing from Southeast Iran/Afghanistan/Pakistan territory.
    So it might be not all crystal clear until we have enough geographic coverage for the 8000-11000 BC timeframe.

    EDIT
    Quote Originally Posted by aaronbee2010 View Post
    All male samples found in Neolithic Ganj Dareh by Narasimhan et al. 2019 come under R2a-M124, so that's another subclade to include for Ganj_Dareh_N.
    Thx, with quick look could not find the individual descriptions/IDs
    Last edited by ChrisR; 08-05-2021 at 10:14 AM. Reason: edit re aaronbee2010
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    https://www.biorxiv.org/content/10.1101/423079v1#page

    Study says Neolithic Iranians were a mixture of Dzudzuana and ANE. And modern Iranians today are 23.2-42.5% Neolithic Iranian (using average populations). 08543257-1F56-4DA8-9920-E1288D78AC9A.jpeg

    So this makes me wonder if ANE were P, afaik. How much R1a/R1b derives from the ANE from neolithic Iranians. Rather than Steppe. And I suppose Dzudzuana was something like J, no? J2 is considered too be Iranian farmer, so I guess Dzudzuana was J2, I can’t find much journals or studies explaining there haplo.

    What makes me even more confused, were CHG and IHG the same people just with different percentages of Dzudzuana and ANE?

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    Quote Originally Posted by KHAN View Post
    https://www.biorxiv.org/content/10.1101/423079v1#page

    Study says Neolithic Iranians were a mixture of Dzudzuana and ANE. And modern Iranians today are 23.2-42.5% Neolithic Iranian (using average populations). 08543257-1F56-4DA8-9920-E1288D78AC9A.jpeg

    So this makes me wonder if ANE were P, afaik. How much R1a/R1b derives from the ANE from neolithic Iranians. Rather than Steppe. And I suppose Dzudzuana was something like J, no? J2 is considered too be Iranian farmer, so I guess Dzudzuana was J2, I can’t find much journals or studies explaining there haplo.

    What makes me even more confused, were CHG and IHG the same people just with different percentages of Dzudzuana and ANE?
    R1a and r1b? Probably 0. The only R variant seen with them is R2. I doubt that the ANE derived populations where R1 diversified into R1a and R1b were the same donor populations of ANE ancestry in Neolithic Iranians.

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