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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. Lootah, Pille Hallast, Saeed Al Turki, Hilary C Martin, Yali Xue, Chris Tyler-Smith
    Abstract
    The Middle East is an important region to understand human evolution and migrations, but is underrepresented in genetic studies. We generated and analysed 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 find Arabians have elevated Basal Eurasian ancestry that dilutes their Neanderthal ancestry. A divergence in population size within the region starts before the Neolithic, 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 archaeologically-documented 4.2 kiloyear aridification of the area, while regional migrations increased genetic structure, and may have contributed to the spread of the Semitic languages. We identify new variants that show evidence of selection, some dating from the onset of the desert climate in the region. Our results thus provide detailed insights into the genomic and selective histories of the Middle East.

    Supplementary pdf here.

    A few of the highlights:

    Another contrast between the Levant and Arabia is the excess of African ancestry in
    Arabian populations. We find that the closest source of African ancestry for most populations
    in our dataset is Bantu Speakers from Kenya, in addition to contributions from Nilo-Saharan
    speakers from Ethiopia specifically in the Saudi population. We estimate that African
    admixture in the Middle East occurred within the last 2,000 years, with most populations
    showing signals of admixture around 500-1,000 years ago (Figure S5 and Table S2).

    These results collectively suggest that present-day Middle Eastern populations do not harbour any
    significant traces from an earlier expansion out of Africa, and all descend from the same
    population that expanded out of the continent ~50-60 kya.
    ...
    In addition to the local ancestry from Epipaleolithic/Neolithic people, we find an ancestry
    related to ancient Iranians that is ubiquitous today in all Middle Easterners (orange
    component in Figure 1C; Table S1). Previous studies showed that this ancestry was not
    present in the Levant during the Neolithic period, but appears 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 3,900 and
    5,600 ya (Table S3), followed by admixture in Egypt (2,900-4,700 ya), East Africa (2,200-
    3,300) and Arabia (2,000-3,800). 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 S8).
    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,
    4.8-6.5] kya, agreeing with a potential Bronze Age expansion; however, we do find rarer
    earlier diverged lineages coalescing ~17 kya (Figure S9)
    ...
    To investigate Neanderthal introgression in our dataset, we exploited the
    accurate phasing of our samples and compared cross-coalescent rates with the high
    coverage Vindija Neanderthal genome (PrŁfer et al., 2017). All Middle Easterners showed an
    archaic admixture signal at a time point similar to other Eurasians (Figure 3A).
    ...
    Previous studies identified two correlated variants (rs41380347 and rs55660827)
    in the LCT region, distinct from the known European variant (rs4988235), that are associated
    with lactase persistence in Arabia (Imtiaz et al. 2007; Enattah et al. 2008). For the Arabian
    LCT variant rs41380347, we found evidence for strong selection (s = 0.011, logLR = 13.27 in
    Saudis), similar to, but slightly weaker than, the reported strength of selection at rs4988235
    in Europeans
    Last edited by pmokeefe; 10-19-2020 at 04:48 PM.
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  3. #2
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    In case, like me, you were wondering about this event:
    Around this period, we found that all populations experienced a bottleneck
    coinciding with the 4.2 kiloyear aridification event.

    Are there potential signals of this event mentioned in other DNA papers?
    Last edited by pmokeefe; 10-19-2020 at 05:27 PM.
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    [Finally they recognized Y-DNA J1 was originally an Iranian marker.

    133 In addition to the local ancestry from Epipaleolithic/Neolithic people, we find an ancestry
    134 related to ancient Iranians that is ubiquitous today in all Middle Easterners (orange
    135 component in Figure 1C; Table S1). Previous studies showed that this ancestry was not
    136 present in the Levant during the Neolithic period, but appears in the Bronze Age where
    139 ~50% of the local ancestry was replaced by a population carrying ancient Iran-related
    140 ancestry (Lazaridis et al., 2016). We explored whether this ancestry penetrated both the
    141 Levant and Arabia at the same time, and found that admixture dates mostly followed a North
    142 to South cline, with the oldest admixture occurring in the Levant region between 3,900 and
    143 5,600 ya (Table S3), followed by admixture in Egypt (2,900-4,700 ya), East Africa (2,200-
    144 3,300) and Arabia (2,000-3,800). These times overlap with the dates for the Bronze Age
    145 origin and spread of Semitic languages in the Middle East and East Africa estimated from
    146 lexical data (Kitchen et al., 2009; Figure S8). This population potentially introduced the Y
    147 chromosome haplogroup J1 into the region (Chiaroni et al., 2010; Lazaridis et al., 2016). The
    148 majority of the J1 haplogroup chromosomes in our dataset coalesce around ~5.6 [95% CI,
    149 4.8-6.5] kya, agreeing with a potential Bronze Age expansion;
    Last edited by RCO; 10-19-2020 at 06:10 PM.
    J1 FGC5987 to FGC6175 (188 new SNPs)
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    North_Swedish + PT + PT + PT @ 3.96 EUtest 4

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    The paper confirms the J1 Iranian invasion of the Mesopotamian Lowlands, Levant, Arabia, Eastern Africa and the Steppe, because the Middle Eastern areas were already "densely" populated they kept their Semitic languages, but in the Steppe they also changed to new Iranian Indo-European languages. What kind of population from Iran would expand to all places around the Bronze Age with such a power and impact ? They should have a big social economic, technological, military and political superiority in that period because the Iranian (orange) component is everywhere.
    Last edited by RCO; 10-19-2020 at 10:47 PM.
    J1 FGC5987 to FGC6175 (188 new SNPs)
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    Y-DNA - Milhazes, Barcelos, Minho, Portugal.
    mtDNA - Ilha Terceira, Azores, Portugal
    North_Swedish + PT + PT + PT @ 3.96 EUtest 4

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    Quote Originally Posted by RCO View Post
    The paper confirms the J1 Iranian invasion of the Mesopotamian Lowlands, Levant, Arabia, Eastern Africa and the Steppe, because the Middle Eastern areas were already "densely" populated they kept their Semitic languages, but in the Steppe they also changed to new Iranian Indo-European languages. What kind of population from Iran would expand to all places around the Bronze Age with such a power and impact ? They should have a big social economic, technological, military and political superiority in that period because the Iranian (orange) component is everywhere.
    As far as I remember before the Semitic Akkad language appeared in Mesopotamia the Sumerian language was widely spoken there

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    Quote Originally Posted by RCO View Post
    The paper confirms the J1 Iranian invasion of the Mesopotamian Lowlands, Levant, Arabia, Eastern Africa and the Steppe, because the Middle Eastern areas were already "densely" populated they kept their Semitic languages, but in the Steppe they also changed to new Iranian Indo-European languages. What kind of population from Iran would expand to all places around the Bronze Age with such a power and impact ? They should have a big social economic, technological, military and political superiority in that period because the Iranian (orange) component is everywhere.
    J-P58 is originally associated with Iran Neolithic-type people from somewhere in the highland West Asian realm, no doubt. But Indo-Iranian languages and their speakers? Fat chance.
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    Quote Originally Posted by hartaisarlag View Post
    J-P58 is originally associated with Iran Neolithic-type people from somewhere in the highland West Asian realm, no doubt. But Indo-Iranian languages and their speakers? Fat chance.
    Indo-Iranian languages are R1a-Z93-Y3. The Mittani language is probably R1a-Z93-Z2124

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    Quote Originally Posted by VladimirTaraskin View Post
    Indo-Iranian languages are R1a-Z93-Y3. The Mittani language is probably R1a-Z93-Z2124
    I generally agree with you that this is more on the mark, but I don't deny the possibility that there were other non-R1a lineages in the mix.
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  16. #9
    I doubt that Proto-Semitic or Central Semitic spread with J1. The physical characteristics of the Proto-Semites match Bedja and North Africans rather than Iranians and Modern Middle Easterners (Lipiński 2001:47). Furthermore, J1 was only found among low status individuals in the Bronze Age Levant and is only found at low frequencies among Ethio-Semitic speakers.

    More importantly, the Hebrews seem to have specifically targeted J1 carriers when they ethnically cleansed (Herem-warfare) non-Semitic speakers from the Levant, so it is doubtful that J1 carriers were considered "Semitic" by Iron Age & Bronze Age Semitic speakers.

    Quote Originally Posted by The Genomic History of the Bronze Age SouthernLevant - Agranat-Tamir et al. 2020
    Level K-4 Late Iron I, large courtyard house destroyed in big fire. The individual (I4517) seems to have perished during the devastation of the city.
    I4517 ---- Megiddo_IA ---- J1a2a1a2d2b2b2c2:S16807/S21060

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    Quote Originally Posted by pmokeefe
    In addition to the local ancestry from Epipaleolithic/Neolithic people, we find an ancestry
    related to ancient Iranians that is ubiquitous today in all Middle Easterners (orange
    component in Figure 1C; Table S1). Previous studies showed that this ancestry was not
    present in the Levant during the Neolithic period, but appears 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
    This is also largely visible in modern Arabians, where their Levant_N / Iran_ChL ratios are way tilted in favor of Levant_N.

    I wonder if just as there was a slow diffusion of Iranian-like and later on Caucasus-originated geneflow to the Levant (and Iranian-like all the way to the Arabian peninsula), as has been shown in the last several ancient Levant papers (like Haber et al. or Agranat-Tamir et al.), if there was also a slow diffusion "back" north of Levant_N-rich admixture to the Levant. If so, that would vindicate several theories which have been discussed by many of us here:

    1. That there was a genetic pendulum in the Levant which "countered" the additional Aegean, Anatolian, Caucasus and Iranian-like admixtures which have entered the Levant during the LBA and especially late IA (especially IAIII) and Persian, Hellenistic and Roman eras. This would make a lot of sense to be honest, as samples from the Levant shown in those studies show substantial such admixtures, while modern-day Levantines seem to be way too close to Bronze Age Levantines, as if all these admixtures simply didn't take place.

    2. One specific case is of course the Samaritans - their autosomal similarity to Bronze Age Levantines, while gave them a certain prestige in our community as some sort of ancient genetic relic of the region, might have got some admixture from Levant_N-rich population which would explain how a Levant_IAIII population, which they would descend from, became Levant_MBA-like.

    3. This might also be the key to where the genetic impact of the Ghassanids and the Nabataeans in the Levant disappeared to - it didn't, and modern-day Christian Levantines, which on the face of it do not show any significant "Arabian" admixture as opposed to their Muslim co-patriots, actually do have such admixture just from pre-Islamic Arabs which elevated their Levant_N and "diluted" their Aegean and Persian admixtures.
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