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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

    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.

    https://www.biorxiv.org/content/10.1...10.18.342816v1

    Interesting stuff:

    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 (Prüfer 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 Anfänger; 20-10-20 at 13:37.

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    Quote Originally Posted by Anfänger View Post
    The Genomic History of the Middle East

    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.

    https://www.biorxiv.org/content/10.1...10.18.342816v1

    Interesting stuff from the Supplementary:

    Indeed. It would seem to imply the spread of Semitic from north to south or do they leave that open?


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    Quote Originally Posted by Angela View Post
    Indeed. It would seem to imply the spread of Semitic from north to south or do they leave that open?
    Yes, that's exactly what they imply in the paper:


    1. An additional source of ancestry needed to model modern Middle Easterners is related to ancient Iranians. Our admixture tests show that this ancestry first reached the Levant, andsubsequently reached Egypt, East Africa and Arabia. The timings of these events interestingly overlap with the origin and spread of the Semitic languages (Kitchen et al.,2009), suggesting a potential population carrying this ancestry may have spread the language. Around this period, we found that all populations experienced a bottleneck coinciding with the 4.2 kiloyear aridification event. This severe drought has been suggestedto have caused the collapse of kingdoms and empires in the Middle East and South Asia, potentially reflected genetically in the signal we identify.



    From the Supplementary Material:

    Bildschirmfoto 2020-10-20 um 13.45.41.png

    J1 and ancient Iranian ancestry from the North. I think it was you, Angela and also Ygorcs who wrote J1 and Semetic languages are possibly from the North few months ago.

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    1 members found this post helpful.
    Thanks for sharing
    I don't know if j1 is related
    To the spread of iranian
    ancestery...🤔
    Or to semitic languages🤔
    But i do believe it came from the
    North and reduced the number
    of e1b1b1 in the levant ...😐
    this something i supected before this paper
    Came out...🤔
    known ancestery:
    Sefhardi/ aschenazi/ mizrahi/ bulgarian
    Eurogenes k13 updated closest:
    4.70345618 Greek_Andros_Island

    eurogenes k13 ancient closeset:
    4.86806943 R136_Lazio_Rome_italy_Late_Antiquity
    http://www.ianlogan.co.uk/sequences_by_group/h3aa-av_genbank_sequences.htm

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    Quote Originally Posted by Anfänger View Post
    Yes, that's exactly what they imply in the paper:



    From the Supplementary Material:

    Bildschirmfoto 2020-10-20 um 13.45.41.png

    J1 and ancient Iranian ancestry from the North. I think it was you, Angela and also Ygorcs who wrote J1 and Semetic languages are possibly from the North few months ago.
    I've thought for years that was the most likely scenario. J1 coming from the north was always pretty clear. Why couldn't the coming of a new y lineage be the agent for a language change? Most linguists disagreed, the amateur ones on other sites most vociferously, saying the new conquerors adopted the language of the locals, which is possible but more unlikely in this scenario, I think. E was virtually wiped out. Why couldn't it be that the language spread all the way south into Africa. Levantine genes brought lots of changes to Africa.

    I'm going to read the paper and supplement with great interest.

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    Razib Khan has opined. I agree with most of what he says, but not all. He's always been a flag waver for lots of R1a and steppe everywhere, perhaps related to his own y.

    A total of 5-10% "European like-steppe admixed ancestry" in more northern areas of the Near East is hardly earth shattering. I think he gives far too little credit to the long Byzantine domination of the whole of the Near East down to but not including Arabia. Yes, there were Mitanni in some areas, but who knows how much of a genetic impact they had.

    At any rate it's impossible to parse out how much is from them and how much from later European domination of the area. One study found that in one area the Philistines seem to have left no lasting impact, but in another area it seems perhaps to have been different.

    Plus, there are all the Greek settlements and then, as I said, the long years of Ottoman control, with people setting in the area from the Slavic countries (slaves and soldier slaves), from Greece and from areas in the Caucasus. Circassians are a big presence in the Levant (and Turkey), forming large segments of the military and civilian administration. They founded Amman for goodness sakes.

    See:
    https://en.wikipedia.org/wiki/Circassians_in_Jordan

    It's the same story in Syria.

    That's not to mention that for much of Ottoman rule Circassian women were the most prized for harems. Goodness knows how many were sold or kidnapped for the slave marts. African dna entered the Near East in the same way, and their women were far less prized, the offspring sometimes being killed at birth.

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    Razib is r1a???😲
    Wow that shows that y haplogroup
    Have no connection to look ..
    He looks nothing like beniamin nethanyahu
    Or tom hanks
    Both confirmed r1a...

    P.s
    I hope he is not obsesed with
    r1a=steppe spread
    Like other people in the net 🤔😉
    I agree with you that later influence than mitanni could
    Increase steppe ancestery in levant and north middle-east😉

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    i think it's rather unlikely that ancient greeks could have siginificantly increased steppe ancestry in near east. more likely that it was from migrations directly from north of caucasus, maybe the ottomans themselves, contributed most to the increase of this ancestry in anatolia but it seems they didn't look at this region here.
    there are also large kurdish comunities in countries like syria, iraq.

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    Razib Khan writes:

    "Some of these dates are hard to credit. For example, I obtain a midpoint estimate of Iranian admixture into Egypt around 1836 BC! ... The authors talk about Semitic languages, and ancient Egyptian is not Semitic. So it could be a minority population mixed into the Egyptians, but this is a massive event that we don’t have records of."


    On the contrary there is plenty of evidence for large scale settlement of Semites in Egypt c. 1800 BC.


    https://en.wikipedia.org/wiki/Hyksos...rival_in_Egypt

    https://en.wikipedia.org/wiki/Fourte...nasty_of_Egypt

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    Other groups that could spread
    Some steppe ancestery are
    Hurrians and hittites not only mitanni
    P.s
    Alichu mention the kurdish community
    In syria so that could increase steppe
    Ancestery in modern syrians.
    Basically
    The lowest steppe in the middle east
    Is in south arabia
    And they have also 10-16% african
    Ancestery autosomaly speaking...🤔
    They also have the lowest neaderthal
    Admixture compare to levantines( represented by syrians, jordanians in this study)
    The auther concludes that it is not only african ancestery which reduced the neaderthal allells
    Since saudi core sample and emirati core sample both carry only 3% african ancestery not high.. 🤔
    The other big thing which reduced
    The neaderthall allells is basal euroasian
    Ancestery which is high in arabia
    And higher compare to levant..

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    [QUOTE=Angela;614176]Yes, Razib is a Brahmin, although a Bengali one, so not so unusual. I've always held that ydna has nothing to do with physical appearance.

    A lot of people are still enamored of the hordes from the steppes spreading their genes everywhere. They certainly spread their genes and language around, including in Italy. My point is just that there are a lot of source populations which could contribute something to that 5-10%.

    As for the Basal Eurasian, from the horse's mouth:

    "Iosif Lazaridis


    I'm quite excited about this paper as it seems to provide new evidence for the idea I proposed in 2016 that Basal Eurasian ancestry in the ancient Near East diluted Neandertal ancestry."


    However, pinning down for modern populations is tricky, as (a) these have less Basal Eurasian ancestry -- Neolithic Iranians/Natufians admixed with others and (b) they also often have some African admixture which also dilutes Neandertal ancestry


    So, it is quite exciting to see that the authors have been able to study this with full genomes (which are great for teasing out variation in Neandertal ancestry) and while controlling for African ancestry (see their Fig. 3c)









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    @kingjohn

    There are so many source populations for 5-10% Steppe ancestry in Levantines(Peninsula Arabs have no steppe). Greeks,Romans,IE Iranian,Ottomans,Armenians,Slaves from northern Caucasus,... .

    @Angela

    Thanks for sharing. I am pretty sure there will be Basaleurasian samples in the future and Lazaridis will finally have ancient DNA to proof his idea of Basaleurasians.

    Btw, I like the idea that CHG/Iran and J1 and J2 pop up everywhere. Not that bad steppe guys, hu ?

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    Attachment 12372
    Table s1: ( from paper page 37)
    What is the EHG represent here. ?

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    Quote Originally Posted by kingjohn View Post
    Attachment 12372
    Table s1: ( from paper)
    What is the EHG represent here. ?
    This one? :

    Bildschirmfoto 2020-10-20 um 20.06.43.jpg

    Good question... but I think some HGs from Eastern Europe maybe Samara_HG or Karelia_HG. Both are very very much alike.

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    Quote Originally Posted by Anfänger View Post
    This one? :

    Bildschirmfoto 2020-10-20 um 20.06.43.jpg

    Good question... but I think some HGs from Eastern Europe maybe Samara_HG or Karelia_HG. Both are very very much alike.

    Yes this one

    Yemenites score here 4-6% EHG
    thats why i thought even arabians have some steppe ancestery🤔
    Since the steppe ancestery was combination
    Of EHG+CHG.
    ..🤔

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    Quote Originally Posted by kingjohn View Post
    Yes this one
    Yemenites score here 4-6% EHG
    thats why i thought even arabians have some steppe ancestery������
    Since the steppe ancestery was combination
    Of EHG+CHG.
    ..������
    Hmm... i am not familiar with qpAdm modelling. Maybe they should have included CHG. The other EHG results also don't seem right to me.





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    Iranian-related ancestry in the Levant = Semitic and other non-IE languages, in India = Dravidian and other non-IE languages, in Central Asia = Altaic and and other non-IE languages, in Caucasus = Caucasian and and other non-IE languages, in Europe = Etruscan and other non-IE languages, in Anatolia = Hattic and other non-IE languages, in North of Eurasia = Uralic and and other non-IE languages, ... The most interesting is that the original language of people who lived in Iran is said to be Elamite which was an isolated language with absolutely no relation to other languages!

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    Problem is that Etruscans genetically obviously came into Italy from Central Europe.
    Last edited by Angela; 26-10-20 at 16:27.

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    Etruscan is certainly an European language, Semitic and Egyptian are certainly Afro-Asiatic languages,... they have nothing to do with Iran.

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    The land in the east of Elam in the 3rd millennium BC was Parhasi in the Akkadian sources, the same land that Achaemenids called Pars (Persia) but in the ancient Egyptian sources, name of Persia was Peles, for example look the name of this land on the statue of Darius the Great which was carved in Egypt:



    We see nothing about Parhasi in the Mesopotamian sources in the 2nd millennium BC but in the ancient Egyptian sources we read about Peleset as a land in the south coast of Canaan (Palestine), about 3200 years ago they invaded to Egypt too.


    Peleset, captives of the Egyptians, from a graphic wall relief at Medinet Habu, in about 1185-52 BC, during the reign of Ramesses III

    Those are fluted hats.


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