Friday, June 17, 2016

The genetic structure of the world's first farmers

Abstract for pre-print:


"We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to drastically reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those from Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia."


I haven't read through the pre-print yet (just looked at the abstract so far) and will do a post concerning it sometime soon, I'm sure. Enjoy...



List of Y-Chromosome Haplogroups for the new samples:

Armenia_Chalcolithic:

I1407: L1a
I1632: L1a
I1634: L1a

Iran_Mesolithic (Hotu Cave):

I1293: J(xJ2a1b3, J2b2a1a1)

Iran_Neolithic:

I1945: P1(xQ, R1b1a2, R1a1a1b1a1b, R1a1a1b1a3a, R1a1a1b2a2a)

I1949: CT

Iran_Late Neolithic:

I1671: G2a1(xG2a1a)

Iran_Chalcolithic:

I1662: J(xJ1a, J2a1, J2b)
I1674: G1a(xG1a1)

Natufians (Epipaleolithic Levant):

I0861: E1b1b1b2(x E1b1b1b2a, E1b1b1b2b)
I1069: E1b1(xE1b1a1, E1b1b1b1)
I1072: E1b1b1b2(xE1b1b1b2a, E1b1b1b2b)
I1685: CT
I1690: CT

Levant_Neolithic:

I0867: H2 (PPNB)
I1414: E(xE2, E1a, E1b1a1a1c2c3b1, E1b1b1b1a1, E1b1b1b2b) (PPNB)
I1415: E1b1b1 (PPNB)
I1416: CT (PPNB)
I1707: T(xT1a1, T1a2a) (PPNB)
I1710: E1b1b1(x E1b1b1b1a1, E1b1b1a1b1, E1b1b1a1b2, E1b1b1b2a1c) (PPNB)
I1727: CT(xE, G, J, LT, R, Q1a, Q1b) (PPNB)
I1700: CT (PPNC)

Levant_Bronze Age:

I1705: J1(xJ1a)
I1730: J(xJ1, J2a, J2b2a)


Link

10 comments:

  1. Ooops Awale, I posted a response on the wrong page lol. Just don't approve that one and approve this one.

    So are the neolithic levantines direct ancestors to horners (where most of east africans west eurasian comes from), or are they simply a neolithic best fit proxy population?

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    1. Heheh, it's all good. (Nice Tobi/Obito Avatar btw... I'm a Manga~Anime fan myself, I partially grew up on that stuff ;-)).

      Anyway, it does seem like the Neolithic Levantines are a "best fit" of some sort, although they did pull some weird model in the supplementary regarding Somalis:

      http://oi67.tinypic.com/wvemgj.jpg
      "Somali are a mixture of Mota and a population on the Iran_ChL→Levant_BA cline."

      So it may just be that they're a good fit but not a perfect fit. They also made this diagram:

      http://oi65.tinypic.com/311pgrq.jpg

      You can see qpAdm based mixture proportions on the arrows. The "East Africans" (Horn Africans) in question seem to be ~40% Neolithic Levantine-related and ~60% Mota-related. No idea if they used Somalis or any one population or if that's some funky composite of all the substantially West Eurasian groups in the region. We'll have better fits and estimates once David and co. get their hands on these genomes in a month or so once the paper's published in a journal.

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  2. Thanks man lol. Orange mask serious Tobi is my favorite Naruto character by far. He was essentially a high brow Edo Tensei Madara who got the job done. Imo Orange mask Tobi was a better Madara than the real Madara, although I liked the real Madara as well. You have a fav?

    Considering the percentages they probably used Somalis or the oromos who are closest to the Somali eurasian/ssa ratio. I don't see Habeshas droping like 8 eurasian points or Borana Oromo increasing their eurasian by that much.

    Thanks for the diagram.
    Natufians appear to be very arabian like. Levantine neolithic appears to be 1/3 antolian farmer like and bronze age levantines got according to the diagram anatolia chl.

    Are bronze age levantines similar to modern levantines minus the recent SSA for the most part?
    Also I know the purer arabian groups are the most similar to natufians (or so I think), what modern group appear to be the closest to Levantine neolithic?

    lol part of the pains of being a horner is that you don't peak at anything.

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  3. "Thanks man lol. Orange mask serious Tobi is my favorite Naruto character by far. He was essentially a high brow Edo Tensei Madara who got the job done. Imo Orange mask Tobi was a better Madara than the real Madara, although I liked the real Madara as well. You have a fav?"

    I agree with you about him being a better Madara. I was actually really hoping he'd keep being Madara and not be revealed to be Obito because 1) the Obito reveal seemed too obvious & 2) He was, as you said, a better Madara. I actually grew disillusioned with the entire series for a while when he was revealed to be Obito... I regained my love for it gradually and I ultimately liked the ending. As for my favorite character:

    https://www.youtube.com/watch?v=hctF9Ou1glk

    "Considering the percentages they probably used Somalis or the oromos who are closest to the Somali eurasian/ssa ratio. I don't see Habeshas droping like 8 eurasian points or Borana Oromo increasing their eurasian by that much."

    I emailed Lazaridis and asked him about that and:

    http://oi66.tinypic.com/15f19ix.jpg

    He's talking about these mixture proportions:

    http://oi65.tinypic.com/95o7pe.jpg
    http://oi68.tinypic.com/25s3jid.jpg
    http://oi67.tinypic.com/14y3yc.jpg

    Ignore the results for Neolithic Iranian and the Hotu Cave Iranian as the standard errors for them are off the charts and the results are unsurprisingly ridiculous. But basically, they took the least Neolithic Levantine population (0%) and Amharas (~42% Neolithic Levantine) and used their mixture proportions in that figure.

    Somalis look ~35% Neolithic Levantine and Tigrinyas seem 44% Neolithic Levantine but oddly Somalis seem ~41% Bronze Age Levantine and Tigrinyas seem ~53% Bronze Age Levantine. I'd say these somewhat funky results are sadly caused by how they're using Mota as a proxy for our African side which, as you know, is misguided. He messed with that older study's stats as well... They'd have been better off just using Southern Sudanese folk even with their West-Central African-related admixture. I'd wager the admixture levels for Neolithic Levantine ancestry will go up by ~5-6% or so once this is done by someone like David. And the other results (i.e. with Bronze Age Levantines) won't look so ridiculous perhaps. Time will tell.

    "Thanks for the diagram.
    Natufians appear to be very arabian like. Levantine neolithic appears to be 1/3 antolian farmer like and bronze age levantines got according to the diagram anatolia chl."

    Well, at least in regards to Fst; Arabians are much closer to Neolithic and Bronze Age Levantines than Natufians and I have a feeling Arabians' Basal Eurasian levels will be more in line with those of Neolithic Levantines tbh. But we'll see in due time, I hope.

    https://docs.google.com/spreadsheets/d/1Q_xf0SDWv-jA6PT55KQihYKztSR5T8wdkCA0KM50mkw/edit#gid=661149763

    "Are bronze age levantines similar to modern levantines minus the recent SSA for the most part?"

    Yes, that seems to be the case. Though it's actually possible that these Bronze Age Levantines are part African. That might be why Horners show more ancestry from them (granted, we oddly get similar results with Chalcolithic Iranians which makes no sense). They also seem to cluster among Syrians and such... ~5-10% African populations right there. We'll see soon enough when the genomes are publicly available.

    "lol part of the pains of being a horner is that you don't peak at anything"

    Lol, well we can peak for certain ancestries within our own region if that's any consolation. ;-)

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    1. Dude I am with you 100%. Naruto lost it's luster right about that time. The author clearly wanted to finish the series with the number 700 (I believe the reveal was in chapter 600 or something). The ending was ok, and during the Kaguya fight I was holding on to the belief that Madara was going to take over Kaguya or something lol.

      JMAN! lol, probably the funniest character in the entire series. I wonder if things would have been different if he was alive in the series? The pain arc was probably the best story line wise in shippuden.

      True, I remember seeing the Mota reference and wondered why they didn't use proper reference for the African proxy. It's good that others like yourself thought the same.
      I guess we will have to play the wait and see game a bit more.

      Even though the African references were Youraba, what did you think of Somalis being very Natufian like and lacking anatolian admixture in that run on anthrogenica? Seriously the Natufian result was more than the ssa. Of course we'll have to wait and see, but I find this very interesting. The african reference is an issue as well as the possibility that the Natufian component is absorbing some SSA, but still very interesting.

      Doesn't it raise the possibility that a Natufian like populating contributed to horner genetics rather than Levantine Farmers?

      Yea. Somalis increasing in affinity with bronze age Levantines makes no sense. why does it seem like these studies sometimes give us more confusion (sarcasm) lol. But yes I agree with your insights.

      "Lol, well we can peak for certain ancestries within our own region if that's any consolation. ;-)"
      True enough lol.


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    2. "Dude I am with you 100%. Naruto lost it's luster right about that time. The author clearly wanted to finish the series with the number 700 (I believe the reveal was in chapter 600 or something). The ending was ok, and during the Kaguya fight I was holding on to the belief that Madara was going to take over Kaguya or something lol."

      Hahahah.... I didn't actually mind the Kaguya reveal at all and liked the irony of Madara, the mastuh manipulatuh, being manipulated himself but what was disappointing was how she turned out. Seemed like a "shallowly written" character, ultimately. But yes, the Obito reveal occurred around chapter ~600 and it was indeed when the series slowed down for me but it got back up around when Orochimaru summoned the former Kages for Sasuke, I think. But even then... Took a while to restore my faith, lol.

      "JMAN! lol, probably the funniest character in the entire series. I wonder if things would have been different if he was alive in the series? The pain arc was probably the best story line wise in shippuden."

      Hhahaha, yes, J-Man! He's probably who I'd want to be in the Naruto world, quite frankly. ;-) And while I really enjoyed the Pain story-line; I never quite chose a favorite story-line tbh. I hate picking favorites, lol. But yes, the whole Pain story-line and when Tobi/Obito started revealing the Uchiha~Senju History to Sasuke is when the series really started getting "amazing" plot wise. For me, anyway.

      "True, I remember seeing the Mota reference and wondered why they didn't use proper reference for the African proxy. It's good that others like yourself thought the same.
      I guess we will have to play the wait and see game a bit more.

      Even though the African references were Youraba, what did you think of Somalis being very Natufian like and lacking anatolian admixture in that run on anthrogenica? Seriously the Natufian result was more than the ssa. Of course we'll have to wait and see, but I find this very interesting. The african reference is an issue as well as the possibility that the Natufian component is absorbing some SSA, but still very interesting."

      I'd like to get more detailed about this with you but there's a lot to be said about Kurd's analysis there. Email me at Awaleking@gmail.com

      "Doesn't it raise the possibility that a Natufian like populating contributed to horner genetics rather than Levantine Farmers?"

      Honestly, I still think Neolithic Levantines are a better fit especially because of their slight shift toward the Villabruna/WHG cluster (check David over at Eurogenes' Pan-West Eurasia PCA) which could explain why groups like Somalis have "Mediterranean"-like affinities which these Natufians, in my humble opinion, will lack and prove mostly "Southwest Asian"-like.

      "True enough lol."

      Hhehe.


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    3. So the second time I've been gone for almost 2 months (like 7 weeks) hahahah
      Sorry about that man. I don't think I'll go on 7 weeks without replying again, but the next time if it has too happen again I'll give you a heads up if I am busy with something.

      I'll be replying via email by this time tomorrow. I'm only typing this here because of the notification system lol. Just came by to let you know bro, again I'm sorry.

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    4. It's all good, mayne. Take your time. :-)

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  4. Nyeh. They keep using Mota as the source of ancestry in Horners. It might help abit but It probably doesnt match exactly good.
    I guess it would be better to extract the East African nature of the Horner cluster
    Is that possible?

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    1. No, I don't think that's possible in some of these stats but I'm not sure tbh.

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