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Thread: The genetic structure of the world’s first farmers

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    Quote Originally Posted by epoch View Post
    I didn't read that. The paper states:
    Got it now, thanks for explaining.

    CHG was paleolithic and mesolithic.
    Yes, but overlapping with Iranian Neolithic as perf figure 1a.

    Any idea why Figure 1c is not in tune with Figure 4b? According to 1c Anatolian N is mixture of mostly Natufian/Levant farmer with WHG. According to 4b mostly Iranian N, then Levant N, and some WHG. 1b PCA chart also plots Anatolian and European farmer between position of Natufians and WHG. Iranian N being very far away.

    A very short look at archaeology could have told you that as well.
    Right



    No, the 50/50 basis for Yamnaya hasn't changed.
    Or was it Corded Ware with very small farmer input?
    Be wary of people who tend to glorify the past, underestimate the present, and demonize the future.

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    For all doubters of Steppe invasion into South Asia and India here is a genetic proof:
    In South Asia, our dataset provides insight into the sources of Ancestral North Indians (ANI), a West Eurasian related population that no longer exists in unmixed form but contributes avariable amount of the ancestry of South Asians, (Supplementary Information, section 9) (Extended Data Fig. 4). We show that it is impossible to model the ANI as being derived from any single ancient population in our dataset. However, it can be modelled as a mix of ancestry related to both early farmers of western Iran and to people of the Bronze Age Eurasian steppe; all sampled South Asian groups are inferred to have significant amounts of both ancestral types. The demographic impact of steppe related populations on South Asia was substantial, as the Mala, a south Indian population with minimal ANI along the ‘IndianCline’ of such ancestry, is inferred to have ~18% steppe-related ancestry, while the Kalashof Pakistan are inferred to have ~50%, similar to present-day northern Europeans.

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    Quote Originally Posted by LeBrok View Post
    For all doubters of Steppe invasion into South Asia and India here is a genetic proof:
    There was without a doubt Steppe influx into India the Out of India theory doesn't make much sense so I don't bother, however the figure of 50% for other South Asians is far too high even tribal Indians are shown wth ~18% Steppe admixture which is exactly the reason that brings the authors to the idea that something very EHG like did already exist in the region prior to the Indo_Iranian migration. So not all of the "Steppic" ancestry there is really Steppic but could be even more ancient.

    And this would also explain where the ~13% EHG admixture in the mesolithic and calcolthic Iranian samples come from.

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    Quote Originally Posted by LeBrok View Post
    For all doubters of Steppe invasion into South Asia and India here is a genetic proof:

    In South Asia, our dataset provides insight into the sources of Ancestral North Indians (ANI), a West Eurasian related population that no longer exists in unmixed form but contributes avariable amount of the ancestry of South Asians, (Supplementary Information, section 9) (Extended Data Fig. 4). We show that it is impossible to model the ANI as being derived from any single ancient population in our dataset. However, it can be modelled as a mix of ancestry related to both early farmers of western Iran and to people of the Bronze Age Eurasian steppe; all sampled South Asian groups are inferred to have significant amounts of both ancestral types. The demographic impact of steppe related populations on South Asia was substantial, as the Mala, a south Indian population with minimal ANI along the ‘IndianCline’ of such ancestry, is inferred to have ~18% steppe-related ancestry, while the Kalashof Pakistan are inferred to have ~50%, similar to present-day northern Europeans.
    If Bronze-Age-Eurasian-steppe-like people were already in North India and early-farmers-of-Western-Iran migrated there we could have the same result.

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    This is what we've been waiting for.

    I haven't had a chance to read this as an old college buddy passing through town compelled me to compromise my faculties for the past 18 hours.

    A couple things.

    I while ago I noticed that there was a surged in Teal in steppe EHG prior to any evidence of contact with the Caucuses. On this notion I proposed early contacts with the South East/Iranian Plateau. The evidence of a freakishly early neolithic on the Volga is also consistent with this.

    Also I think Basal Eurasian comes from South Asia.

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    Quote Originally Posted by A. Papadimitriou View Post
    If Bronze-Age-Eurasian-steppe-like people were already in North India and early-farmers-of-Western-Iran migrated there we could have the same result.
    Before bronze age Steppe people had different admixture signature, were genetically different from Bronze age steppe people. I'm sure the authors of this paper would recognize Steppe Bronze signature in Indian population from any other.

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    Quote Originally Posted by LeBrok View Post

    Any idea why Figure 1c is not in tune with Figure 4b? According to 1c Anatolian N is mixture of mostly Natufian/Levant farmer with WHG. According to 4b mostly Iranian N, then Levant N, and some WHG. 1b PCA chart also plots Anatolian and European farmer between position of Natufians and WHG. Iranian N being very far away.
    There seems to be a serious discrepancy with prediction model and actual samples for Anatolian Neolithic. Look at Extended Data Figure 5, top of the page in the middle. The prediction model is much closer in agreement to what Figure 4 represents (Iranian N/Levant N/WHG), while actual data agrees more with Figure 1c (Levant/WHG). Is Figure 4 from some sort of prediction, and Figure 1c is actual data?
    What am I missing here?

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    1 out of 1 members found this post helpful.
    Quote Originally Posted by holderlin View Post
    .

    Also I think Basal Eurasian comes from South Asia.
    Yep, as Alan said and I agree, it most likely comes from Arabian peninsula.

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    LeBrok, can you try the fst chart? It works for me.


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    1 out of 1 members found this post helpful.
    I don't think there's any way of knowing at this stage where the Basal Eurasian was hiding, but one of the points against an Arabian refugia is that Levant Neolithic has less of it than Iranian hunter-gatherer (44% to 64%). On the other hand, both Levant Neolithic and Iranian Neolithic have about the same amount-44%-so the argument could be made that Basal was diluted in the west by something WHG like and in the east by something EHG or maybe ANE like.

    The other alternative often mentioned is a Persian Gulf refugia, which is actually I think what Alan said?

    @Holderlin,
    I've considered that too. It would certainly explain why we haven't stumbled upon it yet, given that we have nothing really old from that region.

    @Alan,
    That makes sense to me, and I think the statements in the paper alluding to perhaps more "proximate" contacts was included. So, not that there wasn't actual steppe movement to India, but that there are older processes which may be inflating the figures.

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    Quote Originally Posted by Angela View Post
    LeBrok, can you try the fst chart? It works for me.
    Both work now.

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    Quote Originally Posted by Angela View Post
    It is interesting that Jews plot with Neolithic Levant and Palestinians with Bronze Age Levant. Like Jews were sheltered from Bronze Age genetic influence. Well, they really must have hidden in a desert, not for 40 but 1,000 years. ;) Bedouins and Saudis are closer to Natufians though.

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    1 out of 1 members found this post helpful.
    Looking at PCA, post above, it is interesting how Steppe Late Neolithic/Early Bronze is composed pretty much of two elements the EHG and Iranian N/Chl (Steppe EMBA). No EEF farmer input what so ever. Also in Extended figure 5.
    By mid Bronze Age the Steppe group is strongly influenced only by Anatolian/European Neolithic farmer genetics at strong 30% level, Steppe MLBA. Strong EEF genetic flow. I'm assuming this could have been done by mixing heavily with Cucuteni farmers in West Yamnaya. Or EMBA was East Yamnaya and MLBA West Yamnaya. If I understood the paper this latter MLBA became dominant in the Steppe. However there is still this IA sample which is much closer to the EMBA population. I guess stepp was mixed and varied by cultures.

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    1 out of 1 members found this post helpful.
    Quote Originally Posted by LeBrok View Post
    Any idea why Figure 1c is not in tune with Figure 4b? According to 1c Anatolian N is mixture of mostly Natufian/Levant farmer with WHG. According to 4b mostly Iranian N, then Levant N, and some WHG. 1b PCA chart also plots Anatolian and European farmer between position of Natufians and WHG. Iranian N being very far away.
    If I understand it all correctly ADMIXTURE takes a whole lot of f3 stats and plots them. If it finds some samples clustering (i.e. a number of instances all with very low different f3 stats) it will consider it a population and measure the "distance" of others towards it as admixture proportions. You can imagine that for very old samples this will not work. They will have contributed for instance to population A as well as population B and C. The old samples will also have their own - lost - drift. This will be calculated as a mixture of A, B and C even if it is not.

    ADMIXTURE will try to find a new cluster each step it takes.

    So as long as Levant_N and Anatolia_N aren't considered different populations 1c is valid. As soon as both are considered separate populations 4b. In other words: 1c means K=11, 4b means K>11.

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    3 out of 3 members found this post helpful.
    I have been busy and only saw this paper now. Finally some Natufian and Early Levantine Neolithic genomes! That's great news. I haven't had time to read the paper yet. Only the comments posted here and quickly browsing through the Y-DNA and mtDNA results.

    I am surprised like most of you not to find any trace of Y-haplogroup G among the Pre-Pottery Neolithic Levantines, but I am pleased that we finally have some Y-DNA T and that it was indeed as I thought found among the earliest farmers. Note that the Mesolithic Natufians appear to belong exclusively to CT and E1b1b, while early pre-pottery farmers also have H2 and T. So it could be that H2 and T colonised the southern Levant from further north (e.g. northern Mesopotamia or Syria).

    I do expect to find G2a among Early Farmers further north though, either in Syria or southern Turkey. They had to come from somewhere, and it is extremely unlikely that cereal farming spread almost exclusively through diffusion from the southern Levant to Anatolia while it spread almost exclusively by migration from Anatolia to all Europe. That wouldn't make any sense. Anyway it is sure that some T and H2 people were among the predominantly G2a Early European Farmers, but it's somewhat odd that only one T and no E-M123 have been found in Neolithic Europe or Anatolia to date. H2 looks like the strongest unifier of Near Eastern and European Neolithic people, which makes even less sense as it is almost extinct everywhere today.

    Just as I expected there was no R1b, J1 or J2 in the Levant at the time. R1b-V88 would have arrived from the northern Fertile Crescent with cattle herders a bit later in the Neolithic, with J1 and J2 could have come with some goat herders in the Neolithic and/or Chalcolithic. More of them certainly came during the great Bronze Age expansions of the Indo-Europeans (R1a, R1b) and of the Kura-Araxes culture (J1, J2, G2a).

    I wasn't sure about when E-M123 had entered the Levant from Africa. We now know that it was at least since the Mesolithic with the Natufians. That's interesting because it would mean that E-M123 wasn't brought by Proto-Semitic people during the Chalcolithic. Or else perhaps Proto-Semitic did really arrive in the Chalolithic but with a different wave of E-M34 people. In that case the E-M123 or other E1b1b would only be distantly related and all/most of these Natufian E1b1b lineages are now extinct, just like CT. This second hypothesis seems the most likely.

    It's a bit disappointing that they only managed to test a single Natufian mtDNA sample. It's hard to believe that they couldn't sequence any when mtDNA is the easiest part of the genome to sequence. It turns out to belong to haplogroup N1b, which is almost exclusively found in the Middle East today.

    The mtDNA from the Pre-Pottery Neolithic in the Levant is K1a4b, R0a and T1a2, three almost exclusively Middle Eastern lineages today (K1a4b is found chiefly among the Druzes). This, combined with the Y-DNA results, strongly suggests that the Levantine Neolithic is not the source of any European Neolithic culture.

    Early Iranian Neolithic samples only yielded mt-haplogroup X2 (found all over Europe today) and J1c10, (found nowadays in central and western Europe, continental Italy, Sardinia and Morocco). Both were found among European Neolithic farmers.

    Therefore, based on the (very scarce) Y-DNA and mtDNA data, it looks like European farmers came from Anatolia and Iran, or more probably a common source in the northern Fertile Crescent around modern Kurdistan, but not from the Levant.

    Iranian Chalcolithic samples belonged to I1c, K1a12a (2x), H29, U3a'c and U7a, the Armenian Chalcolithic belonged to K1a8 (2x), H2a1 and U4a, while the Anatolian Chalcolithic had just one K1a17. Those lineages are still typical of the northern Middle East today and are much rarer in Europe than the Neolithic mtDNA from Anatolia and Iran. The only exceptions are I1c, H2a1 and U4a, which are found especially in central and eastern Europe today, but did not show up in Europe until the Indo-European invasions with the Corded Ware culture. It is highly interesting that these were found in Chalcolithic Armenia and Iran, as it appears to confirm that Proto-Indo-Europeans originated in that region before crossing the Caucasus to found the Yamna culture in the Pontic-Caspian Steppe. More intriguing still, these three lineages (H2a1, I1c and U4a) are actually linked to the R1a-dominant Corded Ware and Catacomb cultures, not the R1b-dominant Yamna culture. We still have to determine what could be the link between Armenia-Iran and the northern forest steppe of Russia. It could be the same population that brought CHG admixture to both Yamna and Corded Ware and it does appear to have been maternally mediated, as clearly Chalcolithic Armenians and Iranians had completed different Y-DNA from Steppe people (L1a, G1, G2a and J vs R1a and R1b).
    Last edited by Maciamo; 19-06-16 at 00:40.
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    1 out of 1 members found this post helpful.
    Quote Originally Posted by LeBrok View Post
    Looking at PCA, post above, it is interesting how Steppe Late Neolithic/Early Bronze is composed pretty much of two elements the EHG and Iranian N/Chl (Steppe EMBA). No EEF farmer input what so ever. Also in Extended figure 5.
    By mid Bronze Age the Steppe group is strongly influenced only by Anatolian/European Neolithic farmer genetics at strong 30% level, Steppe MLBA. Strong EEF genetic flow. I'm assuming this could have been done by mixing heavily with Cucuteni farmers in West Yamnaya. Or EMBA was East Yamnaya and MLBA West Yamnaya. If I understood the paper this latter MLBA became dominant in the Steppe.
    That's how I read it as well. We don't have any yDna from West Yamnaya, correct? Maybe that's where R1b L51+ has been hiding.

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    @LeBrok,
    Do you mean the Ashkenazim? They don't plot near ancient Levantine farmers from what I can see. They plot right near the Sicilians and Maltese. If I'm reading the modern PCA correctly, it's parallel to the Anatolian Chalcolithc sample. It's true though that a lot of Jews carry E-M123, but so do some Palestinians, I think.

    Another handy graphic:

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    Quote Originally Posted by Alpenjager View Post
    Ancestral = Negative, He doesn't belong to P322.
    yes , you are correct................so there in no link between the T (i1707) in the levant and the 2 early neolitihc T found in germany.

    It means the German T's came from another area.


    currently the highest % of T in this area apart from the kurds are the syrian who declare themselves assyrian in ethnicity
    có che un pòpoło no 'l defende pi ła só łéngua el xe prónto par èser s'ciavo

    when a people no longer dares to defend its language it is ripe for slavery.

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    Quote Originally Posted by Maciamo View Post
    It's a bit disappointing that thy didn't test (or didn't report yet?) any Natufian mtDNA. It's hard to believe that they couldn't sequence any when mtDNA is the easiest part of the genome to sequence.
    Perhaps it will follow. IIRC other pre-print papers added more data as well. Possibly they will update the Y-DNA P1(Xa whole lot) as well.

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    1 out of 1 members found this post helpful.
    Some of you may have seen this tweet from Lazaridis already:
    Iosif Lazaridis ‏@iosif_lazaridis
    I1635 (Armenia_EBA) is R1b1-M415(xM269). We'll be sure to include in the revision. Thanks to the person who noticed!

    This is Kura Araxas.

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    Quote Originally Posted by Angela View Post
    Some of you may have seen this tweet from Lazaridis already:
    Iosif Lazaridis ‏@iosif_lazaridis
    I1635 (Armenia_EBA) is R1b1-M415(xM269). We'll be sure to include in the revision. Thanks to the person who noticed!

    This is Kura Araxas.
    HA antoher one, I know I sound selfish and like a broken recorder but I pointed out the similarities between Kura Araxes and Steppic folks. I did point out Kura Araxes had both Kurgan and pit graves and horses there predate horses in Sintashta by several hundred years.

    So far Kura Araxes period Haplogroups are L1a and R1b.

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    Quote Originally Posted by Angela View Post
    @LeBrok,
    Do you mean the Ashkenazim? They don't plot near ancient Levantine farmers from what I can see. They plot right near the Sicilians and Maltese. If I'm reading the modern PCA correctly, it's parallel to the Anatolian Chalcolithc sample. It's true though that a lot of Jews carry E-M123, but so do some Palestinians, I think.

    Another handy graphic:
    Nope, all the other Jews in the area, especially the Libyan and Tunisian Jews. Look at modern population PCA in Extended Figure 1. Compare it to PCA Figure 1b

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    Imo if Kura Araxes had R1b, than Maykop which is roughly from the same timeframe further North had it too.

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    Quote Originally Posted by Maciamo View Post

    Just as I expected there was no R1b, J1 or J2 in the Levant at the time. R1b-V88 would have arrived from the northern Fertile Crescent with cattle herders a bit later in the Neolithic, with J1 and J2 could have come with some goat herders in the Neolithic and/or Chalcolithic. More of them certainly came during the great Bronze Age expansions of the Indo-Europeans (R1a, R1b) and of the Kura-Araxes culture (J1, J2, G2a).

    I wasn't sure about when E-M123 had entered the Levant from Africa. We now know that it was at least since the Mesolithic with the Natufians. That's interesting because it would mean that E-M123 wasn't brought by Proto-Semitic people during the Chalcolithic. Or else perhaps Proto-Semitic did really arrive in the Chalolithic but with a different wave of E-M34 people. In that case the E-M123 or other E1b1b would only be distantly related and all/most of these Natufian E1b1b lineages are now extinct, just like CT. This second hypothesis seems the most likely.

    It's a bit disappointing that they only managed to test a single Natufian mtDNA sample. It's hard to believe that they couldn't sequence any when mtDNA is the easiest part of the genome to sequence. It turns out to belong to haplogroup N1b, which is almost exclusively found in the Middle East today.

    The mtDNA from the Pre-Pottery Neolithic in the Levant is K1a4b, R0a and T1a2, three almost exclusively Middle Eastern lineages today (K1a4b is found chiefly among the Druzes). This, combined with the Y-DNA results, strongly suggests that the Levantine Neolithic is not the source of any European Neolithic culture.Early Iranian Neolithic samples only yielded mt-haplogroup X2 (found all over Europe today) and J1c10, (found nowadays in central and western Europe, continental Italy, Sardinia and Morocco). Both were found among European Neolithic farmers.

    Therefore, based on the (very scarce) Y-DNA and mtDNA data, it looks like European farmers came from Anatolia and Iran, or more probably a common source in the northern Fertile Crescent around modern Kurdistan, but not from the Levant.
    The only squeaky wheel in it is that Anatolian farmers have 34% of autosomal Levant Neolithic in them. I see two possibilities to explain. Either Levant Y and mtDNA got deleted by better fit Iranian and local types uniparental DNA, which is not impossible knowing how fast they can bloom and die due to bottlenecking (8.2k event) and other evolutionary forcings. Second solution is that 34% of what appears to be Levant DNA is actually from a group of very related to them HGs in Central Anatolia, possibly carriers of G2a. Therefore all farmers genes come from Iranian Farmers, the rest from local hunters. That's quite a twist to what we assumed just days ago, but it is what it is. Well, possible by now, till dust settles.

    samples belonged to I1c, K1a12a (2x), H29, U3a'c and U7a, the Armenian Chalcolithic belonged to K1a8 (2x), H2a1 and U4a, while the Anatolian Chalcolithic had just one K1a17. Those lineages are still typical of the northern Middle East today and are much rarer in Europe than the Neolithic mtDNA from Anatolia and Iran. The only exceptions are I1c, H2a1 and U4a, which are found especially in central and eastern Europe today, but did not show up in Europe until the Indo-European invasions with the Corded Ware culture. It is highly interesting that these were found in Chalcolithic Armenia and Iran, as it appears to confirm that Proto-Indo-Europeans originated in that region before crossing the Caucasus to found the Yamna culture in the Pontic-Caspian Steppe. More intriguing still, these three lineages (H2a1, I1c and U4a) are actually linked to the R1a-dominant Corded Ware and Catacomb cultures, not the R1b-dominant Yamna culture. We still have to determine what could be the link between Armenia-Iran and the northern forest steppe of Russia. It could be the same population that brought CHG admixture to both Yamna and Corded Ware and it does appear to have been maternally mediated, as clearly Chalcolithic Armenians and Iranians had completed different Y-DNA from Steppe people (L1a, G1, G2a and J vs R1a and R1b).
    Well, if we assume that proto IE is actually Iranian Neolithic, which fed Anatolian Neolithic, which fed European Neolithic, it makes European Neolithic proto IE too. Meaning all old Europe spoke proto IE language, plus half of Middle East. It makes irrelevant whichever farmers, Maykop or Cucuteni, taught language to Steppe people via farming and mingling, it was all proto IE. Actually it would make it easier to understand why the steppe invaders were so successful teaching all Europe and half Asia to speak their language. It was already very similar to local languages.
    Well, one of possibilities at the moment.

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    @Maciamo

    I do expect to find G2a among Early Farmers further north though, either in Syria or southern Turkey. They had to come from somewhere, and it is extremely unlikely that cereal farming spread almost exclusively through diffusion from the southern Levant to Anatolia while it spread almost exclusively by migration from Anatolia to all Europe.
    The model i have in my head is multiple farmer groups in the region expanding out from their start point until they bump into each other and with none stronger than the others they create an equilibrium - so in this interior regions crops and animals diffuse across the borders by trade.

    It is their expansion *away* from each other where they are competing with HGs which happens by migration.

    #

    @Holderlin

    Also I think Basal Eurasian comes from South Asia.
    Flooded Persian Gulf is my current guess.

    #

    edit: example of first point

    say the start points were
    - aegean (G?)
    - nile delta (E?)
    - persian gulf (BE?)
    - south caspian (J?)

    and then they all expanded they'd bump into each other in the middle

    but their outward expansion would be over HGs

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