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    The genetic structure of the world’s first farmers

    Very nice new paper up. Dynamite: Natufians were only half Basal Eurasian and Basal Eurasian appears to have had no Neanderthal! Furthermore, the CHG part of Steppe appears to be made of Caucasian HG and part Iranian Chalcolithic. Fitted mixture proportions are 52.7% EHG, 18.1% CHG, 29.2% Iran_Ch.

    Preprint: http://biorxiv.org/content/early/2016/06/16/059311
    Supp Info: http://biorxiv.org/content/early/201...1.figures-only

    The Neanderthal is very interesting as well. O, and Basal is not African. It is buried somewhere in the supp info tables.

    EDIT: Y-DNA of Natufians were E1b and some J1. Iran G1a G2a and some J.
    Last edited by epoch; 17-06-16 at 19:19.

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    Y DNA results. All but a few Neolithic Levant samples had E1b, no suprise. Most had M123 though not M78(like most E1b in Europe and West Asia today).

    Armenia_ChL (Chalcolithic Armenia)

    I1407: L1a
    I1632: L1a
    I1634: L1a


    Iran_Mesolithic (Hotu Cave)


    I1293: J(xJ2a1b3, J2b2a1a1)


    Iran_N


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


    My guess here is that this is R2, and hopefully we shall see when the bam files are released.


    I1949: CT


    Iran_LN


    I1671: G2a1(xG2a1a)


    Iran_ChL (Chalcolithic Iran)


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


    Natufians


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


    Levant_N


    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_BA


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

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    The reduced Neanderthal in Basal... It has me thinking. Could that be the cause for the perceived increasing middle-eastern in WHG? It would be a nice way to explain for the slight increase in El Miron. Also, it shows that either Basal wasn't surviving in the Asian part of the Middle-East and thus the Basal Urheimat (I am laughing as I type these words ;.) must have been Egypt, or the Neanderthal admixture took place more north.

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    Quote Originally Posted by epoch View Post
    The reduced Neanderthal in Basal... It has me thinking. Could that be the cause for the perceived increasing middle-eastern in WHG? It would be a nice way to explain for the slight increase in El Miron. Also, it shows that either Basal wasn't surviving in the Asian part of the Middle-East and thus the Basal Urheimat (I am laughing as I type these words ;.) must have been Egypt, or the Neanderthal admixture took place more north.
    Reduced Neanderthal in Basal makes a lot of sense. WHG and El Miron didn't have Basal Eurasian ancestry. East Asians are equally close to them as to earlier Europeans, confirming they don't have Basal Eurasians.

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    no G2a2 found, none
    is G2a2 exclusive to Anatolian & European neolithic?

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    Quote Originally Posted by Fire Haired14 View Post
    Reduced Neanderthal in Basal makes a lot of sense. WHG and El Miron didn't have Basal Eurasian ancestry. East Asians are equally close to them as to earlier Europeans, confirming they don't have Basal Eurasians.
    Mota Cave HG E1b1a didn't have Neanderthal, probably Natufian E-Z830 didn't have either before coming to Asia.
    It hints at arrival of E-Z830 from Africa.

    I'm not sure Basal Eurasian originated in Africa though.
    The reduced Neandertahl may be related to admixture with E-Z830 and unrelated to the Basal Eurasian.

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    Anatolia_Neolithic found a brother in Neolithic/Paleo Levant. Also, Neolithic/Paleo Levant clusters in West Eurasia exactly where we expected, just south of Anatolia_Neolithic by modern SouthWest Asians.

    Huge Genetic shift in Chalolithic Anatolia.

    Our about 6,000 year old genome from Western Turkey(same location as Neolithic Anatolians) is most similar to modern NorthWest Asians. So finally we have an answer as to when Turkey went from EEF to what it is today(for the most part).
    Last edited by Fire Haired14; 17-06-16 at 15:39.

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    Quote Originally Posted by bicicleur View Post
    Mota Cave HG E1b1a didn't have Neanderthal, probably Natufian E-Z830 didn't have either before coming to Asia.
    It hints at arrival of E-Z830 from Africa.

    I'm not sure Basal Eurasian originated in Africa though.
    The reduced Neandertahl may be related to admixture with E-Z830 and unrelated to the Basal Eurasian.
    The authros don't think Basal Eurasian came from Africa, because Basal Eurasian peaks in Neolithic Iranians.

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    Quote Originally Posted by Alan View Post
    The authors don't think Basal Eurasian came from Africa, because Basal Eurasian peaks in Neolithic Iranians.
    But while HG's all had Basal, no one was a pure Basal. It clearly is not African - this paper reaffirms that - so how can that be?

    It must therefore be something very old and it needs to have happened before the UP. So, Basal remained in ME, admixture with Neanderthals happened in the Caucasus or Anatolia and the latter back migrated. Then diversified.

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    1 out of 1 members found this post helpful.
    Quote Originally Posted by bicicleur View Post
    Mota Cave HG E1b1a didn't have Neanderthal
    I glossed over this, sort of interesting. So you're thinking E1b was African rather than Basal Eurasian. When I first read that I thought you were driving at Natufian being Basal Eurasion.

    I think it's relevant to note that R1b-V88 SSAs don't have any Neanderthal left either.
    Last edited by holderlin; 25-06-16 at 03:42. Reason: I didn't read his whole post

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    Quote Originally Posted by holderlin View Post
    I glossed over this, sort of interesting. So you're thinking E1b was African rather than Basal Eurasian. When I first read that I thought you were driving at Natufian being Basal Eurasion.

    I think it's relevant to note that R1b-V88 SSAs don't have any Neanderthal left either.
    I see Natufian as an admixture of E1b1b1 and Basal Eurasian.
    For Basal Eurasian I guess G and/or H.
    However if G is Basal Eurasian NW Anatolian, LBK and Cardial Ware should have had more of it.

    I don't think of E as the source of Basal Eurasian, because Hotu Cave mesolithic had even more of it.
    Both E and Basal Eurasian were very low on Neanderthal admixture.


    I think it's relevant to note that R1b-V88 SSAs don't have any Neanderthal left either.
    Where did you get this info?

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    there were 3 populations :

    Iran neolithic which expanded to South Asia & Central Asia
    Natufians expanded to Africa
    3rd population expanded to NW Anatolia & Europe : : they were seafaring fishermen that converted into agriculture,
    you'll find them here :


    http://biorxiv.org/content/early/2015/11/25/032763




    Greece Theopetra, Thessaly [Theo5]
    7605–7529 BC

    K1c Hofmanová 2015

    Greece Theopetra, Thessaly [Theo1]
    7288–6771 BC

    K1c Hofmanová 2015

    Greece Revenia [Rev5] F 6438–6264 BC

    X2b Hofmanová 2015

    Greece Paliambela [Pal7] F 4452– 4350 BC

    J1c1 Hofmanová 2015

    Greece Kleitos [Klei10] M 4230-3995 BC G2a2a1b
    K1a2 Hofmanová 2015

    Turkey Barcın [I0707/BAR2 / L11-213] F 6500-6200 BC

    K1a4 Mathieson 2015

    Turkey Barcın [I0708/BAR6 / L11-439] M 6500-6200 BC J2a M410, L559, L212; J2a-M410 > PF4610 > Z6049 > Z6048(xS20392) N1b1a Mathieson 2015; Additional info on Y-DNA SNPs from Chris Rоttеnѕtеіnеr

    Turkey Barcın [I0709/BAR20 / M13-170] M 6500-6200 BC H2 L281, P96, L284, L285, L286 U3 Mathieson 2015

    Turkey Barcın [I0736/L11-216] F 6500-6200 BC

    N1a1a1a Mathieson 2015

    Turkey Barcın [I0744/M10-275] M 6500-6200 BC G2a2b2a Z3077, CTS688, PF3329, CTS4454, CTS10366, P303, Z3243, PF3342, Z3481, PF3343 J1c11 Mathieson 2015

    Turkey Barcın [I0745/M11-363] M 6500-6200 BC H2 L281, P96, L284, L285, L286 U8b1b1 Mathieson 2015

    Turkey Barcın [I0746/L11-322] M 6500-6200 BC G2a2b2a1c CTS342 K1a or K1a1 Mathieson 2015

    Turkey Barcın [I1096/BAR26/M10-76] M 6500-6200 BC I2c L596, L597 N1a1a1 Mathieson 2015

    Turkey Barcın [I1097/BAR271 / M10-271] M 6500-6200 BC G2a2b2a Z3077, CTS946, PF3329, CTS4454, CTS10366, Z3243, PF3342, Z3481 W1-T119C Mathieson 2015

    Turkey Barcın [I1098/BAR99 / M10-352] F 6500-6200 BC

    X2d2 Mathieson 2015

    Turkey Barcın [I1099/L11-S-488] M 6500-6200 BC G2a2a1b L91 T2b Mathieson 2015

    Turkey Barcın [I1100/M11-351] F 6500-6200 BC

    K1a or K1a6 Mathieson 2015

    Turkey Barcın [I1101/M11-352a] M 6500-6200 BC

    T2b Mathieson 2015

    Turkey Barcın [I1102/M11-354] M 6500-6200 BC C1a2 V20 K1a3a Mathieson 2015

    Turkey Barcın [I1103/M11-S-350] M 6500-6200 BC G2a2a1b1 PF3247 K1b1b1 Mathieson 2015

    Turkey Barcın [I1579/M13-72] F 6500-6200 BC

    K1a-C150T Mathieson 2015

    Turkey Barcın [I1580/L12-393] F 6500-6200 BC

    H5 Mathieson 2015

    Turkey Barcın [I1581/L12-502] F 6500-6200 BC

    U3 Mathieson 2015

    Turkey Barcın [I1583/L14-200] M 6500-6200 BC G2a2a1b L91 K1a2 Mathieson 2015

    Turkey Barcın [I1585/M11-59] F 6500-6200 BC

    J1 or J1c Mathieson 2015

    Turkey Barcın [I0854/L11-215] F 6500-6200 BC

    N1a1a1a Mathieson 2015
    Fikirtepe Turkey Menteşe [I0723/T1, M229 / UH] M 6400-500 BC G2a2a PF3165, PF3166, PF3175, PF3184 X2m2 Mathieson 2015
    Fikirtepe Turkey Menteşe [I0724/T2 / UP] M 6400-500 BC I CTS6231 K1a4 Mathieson 2015
    Fikirtepe Turkey Menteşe [I0726/M15, M15.2, M15.2 / UF] F 6400-500 BC

    H or H5-C16192T Mathieson 2015
    Fikirtepe Turkey Menteşe [I0727/M24 / UA JK 16] M 6400-500 BC G CTS11294 K1a2 Mathieson 2015
    Fikirtepe Turkey Menteşe [I0725/T4 / SSK15] F 6400-500 BC

    N1a1a1a Mathieson 2015

    Turkey Barcın [Bar31] M 6419–6238 BC G2a2b > genetiker G2a2b-L30*
    X2m Hofmanová 2015

    Turkey Barcın [Bar8] F 6212–6030 BC

    K1a2 Hofmanová 2015




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    big surprises in unchartered territory
    very interesting but I'll need some time to digest

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    Natufians are E-Z830 x(E-M123, M293), TMRCA 19.2 ka
    That leaves open 2 possibilities : E-Z830* or E-V42.
    That is : Natufians are extinct or surviving in Ethiopia ????

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    1 out of 1 members found this post helpful.

    No Gene flow between Neolithic Iran and Levant

    @Angela,

    Genetic continuum in Iran from Mesolithic to Neolithic.

    The origin of the Neolithic of Iran does not appear to be related to either Anatolia or the Levant, as theNeolithic and Mesolithic of Iran are symmetrically related to either population (Fig. S7.5), providingno evidence for gene flow from either region into the Zagros, but hinting strongly that whatever rolethe exchange of ideas and technology may have played in the emergence of the Neolithic in theZagros, this was not accompanied with any substantial gene flow from other ancient Near EasternNeolithic centers of domestication.
    Genetic continuum from Paleolithic to Neolithic Levant.

    Among first farmers, those of the Levant trace ~2/3 of their ancestry to people related toNatufian hunter-gatherers and ~1/3 to people related to Anatolian farmers (Supplementary
    Information, section 7).
    Last edited by Fire Haired14; 17-06-16 at 15:38.

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    In ADMIXTURE analysis....

    >Anatolia Neolithic comes out as a mixture of Natufians and WHG/EHG.
    >Armenia Chalolithic and Bronze, Anatolia Chalolithic, come out as Natufian+Iran Neo/CHG+WHG/EHG.
    >Levant BA is Natufian+Iran Neo/CHG.

    So all of this was expected. None of this is a surprise. For years now we've known "SouthWest Asian"(Natufian) and "Meditreaen"(Anatolia Neolithic) were closely related. We've also known that West Asians are a mixture of "SouthWest Asian" and "Caucasus"(CHG, Iran Neo).

    This paper has supported another event we already knew. South Asian's West Eurasian ancestry is a mixture of Iran Neolithic and European/Steppe Bronze age.

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    Quote Originally Posted by Fire Haired14 View Post
    In ADMIXTURE analysis....

    >Anatolia Neolithic comes out as a mixture of Natufians and WHG/EHG.
    >Armenia Chalolithic and Bronze, Anatolia Chalolithic, come out as Natufian+Iran Neo/CHG+WHG/EHG.
    >Levant BA is Natufian+Iran Neo/CHG.

    So all of this was expected. None of this is a surprise. For years now we've known "SouthWest Asian"(Natufian) and "Meditreaen"(Anatolia Neolithic) were closely related. We've also known that West Asians are a mixture of "SouthWest Asian" and "Caucasus"(CHG, Iran Neo).

    This paper has supported another event we already knew. South Asian's West Eurasian ancestry is a mixture of Iran Neolithic and European/Steppe Bronze age.
    Furthermore it confirms 25% ANE in WHG, ANE in Han. Although I have a tad problems with the numbers: They seem to change over the papers. Fu 2016 has slightly different numbers if I recall correctly: No ANE in Han or WHG due to no D-stat confirming it when Mal'ta is used.

    And the three farmer populations was more or less already known from archaeology. The hotspots of the earliest neolithic transition were, according to archaeology: Zagros mountains, Catal Huyuk and the Levant.

    EDIT: Fig. S11.3 models WHG as 7% ANE and 93% Bichon. Damn shame they didn't use the UP samples. Miss Fu worked at both papers, so I don't know exactly why. WHG proper is Loschbour?

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    1 out of 1 members found this post helpful.
    I guess I'll call my friend and postpone that walk. :)

    Where is Alan? He had it right about there being three farmer populations in the Near East, and without benefit of a leak from an about to be published paper.

    I'll be back when I've read it carefully too, Bicicleur.


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    Quote Originally Posted by Angela View Post
    I guess I'll call my friend and postpone that walk. :)

    Where is Alan? He had it right about there being three farmer populations in the Near East, and without benefit of a leak from an about to be published paper.

    I'll be back when I've read it carefully too, Bicicleur.
    thanks for mentioning me. :)

    I remember Maciamo giving me a thumps up back than which means he agreed with this already back than.

    I wrote allot of things in the other thread.

    Here are my posts I wrote in the other thread.

    HA I knew it I said it, but some people just jumped on wrong conclusions merely out of the fact that they don't like the idea of Yamna possibly being from Iranian Plateau.

    Even the sentence "no direct geneflow" should have made anyone suspecious that they don't exclude indirect geneflow.


    It makes archeological 100% sense. Maykop culture is descend of the Layla Tepe culture which according to archeologists derives from the Iranian Plateau.

    I always said it

    Iranian Plateau => Caucasus=> Steppes.

    OR Eastern Iranian Plateau => Central Asia => Steppes.
    From the paper Iran_N(Neolithic)
    Iran_N

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


    So it seems there was R Haplogroup in Neolithic Iran. Take that all you haters ^^

    Edit: I see the guys at Eurogenes are still in denial X)
    The paper also perfectly proves my hypothesis that THREE distinct groups were living in the Near East at least by Neolithic.

    A Southwestern farmer, A Anatolian farmer and a Iranian Plateau farmer/Herder group.

    The Natufians were quite similar to Anatolian_Farmers but had some differences. And it seems that the Caucasian DNA in East Africa came via the Natufians rather than Anatolian_Farmers.
    The Natufians were full of E1b1b and CT Haplogroups. Seems like we have found the source of the Egyptian culture in Levant_Neo. The whole Afro_asiatic family seems to be descend from the Levantine Neolithic.

    Natufians and Anatolian farmers are very similar but still distinct, while Zagros farmers are significantly different from the former both.

    Mesolithic Zagros H&G were more Basal Eurasian than Natufians which indicates that Basal Eurasian in fact derives from further East than South. Possibly Iranian coastle region.

    And there seems to be EHG like ancestry in mesolithic Iran.

    Mal'ta is modeled as ~28% Iranian Neolithic like, 15% CHG and ~35% WHG like

    EHG is modeled as 80% WHG, 7% Iranian Neolithic and 10% CHG like.
    Last edited by Alan; 25-06-16 at 03:33.

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    Wow, so many surprises! And it looks really rich in infor, and we have Natufians!!! I'm so excited, I'm skipping job today...., no, can't do that, lol. Cya guys later.
    Lol, Natufians are E1b, my first guess before changing my mind to G2a based on EEF samples. Once again we have an example how Y DNA can shift quickly. But let's see where ENF genome comes from, maybe it is not Natufian but from Iranian farmer mostly. Later...
    Be wary of people who tend to glorify the past, underestimate the present, and demonize the future.

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    @Maleth,
    It appears that the Natufians carry the precursor to E-M34. Thought you'd want to know. :)

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    More explained: Gedrosia is introduced from Iran to Steppe. Is also interesting to notice that the Caucasus has lot of the mentioned Y-DNA. Shame the paper has no mtDNA. I have a hunch there will be quite some updates.

    EDIT: SI has no mtDNA, but supplementary data does. So I was lazy
    Last edited by epoch; 17-06-16 at 21:55.

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    Quote Originally Posted by Angela View Post
    @Maleth,
    It appears that the Natufians carry the precursor to E-M34. Thought you'd want to know. :)
    This is really exciting. And I thought we would never get any results from these regions....but here they are.

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    For ease of reference:

    Lazaridis Neolithic paper admixture chart.PNG

    In this Admixture analysis, the Anatolia Neolithic appears to be a mix of Levant Neolithic, as defined as south Levant Neolithic (Jordan/Palestine), Iranian Neolithic, and some WHG.

    By the time we get to the Anatolian Chalcolithic, or Copper Age, which some researchers call the Late Neolithic, we have an increase in the Iranian Neolithic, a bit of EHG, and a corresponding slight decrease in the WHG and Levant Neolithic. Yes?

    How are we supposed to interpret this in light of the fact that the authors say these are genetically distinct populations? Is it partly a function of the time periods in question?

    These are the dates provided in the paper itself for these samples:
    "The samples include Epipaleolithic Natufian hunter-gatherers from Raqefet 125 Cave in the Levant (12,000-9,800 BCE); a likely Mesolithic individual from Hotu Cave in the 126 Alborz mountains of Iran (probable date of 9,100-8,600 BCE); Pre-Pottery Neolithic farmers 127 from ‘Ain Ghazal and Motza in the southern Levant (8,300-6,700 BCE); and early farmers 128 from Ganj Dareh in the Zagros mountains of western Iran (8,200-7,600 BCE). The samples 129 also include later Neolithic, Chalcolithic (~4,800-3,700 BCE), and Bronze Age (~3,350- 130 1,400 BCE) individuals.

    I haven't gotten to the supplement yet. Does anyone know if all the Anatolian samples they used are from about 4800 BCE or later? If they are, there's a few thousand years for some admixture to have already occurred.

    I'm not sure what to make of the Armenia Chalcolithic. Yes, they have some EHG and WHG, but so did the even earlier CHG hunter-gatherer. Indeed, so did the Iran_HotuIIIb sample. Then in the Early Bronze Age, the EHG decreases, probably as the result of further movement from the south, only for the EHG to increase again in the Middle Bronze Age.

    Far from being a barrier to gene flow, the Caucasus range seems to have been remarkably porous. In that regard, perhaps some of this incoming EHG was by way of bride exchange between the Caucasus and steppe groups? So, no, I hate to dash anyone's fantasies, but probably not he-men steppe cowboys riding into the Caucasus to raid and steal wives.

    Speaking of the steppe, this shows not only Iranian Neolithic genes on the steppe in the Early/Middle Bronze Age, but a bit of Levant Neolithic and WHG, which increases in the Middle/Late Bronze Age. So, did the latter two come with the people who came onto the steppe from the West Asian Highlands, or is it being picked up from people moving east from "Old Europe", since European EN here appears to be a three way mix of Iranian Neolithic, Levant Neolithic and WHG?

    In Europe, the transition from the MiddleN/Chal to LN/Bronze sees the arrival of EHG, and a corresponding decrease in WHG and Levant Neolithic, but Iranian Neolithic stays the same.

    I hate to be greedy when there is such a wealth of information here, but the only place from which we don't have farmer dna is precisely the area from which we know, or think we know, from the archaeology, that farmers set out for Cyprus, and, it was thought, other islands in the Aegean, and that is the area between southeast Anatolia and the northern Levant, approximately the area around northern Syria. I wonder if they would have been intermediate between northwest Anatolian farmers and Levant farmers?

    This is probably why the authors are careful to say that there was no direct input from south Levant farmers into Europe. It was mediated by more northerly groups.

    "To the west, the 270 early farmers of mainland Europe were descended from a population related to Neolithic northwestern Anatolians8 271 . This is consistent with an Anatolian origin of farming in Europe, 272 but does not reject other sources, since the spatial distribution of the Anatolian/European-like 273 farmer populations is unknown. We can rule out the hypothesis that European farmers stem directly from a population related to the ancient farmers of the southern Levant30,31 274 , however,"

    @Epoch,
    Maybe they were rushed because the paper had been leaked...

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    @Angela

    Nah. I simply overlooked it. The Anatolians are Mathiesons, IIRC.

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