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Thread: The genomic history of southeastern Europe-Mathiesen et al

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    4 members found this post helpful.

    The genomic history of southeastern Europe-Mathiesen et al

    All I can say is Wow!
    See:
    http://biorxiv.org/content/biorxiv/e...35616.full.pdf

    This is the abstract.

    "Farming was first introduced to southeastern Europe in the mid-7th millennium BCE - brought by migrants from Anatolia who settled in the region before spreading throughout Europe. However, the dynamics of the interaction between the first farmers and the indigenous hunter-gatherers remain poorly understood because of the near absence of ancient DNA from the region. We report new genome-wide ancient DNA data from 204 individuals-65 Paleolithic and Mesolithic, 93 Neolithic, and 46 Copper, Bronze and Iron Age-who lived in southeastern Europe and surrounding regions between about 12,000 and 500 BCE. We document that the hunter-gatherer populations of southeastern Europe, the Baltic, and the North Pontic Steppe were distinctive from those of western Europe, with a West-East cline of ancestry. We show that the people who brought farming to Europe were not part of a single population, as early farmers from southern Greece are not descended from the Neolithic population of northwestern Anatolia that was ancestral to all other European farmers. The ancestors of the first farmers of northern and western Europe passed through southeastern Europe with limited admixture with local hunter-gatherers, but we show that some groups that remained in the region mixed extensively with local hunter-gatherers, with relatively sex-balanced admixture compared to the male-biased hunter-gatherer admixture that we show prevailed later in the North and West. After the spread of farming, southeastern Europe continued to be a nexus between East and West, with intermittent steppe ancestry, including in individuals from the Varna I cemetery and associated with the Cucuteni-Trypillian archaeological complex, up to 2,000 years before the Steppe migration that replaced much of northern Europe's population.""


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    2 members found this post helpful.
    Some nuggets:

    Globular Amphora is 75% farmer and 25% HG, like Iberian Neolithic...no steppe.

    As to LBK, Cardial, and Balkan Neolithic, " These three populations form a clade with Northwest Anatolians as an outgroup, consistent with a single migration from a population closely related to the northwestern Anatolian Neolithic farming population into the Balkan peninsula, which then367 split into two populations that followed the Danubian and Mediterranean routes."

    I knew it.

    Early Greek Neolithic was different: "four southern Greek (Peloponnese) Neolithic individuals – three from Diros Cave and onefrom Franchthi Cave, plus one previously published individual from Diros – are not consistent with descending from the same source population as other European farmers...have less WHG related ancestry than Anatolia Neolithic ones...suggesting an independent migration into Europe from a population that split off from the ancestors of the northwest Anatolian individuals from which we have data... their Near Eastern ancestry is derived from a lineage that is close, or basal, to the non-WHG component of Anatolian Neolithic ancestry. One possibility is that this independent migration is related to an earlier Aceramic Neolithic in Greece that was derived from the pre-pottery Neolithic(PPNB) of Cyprus and the Levant. Under this model, the earliest Neolithic populations in Greece migrated from the Levant, perhaps via the southwestern Anatolian coast as early as7000 BCE, but the majority of Neolithic ancestry arrived around 500 years later via a route that passed through northwestern Anatolia... Populations related to the Peloponnese Neolithic potentially made a small contribution to the ancestry of other Mediterranean Neolithic populations like Early NeolithicIberia and Neolithic farmers from northern Greece but we do not strongly reject models395 without such a contribution (Supplementary Information, section 3).

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    early farmers from southern Greece are not descended from the Neolithic population of northwestern Anatolia
    Are they saying that Greece had distinct and earlier farming population, not related to ENF?!!!

    Looks like we will get Cucuteni genomes finally. :)
    Be wary of people who tend to glorify the past, underestimate the present, and demonize the future.

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    Quote Originally Posted by Angela View Post
    Some nuggets:

    Globular Amphora is 75% farmer and 25% HG, like Iberian Neolithic...no steppe.

    As to LBK, Cardial, and Balkan Neolithic, " These three populations form a clade with Northwest Anatolians as an365 outgroup, consistent with a single migration from a population closely related to the366 northwestern Anatolian Neolithic farming population into the Balkan peninsula, which then367 split into two populations that followed the Danubian and Mediterranean routes."

    I knew it.

    Early Greek Neolithic was different: "four southern Greek (Peloponnese) Neolithic individuals – three from Diros Cave and onefrom Franchthi Cave, plus one previously published individual from Diros – are not consistent with descending from the same source population as other European farmers...have less WHG-379 related ancestry than Anatolia Neolithic ones...suggesting an independent migration into Europe from a population that split off from the ancestors of the northwest Anatolian individuals from which we have data... their Near Eastern ancestry is derived from a lineage that is close, or basal, to the non-WHG component of Anatolian Neolithic ancestry. One possibility is that this independent migration is related to an earlier Aceramic Neolithic in Greece that was derived from the pre-pottery Neolithic(PPNB) of Cyprus and the Levant. Under this model, the earliest Neolithic populations in Greece migrated from the Levant, perhaps via the southwestern Anatolian coast as early as7000 BCE, but the majority of Neolithic ancestry arrived around 500 years later via a route that passed through northwestern Anatolia... Populations related to the Peloponnese Neolithic potentially made a small contribution to the ancestry of other Mediterranean Neolithic populations like Early NeolithicIberia and Neolithic farmers from northern Greece but we do not strongly reject models395 without such a contribution (Supplementary Information, section 3).
    Thanks, picture is getting clearer now. I wonder if early farming in Cyprus was also related to Greece Neolithic and Levant?

    I wonder if this first Greek population was totally or almost totally replaced, as we are not getting much of levant signal from modern Greeks at all. Well, except Cyprus.

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    "In the Balkan Neolithic there is no evidence of sex bias. However, in the Middle Neolithic and later populations, this effect reverses. In the Balkan Copper Age there is weak evidence of bias (Z=1.77) but in Iberia and central Europe Middle409 Neolithic there is clear bias is in favor of male hunter-gatherer ancestry This result is independently supported by uniparental markers (Figure 3C). Proportions of typically hunter-gatherermitochondrial haplogroups (haplogroup U) are low in all populations. On the other hand, hunter-gatherer Ychromosomes (haplogroups I2, R1 and C1) are much more common: 6/7 in the Iberian415 Neolithic/Copper Age and 7/8 in Middle-Late Neolithic central Europe (Central_MN andGlobular_Amphora)...in the central European Middle Neolithic population that shows the strongest evidence of sex bias, 35-50% of the male ancestors were hunter-gatherers, compared to 0-5% of the female ancestors (Extended Data Figure 4)."

    "1 The merging of hunter-gatherer and farmer populations was a dynamic process that unfolded over thousands of years, and proceeded in a profoundly different way in different parts of Europe... in some places – for example at Malak Preslavets in Bulgaria – there was extensive mixing between hunter-gatherers and farmers, likely driven by the high local hunter-gatherer population density. In other places–in particular in western, central and northern Europe–hunter-gatherers and farmers lived in close proximity for long periods oftime with minimal mixture. When they did finally mix...admixture was male-biased, implying a different dynamic. Farming was initially unable to expand widely in central and northern Europe because early farming techniques were only suitable for specific regions within the loess belt of the northern European plain.Thus, northern and central European hunter-gatherers were protected from the demographic impact of farming migrations, resulting in persistent frontiers between farmers and huntergatherers.This may have given hunter-gatherers and farmers time to learn from each other434 and interact in a different way than during the more rapid expansion of the first farmers in the435 South."

    That still doesn't explain why it was male mediated. What happened to their women?

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    Did they get any ydna, mtdna?

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    1 members found this post helpful.
    Hunter gatherer women didn't get much love in west,central and northern Europe? Or does this mean that those male hg were more aggressive to the farmers, raped a bunch of their women and the farmers in those regions were in smaller number.

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    Cold water is indeed thrown on the Anatolian branch of IE entering Anatolia through the Balkans.

    "While we find steppe ancestry in Balkan Copper Age and Bronze Age individuals, this ancestry is sporadic across individuals in the Copper Age, and at low levels in the Bronze Age. Moreover, whileBronze Age Anatolian individuals have CHG / Iran Neolithic related ancestry, they haveneither the EHG ancestry characteristic of all steppe populations sampled to date, nor the WHG ancestry that is ubiquitous in southeastern Europe in the Neolithic.

    The following is in Wow territory, particularly in light of the fact that so many of the world's foremost geneticists, and not just the Reich lab, have signed on, and that they know what the Caucasus samples will show. I guess I wasn't crazy years ago when I kept on arguing with Aberdeen and others about data from Grigoriev.

    "An alternative hypothesis is that the ultimate homeland of Proto-Indo European languages was in the Caucasus or in Iran. In this scenario, westward movement contributed to the dispersal of Anatolian languages, and northward movement and mixture with EHG was responsible for the formation of the population associated with the Yamnaya complex. These steppe pastoralists plausibly spoke a “Late Proto-Indo European” language that is ancestral tomany of the non-Anatolian branches of the Indo-European language family. On the other hand, our data could still be consistent with the Steppe-Balkans-Anatolia route hypothesis model, albeit with constraints. It remains possible that populations dating to around 1600 BCE in the regions where the Indo-European Luwian, Hittite and Palaic languages were spoken did have European hunter-gatherer ancestry. However, our results would require that such ancestry was not ubiquitous in Bronze Age Anatolia, and was perhaps tightly linked to Indo-European speaking groups. We predict that additional insight about the genetic origins of the potential speakers of early Indo-European languages will be obtained when ancient DNA data become available from additional sites in this key period in Anatolia and the Caucasus."

    I predict that in addition to a spike in prescriptions for xanax we will shortly see protestations that it never mattered to anyone where it arose, just the launching point to Europe. :)

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    "Mesolithic and Neolithicindividuals from Ukraine, Latvia and the Iron Gates have, like Scandinavian and Easternhunter-gatherers, intermediate to high frequencies of the derived skin pigmentation allele atSLC24A5. However, unlike Scandinavian and Eastern hunter-gatherers, they have lowfrequency of the derived SLC45A2 allele. The derived HERC2 allele that is associated withlight (particularly blue) eye color is common in WHG, SHG, and hunter-gatherers fromLatvia, but at low frequency in hunter-gatherers from Ukraine and the Iron Gates. This alleleappears to be differentiated in a North-South gradient, as it is today. The apparent WHGphenotype of light eye and dark skin pigmentation therefore appears to be restricted towestern Europe, with light skinpigmentation being common in Northern and Eastern Europe before the appearance ofagriculture."

    Well, that's a relative term. CHG had derived SLC 24A5. Anatolian farmers had a similar profile, as did Yamnaya, as do some South Asians. It's additive, so the total mix of depigmentation snps is important.

    Blonde hair is from ANE:
    "The derived allele of the KITLG SNP rs12821256 that is associated with – and likely causalfor – blond hair in Europeans4,5 is present in one hunter-gatherer from each of Samara, Motalaand Ukraine (I0124, I0014 and I1763), as well as several later individuals with Steppeancestry. Since the allele is found in populations with EHG but not WHG ancestry, it suggeststhat its origin is in the Ancient North Eurasian (ANE) population. Consistent with this, weobserve that earliest known individual with the derived allele is the ANE individual Afontova Gora."

    LP:
    "The WHG individual Ibousierres-25 appears to carry the derived allele at the SNP rs4988235that is strongly associated with lactase persistence in present-day Northern Europeans. Fourreads at this SNP all carry the derived allele, although we caution that this is a C>T SNP in anon-UDG treated sample and so might be affected by deamination, and two reads atneighboring SNPs do not support the persistence haplotype, at least in a homozygous state(Supplementary Figure S2.3). The observation of this allele, long before domestication anddairying, would be surprising, but might be consistent with observation of lactase persistencein early Neolithic populations in Iberia and Sweden – observations that were themselvessurprising based on the absence of persistence in large samples of Anatolian Neolithic andLBK individuals. One possibility is that the allele was widely distributed at low frequenciesbefore being strongly selected in the Bronze Age, perhaps due to changes in use or cattle."

    Only one example of EDAR.

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    "Anatolian Neolithic and Bronze AgeNorthwest Anatolian Samples from Barcın can be modeled as a mixture of a populationrelated to WHG, and a diverged population that is related to Iran Neolithic (and also to theNeolithic Levant)4. Neolithic samples from Tepecik Ciflik3 are very similar, possibly withless WHG ancestry, while those from Kumtepe5 can be modeled as having 12% additionalIran Neolithic related ancestry compared to 29% additional in the Anatolian Bronze Age."

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    1 members found this post helpful.
    Quote Originally Posted by Apsurdistan View Post
    Hunter gatherer women didn't get much love in west,central and northern Europe? Or does this mean that those male hg were more aggressive to the farmers, raped a bunch of their women and the farmers in those regions were in smaller number.
    Hallo

    the virgin huntress is a supreme deity to all ancient cultures.




    I wonder,
    did they remained virgins?

    the story of virgin huntress Atalante
    https://en.wikipedia.org/wiki/Atalanta

    ΟΘΕΝ ΑΙΔΩΣ OY EINAI
    ΑΤΗ ΛΑΜΒΑΝΕΙΝ ΑΥΤΟΙΣ
    ΥΒΡΙΣ ΓΕΝΝΑΤΑΙ
    ΝΕΜΕΣΙΣ ΚΑΙ ΤΙΣΗ ΑΚΟΛΟΥΘΟΥΣΙ ΔΕ

    When there is no shame
    Divine blindness conquers them
    Hybris (abuse, opprombium) is born
    Nemesis and punishment follows.

    Εχε υπομονη Ηρωα
    Η τιμωρια δεν αργει.

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    An alternative hypothesis is that the ultimate homeland of Proto-Indo European languages was in the Caucasus or in Iran. In this scenario, westward movement contributed to the dispersal of Anatolian languages, and northward movement and mixture with EHG was responsible for the formation of the population associated with the Yamnaya complex.
    I don't know, the problem with this westward movement giving rise to Anatolians idea is Y-dna, I can't think of a possible clade of R1b or R1a that could possibly fit this movement, except if Anatolian IE's weren't R1b or R1a but were something else, then maybe, but then what is that ?

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    Quote Originally Posted by Apsurdistan View Post
    Hunter gatherer women didn't get much love in west,central and northern Europe? Or does this mean that those male hg were more aggressive to the farmers, raped a bunch of their women and the farmers in those regions were in smaller number.
    The most obvious explanation is that early farming was volatile and prone to crop failure so the Y-DNA lineages that spread with it were more likely to decline in frequency. The HGs were better adapted to the environment which put them at an advantage even after they adopted agricultural economies.

    Just stop with the rape stuff for god's sake.

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    Quote Originally Posted by Angela View Post
    Cold water is indeed thrown on the Anatolian branch of IE entering Anatolia through the Balkans.

    "While we find steppe ancestry in Balkan Copper Age and Bronze Age individuals, this ancestry is sporadic across individuals in the Copper Age, and at low levels in the Bronze Age. Moreover, whileBronze Age Anatolian individuals have CHG / Iran Neolithic related ancestry, they have neither the EHG ancestry characteristic of all steppe populations sampled to date, nor the WHG ancestry that is ubiquitous in southeastern Europe in the Neolithic.
    Ah, so this Bronze Age Anatolia/Armenia invasion, that increased so much Caucasian admixture in Balkans, happened before IE invasion from North Europe to Balkans. Possibly this Anatolia invasion is IE Mycenaean and some others.


    The following is in Wow territory, particularly in light of the fact that so many of the world's foremost geneticists, and not just the Reich lab, have signed on, and that they know what the Caucasus samples will show. I guess I wasn't crazy years ago when I kept on arguing with Aberdeen and others about data from Grigoriev.

    "An alternative hypothesis is that the ultimate homeland of Proto-Indo European languages was in the Caucasus or in Iran. In this scenario, westward movement contributed to the dispersal of Anatolian languages, and northward movement and mixture with EHG was responsible for the formation of the population associated with the Yamnaya complex. These steppe pastoralists plausibly spoke a “Late Proto-Indo European” language that is ancestral tomany of the non-Anatolian branches of the Indo-European language family. On the other hand, our data could still be consistent with the Steppe-Balkans-Anatolia route hypothesis model, albeit with constraints. It remains possible that populations dating to around 1600 BCE in the regions where the Indo-European Luwian, Hittite and Palaic languages were spoken did have European hunter-gatherer ancestry. However, our results would require that such ancestry was not ubiquitous in Bronze Age Anatolia, and was perhaps tightly linked to Indo-European speaking groups. We predict that additional insight about the genetic origins of the potential speakers of early Indo-European languages will be obtained when ancient DNA data become available from additional sites in this key period in Anatolia and the Caucasus."

    I predict that in addition to a spike in prescriptions for xanax we will shortly see protestations that it never mattered to anyone where it arose, just the launching point to Europe. :)
    I never had problem with this. One of the sources of IE language could have been Iranian Farmer (like) to whom I "rewarded" quarter of Yamnaya ancestry. Questing is still open. However the IE package came later from BA Steppe.

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    The IE language first split from PIE in Anatolia ~4000BC ...........it has been said that it came from PIE in the north-caucasus and not from the balkans
    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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    1 members found this post helpful.
    Then the Ancient Greeks are indeed the most ancient in Europe. Makes perfect sense.

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    Quote Originally Posted by MarkoZ View Post
    The most obvious explanation is that early farming was volatile and prone to crop failure so the Y-DNA lineages that spread with it were more likely to decline in frequency. The HGs were better adapted to the environment which put them at an advantage even after they adopted agricultural economies.

    Just stop with the rape stuff for god's sake
    Ok the farmer women married the hg men and the farmer men just gave them away to the gentrified hunter gatherers.

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    Quote Originally Posted by LeBrok View Post
    Ah, so this Bronze Age Anatolia/Armenia invasion, that increased so much Caucasian admixture in Balkans, happened before IE invasion from North Europe to Balkans. Possibly this Anatolia invasion is IE Mycenaean and some others.


    I never had problem with this. One of the sources of IE language could have been Iranian Farmer (like) to whom I "rewarded" quarter of Yamnaya ancestry. Questing is still open. However the IE package came later from BA Steppe.
    I'm not sure about the Greek part.

    None of the IE Package originated on the steppe except the domesticated horse and possibly the spoked wheel chariot.

    All the models seem to put CHG "like" or "southern" ancestry at 40-50%

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    3 members found this post helpful.
    The ydna and mtdna are in Table 1. These are just some I noticed. There are some big surprises.

    Iberia H/G 10,000 BC: J:P209:19179335T->C; IJ:P126:21225770C->G

    Harmonren Turkey 1 J1a
    One J2 in LBK

    Barcin 3 H2, 1J2a, 6 G2a2a1a2a, 1C1a2V20, 1 I2c, L596, 9 no result

    Cardial, Croatia E1b1b1a1b1

    Iron Gates Hunter- Gatherers: 3 R1b1a:A702:10038192G->A; R1b1a:CTS4244:15510064T->G; R1b1a:CTS8436:18026855G->A; R1b1a:FGC41:7900883C->A; R1b1a:L1345:21558298G->T; R1b1:CTS2229:14226692T->A; R1:CTS2565:14366723C->T; R:CTS8311:17930099C->A; R:FGC1168:15667208G->C;

    One sample goes all the way back to about 10,000 BC. I wonder what Gioiello is doing. J

    Lepinski Vir Neolithic 6222-5912 calBCE (7179±73* BP, OxA-25211)
    : R1b1a:CTS4244:15510064T->G; R1b1:L822:7960019G->A; R:F652:23631629C->A; R:M799:23134896C->T

    Greece Final Neolithic Kletios-G2a2a1a2

    Greek Peloponnesus Neolithic- no results

    Ukraine Mesolithic 8825-8561 BC- R1a

    Ukraine “Neolithic”, which is much more WHG, has a lot of R1b1a

    Globular Amphora is mostly I2, plus one each of:
    BT
    CT


    Varna: CT-I think this is the gold encrusted one, but someone check, R1, G2a2b2b, G2a
    Tryphilia: 3 G2a2...…and one E

    Smyadova Bulgaria 4545-4400 B C- 1 Late Chalcolithic R1b1a:A702, R P280:2184

    Vucedol: R1b1a1a2a2, G2a2a1a2a

    Croatia: EM Bronze-J2b

    Can this be right? Ust-Isham 45530-40610 calBCE : R1a1a1b

    And look at this: Iran Neolithic:
    R:M718:17334694G->T
    R:CTS2426:14300457G->A; R:FGC1168:15667208G->C

    Now, my brain is fried.

  20. #20
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    The Ust-Ishim one has to be a mistake. They left the SNP column blank too.

    This one is interesting as well:

    Iboussieres31-3 - France ~11725 BP mtDNA: U5b1 y-DNA: R

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    I don't see I1 anywhere, of course. It's basically non existent in ancient DNA before bronze age.

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    Quote Originally Posted by Angela View Post
    I'm not sure about the Greek part.

    None of the IE Package originated on the steppe except the domesticated horse and possibly the spoked wheel chariot.

    All the models seem to put CHG "like" or "southern" ancestry at 40-50%
    The Olade et al admixture plot shows what looks to be about 35% for Yamnaya-Samara.

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    Quote Originally Posted by Apsurdistan View Post
    I don't see I1 anywhere, of course. It's basically non existent in ancient DNA before bronze age.
    And what's the explanation for all the R1b in the Balkan hunter gatherers?

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    Now it's seems quite clear the R1b was really a Paleolithic clade as thought some years ago: it pops up in Italy (Villabruna), Romania (Iron Gates), Germany, Samara, Latvia... all LGM refuges were used (Italy, Balkans, Caucasus).

    The papers provides 36 Y-DNA samples from Ukraine, only 8 are R1b, mainly from the outliers of Dereivka. It seems that the western steppe origin for L51 is fading...

    When I was pointing out that IE languages were based on R1a pops is now more certain after finding a R1a in Kairyaka necropolis (1750-1625), as by such dates Greeks and Hitties where in their places.
    "What I've seen so far after my entire career chasing Indoeuropeans is that our solutions look tissue thin and our problems still look monumental" J.P.Mallory

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    Quote Originally Posted by Angela View Post
    The ydna and mtdna are in Table 1. These are just some I noticed. There are some big surprises.

    Iberia H/G 10,000 BC: J:P209:19179335T->C; IJ:P126:21225770C->G

    Harmonren Turkey 1 J1a
    One J2 in LBK

    Barcin 3 H2, 1J2a, 6 G2a2a1a2a, 1C1a2V20, 1 I2c, L596, 9 no result

    Cardial, Croatia E1b1b1a1b1

    Iron Gates Hunter- Gatherers: 3 R1b1a:A702:10038192G->A; R1b1a:CTS4244:15510064T->G; R1b1a:CTS8436:18026855G->A; R1b1a:FGC41:7900883C->A; R1b1a:L1345:21558298G->T; R1b1:CTS2229:14226692T->A; R1:CTS2565:14366723C->T; R:CTS8311:17930099C->A; R:FGC1168:15667208G->C;

    One sample goes all the way back to about 10,000 BC. I wonder what Gioiello is doing. J

    Lepinski Vir Neolithic 6222-5912 calBCE (7179±73* BP, OxA-25211)
    : R1b1a:CTS4244:15510064T->G; R1b1:L822:7960019G->A; R:F652:23631629C->A; R:M799:23134896C->T

    Greece Final Neolithic Kletios-G2a2a1a2

    Greek Peloponnesus Neolithic- no results

    Ukraine Mesolithic 8825-8561 BC- R1a

    Ukraine “Neolithic”, which is much more WHG, has a lot of R1b1a

    Globular Amphora is mostly I2, plus one each of:
    BT
    CT


    Varna: CT-I think this is the gold encrusted one, but someone check, R1, G2a2b2b, G2a
    Tryphilia: 3 G2a2...…and one E

    Smyadova Bulgaria 4545-4400 B C- 1 Late Chalcolithic R1b1a:A702, R P280:2184

    Vucedol: R1b1a1a2a2, G2a2a1a2a

    Croatia: EM Bronze-J2b

    Can this be right? Ust-Isham 45530-40610 calBCE : R1a1a1b

    And look at this: Iran Neolithic:
    R:M718:17334694G->T
    R:CTS2426:14300457G->A; R:FGC1168:15667208G->C

    Now, my brain is fried.
    So basically we have R1b all over Balkans,pure gold.
    Last edited by Milan.M; 11-05-17 at 02:09.

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