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Thread: Late Pleistocene human genome suggests a local origin for the first farmers of centra

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    4 out of 4 members found this post helpful.

    Late Pleistocene human genome suggests a local origin for the first farmers of centra

    Anatolia was home to some of the earliest farming communities. It has been long debated whether a migration of farming groups introduced agriculture to central Anatolia. Here, we report the first genome-wide data from a 15,000-year-old Anatolian hunter-gatherer and from seven Anatolian and Levantine early farmers. We find high genetic continuity (~80–90%) between the hunter-gatherers and early farmers of Anatolia and detect two distinct incoming ancestries: an early Iranian/Caucasus related one and a later one linked to the ancient Levant. Finally, we observe a genetic link between southern Europe and the Near East predating 15,000 years ago. Our results suggest a limited role of human migration in the emergence of agriculture in central Anatolia.

    https://www.nature.com/articles/s414...oH1GZFfwlIQmug

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    Quote Originally Posted by bicicleur View Post
    Anatolia was home to some of the earliest farming communities. It has been long debated whether a migration of farming groups introduced agriculture to central Anatolia. Here, we report the first genome-wide data from a 15,000-year-old Anatolian hunter-gatherer and from seven Anatolian and Levantine early farmers. We find high genetic continuity (~80–90%) between the hunter-gatherers and early farmers of Anatolia and detect two distinct incoming ancestries: an early Iranian/Caucasus related one and a later one linked to the ancient Levant. Finally, we observe a genetic link between southern Europe and the Near East predating 15,000 years ago. Our results suggest a limited role of human migration in the emergence of agriculture in central Anatolia.

    https://www.nature.com/articles/s414...oH1GZFfwlIQmug
    Thanks, Bicicleur. I'll read it with interest. Krause and Haak again, I see.

    I want to see, in particular, what evidence they have that the people in that 20% "new" ancestry group didn't bring agriculture with them. Also, does this conflict with prior analyses showing a higher proportion of Levantine Neolithic ancestry? Perhaps there were differences over time or by location? Agriculture reached coastal Anatolia before it reached Central Anatolia if I remember correctly.


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    1 out of 2 members found this post helpful.
    Well, they answer some questions right away.

    " Strikingly, the AHG individual is positioned near both AAF and later Anatolian Ceramic farmers12 (7000–6000 cal BCE). These three prehistoric Anatolian populations (AHG, AAF, and ACF), representing a temporal transect spanning the transition into farming, are positioned along PC1 between Mesolithic western European hunter-gatherers (WHG)4,7,12 who are at one extreme of PC1 and Levantine Epipaleolithic Natufians6 who are at the other. Along PC2, ancient Anatolians, WHG, and Natufians have similar coordinates. The newly reported Levantine Neolithic farmers (BAJ001 and KFH2) are positioned near the previously published Levantine Neolithic farmers6(Supplementary Note 2). In ADMIXTURE analysis AHG, AAF, and ACF are inferred as a mixture of two components that are each maximized in Natufians and WHG, consistent with their intermediate positions along PC1 in PCA (Supplementary Figure 1)."

    "
    Strikingly, the AHG individual is positioned near both AAF and later Anatolian Ceramic farmers12 (7000–6000 cal BCE). These three prehistoric Anatolian populations (AHG, AAF, and ACF), representing a temporal transect spanning the transition into farming, are positioned along PC1 between Mesolithic western European hunter-gatherers (WHG)4,7,12 who are at one extreme of PC1 and Levantine Epipaleolithic Natufians6 who are at the other. Along PC2, ancient Anatolians, WHG, and Natufians have similar coordinates. The newly reported Levantine Neolithic farmers (BAJ001 and KFH2) are positioned near the previously published Levantine Neolithic farmers6(Supplementary Note 2). In ADMIXTURE analysis AHG, AAF, and ACF are inferred as a mixture of two components that are each maximized in Natufians and WHG, consistent with their intermediate positions along PC1 in PCA (Supplementary Figure 1)."

    "
    Accordingly, a mixture of AHG and Neolithic Iranians provides a good fit to AAF in our qpAdm modeling (χ2p = 0.296), in which AAF derive most of their ancestry (89.7 ± 3.9%) from a population related to AHG (Supplementary Tables 4 and 6)...The additional Neolithic Iranian-related ancestry (10.3 ± 3.9%) presumably diffused into central Anatolia during the final stages of the Pleistocene or early Holocene, most likely via contact through eastern Anatolia. This provides evidence of interactions between eastern and central Anatolia in the Younger Dryas or the first millennium of the Holocene, currently poorly documented archeologically."

    "
    Likewise, qpAdm modeling suggests that the AAF gene pool still constitutes more than 3/4 of the ancestry of ACF 2000 years later (78.7 ± 3.5%; Supplementary Tables 4 and 7) with additional ancestry well modeled by the Neolithic Levantines (χ2p = 0.115) but not by the Neolithic Iranians (χ2p = 0.076; the model estimated infeasible negative mixture proportions) (Supplementary Tables 4 and 7). These results suggest gene flow from the Levant to Anatolia during the early Neolithic. In turn, Levantine early farmers (Levant_Neol) that are temporally intermediate between AAF and ACF could be modeled as a two-way mixture of Natufians and AHG or AAF (18.2 ± 6.4% AHG or 21.3 ± 6.3% AAF ancestry; Supplementary Tables 4 and 8 and Supplementary Data 4), confirming previous reports of an Anatolian-like ancestry contributing to the Levantine Neolithic gene pool6. These two distinct detected gene flows support a reciprocal genetic exchange between the Levant and Anatolia during the early stages of the transition to farming."

    [IMG][/IMG]

    Am I making too much of the fact that the sample from Israel is significantly shifted from the sample from Jordan?

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    "Our results suggest that the non-Basal Eurasian ancestry of ancient Anatolians and Levantines derived from a gene pool related to the Villabruna cluster prior to its expansion within Europe observed after 14,000BP."

    [IMG][/IMG]

    "Iron Gates HG have been previously modeled as a mixture of WHG (~85%) and eastern European hunter-gatherers (EHG; ~15%)18, the latter of which shares a much lower affinity with ancient Near Easterners in respect to other European HG (Fig. 3a). Since the previously reported WHG and EHG model did not fit well (χ2p = 0.0003) and since Iron Gates HG harbored Near-Eastern-like mitochondrial groups, an affinity with Anatolians beyond the WHG + EHG model has been hypothesized18. Accordingly, we find that Iron Gates HG can be modeled as a three-way mixture of Near-Eastern hunter-gatherers (25.8 ± 5.0 % AHG or 11.1 ± 2.2 % Natufian), WHG (62.9 ± 7.4% or 78.0 ± 4.6%, respectively) and EHG (11.3 ± 3.3% or 10.9 ± 3%, respectively); (χ2p = 0.308 and χ2p = 0.589 respectively; Supplementary Tables 4 and 9)."

    "
    To estimate the Basal Eurasian ancestry proportion (“α”), we followed a previously established qpAdm-based approach that uses an African reference (the ancient Ethiopian Mota genome19) as a proxy6 (Supplementary Table 10). We estimated αto be 24.8 ± 5.5% in AHG and 38.5 ± 5.0% in Natufians (Fig. 3b, Supplementary Table 10), consistent with previous estimates for the latter6. In turn, the Iron Gates HG could be modeled without any Basal Eurasian ancestry or with a non-significant proportion of 1.6 ± 2.8% when forced to have it as a third source (Fig. 3b and Supplementary Table 10). In contrast to the above direct estimate, the three-way admixture model of WHG + EHG + AHG predicts α = 6.4 ± 1.9% for Iron Gates, calculated as (% AHG in Iron Gates HG) × (α in AHG), suggesting that unidirectional gene flow from the Near East to Europe alone may not be sufficient to explain the excess affinity between the Iron Gates HG and the Near-Eastern hunter-gatherers. Thus, it is plausible to assume that prior to 15,000 years ago there was either a bidirectional gene flow between populations ancestral to Southeastern Europeans of the early Holocene and those ancestral to Anatolians of the Late Glacial or a genetic influx from the populations ancestral to Southeastern Europeans into the Near East."

    "Two additional scenarios, both involving gene flow from the ancestors of Iron Gates HG to the ancestors of AHG, can help explain the extra affinity between Iron Gates HG and AHG. One assumes a secondary gene flow from Southeastern Europe to Anatolia after the initial formation of the Near-Eastern gene pool as a mixture of the Basal Eurasian and the Villabruna-related gene pools. The other assumes that Iron Gates HG are indeed the most closely related group among European hunter-gatherers to the Villabruna-related ancestry in ancient Near Easterners. Further sampling in Anatolia and Southeastern Europe is needed to specify the spatiotemporal extent of the genetic interactions that we observe."

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    2 out of 3 members found this post helpful.
    Here's some nice info on uniparentals. How they change over time, especially the y.

    "The uniparental marker analysis placed AHG within the mitochondrial sub-haplogroup K2b and within the Y-chromosome haplogroup C1a2, both rare in present-day Eurasians (Table 1 and Supplementary Data 6). Mitochondrial Haplogroup K2 has so far not been found in Paleolithic hunter-gatherers20. However, Y-haplogroup C1a2 has been reported in some of the earliest European hunter-gatherers8,17,21. The early farmers belong to common early Neolithic mitochondrial (N1a, U3 and K1a) and Y chromosome types (C and G2a), with the exception of the Levantine BAJ001, which represents the earliest reported individual carrying the mitochondrial N1b group (Table 1 and Supplementary Data 6)."

    As to phenotype, interesting stuff about blue eyes. That old paper saying they came from somewhere around the Caucasus may be correct.

    '
    We examined alleles related to phenotypic traits in the ancient genomes (Supplementary Data 7). Notably, three of the AAF carry the derived allele for rs12193832 in the HERC2 (hect domain and RLD2) gene that is primarily responsible for lighter eye color in Europeans22. The derived allele is observed as early as 14,000–13,000 years ago in individuals from Italy and the Caucasus8,23, but had not yet been reported in early farmers or hunter-gatherers from the Near East."


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    While these results do not suggest that the AHG gene pool originated as a mixture of Levant_N and WHG, both of which lived millennia later than AHG, it still robustly supports that AHG is genetically intermediate between WHG and Levant_N. This cannot be explained without gene flow between the ancestral gene pools of those three groups.

    Why didn't they bring Dzudzuana into the equasion?

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    Isn't C1a2 a proof in itself that there was Gene Flow between at least Balkans and Anatolia? And i think they are wrong to assume " Villabruna expansion in Europe after 14'000 BP " If we already sees Villabruna in Vestonice, it's probably way older in Europe and have stationned way before 14'000 BP already in the Balkans. I actually bet that Common West-Eurasian meaning Villabruna/Dzudzuana early ancestry came in Europe with y-dna I.

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    0 out of 1 members found this post helpful.
    Quote Originally Posted by bicicleur View Post
    While these results do not suggest that the AHG gene pool originated as a mixture of Levant_N and WHG, both of which lived millennia later than AHG, it still robustly supports that AHG is genetically intermediate between WHG and Levant_N. This cannot be explained without gene flow between the ancestral gene pools of those three groups.

    Why didn't they bring Dzudzuana into the equasion?
    That's a good question. It would be a whole other way of looking at things. Dzudzuana plus something related to Iron Gates HG?

    It's not those specific populations, which come from a later time period, but from populations related to them. I think it's undeniable.

    Also, given the data on the Iron Gates type hg's, it's clear there was ancient gene flow from Anatolia into the Balkans as well as the other way around.

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    Quote Originally Posted by Angela View Post
    That's a good question. It would be a whole other way of looking at things. Dzudzuana plus something related to Iron Gates HG?

    It's not those specific populations, which come from a later time period, but from populations related to them. I think it's undeniable.

    Also, given the data on the Iron Gates type hg's, it's clear there was ancient gene flow from Anatolia into the Balkans as well as the other way around.
    C1a2 hints at an early (LGM ?) flow from Europe into Anatolia
    and Greek mesolithic doesn't look like European, but Anatolian
    we also have some Anatolian mtDNA in the Iron Gates

    but all this was already known before

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    Feldman 2018 dealt with the same genomes :

    https://www.biorxiv.org/node/127252.article-info

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    I throw this out now, in case one day it's confirmed by sampling. But i bet to an Europe -> Anatolian ( Middle-East ) migration bringing C1a2 and mtdna U8b in the territory.

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    I am wondering were does E-V13 hide so far. I want to know a hub from where E-V13 initially migrated.

    Initially they were either Natufian-like, who amalgamated among the AHG, or if they migrated directly from North Africa they were more like Iberomaurusians.

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    1 out of 1 members found this post helpful.
    Well, we have the immediate precursor lineage in Neolithic Croatia and Spain. So they'd hardly be Natufian like or Iberomaurian by that point.

    Perhaps it traveled with Cardial Ware Neolithic farmers into Europe.

    What we do know is that there was a star like expansion in the Bronze Age.

    Maciamo has proposed that there might have been a lot of it in the Cuteni-Tripolye farmer areas and some was picked up by Indo-European groups and went both west and east.

    Once we find some proximate Bronze Age samples we'll know more.

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    1 out of 2 members found this post helpful.
    Quote Originally Posted by Angela View Post
    Well, we have the immediate precursor lineage in Neolithic Croatia and Spain. So they'd hardly be Natufian like or Iberomaurian by that point.

    Perhaps it traveled with Cardial Ware Neolithic farmers into Europe.

    What we do know is that there was a star like expansion in the Bronze Age.

    Maciamo has proposed that there might have been a lot of it in the Cuteni-Tripolye farmer areas and some was picked up by Indo-European groups and went both west and east.

    Once we find some proximate Bronze Age samples we'll know more.
    I know one other thing: if Maciamo is correct, the TMRCA of the E-V13 in Italy is very young, around 1000 BC. That spells the Greeks as far as I'm concerned, which the Boattini group said a couple of years ago.

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    so , what I am taking away from the information posted here : Anatolia farmers are more closely related to the hunters and gatherers, the earliest ancestors came from Iranian /Caucasus .
    Quote Originally Posted by bicicleur View Post
    Anatolia was home to some of the earliest farming communities. It has been long debated whether a migration of farming groups introduced agriculture to central Anatolia. Here, we report the first genome-wide data from a 15,000-year-old Anatolian hunter-gatherer and from seven Anatolian and Levantine early farmers. We find high genetic continuity (~80–90%) between the hunter-gatherers and early farmers of Anatolia and detect two distinct incoming ancestries: an early Iranian/Caucasus related one and a later one linked to the ancient Levant. Finally, we observe a genetic link between southern Europe and the Near East predating 15,000 years ago. Our results suggest a limited role of human migration in the emergence of agriculture in central Anatolia.


    https://www.nature.com/articles/s414...oH1GZFfwlIQmug

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    Well, we have the immediate precursor lineage in Neolithic Croatia and Spain. So they'd hardly be Natufian like or Iberomaurian by that point.

    Perhaps it traveled with Cardial Ware Neolithic farmers into Europe.

    my question is , where Cardial ware neolithic farmers came from and into Europe ? Did they come from outside Europe? Then what dividing landmark we are using ? the Ural mountain? or the Anatolia ?

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