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Thread: Admixture Across Ancient Inner Eurasia

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    Admixture Across Ancient Inner Eurasia

    See:

    Characterizing the genetic history of admixture across inner Eurasia

    View ORCID ProfileChoongwon Jeong, Oleg Balanovsky, Elena Lukianova, Nurzhibek Kahbatkyzy, Pavel Flegontov, Valery Zaporozhchenko, Alexander Immel, Chuan-Chao Wang, Olzhas Ixan, Elmira Khussainova, Bakhytzhan Bekmanov, Victor Zaibert, Maria Lavryashina, Elvira Pocheshkhova, Yuldash Yusupov, Anastasiya Agdzhoyan, Koshel Sergey, Andrei Bukin, Pagbajabyn Nymadawa, Michail Churnosov, Roza Skhalyakho, Denis Daragan, Yuri Bogunov, Anna Bogunova, Alexandr Shtrunov, Nadezda Dubova, Maxat Zhabagin, Levon Yepiskoposyan, Vladimir Churakov, Nikolay Pislegin, Larissa Damba, Ludmila Saroyants, Khadizhat Dibirova, Lubov Artamentova, Olga Utevska, Eldar Idrisov, Evgeniya Kamenshchikova, Irina Evseeva, Mait Metspalu, Martine Robbeets, Leyla Djansugurova, Elena Balanovska, Stephan Schiffels, Wolfgang Haak, David Reich, Johannes Krause

    https://www.biorxiv.org/content/bior...27122.full.pdf


    "
    The indigenous populations of inner Eurasia, a huge geographic region covering the central Eurasian steppe and the northern Eurasian taiga and tundra, harbor tremendous diversity in their genes, cultures and languages. In this study, we report novel genome-wide data for 763 individuals from Armenia, Georgia, Kazakhstan, Moldova, Mongolia, Russia, Tajikistan, Ukraine, and Uzbekistan. We furthermore report genome-wide data of two Eneolithic individuals (~5,400 years before present) associated with the Botai culture in northern Kazakhstan. We find that inner Eurasian populations are structured into three distinct admixture clines stretching between various western and eastern Eurasian ancestries. This genetic separation is well mirrored by geography. The ancient Botai genomes suggest yet another layer of admixture in inner Eurasia that involves Mesolithic hunter-gatherers in Europe, the Upper Paleolithic southern Siberians and East Asians. Admixture modeling of ancient and modern populations suggests an overwriting of this ancient structure in the Altai-Sayan region by migrations of western steppe herders, but partial retaining of this ancient North Eurasian-related cline further to the North. Finally, the genetic structure of Caucasus populations highlights a role of the Caucasus Mountains as a barrier to gene flow and suggests a post-Neolithic gene flow into North Caucasus populations from the steppe."

    Here we go again. :)
    Last edited by Angela; 09-05-19 at 18:59.


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    " Individuals from northern Eurasia, speaking Uralic or Yeniseian languages, form a cline303 connecting northeast Europeans and the Uralic (Samoyedic) speaking Nganasans from northern Siberia304 (“forest-tundra” cline). Individuals from the Eurasian steppe, mostly speaking Turkic and Mongolic305 languages, are scattered along two clines below the forest-tundra cline. Both clines run into Turkic- and306 Mongolic-speaking populations in southern Siberia and Mongolia, and further into Tungusic-speaking307 populations in Manchuria and the Russian Far East in the East; however, they diverge in the west, one heading to the Caucasus and the other heading to populations of the Volga-Ural area (the “southern steppe”309 and “steppe-forest” clines, respectively; Figure 2 and Figure S2)"

    "Overall, the proportions of ancestry components associated with eastern or western Eurasians312 are well correlated with longitude in inner Eurasians (Figure 3A). Notable outliers from this trend include313 known historical migrants such as Kalmyks, Nogais and Dungans. The forest-tundra cline populations314 derive most of their eastern Eurasian ancestry from a component most enriched in Nganasans, while those315 on the steppe-forest and southern steppe clines have this component together with another component316 most enriched in populations from the Russian Far East, such as Ulchi and Nivkh. The southern steppe317 cline groups are distinct from the others in their western Eurasian ancestry profile, in the sense that theyhave a high proportion of a component most enriched in Mesolithic Caucasus hunter-gatherers (“CHG”)28 318and Neolithic Iranians (“Iran_N”)19 319 and frequently harbor another component enriched in South Asians."

    "The European donors provide a major contribution for the western Eurasian-related source in the forest367tundra and steppe-forest recipients while the Caucasus/Iranian donors do so in the southern steppe368 recipients. Similarly, Siberian donors make the highest contribution to the eastern Eurasian-related source369 in the forest-tundra recipients, followed by the steppe-forest and southern steppe ones."

    "We estimated the proportion of East Asian ancestry in Botai using qpAdm. The two-wayadmixture model of AG3+Korean provides a good fit to Botai with 17.3% East Asian contribution (χ2 392 p =0.286; Table S5), while the models EHG+EAS do not fit (χ2p ≤ 1.44×10-7 393 ). However, we find that Botai394 harbors an extra affinity with Mesolithic western European hunter-gatherers (“WHG”) unexplained by395 this model:

    "Thus, we conclude that the ANE404related ancestry in Botai is intermediate between EHG and AG3, which corresponds to its intermediate405 geographic position. This suggests a genetic cline of decreasing ANE-related ancestry stretching from406 AG3 in Siberia to WHG in Western Europe. A substantial East Asian contribution into Botai make them407 offset from the WHG-ANE cline. A strong genetic affinity between Botai and the Middle Bronze Age408 Okunevo individuals in the Altai-Sayan region also suggests a wide geographic and temporal distribution409 of Botai-related ancestry in central Eurasia (Figure S6C)."

    "ANE404related ancestry in Botai is intermediate between EHG and AG3, which corresponds to its intermediate405 geographic position. This suggests a genetic cline of decreasing ANE-related ancestry stretching from406 AG3 in Siberia to WHG in Western Europe. A substantial East Asian contribution into Botai make them407 offset from the WHG-ANE cline. A strong genetic affinity between Botai and the Middle Bronze Age408 Okunevo individuals in the Altai-Sayan region also suggests a wide geographic and temporal distribution409 of Botai-related ancestry in central Eurasia (Figure S6C)."

    "The Y-chromosome of the male Botai individual (TU45) belongs to the haplogroup R1b (TableS6). However, it falls into neither a predominant European branch R1b-L5165 411 nor into a R1b-GG400 branch found in Yamnaya individuals.66 412 Thus, phylogenetically this Botai individual should belong to the413 R1b-M73 branch which is frequent in the Eurasian steppe (Figure S9). This branch was also found inMesolithic samples from Latvia67 414 as well as in numerous modern southern Siberian and Central Asian415 groups."

    "
    Among the ancient groups, Sintashta+EAS generally fits Andronovo individuals well with a430 small eastern Eurasian contribution (6.4±1.4% for estimate ± 1 SE with Nganasans), while later Karasuk431 or Iron Age individuals from the Altai are modeled better with the older Afanasievo as their WSH-related432 source (Table S7). If the pre-Bronze Age populations of the Altai-Sayan region were related to either433 Botai in the west or the Upper Paleolithic Siberians in the east, these results suggest that these pre-Bronze434 Age populations in southern Siberia did not leave a substantial genetic legacy in the present-day435 populations in the region. The Okunevo individuals are the only case that WSH+EAS mixture cannotexplain (χ2p ≤ 3.85×10-4); similar to Botai, a model of AG3+EAS provides a good fit (χ2 436 p = 0.396 for437 AG3+Korean; Table S5)."

    "WHG, WSH (represented by “Yamnaya_Samara”), and early Neolithic European farmers441 (EEF; represented by “LBK_EN”; Table S2). Adding Nganasans as the fourth reference, we find that442 most Uralic-speaking populations in Europe (i.e. west of the Urals) and Russians are well modeled by thisfour-way admixture model (χ2 443 p ≥ 0.05 for all but three groups; Figure 5 and Table S8). Nganasan-related444 ancestry substantially contributes to their gene pools and cannot be removed from the model without asignificant decrease in model fit (4.7% to 29.1% contribution; χ2p ≤ 1.12×10-8 445 ; Table S8). The ratio of446 contributions from three European references varies from group to group, probably reflecting genetic447 exchange with neighboring non-Uralic groups. For example, Saami from northern Fennoscandia contain a448 higher WHG and lower WSH contribution (16.1% and 41.3%, respectively) than Udmurts or Besermyans449 from the Volga river region do (4.9-6.6% and 50.7-53.2%, respectively), while the three groups have450 similar amounts of Nganasan-related ancestry (25.5-29.1%)."

    "Compared to both northwest480 and northeast groups, South Caucasians show extra affinity to Near Eastern populations, such as Neolithic481 Levantines and Anatolians (“Levant_N” and “Anatolia_N”, respectively; Table S2). In turn, North482 Caucasus populations have extra affinity with populations of the steppe and broadly of eastern Eurasia.483 Northeast Caucasians, for example Laks and Lezgins, show the strongest signals with ANE- and WSH484related ancient groups, with MA-1, AG3, Botai and EHG at the top. Northwest Caucasians (e.g. Adygei485 and Ossetians) are closer to East Asians than Northeast or South Caucasians are. We speculate that these486 results may suggest at least two layers of gene flow into the North Caucasus region: an older layer related487 to the ANE- or WSH-related ancestries and the younger layer related to East Asians. The former may488 have involved an interaction with Iron Age nomads, such as Scythians or Sarmatians. The latter most489 strongly affected Northwest Caucasians and might be related to historical movements of Turkic populations with some East Asian ancestry into the Caucasus. The genetic legacy of this movement is491 obvious for the Nogais that are scattered along PC1 between the rest of Caucasus populations and Central492 Asians (Figures S1-S2)."

    "For 7 of 22 Caucasus populations, a twowayadmixture model using Armenians and an ancient Scythian individual31 is sufficient (χ2 495 p ≥ 0.05;496 Table S9). Except for Georgians from the South Caucasus (6.8% contribution from Scythians), all the497 other groups have a substantial contribution from Scythians (38.0-50.6%). When we add Nanais as the498 third reference to model potential gene flow from Eastern Eurasians, most of the Caucasus populationsare consistent with the model: 15 of 22 Caucasus populations with χ2p ≥ 0.05 and another three with χ2 499 p500 ≥ 0.01 (Table S9). 9 of the 15 groups are adequately modeled by the three references but not by the two:501 they indeed have positive admixture coefficients for Nanais. Except for Nogais (19.8% for Nogai1 and502 48.0% for Nogai2), the other seven groups have only a small amount of East Asian ancestry that is503 prominent neither in PCA nor in ADMIXTURE (2.7-5.1%; Table S9)"

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    Interesting. The Y-DNA of the Botai was R1b-M73.
    They also write in the paper that R1b-M73 has also been found in Latvian hunter gatherers.

    But it doesn't seem like they survived in the areas that would later become occupied by yamnaya. Or at least they didn't ride the yamna train to Europe.

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    1 out of 1 members found this post helpful.
    [IMG][/IMG]

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    Quote Originally Posted by Ernekar View Post
    Interesting. The Y-DNA of the Botai was R1b-M73.
    They also write in the paper that R1b-M73 has also been found in Latvian hunter gatherers.

    But it doesn't seem like they survived in the areas that would later become occupied by yamnaya. Or at least they didn't ride the yamna train to Europe.
    I think they seems to be genetically related with Q1a2 of MayKop steppe where the oldest wagon was buried.
    Problem is how yamna trespassed the botai zone. Actually they were wild horse killers, so nothing but butchers. David Anthony found botai horse culture in afanasievo (but no wagon and no mound). So he tried to connected yamna to afansievo by the botai horse culture. Of course some afansievo is Q1a.

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    2 out of 2 members found this post helpful.
    Quote Originally Posted by Angela View Post
    [IMG][/IMG]
    Is EHG and EHG component of yamna different?
    Is it possible for European not to have EHG component?
    I think EHG culture has nothing to do with yamna culture.

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    Quote Originally Posted by johen View Post
    Is EHG and EHG component of yamna different?
    Is it possible for European not to have EHG component?
    I think EHG culture has nothing to do with yamna culture.
    As a rough estimate, Yamnaya is anywhere from 50-60% EHG. According to Anthony, Yamnaya as a culture is around 3500-3000 BC, and by then its people were mixed, and many of its cultural influences came from the south. The "pure" EHG were fisher/hunter/gatherers.

    The WHG is close to accurate because they're using LBK EN, which only had about 5% WHG picked up in Europe.

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    1 out of 1 members found this post helpful.
    Quote Originally Posted by Angela View Post
    The ancient Botai genomes suggest yet another layer of admixture in inner Eurasia that involves Mesolithic hunter-gatherers in Europe, the Upper Paleolithic southern Siberians and East Asians. Admixture modeling of ancient and modern populations suggests an overwriting of this ancient structure in the Altai-Sayan region by migrations of western steppe herders, but partial retaining of this ancient North Eurasian-related cline further to the North. Finally, the genetic structure of Caucasus populations highlights a role of the Caucasus Mountains as a barrier to gene flow and suggests a post-Neolithic gene flow into North Caucasus populations from the steppe."
    These results about an "overwriting" of the Botai-like ancient structure in the Altai-Sayan, but partial preservation of it to the north (I presume they're talking of the formerly heavily Yeniseian-speaking areas in central-north Siberia), reinforce some hypothesis that has apparently gained some ground lately: the supposed linguistic (and maybe also genetic?) connections between Yeniseian and Burushaski. We know that even before BA steppe ancestry arrived in South Asia the West Siberian component was already there, and maybe it was much more relevant and more concentrated in a few areas than in most others, thus getting to impose their Central Asian/South-Central Siberian language. Do we have analysis of Burusho people's ancestry investigating for the West Siberian-related admixture in them? If Burushaski is really connected to a North Asian language family, it would make sense that it came before Indo-Europeanization of Central Asia.

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    0 out of 1 members found this post helpful.
    I guess this paper happened in good times to affirme the newly hypothetized CHG " Indo-European " and EHG " Uralic " theory from Jena and Harvard.

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    1 out of 1 members found this post helpful.
    Quote Originally Posted by halfalp View Post
    I guess this paper happened in good times to affirme the newly hypothetized CHG " Indo-European " and EHG " Uralic " theory from Jena and Harvard.
    The smartest guy, Rob in Eurogenes also tried to connect steppe R1b to CHG from south.
    Rob said...

    “PG2004, PG2001, VJ1001 from this study - R1b and probably 50-60% CHG looking at their admixture bar. Not to mentioned the Z2103's throughout Yamnaya with ~ 40% 'CHG'. That's 'CHG rich' is it not ?
    There's also I1635 (L388 xM269) from Kalavan Cave, Kura Araxes , Armenia c. 3000 BC, ~ 70% CHG. So plenty of R1b in/ from "CHG rich' areas.”


    Problem is the burial type of R1b. Even if there are two type burials in yamna kurgan, I think R1b guys in yamna, afanasievo, and Khvalynsk were buried in supine position with legs raised. As far as I know, the position appeared only in steppe.

    Next time Harvard lab need to focus upon Kura Araxes burial with wagon, where steppe gene (maybe Z2103 with convex nose skull) will be found.

    “However, by 2400 BC changes are consistently visible, starting with settlement patterns; the abandonment of the former Kura-Araxes villages and a shift toward less permanent occupations and higher mobility coupled with the construction of monumental funerary tumuli (Edens, 1995). These earthen kurgans—with their preserved wooden-log funerary chambers containing wheeled wagons (Djaparidze, 2003; Makharadze and Murvanidze, 2014; Lyonnet, 2014) and rich funerary inventories composed of skillfully crafted golden and silver artifacts, arsenical copper, and tin-bronze objects (Chernykh, 1992; Carminati, 2014)—are paradigmatic of the radical changes in the region.”

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    1 out of 1 members found this post helpful.
    Quote Originally Posted by johen View Post
    The smartest guy, Rob in Eurogenes also tried to connect steppe R1b to CHG from south.
    Rob said...

    “PG2004, PG2001, VJ1001 from this study - R1b and probably 50-60% CHG looking at their admixture bar. Not to mentioned the Z2103's throughout Yamnaya with ~ 40% 'CHG'. That's 'CHG rich' is it not ?
    There's also I1635 (L388 xM269) from Kalavan Cave, Kura Araxes , Armenia c. 3000 BC, ~ 70% CHG. So plenty of R1b in/ from "CHG rich' areas.”
    Kura-Araxes is too late to account for the CHG genes in the steppes, which are present in high percentage even before Yamnaya. It is possible that Kura-Araxes also absorbed some of the same source of CHG/R1b that also contributed to the steppe populations much earlier, but I'm not sure yet. We aren't even sure that R1b Z2103 from Chalcolithic Iran was really confirmed, as there were so many apparently wrong "signatures" in that preprint.

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    4 out of 4 members found this post helpful.
    Tomenable is even downvoting papers in order to "get" at me. How incredibly childish.

    Why don't you go out, kick a football around, chase some girls, or if you're not that type, take some courses. Whatever. Just get a life and stop sending sexuallly harassing e-mails to a woman old enough to be your mother.

    You're pathetic, and I'll keep on pointing that out every time you do it, so that everyone here can see it.

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    1 out of 1 members found this post helpful.
    So on the subject of the Steppe Maykop and the Botai hunters, do the Steppe Maykop samples have East Asian ancestry or do they share a common ancestry with the Botai hunters. Also do the Botai hunters have East Asian ancestry or is it this unspecified ancestry related to the Kennewick man and modern East Asians? I remember one of these papers said something about a new ancestral component that existed throughout Siberia that was not necessarily Ancient North Eurasian, and this component existed in the Steppe Maykop samples and the Botai samples. Also the existence of both R1b and Q1a in the Steppe Maykop, Khvalynsk culture, and Mesolithic Latvia leads me to believe there is some link between R1b, R1a, Q1a, and to a lesser extent I2a2. This might explain why there are specific types of Q1a2 in Scandinavia and other regions of western and northern Europe. Specific subclades of Q1a2 that might be related to Bronze Age Indo-European expansions are Q1a2a1a2 (L804) and its subclade Q1a2a1a2a (L807), Q1a2b1 (L527), and most likely the subclades Q1a2b2 (L938) and Q1a2b2a (L939), which are found in Portugal, Britain, Anatolia/Turkey, and Lithuania.

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    Quote Originally Posted by halfalp View Post
    I guess this paper happened in good times to affirme the newly hypothetized CHG " Indo-European " and EHG " Uralic " theory from Jena and Harvard.
    could you develop please?
    thanks

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    2 out of 2 members found this post helpful.
    Paper is finally out.

    ""The genetic history of admixture across inner Eurasia"

    https://www.nature.com/articles/s41559-019-0878-2

    "The indigenous populations of inner Eurasia—a huge geographic region covering the central Eurasian steppe and the northern Eurasian taiga and tundra—harbour tremendous diversity in their genes, cultures and languages. In this study, we report novel genome-wide data for 763 individuals from Armenia, Georgia, Kazakhstan, Moldova, Mongolia, Russia, Tajikistan, Ukraine and Uzbekistan. We furthermore report additional damage-reduced genome-wide data of two previously published individuals from the Eneolithic Botai culture in Kazakhstan (~5,400 BP). We find that present-day inner Eurasian populations are structured into three distinct admixture clines stretching between various western and eastern Eurasian ancestries, mirroring geography. The Botai and more recent ancient genomes from Siberia show a decrease in contributions from so-called ‘ancient North Eurasian’ ancestry over time, which is detectable only in the northern-most ‘forest-tundra’ cline. The intermediate ‘steppe-forest’ cline descends from the Late Bronze Age steppe ancestries, while the ‘southern steppe’ cline further to the south shows a strong West/South Asian influence. Ancient genomes suggest a northward spread of the southern steppe cline in Central Asia during the first millennium BC. Finally, the genetic structure of Caucasus populations highlights a role of the Caucasus Mountains as a barrier to gene flow and suggests a post-Neolithic gene flow into North Caucasus populations from the steppe.""

    Behind a pay wall, of course, so don't know what might have changed.




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    http://sci-hub.tw/https://www.nature...559-019-0878-2

    And looks like nothing has changed.

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    M73 is not related with yamna, however I think the M73 would be with Indo-aryan along with z93. Recently I knew that 10% south asian has M73. Copper hoard culture maybe? copper hoard artifacts is very similar to mycenaean shield. I also think andronovo culture could not be connected to Hindu aryan, of which core concept is snake culture. snake means thunderbolt of indra and zeus, sunlight, creation to regerate and regenerate life, and finally fire cult. Any scholars did not mention snake culture in yamna, afanasievo, sintashta, andronovo except okunevo, seima turbino, malta and mesoamerica. Hidu culture is extremely similar to mesoamerica culture. It is not good to connect irrelevant steppe cultures to Hindusim, taking use of siberian shamanism. Moreover, seima turbino culture spread to British isle and iberia at late bronze age.
    looks like SM culture covered whole eurasia.

    Copper Hoard Culture describe find-complexes which occur in the northern part of the Indian subcontinent. These occur mostly in hoards large and small and are believed to date to the later 2nd millennium BCE


    https://anthrogenica.com/showthread....ai-petroglyph& (post 8)



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