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Thread: Global25 automated nMonte for South/Central Asian members

  1. #4501
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    Quote Originally Posted by Dr_McNinja View Post
    What do you suppose AASI_NW represents in terms of real populations? Do you think a population like that existed?
    Per my previous comment, it's a composite of various approximations of AASI found in the BA and IA Pakistani-Afghan samples. So, it's an unweighted average of a ghost component.

    There likely wasn't AA-related admixture embedded within NW_AASI, and there could well be some WSHG and Chokhopani-related ancestry embedded within (IMO likely), so it probably doesn't completely represent the UP HG's that may have been present northwest of the Ganges (or it may have, depending on when or if the potential cryptic WSHG and Chokho-related ancestry filtered its' way southwards).

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  3. #4502
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    FYI, the AASI concept will probably get dropped in the final paper.

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    Quote Originally Posted by bmoney View Post
    Basal Eurasian and the earlier split 'Deep' provides no ancestry to the ENA branch:

    Limits of long-term selection against Neandertal introgression 2019

    https://www.pnas.org/content/pnas/su...38116.sapp.pdf

    The statistic f4(West Eurasian W, Han; Ust’-Ishim, Chimp) has been previously used as a
    test of the presence of Basal Eurasian ancestry in a West Eurasian W (15). Specifically, it
    tests whether a population tree in which W and Han lineages form a clade is consistent
    with the observed data, which results in f4 statistic ~0. On the other hand, significantly
    negative values are evidence for an affinity of Han and Ust’-Ishim lineages, which can be
    most parsimoniously explained by W carrying an ancestry component from a population
    that diverged from other Eurasians prior to the separation of Ust’-Ishim. This “ghost”
    population is commonly referred to as Basal Eurasians
    (16). By analyzing a combined
    early-modern and present-day West Eurasian dataset, we find that this f4 statistic becomes
    consistently negative in the present, which is in agreement with the hypothesis that
    present-day West Eurasians carry (in different proportions) Basal Eurasian ancestry that
    was not present in early European hunter gatherers


    Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry 2018

    All known ancient Near Eastern populations prior to this work were inferred to harbor ‘Basal
    Eurasian’ ancestry9
    141 , a branch that diverged from all other non-Africans (including ESHG and
    142 present-day East Asians and Oceanians) before they split from each other.


    With these caveats in mind, we propose a scenario in which
    (i) Basal Eurasians split from other non-Africans, and may have plausibly not participated in the
    Neandertal admixture of Ust’Ishim and other non-Africans
    . Their divergence from other non69
    Africans has been recently estimated as having occurred 67.4-101kya using an independent
    method.18
    (ii) The Basal Eurasian split from other Eurasians may have involved migration of the ancestors
    of non-Basal Eurasians that brought them into contact with Levantine Neandertal populations
    followed by admixture.
    (iii) Subsequently, this mixed population dispersed across Eurasia established a relatively
    homogeneous ~2%-admixed set of Eurasian populations outside the Near East
    (iv) Admixture between Basal and non-Basal Eurasians in the Near East occurred at some time
    prior to our samples from Dzudzuana Cave.
    Regardless of the accuracy of this scenario, our results provide additional evidence that Basal
    Eurasians did not experience Neandertal admixture and through Near Eastern populations such as
    Dzudzuana diluted this type of ancestry in later West Eurasians


    Onge themselves
    are modeled as mixtures of Han and Papuan which might be tentatively suggestive of a
    Tianyuan→Han→Onge→Papuan cline in eastern non-Africans. However, Papuans are also modeled as a
    mixture of Onge and ~9.5% Mbuti; this does not mean that they have African ancestry, and this
    proportion likely reflects archaic Eurasian admixture from Neandertals and Denisovans18.


    Interesting, this model corresponds quite nicely with the K2 ADMIX runs from the Loosdrecht paper.

    The Yoruba are rendered here with the same ~13% (ancient UP) Eurasian admixture:

    .... .. I have spoken."

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  7. #4504
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    Quote Originally Posted by Generalissimo View Post
    FYI, the AASI concept will probably get dropped in the final paper.
    That would be something! I hope Lazaridis' Basal Eurasian meets a similar end.

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  9. #4505
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    Quote Originally Posted by bmoney View Post
    Basal Eurasian and the earlier split 'Deep' provides no ancestry to the ENA branch:

    Limits of long-term selection against Neandertal introgression 2019

    https://www.pnas.org/content/pnas/su...38116.sapp.pdf

    The statistic f4(West Eurasian W, Han; Ust’-Ishim, Chimp) has been previously used as a
    test of the presence of Basal Eurasian ancestry in a West Eurasian W (15). Specifically, it
    tests whether a population tree in which W and Han lineages form a clade is consistent
    with the observed data, which results in f4 statistic ~0. On the other hand, significantly
    negative values are evidence for an affinity of Han and Ust’-Ishim lineages, which can be
    most parsimoniously explained by W carrying an ancestry component from a population
    that diverged from other Eurasians prior to the separation of Ust’-Ishim. This “ghost”
    population is commonly referred to as Basal Eurasians
    (16). By analyzing a combined
    early-modern and present-day West Eurasian dataset, we find that this f4 statistic becomes
    consistently negative in the present, which is in agreement with the hypothesis that
    present-day West Eurasians carry (in different proportions) Basal Eurasian ancestry that
    was not present in early European hunter gatherers


    Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry 2018

    All known ancient Near Eastern populations prior to this work were inferred to harbor ‘Basal
    Eurasian’ ancestry9
    141 , a branch that diverged from all other non-Africans (including ESHG and
    142 present-day East Asians and Oceanians) before they split from each other.


    With these caveats in mind, we propose a scenario in which
    (i) Basal Eurasians split from other non-Africans, and may have plausibly not participated in the
    Neandertal admixture of Ust’Ishim and other non-Africans
    . Their divergence from other non69
    Africans has been recently estimated as having occurred 67.4-101kya using an independent
    method.18
    (ii) The Basal Eurasian split from other Eurasians may have involved migration of the ancestors
    of non-Basal Eurasians that brought them into contact with Levantine Neandertal populations
    followed by admixture.
    (iii) Subsequently, this mixed population dispersed across Eurasia established a relatively
    homogeneous ~2%-admixed set of Eurasian populations outside the Near East
    (iv) Admixture between Basal and non-Basal Eurasians in the Near East occurred at some time
    prior to our samples from Dzudzuana Cave.
    Regardless of the accuracy of this scenario, our results provide additional evidence that Basal
    Eurasians did not experience Neandertal admixture and through Near Eastern populations such as
    Dzudzuana diluted this type of ancestry in later West Eurasians


    Onge themselves
    are modeled as mixtures of Han and Papuan which might be tentatively suggestive of a
    Tianyuan→Han→Onge→Papuan cline in eastern non-Africans. However, Papuans are also modeled as a
    mixture of Onge and ~9.5% Mbuti; this does not mean that they have African ancestry, and this
    proportion likely reflects archaic Eurasian admixture from Neandertals and Denisovans18.


    Yes I was referring to Basal Eurasian at split t=0 (Main Eurasian/Basal Eurasian node in the figure ~50000ybp) as being ancestral to the Ongee via a Ust Ishim type (Ust Ishim/Tianyuan node circa 45000ybp) population.

  10. #4506
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    Quote Originally Posted by NiloSaharan View Post
    Interesting, this model corresponds quite nicely with the K2 ADMIX runs from the Loosdrecht paper.

    The Yoruba are rendered here with the same ~13% (ancient UP) Eurasian admixture:

    No doubt and the Dinka have even higher, while the Mbuti are much lower, which is consistent with the Ust Ishim D stat.


  11. #4507
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    Yes, these "meta-clades" (AASI, ENA, BE) will all eventually become defunct terms when the obligatory ancient samples are surfaced. Much the same way "ANI" has been rendered obsolete (or at least it should be).

    How soon, is the question.

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  13. #4508
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    Quote Originally Posted by DMXX View Post
    Yes, these "meta-clades" (AASI, ENA, BE) will all eventually become defunct terms when the obligatory ancient samples are surfaced. Much the same way "ANI" has been rendered obsolete (or at least it should be).

    How soon, is the question.
    I agree, we tend to make models based on these ancient groups as if they were relatively homogenous or unitary, when the reality is that humans have been moving and mixing for hundreds of thousands of years. My only issue with the "meta-clade update" is that I become very much detached from them - even talking about Western Hunter-Gatherers feels so distant it's almost abstract to me, let alone whatever else came before them.
    Or maybe it's just me, since I have a strong bias in favour of the metal ages (and early medieval periods), and while older periods are also fascinating, they just don't capture my imagination enough to lose some of my time modeling or exploring them
    Last edited by Ruderico; 05-09-2019 at 08:27 AM.
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    [1] "distance%=1.6023"

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    Quote Originally Posted by parasar View Post
    That would be something! I hope Lazaridis' Basal Eurasian meets a similar end.
    Whys that?

  16. #4510
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    Quote Originally Posted by Mingle View Post
    Why are both "Simulated_AASI_South_by_DMXX" and "Simulated_AASI_NW_by_DMXX" being used in this model that you did for Kerala Nairs? Shouldn't only South AASI be used here? Are both being used for Kerala Nairs here because they have both North Indian and South Indian ancestry? If that's the case, then does that mean most populations in the region should be using only only one simulated AASI instead of both? Or does using both apply to all populations in the region?

    Do you think the difference between Simulated AASI NW and Simulated AASI South is mostly due to genetic drift or they have some other components that were difficult to remove during the simulation?

    How come there haven't been any Simulated AASIs done for the Gangetic Plains and East Iran (SIS3)? Are they not different enough to warrant a separate simulation?

    Do you know what the genetic difference between Dzharkutan1, Dzharkutan2, and Sappali Tepe is?
    Mingle posted this question a while ago. I am also curious if we can extract some kind of simulated Iran_N? How different would it be from Tepe Hisar or Ganj Dareh? Is Iran_N a composite of various ancestries?

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