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Thread: Global25 automated nMonte for South/Central Asian members

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    Quote Originally Posted by Kulin View Post
    @DMXX, not very related to the current topic being discussed, but what is the exact component that allows for South Asians to have some affinity towards Ust Ishim and be relatively close to it in distance. I'm not noticing a pattern here in regards to AASI/W Eurasian/East Asian etc. Also, for some reason, I am much closer to it than the Bengali_average in the dataset.

    "closestDistances": [
    "Onge:undefined: 14.79887",
    "Kulin_scaled:undefined: 14.84697",
    "Bengali_Bangladesh:undefined: 16.91125",
    "Paniya:undefined: 19.20747",
    "Shahr_I_Sokhta_BA3:undefined: 20.75658",
    "Thai:undefined: 31.05514"
    Ust' Ishim is a very archaic (~45kya) UP Eurasian HG from Siberia who didn't appear to contribute to any modern Eurasian populations.

    Due to its' great age, in simple terms, Ust' Ishim lacks the sort of informative drift that's necessary to form components in admixture models with programs like ADMIXTURE, and the same presumably holds true with David's G25 data. As such, Ust' Ishim's ancestry is erroneously categorised.

    You'll note from here that, in ADMIXTURE, Ust' Ishim comes out as predominantly SC Asian, Australasian and E Asian. It sits in a similar space in most PCA dimension pairs. That space is aligned with the direction from which AASI would have arisen.

    That is why Ust' Ishim's overall fit tends to be not-so-bad here with modern AASI-rich individuals, and indeed, why it seemed to serve as an accidentally useful ancient when modelling modern South Asians.

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    Quote Originally Posted by Mingle View Post
    Would you be using SISBA1 alongside SISBA3 for Balochis and South Iranians?

    And why would you use simulated AASI as well?
    No, because SiSBA3 is clearly an AASI-admixed iteration of SiSBA1, and there's no evidence to suggest that southern Iranians and Balochis derived a big chunk of their ancestry from a population similar to SiSBA3, rather than the more autochthonous iteration (SiSBA1). AASI in SC Asia was absent until the Bronze Age, per our current data, and with the exception of SiSBA2+3, most groups didn't score much.

    I would use the simulated AASI in case there's additional AASI in these populations that isn't sufficiently captured by SiSBA1.

    Shouldn't it already be embedded in SISBA?
    Won't know until we've performed the model, no?
    Last edited by DMXX; 05-07-2019 at 08:39 PM. Reason: amendment, we have no truly S Iranian aDNA

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    Quote Originally Posted by DMXX View Post
    Thou hath sinned against our righteous dogma, O Winged Equine of the Aegean.

    On a serious note, I think I understand why he did that - the region bounded between Tepe Hissar, SiSBA3 and Dzharkutan (NE Iran, SE Iran-SW Afghanistan, W Uzbekistan) is the bounded area from which the early East Iranians filtered down through after the Andronovo-BMAC hybrid cultures formed just to the north (we don't know what these looked like genetically just yet, though IMO they resembled Turkmenistan_IA).

    I suspect pegasus wanted to "cast a net" rather than pinning this ancestral component to just Gonur1_BA, which would've been my only pick for such a model. If you wanted to run a pan-Bronze Age model for yourself that cleanly separated the ancestral streams, then I'd go for Gonur1_BA, SiSBA3, Sintashta, Chokhopani_Nepal (to cover for any pre-TB ENA) and Hovsgol_BA (other ENA).
    Yes that was the idea, though I suspect populations further down where Amu Darya ends will have more AASI and WSHG, because Darra I khur, and 3 Udegram samples (not in the formal paper) strongly point to a population which I would imagine living in the Afghan highlands in the late Bronze Age.
    Last edited by pegasus; 05-07-2019 at 10:07 PM.

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    Quote Originally Posted by Kulin View Post
    @DMXX, not very related to the current topic being discussed, but what is the exact component that allows for South Asians to have some affinity towards Ust Ishim and be relatively close to it in distance. I'm not noticing a pattern here in regards to AASI/W Eurasian/East Asian etc. Also, for some reason, I am much closer to it than the Bengali_average in the dataset.

    "closestDistances": [
    "Onge:undefined: 14.79887",
    "Kulin_scaled:undefined: 14.84697",
    "Bengali_Bangladesh:undefined: 16.91125",
    "Paniya:undefined: 19.20747",
    "Shahr_I_Sokhta_BA3:undefined: 20.75658",
    "Thai:undefined: 31.05514"
    They way I see it is that Basal Eurasian is the ancestral population to the Ongee from about ~50000ybp. Ust Ishim is an ancestral population to the Ongee from 45000ybp.
    The reason I mention specifically the Ongee is that they seem to be a relic population on the path of OoA that have remained isolated for a long time. Most of the change in them over that period is likely some drift and some selection.
    That is why I think on D stats Ust Ishim is closest to the Ongee - just barely so though especially when compared to East Asians (Han); indicating that the Ongee-Han split is very very close in time to Ust Ishim.


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    Quote Originally Posted by parasar View Post
    They way I see it is that Basal Eurasian is the ancestral population to the Ongee from about ~50000ybp. Ust Ishim is an ancestral population to the Ongee from 45000ybp.
    The reason I mention specifically the Ongee is that they seem to be a relic population on the path of OoA that have remained isolated for a long time. Most of the change in them over that period is likely some drift and some selection.
    That is why I think on D stats Ust Ishim is closest to the Ongee - just barely so though especially when compared to East Asians (Han); indicating that the Ongee-Han split is very very close in time to Ust Ishim.

    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.



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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
    That said, this Dec 2018 pre-print was also brought up recently on this forum:

    The X chromosome in non-African populations has less diversity and less Neanderthal introgression than expected. We analyzed X chromosome diversity across the globe and discovered seventeen chromosomal regions, where haplotypes of several hundred kilobases have recently reached high frequencies in non-African populations only. The selective sweeps must have occurred more than 45,000 years ago because the ancient Ust’-Ishim male also carries its expected proportion of these haplotypes. Surprisingly, the swept haplotypes are entirely devoid of Neanderthal introgression, which implies that a population without Neanderthal admixture contributed the swept haplotypes. It also implies that the sweeps must have happened after the main interbreeding event with Neanderthals about 55,000 BP. These swept haplotypes may thus be the only genetic remnants of an earlier out-of-Africa event.
    ἦθος ἀνθρώπῳ δαίμων

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    Quote Originally Posted by traject View Post
    That said, this Dec 2018 pre-print was also brought up recently on this forum:

    The X chromosome in non-African populations has less diversity and less Neanderthal introgression than expected. We analyzed X chromosome diversity across the globe and discovered seventeen chromosomal regions, where haplotypes of several hundred kilobases have recently reached high frequencies in non-African populations only. The selective sweeps must have occurred more than 45,000 years ago because the ancient Ust’-Ishim male also carries its expected proportion of these haplotypes. Surprisingly, the swept haplotypes are entirely devoid of Neanderthal introgression, which implies that a population without Neanderthal admixture contributed the swept haplotypes. It also implies that the sweeps must have happened after the main interbreeding event with Neanderthals about 55,000 BP. These swept haplotypes may thus be the only genetic remnants of an earlier out-of-Africa event.
    Do we know if this non-Neanderthal sweep is Basal Eurasian related?

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    What do you suppose AASI_NW represents in terms of real populations? Do you think a population like that existed?

    I get something equivalent to DMXX's simulated AASI_NW when taking the difference between SiS_BA1 and SiS_BA2 and it's a handy spot on the PCA to form a triangle with West Eurasian and East Eurasian to encompass all the South Asians plus the Onge. But then using it in nMonte completely alters the results with regards to populations outside of South Asia (e.g, a mix of SiS-BA1 and Levant_N plus AASI_NW as opposed to something like Sarazm+AASI_South).
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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?
    I don't know if it was intended to be so, but looking at it, I don't think such a population existed.
    I mean, the pre-neolithic people of the region are not represented by what NW AASI seems to suggest.
    NW AASI seems to have been simulated by removing all the non-ENA of the existing ancient NW subcontinent samples to arrive at the ENA shell. AASI_south however seems to be Paniya-Onge inspired.
    Because of this, the latter retains a crown eurasian affinity( that gives us the "false steppe signal")unlike the former.

    to illustrate-
    distance from sintashta
    "Onge:undefined: 45.05434"
    "Simulated_AASI_South_by_DMXX:ASI_Sm1: 47.55527",
    "Simulated_AASI_South_by_DMXX:ASI_Sm2: 48.92407",
    "Simulated_AASI_NW_by_DMXX:NW_SiSBA3: 63.90674",
    "Simulated_AASI_NW_by_DMXX:NW_SGPT: 64.00131",
    "Simulated_AASI_NW_by_DMXX:NW_SiSBA2: 72.80715",
    "Simulated_AASI_NW_by_DMXX:NW_GonurBA2: 82.12381"

    distance from villabruna
    "Onge:undefined: 57.887"
    "Simulated_AASI_South_by_DMXX:ASI_Sm1: 60.49855",
    "Simulated_AASI_South_by_DMXX:ASI_Sm2: 61.69358",
    "Simulated_AASI_NW_by_DMXX:NW_SiSBA3: 73.69812",
    "Simulated_AASI_NW_by_DMXX:NW_SGPT: 79.78084",
    "Simulated_AASI_NW_by_DMXX:NW_SiSBA2: 83.20752",
    "Simulated_AASI_NW_by_DMXX:NW_GonurBA2: 91.83615"


    Unless this is how it is supposed to be, I find the premise that NW AASI be bereft of all non-ENA affinities while AASI South(and Onge) retain it to be fallacious. I apologise to DMXX in advance, if I am incorrect in my assessment.

    __
    "sample": "Test1:Shahr_I_Sokhta_BA3",
    "fit": 2.7819,
    "Ganj_Dareh_N": 55.83,
    "Simulated_AASI_NW_by_DMXX-NW_SiSBA3": 44.17,
    vs
    "sample": "Test1:Shahr_I_Sokhta_BA3",
    "fit": 0.4477,
    "Ganj_Dareh_N": 50.83,
    "Simulated_AASI_NW_by_DMXX-NW_SiSBA3": 40.83,
    "West_Siberia_N": 8.33,

    How is it ascertained that this "WSHG" portion is from the Iran side and not already present in the "AASI"? Formal stats? Especially since it is assumed that it is from AASI in the southern context.
    Sorry, I am genuinely new to these things and am still learning.
    Last edited by client; 05-08-2019 at 09:05 AM.

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    Quote Originally Posted by client View Post
    Unless this is how it is supposed to be, I find the premise that NW AASI be bereft of all non-ENA affinities while AASI South(and Onge) retain it to be fallacious. I apologise to DMXX in advance, if I am incorrect in my assessment.
    Where are you even deriving this premise from? That isn't something I or anyone else has proposed at any point, here. Who is claiming this? The part in bold is effectively a strawman argument. I state that to prevent any undue tangents about a premise that doesn't exist rather than to initiate an argument.

    I appreciate this thread is incredibly bloated, but I laid out exactly how I obtained those coordinates, and what is (or isn't) encoded within the simulations.

    In a sentence, NW AASI is a composite of isolated AASI coordinates from several Narasimhan ancients (qpAdm-guided proportions). S AASI is a composite of isolated AASI coordinates from several South Indian tribal populations (qpAdm-guided proportions).

    No artificial "stripping" of ENA, WSHG or other potential cryptic source of ancestry was undertaken - These coordinates exclusively represent the non-MLBA steppe, non-SiSBA3 ancestry which Narasimhan et al. inferred from formal statistical tests. How correct those proportions are remains to be seen, once we have AASI-rich aDNA.

    There definitely is something ENA-related in AASI, and there definitely is something WSHG-related in the Subcontinent, also. So, you're right about that, and you won't find any disagreement on that point with any of us who've followed this thread since the early days.

    We discussed these several times in this thread, so it's understandable if you didn't come across those posts (page 300 onwards is your best bet if you're curious). Frankly, I think we need to consider splitting the big discussion arcs in this thread to prevent the above.

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