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Thread: Population genomics of Bronze Age Eurasia (Allentoft et al. 2015)

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    If I recall, Reich's original paper modeled Pashtuns and various other South Asians as a mix of Lithuanian and Onge. In a subsequent paper by Moorjani, they found that the Georgians were a better fit. Now, obviously, those two papers are already ancient, but they are probably on to something when they found Georgians a better fit than Lithuanians.

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    What does d stat show when Pashtuns are compared to a West Asian population and Sintashta (and Chimp as outgroup)?

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    Quote Originally Posted by everest59 View Post
    If I recall, Reich's original paper modeled Pashtuns and various other South Asians as a mix of Lithuanian and Onge. In a subsequent paper by Moorjani, they found that the Georgians were a better fit. Now, obviously, those two papers are already ancient, but they are probably on to something when they found Georgians a better fit than Lithuanians.
    It was the CEU sample from Utah that was used by Reich. The outgroup was also changed from Papuan to Yoruba by Moorjani.

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    Quote Originally Posted by parasar View Post
    It was the CEU sample from Utah that was used by Reich. The outgroup was also changed from Papuan to Yoruba by Moorjani.
    Oh, that's right. The point being that they found Georgians a better fit.

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    It could be Georgian corresponded to ANI ancestry. It's unlikely Pashtun would just be Steppe + ASI. It would be Steppe + ANI + ASI. Georgians are the best fit for ANI, so perhaps it just used Sintashta to represent the non-Indian ancestry from the Steppe outside of ANI/ASI (represented by Georgians + Dai).

    Kind of like doing a one-sample admixture run, but using the in/out populations to guide the breakdown.

    It would have to be tried with other groups in addition to Georgians + Dai as well.
    Paternal - Y-DNA: J2b2* (J-M241) Z2432+ Z2433+ Y978+ (J2b2a2b1*) (Hidden Content ) (YFull: YF02959) (FTDNA Kit B6225), mtDNA: M18a* (FTDNA Kit 329180) (YFull: YF63773)
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    Quote Originally Posted by parasar View Post
    I have this theory of native component recovery after admixture. Some native markers are selected for and they bring along with them the recovery of their associated component. Recovery of WHG after admixture would therefore be expected in areas where WHG was native and similarly EEF would recover where EEF was native. The converse is also true - Euro WHG type markers would not be selected for in South Asia, and the component would reduce over time in South Asia.
    This is a very interesting theory.
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    Quote Originally Posted by everest59 View Post
    If I recall, Reich's original paper modeled Pashtuns and various other South Asians as a mix of Lithuanian and Onge. In a subsequent paper by Moorjani, they found that the Georgians were a better fit. Now, obviously, those two papers are already ancient, but they are probably on to something when they found Georgians a better fit than Lithuanians.
    Dienekes said it did not make sense, as you already had a large urban population in the IVC already established 4 Kya.
    The dates given 4200- 1900 ya seems a better fit with the arrival of various Indo Iranian groups rather than ANI which arrived in the Paleolithic.

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    Quote Originally Posted by surbakhunWeesste View Post
    Iranian languages have four main dialectological categories:

    North-West Iranian, South-West-Iranian, East-Iranian and South-East-Iranian.

    Pashto is not a NE Iranian language, its plainly eastern Iranian. Eastern Iranian languages are Ossete(North and South Ossetia)-(Scytho-Samaritan descendant), Pashto, Yaghnobi(Sogdian descendant), Pamiri languages....

    Shughni, Sanglechi-Ishkashimi, Wakhi(Pamiri) are actually plain E Iranian language so is Pashto, they have quite similarity. All of these languages have retroflex as well.

    Also,
    Farsi and Tajiki is considered South-West Iranian.
    Zaziki, Kurdish and balochi : North-Western Iranian
    Pashto, Sanglechi-Ishkashimi(sometimes),Shugni, Wakhi : East Iranian
    Parachi: South East Iranian

    Also the modern Pashto spoken in Pakistan is heavily Urdufied much like the pashto spoken in Northern Afghanistan(Mazar and vicinity) is heavily Persianfied.

    Further more Pashto is Neo-Iranian now along with others. I can't derail this thread further more. This can be discussed in the Pashto section.
    Just a quick response:

    In other words, if you don't use the very category of "NE Iranian", Pashto isn't "NE Iranian"! You've simply designated the NE Iranian languages as "East Iranian". It's just a terminological change, not a change in conception. The broad unity of Pamiri languages and Pashto still stands (as does the point concerning Scythian affinities).

    And of course, Pashto has been affected considerably by neighboring languages.

    On topic, here are models using the Kusunda. The Kusunda have a good mix of ASI and East Asian ancestry, and they seem to be around 20%-25% West Eurasian (of Indian extraction). Their West Eurasian ancestry (and that too West Eurasian ancestry from South Asia) makes them less than ideal for a "pure" ASI reference, but it is important to see how things look without the Dai (as always, my thanks go to David for working on this topic, and for trying out models).

    54.9% Sintashta + 25.2% BA Armenian + 19.9% Kusunda

    chisq=0.112

    tail probability=0.945338

    58.9% Sintashta + 21.8% Georgian + 19.3% Kusunda

    chisq=0.395

    tail probability=0.820623

    64.9% Sintashta + 15.5% Armenian + 19.6% Kusunda

    chisq=0.585

    tail probability=0.746248

    As one can see, the Sintashta percentages increase in relation to the "southern" shift of the Caucasian reference. By contrast, the Kusunda percentages don't vary. Obviously, the Kusunda have absorbed some Sintashta-related admixture, since they are 20%-25% West Eurasian, and their West Eurasian admixture is probably quite shifted towards Sintashta, since it came from South Asia.

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    Quote Originally Posted by Sein View Post
    With all due respect, I don't know how you define "direct rebuttals"
    Responses to the arguments which illicit none of the prior fallacies and directly address the previous points raised.

    (and I surely don't see any of those on your part, just rather vague and "mushy" responses that don't address my main argument).
    False. I have consistently used both formal language throughout this discussion (i.e. no "amazing's", "exceeding's", "excellent's" or other unnecessarily descriptive discourse on my part) and have quoted the absolute majority of your posts with direct responses, a service you clearly haven't returned.

    Additionally, you have ignored large portions of my prior response, particularly the archaeological data. The face-value indication of this is apparent for all to read.

    Readers are encouraged to compare and contrast previous posts to negate Sein's attempt at strawman fallacies here.

    Also, unfortunately, the only obfuscation that I'm seeing here is solely from your direction, which is quite disheartening. But I'm not sure if it can really be called "unintentional", in this case at least.

    Be that as it may, I've already addressed much of what you've written (and much of what you've written is just a repeat of what you wrote a few days ago, concerning these models, "argumentum ad nauseam"). But you can find some notes below. Please, do forgive the atrocious theoretical repetition that I am about to unleash (I could teach Deleuze a thing or two):

    1) One has no need to use the "ASI" concept if it doesn't mean "South Asian-specific ENA", since that is what Reich et al. were trying to communicate via "Ancestral South Indian".

    If you have your own idiosyncratic understanding (one which only you are privy to), you need to come up with a new personal term of art.
    Ad hominem fallacies (instigating doubt regarding my intent here, weak personal insult, all above in bold) like these do not support your perspective in the least.

    As irrational as I find your stance on this particular topic, there has been no inkling on my part to personalise the discussion (please do not make the frequent misinterpretation of pointing out fallacies as personalising a discussion).

    The ASI discussion could serve as an interesting one. If there's interest among other members, I'll happily start another thread to explore these ideas further.

    2) You have not addressed why these fits appear paltry for Iranians, from any technical angle.
    I actually have provided possible explanations; for the sake of not committing argumentum ad nauseum myself, please revisit the first post of mine you recently quoted here (summarised; Bronze Age Armenians have likely absorbed the bulk of Iranian steppe-related ancestry, or no modern populations satisfactorily quantify the Iranian genepool).

    3) You don't seem to understand that even if Pashtuns aren't 70%-60% Sintashta admixed in a "literal" sense, these fits basically show that 70%-60% of their genetic ancestry comes from populations that are very similar to Sintashta.
    Ditto above; please revisit earlier posts to understand why I (among others) do not share the perspective you have on this particular topic.

    That can no longer be debated, unless you want to be as flat-out disingenuous as possible.
    Of course it will, and should be, given the numerous points I and others have raised regarding wariness towards immediate extrapolation of these results.

    Feel free to accuse myself (as well as most recent participants in this thread) as disingenuous given those rational objections.

    I can't see where that 70%-60% ancestry (that is basically identical to Sintashta) could come from, besides the steppe. Do you have any ideas that you would like to share with us?
    I have already outlined some possibilities previously in this thread (prior input from Eurasian prehistoric hunter-gatherer tribes, partial "masking" of ASI by Sintashta).

    My default position (as is the case you'll find with most involved in research) is tentative scepticism.

    Other users have appraised or contributed further to some of these. Revisit the past few pages to refamiliarise with the discourse thus far.

    4) I cited Everest's previous work to show that this finding isn't unprecedented, and that it isn't limited to qpAdm.
    The gentlemen above have shown the previous work you are referring to is, apparently, problematic and the finality of even those results is debatable.

    5) I find it rather interesting that you frown upon the drawing of a one-to-one correlation between uniparental data and the genome-wide results.
    Any population geneticist will likely view this outcome as a statistical coincidence and nothing more. It is an established fundamental in population genetics that founder effects and time both shift frequencies in unpredictable ways. If you doubt this, feel free to email a population geneticist of your choosing with the following message ad verbatim and inform us of the outcome:

    Code:
    Dear [their name],
    
    I am an enthusiast researching population genetics and observed that the Y-DNA haplogroup frequency for R1a-M17 among modern Pashtuns is 50-70%. 
    
    Modern Pashtuns are a strongly patrilineal ethnic group who have maintained a tribal structure for hundreds of years. Additionally, the history of Pashtuns beyond the Medieval period is largely unknown and shrouded in much speculation.  
    
    I've recently been using autosomal tools modelling Pashtuns as a mix of ancient and modern populations. I should note that no ancient DNA from the locales Pashtuns currently reside near have been tested. To my surprise, I found Pashtuns score 50-70% of their ancestry with an ancient group that so far appears to mostly be R1a-M17.
    
    Are the similar ranges above an indication of strong association between the two? I have been informed that the above is likely a statistical coincidence because of potentially numerous founder effects and the lack of any ancient DNA from near the Pashtun homeland.
    
    Sincerely yours,
    
    [Your name]
    Fulfil the above, acknowledge it is likely a coincidence as dictated by common sense, or otherwise feel free to either continue asserting this false premise simply to support your perspective.

    Mainly, because you did just that in your previous response concerning the genetic evidence, in relation to the Iranian plateau.
    False attribution. I maintained no one-to-one correlation between the frequencies of any genetic parameters in the Iranian plateau. Readers are once more encouraged to revisit my first post, where I even specified that the genetic contribution of these (assumed) West Iranic speakers in the plateau is currently unquantifiable.

    Instead, I cited the presence of distinct linguistic, archaeological and numerous genetic parameters among Iranians and Kurds relative to their immediate neighbours as evidence of a population influx into the Iranian plateau which may account for some of these. I have maintained this view for years (recent example) and is in keeping with our current (very limited) understanding of the ethnogenesis of Iranians.

    There is, therefore, no contradiction here.

    6) Finally, as one would expect, Burusho + Sintashta + Dai, does not work. But your new request is quite doable.

    HGDP Pashtuns (all samples):

    59.2% Burusho + 22.8% Sintashta + 18% Georgian

    chisq=0.266

    tail probability=0.875585

    Please, pay close attention to the chisq and tail probability. Compare them to what we see with this model.

    HGDP Pashtuns (all samples):

    63.4% Sintashta + 23.1% Georgian + 13.4% Dai

    chisq=0.049

    tail probability=0.975924

    If you haven't noticed, both the chisq and tail probability are "perfect", on the second model (the one which seems to annoy you). By contrast, there is room for improvement on the model you've requested. And even then, the model you requested still has a good amount of Sintashta input.
    Thanks very much for undertaking this. The second fit is certainly better.

    Although, as the primary issue here is one of interpretation and a complete absence of relevant aDNA to definitively conceptualise the ethnogenesis of any one group in West or South Asia, this outcome has no bearing on the criticisms raised here (other than addressing my earlier "hunch" regarding qpAdm modelling).

    Just a side note, but Pashto is a NE Iranian language, it is quite close to the Pamiri languages (if this is something you would like to contest, we can start citing the books and papers. Construing Pashto as "SE Iranian" is rare, and a close relationship to Pamiri languages is universally recognized). Scythian input is expected for Pashtuns, just based on that linguistic fact, and it wouldn't be surprising if Sintashta probably covers for some substantial Scythian ancestry.
    Irrelevant tangent. I asked for archaeological evidence to support your assertions, not the status of Pashto in the Iranic family. You have failed to provide this.

    Again (and again, forgive the "argumentum ad nauseam"), even if Pashtuns aren't "literally" 60%-70% Sintashta, it is undeniably certain that 60%-70% of their ancestry is from populations exceedingly similar (in fact, basically identical) to Sintashta, and the only place for such populations is the steppe, looking at the data that we currently have.
    Once more, just in case there is ambiguity regarding my position; these qpAdm figures are definitely indicative of broad patterns if the statistical probability is strongly in favour, which is the case here. However they do not yield a clear picture regarding specific events culminating in any group's ethnogenesis in the region specifically because these founding populations are unaccounted for, and given the incongruity with the archaeological data.

    I'm pretty confident that South Asian aDNA will back me up, and when that occurs, I'll certainly forgive you for this whole conversation ().
    Given the current absence of any aDNA from West Asia, South-Central Asia or South Asia, compounded by an apparent deficiency in your knowledge regarding Indo-Iranian archaeology, this is an untenable (putting it lightly) position to place stock in.

    Edit: Just for the record, only a few months ago (as most can recall), I repeatedly asserted that IE expansions had little genetic impact on South Asia.
    Duly noted.

    One has to be open-minded, and go where the science takes us.
    Indeed; the caveat-laden considerations of numerous posters here are both open-minded and fully in line with the latter stages of the scientific method. Your approach (using qpAdm results to shape the hypotheses while disregarding the prior adjunct data and not recognises serious current limitations) is anything but scientific.

    A friendly advanced notice - Please remove anything resembling ad hominem fallacies in any future replies to this message. As a former staff member, you know full well how stringent we are on these. Thanks.

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    Quote Originally Posted by Kurd View Post
    I would like to thank Sein for all his informative posts I have enjoyed reading. I also admire his courtesy, professionalism, helpfulness, and being considerate of others' viewpoints, in very Pashtun like fashion . I think he is a great asset here.

    Although I concede that qpAdm is based on more modern & robust algorithms than the slightly older algorithms used in admixture calculators, the output in qpAdm is still dependent on the inputs, and admixture calculation is still a necessary part of the analysis and comparison of ancient genomes to modern ones.

    Sein wrora, the issue many members (me included) are having with the >60% Sintashta based Pashtun model is that it highly dependent on Dai being an input population. As soon as you replace Dai, with a geographically more proximate Indian population to Pashtuns for the source of ASI/S Indian admixture present in Pashtuns, the >60% Sintashta input becomes invalid. Now there is really no evidence to suggest that Pashtuns obtained their ASI/S Indian admixture from Dai or any Dai like population. In fact it is much more likely that they did not, in light of the geographic separation.

    In fact I am not even sure we can rule out Afansievo as a source of steppe ancestry in Pashtuns either.

    Here is a suggestion, fix one input population in qpAdm as a steppe population as 1st Sintashta, and then 2nd as Afansievo. Fix the second input population as BA Armenian, or something else from W Asia, and use various Indian populations as the 3rd input ( I realize there are many ) and see what type of outputs you get.

    Also, if David posts a K8 PCA with Indian populations, that may narrow the search a little, because I believe that qpAdm results should be consistent with PCA based 3 population modeling.

    Finally, with Pashtun areas being at the crossroads of population migratory paths in Asia, a 4 population model can not be ruled out either.
    Wrora,

    What you've requested can be done (and will be done), but I'd just like to mention a few things.

    David has tried Afansievo, and they do not provide as excellent models for Pashtuns as Sintashta does.

    Although a model with an Indian population will be tried, we need to note that an Indian population will absorb Sintashta admixture for Pashtuns. R1a1a is everywhere in South Asia, and Sintashta are directly ancestral to many South Indian males! Basically, the only way to get accurate results for Pashtuns is by using an Indian population free of any IE influence, and everyone in India, including the South, probably has IE ancestry (in the far south, probably via gradual gene-flow from northern India).

    For what it's worth Moorjani et al. found very shallow admixture times for all Indians, which probably indicates that IE expansions left a huge genetic imprint of most South Asian populations.

    And the good thing about the Dai is that they are the closest population we have to ASI (in terms of shared drift).

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