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Thread: Can someone answer something for me really quickly in relation to South Asia?

  1. #21
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    Some Dstats comparing with Papuan. Naga (S Indian tribal) is closer to Papuan than Dai, Han, and Ami. I suspect that the similarity with Naga would be even higher if Onge is used in lieu of Papuan.


    SOURCE 1 SOURCE 2 TARGET OUTGROUP DSTAT Z
    Han NAGA Papuan Gorilla -0.009 -2.015
    Dai NAGA Papuan Gorilla -0.0068 -1.429
    Ami NAGA Papuan Gorilla -0.0052 -1.075
    Han Ami Papuan Gorilla -0.0035 -1.632
    Han Dai Papuan Gorilla -0.0022 -1.188
    Dai Ami Papuan Gorilla -0.0014 -0.545
    Han LaBrana1 Papuan Gorilla 0.0533 8.46
    Dai LaBrana1 Papuan Gorilla 0.0551 8.647
    Ami LaBrana1 Papuan Gorilla 0.0558 8.66
    Han Loschbour Papuan Gorilla 0.0577 10.462
    Dai Loschbour Papuan Gorilla 0.0593 10.449
    Ami Loschbour Papuan Gorilla 0.0608 10.774
    Han Kostenki14 Papuan Gorilla 0.0624 9.981
    Dai Kostenki14 Papuan Gorilla 0.0647 10.115
    Ami Kostenki14 Papuan Gorilla 0.0667 10.364
    Han Stuttgart Papuan Gorilla 0.0732 13.687
    Dai Stuttgart Papuan Gorilla 0.075 13.677
    Ami Stuttgart Papuan Gorilla 0.0763 13.799
    Last edited by Kurd; 09-29-2015 at 01:38 PM.

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  3. #22
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    I see. Well here are the working links first of all.

    The link to the post describing Andamanese and its relationship to East Asians: http://anthromadness.blogspot.com/20...tion-more.html

    It essentially says that the Andamanese and the East Asians form part of the same clade. Essentially, since they are in the same clade, ASI was erroneously assumed to be = to Onge, when in reality, it is East Asian/SE Asian in ancestry. Is this a reason why the two are lumped together/equated to each other in these studies? Does it suggest interchangeability of the two?

    And why would the Han serve as a better proxy than the Onge if ASI was really closer to Onge?

    Also, this paper clearly states that the Onge are closer to South East Asians than to South Asian in the conclusion near the end: http://digitalcommons.wayne.edu/cgi/...ontext=humbiol

    Its one of the latest papers in the field. Also, I have read on the Eurogenes blog (and on the Dienekes blog) that when using the Han Chinese in admixture analysis, they serve as a better proxy than the Onge. Furthermore, as I posted in one of my previous posts, (I just confused ASI for "South Indian" -- for that, I apologize, still learning here) the Fst distances clearly suggest than there is no way that the "South Indian" component is related to Onge.

    The link to the Fst distances: https://docs.google.com/spreadsheets...it?pli=1#gid=2

    I stand corrected, that link expounds upon the "South Indian" - "Papuan" distance but not the "ASI" - "Papuan" distance. So if that means that the "South Indian" component is closer to Western Eurasian populations than even Eastern Eurasian or Papuan populations, it would be safe to say that it is predominantly Western Eurasian in ancestry, correct? And this would discount the possibility of "South Indian" being closer to Papuan than to the other populations outlined in the chart, as I explained earlier.

    These are the fst distances from above, the most widely used measure of genetic distance between populations, between "South Indian" and other populations:

    Caucasian: 0.077
    Baloch: 0.08
    NE Asian: 0.081
    NE Euro: 0.082
    SE Asian: 0.084
    SW Asian: 0.091
    Siberian: 0.093
    Mediterranean: 0.095
    Beringian: 0.116
    E African: 0.122
    American: 0.128
    W African: 0.142
    Papuan: 0.145
    Pygmy: 0.188
    San: 0.203

    If one actually reads this fst distance spreadsheet I posted above (with data from Reich et.al and other Harvard geneticists), it is clear that the "South Indian" component is closest to Gedrosia (at 0.081) followed by Caucasus (at 0.082) and East Asian (at 0.085) and Northern European at (0.086). This clearly shows that it’s actually closer to Gedrosia and Caucasus than the East Asian components. Again, the component is closest to Caucasian, Baloch, NE Asian, NE Euro and SE Asian in that order. So its closer to Western Eurasian populations, followed by a South-East Asian population, followed by a North-Eastern European population.

    In other words, the "South Indian" component is actually closer to Western Eurasian populations than even Eastern Asian populations, and it is nowhere near close to Papuan populations. In fact, it’s even closer to North Eastern Europeans than it is to Papuans and closer to West and East African than the Papuan component! So how can one link "South Indian" to Papuan? I keep reading that South Asians are all admixed with Papuan, and it is really frustrating to read that when it is patently false. Even the so-called tribes of India are not all admixed with the Papuan component, and have more in common with each other than they do with the Onge: http://www.ncbi.nlm.nih.gov/pubmed/6479999
    And if the Papuan component is so far from the "South Indian" component, even if the Onge are relatively closer, they would still be a more distant match than Caucasian, Baloch, NE Asian, NE Euro, etc.

    Finally, I've asked this several times before, but how West Eurasian are castes like the Jatt and Bhatia exactly? If they are 25% South Indian, then it follows that they are 12.5% ASI, and thus that they are 87.5% West Eurasian, considering that there isn't any East Asian admixture apart from the ASI already present. Is this a correct value -- 87.5% West Eurasian? I'd really appreciate it if someone could confirm this for me.
    Last edited by Skyfall; 09-29-2015 at 04:23 PM.

  4. #23
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    There is no evidence whatsoever to suggest that ASI or the South Indian component in Indians is related to modern-day Australoids or even Negritos.
    So I guess the conclusions of a scientific paper by a highly respected team of geneticists counts as "no evidence whatsosever" in your world? If you won't accept that, then why bother asking questions at all? Just believe what you want and stop wasting everyone's time.

    Quote Originally Posted by Skyfall
    This paper clearly states that the Onge are closer to South East Asians than to South Asian in the conclusion near the end: http://digitalcommons.wayne.edu/cgi/...ontext=humbiol
    The question is which East Eurasians South Asians are closer to; it's irrelevant whether or not Onge are closer to Southeast Asians. (And the paper you linked has a nice PCA where the Onge are located close to Indian Austro-Asiatic tribes and far from Southeast Asians.)

    It essentially says that the Andamanese and the East Asians form part of the same clade. Is this a reason why the two are lumped together/equated to each other in these studies? Does it suggest interchangeability of the two?
    Forming a clade means that they are more closely related to each other than either is to any outside group. So Onge, Han, Dai, Papuan, Karitiana etc are all more closely related to each other than any of them is to, say, Europeans. That makes them interchangeable for some purposes, but not all. It doesn't mean they are *equally* related to all outside groups. They could have some minority of shared ancestry that links them to other groups - such as the ANE in Karitiana - or they could be representative of ENA admixture into another population, like ASI.

    And why would the Han serve as a better proxy than the Onge if ASI was really closer to Onge?
    How about you provide actual evidence of this? Davidski at Eurogenes doesn't have the Onge genomes because he doesn't want to sign the waiver restricting their use. There are reasons to choose a different proxy apart from the genetic distance.

    I guess that link expounds upon the "South Indian" - "Onge" distance but doesn't take into account ASI. So if that means that the "South Indian" component is closer to Western Eurasian populations than even Eastern Eurasian or Onge populations, it would be safe to say that it is predominantly Western Eurasian in ancestry, correct?
    As you have already been told that component can be considered roughly 50% West Eurasian. However, ADMIXTURE components do not sum up mathematically, that isn't how they work. But it is good enough for a rough estimate.

    There have been three different papers dealing with admixture proportions in South Asian populations, you could read them and see if the populations you are interested in are listed. Or if you know someone who can run f statistics then you could do f4 ratio estimates yourself. But you aren't going to get any definitive, exact results.

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  6. #24
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    I apologize if that post came across as disrespectful in any way, but I'd appreciate it if you could tone down the rhetoric.

    First of all, if the Fst Distances I posted are correct (from the HAP) then how can one suggest that "South Indian" is more closely related to Papuan or Onge than to the other populations listed? That is why I stated that there is no evidence for the same. In addition, numerous people have stated that the Onge are at a best a poor proxy, and that owing to the problems of genetic drift, they assume ownership of a component, which means that in admixture programs, the program would try to force a fit between Onge and Western Eurasians. Again, this is what I've read, if it is incorrect, please feel free to enlighten me.

    Secondly, if the Andamanese and the East Asians form part of the same clade, how can one decide if one fits better than the other? As you pointed out, that makes them interchangeable for some purposes, but not all. And you also stated that they could have some minority of shared ancestry that links them to other groups - so how does one go about isolating exactly what fits better? Isn't this an arbitrary process at this point? And it is relevant that the Onge are closer to SE Asians than to South Asians, because this would suggest that any linkage between South Asians and the Onge is actually hinting at a South Asian-SE Asian linkage. Furthermore, just because some Austro-Asiatic tribes have some connection to the Onge, (as I pointed out above, and have pointed out below as well) doesn't mean that all 1.2 Billion + South Asians have it as well. In fact, the conclusion of the paper and the evidence I have posted below quite clearly states the opposite.

    Thirdly, I don't have access to the link that states that the Han are a better proxy than the Onge, but I do remember quite vividly, that I read it on the Eurogenes blog.

    Also, isnt it fair to say that ASI is just like the paleolithic ANE influence in Europeans, and half of it is Western Eurasian in nature?

    The Reich et al paper even pointed out that the Onge were at best a poor proxy to get something without ANI admixture and little ASI admixture. The reason they picked the Onge as a (poor) proxy was because they were the only group they could find in that region without ANI admixture and because they are such an old population that has been isolated and separated from mainland populations for a very long period of time. They also have very few individuals left, so owing to the problems of genetic drift, they assume ownership of a component, and the admixture program tries to force the Onge component in an admixture model of South Asians.

    Also, the ASI is massively separated from the Onge. In fact, ASI is just as far from the Onge as the Utah Whites (a group of random Euro-descent samples from Utah in the States) are from the Onge, indicating that ASI is as related to Onge as Utah Whites are. In addition, Indians lack Denisovan admixture and other crucial haplogroups found commonly in the Onge as well. It must also be said that if Indians are erroneously assumed to have proto-Australoid-like ancestry, so are Europeans, owing to the relationship of ANE to ASI and the genetic makeup of the Malt'a individual.

    Finally, if the "South Indian" component is closer to Western Eurasian populations than even Eastern Eurasian or Papuan populations, it would be safe to say that it is predominantly Western Eurasian in ancestry, correct? You stated is is 50% Western Eurasian, but I've read in some places that it is 60% -- what is the correct value? And this would discount the possibility of "South Indian" being closer to Papuan than to the other populations outlined in the chart, as I explained earlier, correct?

    As far as the tribal populations I alluded to earlier are concerned, it is true that some members among them share certain markers with a common ancestor of Papuan-like people, as recent genetic research has shown:

    http://blog.23andme.com/news/direct-...an-aborigines/

    However, this is only limited to a super-small minority of tribes that are exceptionally geographically and racially isolated with no contact with the outside world. Even these tribes have been shown to be more similar to each other than to Australoid-like populations, as has been published in peer-reviewed research:

    http://www.ncbi.nlm.nih.gov/pubmed/6479999

    And if the Papuan component is so far from the "South Indian" component, even if the Onge are relatively closer, they would still be a more distant match than Caucasian, Baloch, NE Asian, NE Euro, etc.

    Also, the South Indian component clusters slightly closer to the West Eurasian components and in particular Gedrosia, a Caucasian component. Being roughly intermediate between the Siberian and Gedrosia components does NOT make the South Asian component Australoid in any way. Especially, when the HAP South Indian component is almost twice as close to the Caucasian component than it is to the Papuan component.

    I’m not saying the South Indian component is completely West Eurasian, but it’s clearly mixed between ANI and ASI with the majority being ANI. In addition, Papuans and the Onge cluster closest to East Eurasians (in particular Southeast Asians) than other populations. The South Indian component is intermediate between Siberian and Gedrosia, Siberian being East Asia, and Gedrosia being Caucasian. It is actually slightly closer to Caucasian components than East Eurasian components, therefore, the component is ~60% Caucasian in nature, as I explained earlier.

    The South Indian component is so distant from the Papuan “Australoid-like” component that its laughable to suggest any connection as I explained above. Again, as the fst distances show, it is actually the furthest from all SSAs, and then Papuans — Papuans are even further removed from the South Indian component than the East and West Africans! So there is no relation to Papuans at all. If anything, there is a pull towards East Asians, who themselves are closest to some Negrito populations but still quite far away from them.

    Some South Asians pull towards East Asians like all of Europe, particularly Northern and Eastern Europe, with the same affinities to the same populations, because of the ASI admixture which is present in Europeans in ANE form, which BTW is also 10% SE Asian and Australoid-like according to the latest research. Furthermore, the unusually high South and Southeast Asian scores in some Europeans can be explained by shared ANE ancestry with South Asians (in the form of ASI). In essence, what I stated is that the ANE found in Europeans links them to Amerindian populations because both groups have ANE ancestry, and the ANE component is composed of 45% Mongoloid and Australoid-like ancestry (similar to the distant relation that some South Asians have to proto-Australoids), and the Malt’a boy also has a proto-Australoid ASE component on the order of 10%., and this ANE component peaks in the Karitiana Indians of South America.



    I’d also like to add that Melanesians and Papuans cluster in an isolated position by themselves and are somewhat divergent from one another, while South Asians are closest to West Eurasians with a pull toward East Eurasians. All that means is that the ASI portion of the South Indian component split less recently from the ancestors of the Papuans compared to other populations and is South-East Asian in nature. In addition, any fst distance over 0.1 is still quite distant.

    Finally, I've asked this several times before, but how West Eurasian are castes like the Jatt and Bhatia exactly? If they are 25% South Indian, then it follows that they are 12.5% ASI, and thus that they are 87.5% West Eurasian, considering that there isn't any East Asian admixture apart from the ASI already present. Is this a correct value -- 87.5% West Eurasian? I'd really appreciate it if someone could confirm this for me, even if it is a rough estimate.
    Last edited by Skyfall; 09-29-2015 at 05:24 PM.

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    Quote Originally Posted by Kurd View Post
    Some Dstats comparing with Papuan. Naga (S Indian tribal) is closer to Papuan than Dai, Han, and Ami. I suspect that the similarity with Naga would be even higher if Onge is used in lieu of Papuan.


    SOURCE 1 SOURCE 2 TARGET OUTGROUP DSTAT Z
    Han NAGA Papuan Gorilla -0.009 -2.015
    Dai NAGA Papuan Gorilla -0.0068 -1.429
    Ami NAGA Papuan Gorilla -0.0052 -1.075
    Han Ami Papuan Gorilla -0.0035 -1.632
    Han Dai Papuan Gorilla -0.0022 -1.188
    Dai Ami Papuan Gorilla -0.0014 -0.545
    Han LaBrana1 Papuan Gorilla 0.0533 8.46
    Dai LaBrana1 Papuan Gorilla 0.0551 8.647
    Ami LaBrana1 Papuan Gorilla 0.0558 8.66
    Han Loschbour Papuan Gorilla 0.0577 10.462
    Dai Loschbour Papuan Gorilla 0.0593 10.449
    Ami Loschbour Papuan Gorilla 0.0608 10.774
    Han Kostenki14 Papuan Gorilla 0.0624 9.981
    Dai Kostenki14 Papuan Gorilla 0.0647 10.115
    Ami Kostenki14 Papuan Gorilla 0.0667 10.364
    Han Stuttgart Papuan Gorilla 0.0732 13.687
    Dai Stuttgart Papuan Gorilla 0.075 13.677
    Ami Stuttgart Papuan Gorilla 0.0763 13.799
    Naga is not a south Indian pop but they are north east Indian tribals .They come up as mostly NE Asian in most admixture runs

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  9. #26
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    "Naga is not a south Indian pop but they are north east Indian tribals .They come up as mostly NE Asian in most admixture runs "

    Exactly. Which is why that distance run doesn't mean anything.

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    The reason HAP's South Indian component is close to the Baloch and Caucasus components is because it's not pure ASI. It has West Eurasian in it. And I strongly doubt that the Bhatia are 12.5 % ASI. In my opinion, they and other groups with very high Baloch are hiding some extra South Indian in their Baloch component. Again, no one knows how West Eurasian NW Indians are. For that, we need ancient DNA from South Asia. We don't exactly know the nature of ASI yet since there is no pure ASI population left in South Asia, not even tribals.

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  12. #28
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    Quote Originally Posted by bored View Post
    The reason HAP's South Indian component is close to the Baloch and Caucasus components is because it's not pure ASI. It has West Eurasian in it. And I strongly doubt that the Bhatia are 12.5 % ASI. In my opinion, they and other groups with very high Baloch are hiding some extra South Indian in their Baloch component. Again, no one knows how West Eurasian NW Indians are. For that, we need ancient DNA from South Asia. We don't exactly know the nature of ASI yet since there is no pure ASI population left in South Asia, not even tribals.
    Interesting. So if it is not pure ASI, what relative % of it is West Eurasian? Is my inference above (of it being between 50-60%) correct? If there are no pure ASI populations left in South Asia, then one cannot reasonably conclude what the ASI looked like, or what population the ASI are closest to, owing to the admixture that they have, correct? And in light of the above evidence that I have posted, it is safe to say that connecting South Indian or even ASI to the Papuans and the Onge is a massive stretch, correct?

    Its interesting that you think the Baloch component is hiding extra ASI. But assuming that it isn't, what is a very rough and general estimate of how West Eurasian a caste like the Bhatia are? I mean a very empirical and hypothetical estimate? It surely has to be at least 75%? Also, what % of ANI is West Eurasian?

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    Quote Originally Posted by Skyfall View Post
    "Naga is not a south Indian pop but they are north east Indian tribals .They come up as mostly NE Asian in most admixture runs "

    Exactly. Which is why that distance run doesn't mean anything.
    Dstat values can be quite useful to determine whether a population is derived from a source population or not . And it's effectiveness depend on populations used .
    Here in this example it just shows naga is just more closer to papuan than han or dai . It doesn't say either naga or han is very close or distant to papuan . From the values we can there is only slight pull towards naga and actually both are closer to each other and only distantly related to papuan.
    On another note I think the slight pull south Asians have is due to the influence of the very early coastal migrations . Even if the present gene pool have only around 1-2% remnant of that ancient population they will still show as closer when compared to others who have none.

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    Using the Naga doesn't make sense, however, for the reasons I listed above. The mainland caste populations like the Jats have nothing to do with them. Isolated tribes and their genetic makeup don't correspond to that of all 1+ Billion South Asians. Plus the Naga live in the NE and are essentially completely East Asian. The fact that they are showing up as closer to Han and only distantly related to Papuan further proves the point that Papuan is related to East Asian. Also the South Indian component, while being 50-60% West Eurasian, and 40-50% ASI, doesn't correspond to the Naga, as far as I can make out, since the Naga are only a part of that ASI component, if at all. The ASI component has been hypothesized to be SE Asian or East Asian in ancestry, so even if the Naga are used, it would only prove the point that ASI is East Asian.
    Last edited by Skyfall; 09-29-2015 at 06:12 PM.

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