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Thread: Waves of migration into South Asia

  1. #1081
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    Quote Originally Posted by Kurd View Post
    By contrast to the steppe samples, Iran N WC1 has the ancestral allele for rs1426654. He is AG at that position. His skin color prediction is for brownish skin. I'll try to do Loschbour and Stuttgart tomorrow

    Here is what I have

    SNPs Iran N-WC1
    rs10777129 GG
    rs13289 NN
    rs1408799 TT
    rs1426654 AG
    rs1448484 NN
    rs16891982 NN
    rs2402130 AA
    rs3829241 GG
    rs6058017 NN
    rs6119471 NN


    And his prediction:



    [IMG][/IMG]


    EDIT: By brownish skin I mean darker than the vast majority of modern Kurds and Iranians, which some are pretty dark. So about the complexion of C Indians , darker Punjabis
    Thanks for all the great work!
    Based on this paper from which the sample WC1 originated, the authors seems to be able to distinguish the origin of neolithic farmer contribution between populations in Europe and S. Asia. In Europe, it is from the EEF (such as those related to Bar8), whereas in South Asia is from populations related to WC1.
    Do you think there would be a way to tease out and distinguish any unique contributions of the western fertile crescent farmer (I guess this would be synonymous with EEF) that can be distinguished from contributions from eastern fertile crescent farmer in present day populations of South/S.C./C. Asia?F4.large.jpg
    Last edited by soulblighter; 12-03-2017 at 05:25 PM.
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  3. #1082
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    Quote Originally Posted by Kurd View Post
    I checked the 2 SNPs they used. Good news is they got those right, since I show AA for rs1426654 and CG for rs16891982. Since they are showing 100% derived allele frequency and we know the ancestral allele is C for rs1426654, the inference is that their samples were AA s for that position which is in agreement with what I have.

    Here is the kicker, rs1426654 is one of the most important alleles for pigmentation. About 100% of Europeans and W Asians are fixed for the derived version of allele (ie AA). The ancestral form CC and AC is found mostly in S Asians and Africans, and this SNP carries alot more weight than rs16891982 which honestly contributes much less to pigmentation than the other one.

    So Yamna is AA there, which is shown as 100% derived, just like all Europeans. So based on this one alone Yamnaya is light, but with the other one it is CG like most W Asians, so a little darker than most Europeans.

    That is why we need more pigmentation SNPs for a verdict, and luckily I found 9 for Yamna from the sequence I genotyped. Verdict coming shortly...
    I think rs1426654 is a brown pigmentation allele rather than a light pigmentation allele. It is almost fixed in many South Asian populations (98% in Kokanasth Brahmans, 88.5% in UP Brahmans) and is near 50% in places like Lanka. http://www.ias.ac.in/article/fulltex...2/01/0135-0139
    That is why it looks like the WHG were darker than the average current South Asians.
    Sample Country Years BP Culture D/T
    Ostuni 1 Italy 27,810–27,430 Gravettian 0/1
    El Mirón Spain 18,830–18,610 Magdalenian 0/1
    Villabruna Italy 14,180–13,780 Epigravettian 0/5
    Ranchot 88 France 10,240–9,930 Mesolithic 0/1
    https://genetiker.wordpress.com/2016...ce-age-europe/

    rs16891982 on the other hand is much lower in frequency in South Asia.

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  5. #1083
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    Quote Originally Posted by parasar View Post
    I think rs1426654 is a brown pigmentation allele rather than a light pigmentation allele. It is almost fixed in many South Asian populations .
    Exactly, and Yamnaya is derived (AA) like all Europeans and most Caucasians. So it doesn't have it.

    N Indians and most Pakistanis are AG (1 copy of the dark allele), with some AAs (fair ones), and the rest GG (fixed dark). I believe one or 2 Punjabis posted AA in the other thread pigmentation thread

    rs16891982 on the other hand is much lower in frequency in South Asia.
    I think you mean derived (GG) is much lower frequency. Most Europeans GG. Most Caucasians and W Asians CG. Many N Indians CG. Yamnaya CG, but this does not have such as much of an impact on darkening. however, I looked at another 7 pigment related in Yamna to come up with the prediction Caucasian and Ukrainian like

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  7. #1084
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    What exactly is a South Asian admixture ? Do you have aDNA from South Asia based on which you're making this argument ? The people from Northern portion of South Asia are majority ANI. Do you think ANI has come into South Asia during the Bronze Age ?

    If your argument is that ASI should have already been present in North India / Pakistan from the Mesolithic/Neolithic if not earlier, you clearly have not read the Moorjani et al paper carefully -
    Ancient East Europeans don't even have Iran_Neolithic/Chalcolithic ancestry, which was definitely also present in South Asia.









    Regarding R1a in South Asia, read this recent article by Chaubey & Thangaraj

    http://www.thehindu.com/opinion/op-e...le19265947.ece



    So hold your horses before aDNA comes out from South Asia.
    buy some tissues before aDNA from South Asia is coming

    Not only that, the R1b subclade found in Yamnaya is also found among the Central Asians and Pashtuns. However, why could this not be because of ancestors of these Pashtuns and Central Asians migrating to the steppe ?
    Any evidences or proofs for these funny claims? Yamnaya has CHG ancestry from the Caucasus and zero links to South Central Asia. The mtdna is very much pointing to the Caucasus and Davidski has various times shown, that Yamnaya has female-mediated CHG ancestry.

    Yet we have significant aDNA from the steppe. Contrast this with ZERO aDNA from Central & South Asia. We simply do not know how these ancient South & Central Asians were like. Before aDNA, would you have said that there were 3 different types of Neolithic groups in the fertile crescent at the start of Neolithic ? So why are ready to come to conclusion before aDNA from SC Asia comes out ?



    If South Asians had very low direct steppe ancestry, why did Lazaridis et al 2016 model all South Asians as having very high level of Yamnaya like ancestry ? Clearly, the situation is complex. The genetic affinites of South Asian populations is not just because of Bronze Age migrations but even earlier migrations dating to as early as the Palaeolithic. There is high ANE affinity in South Asians and this simply cannot be explained as a byproduct of some recent bronzge age migration from the steppe.



    This is just speculative stuff. Show me a steppe population from the 2nd millenium BC, which shows no EEF. We can then talk.

    Again, what is the point ? Even if all steppe ancestry in South Asia is from Yamnaya, this does not disprove the kurgan theory actually it is proving it again.

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  9. #1085
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    Quote Originally Posted by parasar View Post
    I think rs1426654 is a brown pigmentation allele rather than a light pigmentation allele. It is almost fixed in many South Asian populations (98% in Kokanasth Brahmans, 88.5% in UP Brahmans) and is near 50% in places like Lanka. http://www.ias.ac.in/article/fulltex...2/01/0135-0139
    That is why it looks like the WHG were darker than the average current South Asians.
    Sample Country Years BP Culture D/T
    Ostuni 1 Italy 27,810–27,430 Gravettian 0/1
    El Mirón Spain 18,830–18,610 Magdalenian 0/1
    Villabruna Italy 14,180–13,780 Epigravettian 0/5
    Ranchot 88 France 10,240–9,930 Mesolithic 0/1
    https://genetiker.wordpress.com/2016...ce-age-europe/

    rs16891982 on the other hand is much lower in frequency in South Asia.
    Genetiker does an excellent and thorough job wit SNP analysis and Y dna calls, though some of his other stuff is a bit off the wall.


    https://genetiker.wordpress.com/2016...-ancient-iran/

    Yeah what you are saying matches up with his analysis Parasar

    "Below are the genotypes for the SNP rs1042602 in the gene TYR for prehistoric European samples. The derived A allele of this SNP is associated with light skin and an absence of freckles. As the graph here shows, the derived allele has a frequency of around 25–50% in modern European populations. The derived allele is absent in the hunter-gatherer samples and the Yamna samples, but it appears in some of the early Neolithic samples, and it is found later in the Bell Beaker, Corded Ware, and Unetice samples."

    https://genetiker.wordpress.com/2015...storic-europe/

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  11. #1086
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    Quote Originally Posted by Immchr View Post
    What exactly is a South Asian admixture ? Do you have aDNA from South Asia based on which you're making this argument ? The people from Northern portion of South Asia are majority ANI. Do you think ANI has come into South Asia during the Bronze Age ?

    If your argument is that ASI should have already been present in North India / Pakistan from the Mesolithic/Neolithic if not earlier, you clearly have not read the Moorjani et al paper carefully -







    The above clearly supports an argument that before 4000 YBP, it is plausible that the people of the Northerns regions of Indian subcontinent may not have had ASI admixture and were conceivably only ANI. Can you deny then that such an ANI only population could not have impacted the likes of Yamnaya when it received the southern Iran-Chl like admixture ?

    ---------------------------

    Regarding R1a in South Asia, read this recent article by Chaubey & Thangaraj

    http://www.thehindu.com/opinion/op-e...le19265947.ece



    So hold your horses before aDNA comes out from South Asia.



    Not only that, the R1b subclade found in Yamnaya is also found among the Central Asians and Pashtuns. However, why could this not be because of ancestors of these Pashtuns and Central Asians migrating to the steppe ?



    Yet we have significant aDNA from the steppe. Contrast this with ZERO aDNA from Central & South Asia. We simply do not know how these ancient South & Central Asians were like. Before aDNA, would you have said that there were 3 different types of Neolithic groups in the fertile crescent at the start of Neolithic ? So why are ready to come to conclusion before aDNA from SC Asia comes out ?



    If South Asians had very low direct steppe ancestry, why did Lazaridis et al 2016 model all South Asians as having very high level of Yamnaya like ancestry ? Clearly, the situation is complex. The genetic affinites of South Asian populations is not just because of Bronze Age migrations but even earlier migrations dating to as early as the Palaeolithic. There is high ANE affinity in South Asians and this simply cannot be explained as a byproduct of some recent bronzge age migration from the steppe.



    This is just speculative stuff. Show me a steppe population from the 2nd millenium BC, which shows no EEF. We can then talk.
    That Moorjani paper is dated like anything. Those dates correspond with arrival of Steppe groups definitely not Neolithic/Mesolithic Iranian groups. Yes , S/SC Asia is complex because of lot of interconnected groups coming through and intrusions by Paleolithic Siberians from Central Asia, I suspect they brought mtdna U2. There was a paper on Indian Mtdna which alludes to it.

    Yes there is something definitely "pre steppe" related according to 2 friends of mine, but keep in mind there was a genuine movement of people whose origins are in the Yamnaya area. That being said I definitely do think Steppe ancestry in most South Asians is inflated but those NW South Asian groups will still have good to substantial amount of it once the dust is settled. There maybe debate about the type of Steppe peoples but point is it is intrusive to the region.

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  13. #1087
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    Quote Originally Posted by Kurd View Post
    Exactly, and Yamnaya is derived (AA) like all Europeans and most Caucasians. So it doesn't have it.

    N Indians and most Pakistanis are AG (1 copy of the dark allele), with some AAs (fair ones), and the rest GG (fixed dark). I believe one or 2 Punjabis posted AA in the other thread pigmentation thread



    I think you mean derived (GG) is much lower frequency. Most Europeans GG. Most Caucasians and W Asians CG. Many N Indians CG. Yamnaya CG, but this does not have such as much of an impact on darkening. however, I looked at another 7 pigment related in Yamna to come up with the prediction Caucasian and Ukrainian like
    I and most members of my South Indian ethnic background I share with, are AA on rs1426654 and more brown than an average NW south asian (and rs16891982 is CC).
    The skin pigmentation is a complex quantitative inheritance that isnt well understood yet.SLC24A5.png
    Last edited by soulblighter; 12-03-2017 at 09:40 PM.
    Paternal YDNA: G-P303+ -> G-Z30522+
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  15. #1088
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    Quote Originally Posted by soulblighter View Post
    I and most members of my South Indian ethnic background are AA on rs1426654 and more brown than an average NW south asian (and rs16891982 is CC).
    The skin pigmentation is a complex quantitative inheritance that isnt well understood yet.
    Thanks for sharing your info about AA and dark complexion. I think if we look at the complement of your 36 SNPs we would likely come up with brown

    Yes very much so, but we can come up with probabilities of accurate predictions. Since I’m sure most don’t understand how we do this I’ll explain it some:

    - we start with a cohort of say 1000 individuals. Ideally it should be 1000 for each world region.
    - we next group them by actual skin color, say lt med dk
    - next we look at the genotype for each one for a list of pigment SNPs. BTW, those SNPs are within coding genes and thus subject to better mutation control mechanisms than intergenic neutral alleles (used in allele freq pop history studies)
    - we form a probability matrix for ex 90% of the ones in the dark group had at least 1 copy of the G allele at rs1426654 etc so probabilities are assigned to each allele at various loci which can be 0-100%

    the more relevant SNPs we can identify as associated with pigment and the larger our cohort and the more ethnically diverse the cohorts the more accurate our predictions become

    Now based on the 2 SNPs used for Yamna in the above study the prediction accuracy is not very high but AA and CG matches up with Caucasians who are white (maybe a shade darker than N Euros) to olive. The prediction didn’t change even when I used 9 SNPs

    If Yamna had AG like WC1 at rs1426654 then the evidence would have been more compelling that it was brown assuming the remaining 7 SNPs were not light pigment SNPs

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    Quote Originally Posted by pegasus View Post
    Actually cannot use MLBA or Srubna/Androvno/Sintashta, the best South Asian model u can get it is with Kalash and they only take in Yamnaya. Technically and logically it should be MLBA but they simple do not work AT ALL. Though I noticed some Kho and Brahmin samples score SW Euro admixture , which infers EEF but that could represent later flows but over all, Steppe in South Asians will be of the Yamnaya kind. My friend thinks there is something Pre Steppe in SC/C Asia causing this as well but yeah these Steppe groups definitely stream through. Only samples will resolve this strange paradox.
    distance%=0.53 / distance=0.0053 Kalash
    Iran_N 40.0
    Yamnaya_Samara 37.3
    Paniya 22.2
    One thing which is intersting is that Indo Iranians were Yamnaya type not Sintashta/Androvno types because those Nuristani samples which Khana has are exactly like Kalash not like Kho or Pashtuns, so they will model like above. Nuristanis are unique because they are neither Iranic nor Indo Aryan
    What about the Andronovo component that comes up in Kurds K12 Ancients - also I just realised I should clarify that I meant Eastern European Farmer when I said EEF

    Also Iran_N are closer to the Kalash than the Yamyana? - so either Iran_N was Indo-Aryan or Kalash are IVC or BMAC relicts absorbing later Yamnaya
    Last edited by bmoney; 12-03-2017 at 11:06 PM.

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    Interesting study about India. Kashmiris are the lightest, which confirms local stereotypes.

    SNPs:

    rs1426654
    rs2470102



    http://www.jidonline.org/article/S00...16)32648-3/pdf

    https://mobile.twitter.com/i/web/sta...87256761479168

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