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Thread: Automated Global25 nMonte entirely from the web

  1. #21
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    Quote Originally Posted by poi View Post
    Added. Just start typing "Nibelung" and your name should appear.



    Looking at your profile, you joined in 2014 and your first post is to say you love this tool? Added your coordinates along with the others. lol

    Just start searching for "sheepslay3r" and the dropdown should show your name.
    Hi poi, could you please add my scaled G25 coordinates to this tool? Thanks!

    Eihwaz_scaled,0.111547,0.139128,0.003017,-0.037791,0.014464,-0.010598,0.000235,0.000692,0.001841,0.01549,0.0035 73,0.004946,-0.002081,0.013074,-0.007057,-0.013657,-0.011474,0.000887,-0.008045,-0.013632,-0.00836,0.002226,0.007025,0.007109,0.005269
    1 Jew_Ashkenazy_Poland +Volga-German Custom:AGUser_Eihwaz 1.7783 85.83 14.17

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     poi (07-23-2018)

  3. #22
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    Some fits for some Saidu sharif samples.

    The fit gets worse when BMaC or tepe Hissar is used instead of western Iran ChL such as Seh Gabi. Doesn’t make sense archeologically, unless if these steppe groups hopped into Iran first then into South Asia? I dunno.

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  5. #23
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    Quote Originally Posted by sweuro View Post
    there seems to be a bug. When you repeat the run with one fixed sample, the percentages change each run in that same sample.
    That is most likely the error margin, it is bound to fluctuate within the margin as it iterates, since its a statistical model, it approximates.
    Last edited by surbakhunWeesste; 07-22-2018 at 09:10 PM.

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  7. #24
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    Quote Originally Posted by jesus View Post
    Some fits for some Saidu sharif samples.

    The fit gets worse when BMaC or tepe Hissar is used instead of western Iran ChL such as Seh Gabi. Doesn’t make sense archeologically, unless if these steppe groups hopped into Iran first then into South Asia? I dunno.
    ...
    How does that comport with what the Reich group posited?
    "there is no evidence that the main BMAC population contributed genetically to later South Asians. Instead, Steppe communities integrated farther south throughout the 2nd millennium BCE, and we show that they mixed with a more southern population ... We reject BMAC as a primary source of ancestry in South Asians."

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  9. #25
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    Quote Originally Posted by parasar View Post
    How does that comport with what the Reich group posited?
    "there is no evidence that the main BMAC population contributed genetically to later South Asians. Instead, Steppe communities integrated farther south throughout the 2nd millennium BCE, and we show that they mixed with a more southern population ... We reject BMAC as a primary source of ancestry in South Asians."
    Do they mean SwatValley IronAge samples as "later South Asians"? I thought so too when the study came out and I read the that bit. The PCA using 12 "best" nMonte models (out of 5400 that I ran) for BMAC+SwatValley+IVCp+SouthAsians+Iranians kinda shows DISTINCT BMAC as well.

    3D PCA: https://plot.ly/~mpan19/53/#/

    2D PCA:
     


    Last edited by poi; 07-23-2018 at 01:17 AM.
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  11. #26
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    Quote Originally Posted by parasar View Post
    How does that comport with what the Reich group posited?
    "there is no evidence that the main BMAC population contributed genetically to later South Asians. Instead, Steppe communities integrated farther south throughout the 2nd millennium BCE, and we show that they mixed with a more southern population ... We reject BMAC as a primary source of ancestry in South Asians."
    There were vast trading networks on Gold/Silver/Tin & Lapis Lazuli. There is vast documentation on this. You can find Tepe Hissar & Seh Gabi in a lot of Shahr-i-Sokhte3 high poulations like Kamma Velama Reddy etc.. & Baluchi Pathans etc
    nMonte3 current
    Velamas Gujarati_D Muslim_UP Tharus Punjabi_1000genomes
    1.859005 3.210341 4.491247 4.998440 6.040323

    G25 Ancients Dist 0.99 Shahr_I_Sokhta_BA3:S8728.E1.L1 65.2 Saidu_Sharif_IA_o:S7722.E1.L1 17.8 Udegram_IA:I1985 7.8 Jordanian:S_Jordanian-1 4.4 Barikot_IA:I6545 2.2 Scotland_N:I26602 Narva_Lithuania: Donkalnis6

    mtDNA mutation 309.1C 315.1C 522.1A 522.2C G8572A G8860A T11368C T16093a T16154C C16519T
    C195T

  12. #27
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    Quote Originally Posted by Eihwaz View Post
    Hi poi, could you please add my scaled G25 coordinates to this tool? Thanks!

    Eihwaz_scaled,0.111547,0.139128,0.003017,-0.037791,0.014464,-0.010598,0.000235,0.000692,0.001841,0.01549,0.0035 73,0.004946,-0.002081,0.013074,-0.007057,-0.013657,-0.011474,0.000887,-0.008045,-0.013632,-0.00836,0.002226,0.007025,0.007109,0.005269
    "distance%=2.1523"

    Eihwaz_scaled


    Ashkenazi_Jew,33
    Barcin_N,14.8
    Finnish,14.6
    Iraqi_Jew,11.4
    Scottish,9
    Anatolia_BA,6.4
    Anatolia_MLBA,5.4
    Anatolia_ChL,3.6
    Finnish_East,1.4
    Tepe_Hissar_ChL,0.4
    nMonte3 current
    Velamas Gujarati_D Muslim_UP Tharus Punjabi_1000genomes
    1.859005 3.210341 4.491247 4.998440 6.040323

    G25 Ancients Dist 0.99 Shahr_I_Sokhta_BA3:S8728.E1.L1 65.2 Saidu_Sharif_IA_o:S7722.E1.L1 17.8 Udegram_IA:I1985 7.8 Jordanian:S_Jordanian-1 4.4 Barikot_IA:I6545 2.2 Scotland_N:I26602 Narva_Lithuania: Donkalnis6

    mtDNA mutation 309.1C 315.1C 522.1A 522.2C G8572A G8860A T11368C T16093a T16154C C16519T
    C195T

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  14. #28
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    Quote Originally Posted by poi View Post
    Do they mean SwatValley IronAge samples as "later South Asians"? I thought so too when the study came out and I read the that bit. The PCA using 12 "best" nMonte models (out of 5400 that I ran) for BMAC+SwatValley+IVCp+SouthAsians+Iranians kinda shows DISTINCT BMAC as well.

    3D PCA: https://plot.ly/~mpan19/53/#/

    2D PCA:
     


    Yes that is my understanding - Swat IA = later South Asians.

    "while the BMAC was affected by the same demographic forces that later impacted South Asia (the southward movement of Middle to Late Bronze Age Steppe pastoralists described in the next section), it was also bypassed by members of these groups who hardly mixed with BMAC people and instead mixed with peoples further south [Indus Periphery]. In fact, the data suggest that instead of the main BMAC population having a demographic impact on South Asia, there was a larger effect of gene flow in the reverse direction, as the main BMAC genetic cluster is slightly different from the preceding Turan populations in harboring ~5% of their ancestry from the AASI."
    Last edited by parasar; 07-23-2018 at 02:13 AM.

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  16. #29
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    Quote Originally Posted by parasar View Post
    Yes that is my understanding - Swat IA = later South Asians.

    "while the BMAC was affected by the same demographic forces that later impacted South Asia (the southward movement of Middle to Late Bronze Age Steppe pastoralists described in the next section), it was also bypassed by members of these groups who hardly mixed with BMAC people and instead mixed with peoples further south [Indus Periphery]. In fact, the data suggest that instead of the main BMAC population having a demographic impact on South Asia, there was a larger effect of gene flow in the reverse direction, as the main BMAC genetic cluster is slightly different from the preceding Turan populations in harboring ~5% of their ancestry from the AASI."
    There is one Gonur2 bmac sample which clearly clusters with the SouthAsians. And both Dzharkutan2 samples cluster with the Iranians. So even in nmonte based data, we can see geneflow from South Asia and Iran into bmac.
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  18. #30
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    Quote Originally Posted by poi View Post
    There is one Gonur2 bmac sample which clearly clusters with the SouthAsians. And both Dzharkutan2 samples cluster with the Iranians. So even in nmonte based data, we can see geneflow from South Asia and Iran into bmac.
    yeah. I have seen 5-10% coming through Gonur2 but can go to as high as 20+ % in some configurations. It might be related to Tepe Hissar.
    nMonte3 current
    Velamas Gujarati_D Muslim_UP Tharus Punjabi_1000genomes
    1.859005 3.210341 4.491247 4.998440 6.040323

    G25 Ancients Dist 0.99 Shahr_I_Sokhta_BA3:S8728.E1.L1 65.2 Saidu_Sharif_IA_o:S7722.E1.L1 17.8 Udegram_IA:I1985 7.8 Jordanian:S_Jordanian-1 4.4 Barikot_IA:I6545 2.2 Scotland_N:I26602 Narva_Lithuania: Donkalnis6

    mtDNA mutation 309.1C 315.1C 522.1A 522.2C G8572A G8860A T11368C T16093a T16154C C16519T
    C195T

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