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Thread: Global25 automated nMonte for South/Central Asian members

  1. #7691
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    Quote Originally Posted by Sapporo View Post
    @agent_lime

    Am I clustering toward my mother instead of more in between my mother and father? Or is it the dimensions and/or the chip used (they are both on V5 and I am on V3) causing that? You seem to be closer to my father than I am. Though, I'm not sure that would be the case in raw distances.

    In terms of what I was asking for, I was looking for something more in line with what khana has posted in the past or David's South-Central Asian specific G25 PCA (with Pamiris in the top right, Baloch/Brahui in the bottom right and SI tribals in the bottom left).

    Here is an example West Eurasian specific global PCA posted by genica user Michalis Moriopoulos:

    https://i.imgur.com/xvAJLYn.png
    I am only closer to your father on the PCA I ran. Yes, you are a little more towards your mother. Again, it's only this specific PCA. (1 is Baloch vs MENA, other Gujarati vs MENA). I have no idea if this is because of the chips used. That specific PCA you posted is how David was originally doing PCA's. I will have to look at what software it was.

    Here are my distances from the set.
     

    Distance to: agentlime_scaled
    0.02359378 Lollybolly_scaled
    0.02840924 Khana_Uncle
    0.03128098 Kamil_scaled
    0.03517927 Sapporo_AGUser
    0.03517967 M_Grewal
    0.03746686 HRP0393
    0.03750141 Kaido
    0.03909738 Sarmad_Awan-GondalJatt
    0.04006104 S_Grewal
    0.04113333 AGUser_Khanabadoshi
    0.04113333 Khana
    0.04252494 Khana_GF_Sister
    0.04383283 Monkeydluffy_Dad_scaled
    0.04586002 B_Grewal
    0.04588892 Monkeydluffy_Mom_scaled
    0.04610322 Punjabi_Ramgarhia_scaled
    0.04630050 aaronbee2010_Father_scaled
    0.04632874 AmbareenR_scaled
    0.05000467 Gujjar_scaled
    0.05028718 bol_natjatt?_scaled
    0.05065279 ZA_scaled
    0.05210740 HRP0349-Niece
    0.05376358 Amit_Sheoran_scaled
    0.05376358 Western-UP_Jatt
    0.05389868 HRP0349_WGS


    Here are some of the other PCA's I did.

    https://i.imgur.com/6sRTk0U.png
    https://i.imgur.com/d1UMlHX.png
    https://i.imgur.com/Ejb2XFf.png

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  3. #7692
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    Quote Originally Posted by Sapporo View Post
    @agent_lime

    Am I clustering toward my mother instead of more in between my mother and father? Or is it the dimensions and/or the chip used (they are both on V5 and I am on V3) causing that? You seem to be closer to my father than I am. Though, I'm not sure that would be the case in raw distances.

    In terms of what I was asking for, I was looking for something more in line with what khana has posted in the past or David's South-Central Asian specific G25 PCA (with Pamiris in the top right, Baloch/Brahui in the bottom right and SI tribals in the bottom left).

    Here is an example West Eurasian specific global PCA posted by genica user Michalis Moriopoulos:

    https://i.imgur.com/xvAJLYn.png
    Do you have your parents coordinates ? Can you post or send them.

  4. #7693
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    Quote Originally Posted by pegasus View Post
    Yes, but the point was showing an UP shift within that AASI. In any case its all speculation till the real McCoys are found.
    could be related to ydna H1-H3 no?

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  6. #7694
    Quote Originally Posted by kamil154 View Post
    I'm in the process of trying to wrap my head around PCA's and how to interpret them. I'd appreciate if anyone who's planning to plot out PCA's can include me for future runs.
    We've enabled labeling of PCAs, which can be useful for sharing/saving plots. Here is the same NW South Asian PCA with your coordinates used as a selected target as well as the reference. As always, I would encourage you to rotate the 3D PCA plot to get a realistic perspective on relative distances. A flat 2D view can often be deceptive.

    2D PCA
    3D PCA

    Explore your Genealogy

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  8. #7695
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    Nice looking PCA. It's still funny how fringe those Lahore samples are, though. I hope we can get genotype data from that Pakistani study because Punjabis deserve better representation than that.
    Ελευθερία ή θάνατος.

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  10. #7696
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    Quote Originally Posted by GenoPlot View Post
    We've enabled labeling of PCAs, which can be useful for sharing/saving plots. Here is the same NW South Asian PCA with your coordinates used as a selected target as well as the reference. As always, I would encourage you to rotate the 3D PCA plot to get a realistic perspective on relative distances. A flat 2D view can often be deceptive.

    2D PCA
    3D PCA

    Thank you!
    G25 Neolithic model

    "sample": "kamil154",
    "distance": 2.3391,
    "Ganj_Dareh_N": 43.5,
    "Barcin_N": 17.5,
    "Simulated_AASI_NW_by_DMXX": 15.5,
    "Karelia_HG": 9,
    "Tyumen_HG": 5,
    "LAO_Hoabinhian": 4,
    "LapaDoSanto_9600BP": 3,
    "GEO_CHG": 2.5

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     Ahmed Ali (09-21-2020)

  12. #7697
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    2D PCA

    There's a few Pashtuns that are clustering close to mine and some of the Khatri results. I'm guessing they are Yousafzaii?
    G25 Neolithic model

    "sample": "kamil154",
    "distance": 2.3391,
    "Ganj_Dareh_N": 43.5,
    "Barcin_N": 17.5,
    "Simulated_AASI_NW_by_DMXX": 15.5,
    "Karelia_HG": 9,
    "Tyumen_HG": 5,
    "LAO_Hoabinhian": 4,
    "LapaDoSanto_9600BP": 3,
    "GEO_CHG": 2.5

  13. #7698
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    Quote Originally Posted by kamil154 View Post
    2D PCA

    There's a few Pashtuns that are clustering close to mine and some of the Khatri results. I'm guessing they are Yousafzaii?
    I don't know how Genoplot divided up their Pashtun data (eg. HGDP Pathan vs. Daamgaard Yusufzai, Uthmankhel and Tarkalani) but I would assume their "Pashtun" data is a mixture of the HGDP Pathan/Pashtun (coordinates suggest Kurram) + Di Cristofaro Afghan Pashtuns from Kunduz/Baghlan and individual anthrogenica members such as surbakhun (Kandahari). So, the Pashtuns near you and the Khatri cluster are likely some HGDP samples rather than any of the Daamgaard samples who were categorized by tribe. Most of the Uthmankhel and Tarkalani would likely be near the Kalash cluster with Yusufzai filling the space between them and the Punjabi Jatt/Khatris cluster.

    Edit: I'm actually curious about the HGDP Sindhi clustering near the Punjabi Jatt cluster/HGDP Pathan shifted toward the Punjabi Jatt cluster. They seem to be an outlier. Apparently, it is HGDP00197, which is surprising based on their Harappa admixture scores.
    Last edited by Sapporo; 09-21-2020 at 10:16 PM.
    pegasus modeling:
    sample": "Punjabi_Jat:Sapporo_AGUser",
    "fit": 1.1506,
    "IRN_Shahr_I_Sokhta_BA3": 43.33,
    "TKM_Gonur1_BA": 31.67,
    "RUS_Sintashta_MLBA": 25,
    "closestDistances": [

    avatar credit goes out to aaronbee2010

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  15. #7699
    Quote Originally Posted by kamil154 View Post
    2D PCA

    There's a few Pashtuns that are clustering close to mine and some of the Khatri results. I'm guessing they are Yousafzaii?
    Unfortunately we don't have that level of detail on the HGDP samples. With the exception of one HGDP Pashtun (HGDP00222), all the samples closest to you (distance < 3) are Punjabi Khatris

    HGDP00222 appears to be very Khatri like

    HarappaWorld

    S-Indian: 25.89%
    Baloch: 42.89%
    Caucasian: 17.4%
    NE-Euro: 9.28%
    SE-Asian: 0.76%
    Papuan: 0.74%
    American: 1.31%
    Beringian: 1.61%
    SW-Asian: 0.12%

    Sample: Pashtun ► HGDP00222
    Fit: 1.88426
    Results: Indus Periphery 56.8
    Steppe 24.8
    BMAC 18
    Excess East Eurasian 0.4


    Mixed Oracles Distance
    72.4% Khatri + 27.6% Uthmankhel 1.445
    66.6% Khatri + 33.4% Yusufzai 1.4521
    62.6% Yusufzai + 37.4% Gujar Pakistan 1.4688
    82.4% Khatri + 17.6% Tarkalani 1.5064
    77.8% Khatri + 22.2% Punjabi Jatt 1.5072
    50.2% Uthmankhel + 49.8% Gujar Pakistan 1.5345
    56% Yusufzai + 44% Kohistani 1.5358
    57.2% Kohistani + 42.8% Uthmankhel 1.5444
    95.6% Khatri + 4.4% Kohistani 1.6202
    50% Khatri + 50% Khatri 1.623


    Sample Distance
    Khatri: Average 2.161
    Punjabi Jatt: Average 2.5355
    Yusufzai: Average 2.7864
    Kohistani: Average 2.8235
    Gujar Pakistan: Average 3.0726
    Uthmankhel: Average 3.3932
    Tarkalani: Average 3.5281
    Explore your Genealogy

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  17. #7700
    Quote Originally Posted by Sapporo View Post
    Most of the Uthmankhel and Tarkalani would likely be near the Kalash cluster with Yusufzai filling the space between them and the Punjabi Jatt/Khatris cluster.

    Edit: I'm actually curious about the HGDP Sindhi clustering near the Punjabi Jatt cluster/HGDP Pathan shifted toward the Punjabi Jatt cluster. They seem to be an outlier. Apparently, it is HGDP00197, which is surprising based on their Harappa admixture scores.
    Here is the Pashtun cluster zoomed in (including more groups)

    Edit: Added Kohistani samples, note the overlap with Punjabi Jatts and Khatris

    The Sindhi sample (HGDP00197) appears to be shifted upwards due to higher than expected East Asian/Siberian scores

    S-Indian: 28.52%
    Baloch: 41.96%
    Caucasian: 11.88%
    NE-Euro: 8.47%
    NE-Asian: 1.4%
    Papuan: 0%
    American: 2.06%
    Mediterranean: 2.27%
    SW-Asian: 2.83%

    Sample: Sindhi ► HGDP00197
    Fit: 2.130263
    Results: Indus Periphery 50.6
    BMAC 23.6
    Steppe 21
    Excess East Eurasian 4.8



    Last edited by GenoPlot; 09-22-2020 at 01:37 PM. Reason: Added Kohistani
    Explore your Genealogy

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