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Thread: PCA G25_scaled - Africans only (Users & Ancients/Modern Avgs)

  1. #321
    Moderator
    Posts
    700
    Sex
    Ethnicity
    Central/E. Sudanic
    Y-DNA (P)
    A-M13 (A-Y95250*)
    mtDNA (M)
    L3x2b
    Y-DNA (M)
    B2a1
    mtDNA (P)
    L2e*

    Canada Uganda
    "MAR_TonyScaletta" user added:

     




    Updated PCA (All Africans):

     








    ◇= Ancients
    X= Active users
    • = Samples/Modern Avgs


    3D PCA: https://plot.ly/~Angoliga/3/ (allow ~less than a minute to load)

    2D PCA: https://plot.ly/~Angoliga/4/


    + Deep-layer run:
     


    Source Samples:
     

    KEN_LSA,-0.522448,0.044683,-0.010936,0.006137,0.004308,-0.006414,0.085309,-0.06692,0.076287,-0.06925,-0.011367,0.010491,-0.033003,0.000138,0.00855,-0.014983,0.021383,0.038513,-0.002137,-0.005253,-0.007612,-0.002968,0.002342,0.004699,-0.000718
    ETH_4500BP,-0.511066,0.043668,0.000754,0.000969,-0.00277,-0.011435,0.050997,-0.045229,0.089172,-0.087838,-0.012991,-0.002997,-0.031219,0.000688,0.02158,-0.029965,0.027772,0.039273,0.00176,-0.009004,0.000374,0.006183,-0.003451,-0.00241,-0.000838
    KEN_Pastoral_N,-0.3004929,0.0954598,-0.0263607,-0.0737732,0.0007384,-0.0365346,-0.0094944,-0.0014769,0.1220598,-0.0880928,-0.0057811,-0.0097713,-0.0017243,-0.0018993,0.0229232,-0.0209888,0.0222697,-0.0004942,0.0076929,-0.0014882,0.0019467,0.00298,-0.0040671,-0.0013375,-0.0010058
    Levant_JOR_EBA,0.0758823,0.147929,-0.0599623,-0.11402,-0.0056417,-0.0476903,-0.0108887,-0.013307,0.0336783,0.0075323,0.0157517,-0.0196823,0.041526,-0.0008717,-0.0031217,0.0228937,0.0018253,0.0010137,-0.0030583,0.0170917,0.0050743,0.011706,-0.0038617,0.0042577,-0.0071053
    Levant_PPNB,0.072847,0.1639064,-0.0316026,-0.1361132,0.0332986,-0.0645352,-0.0134426,-0.0147684,0.0741604,0.03601,0.0188046,-0.0150764,0.035738,0.0025596,-0.0217696,0.006099,0.0098048,-0.0013176,-0.0047264,0.0188088,-0.001797,0.0071472,0.0008872,-0.0056874,-0.0037602
    Levant_PPNC,0.067156,0.168578,-0.023004,-0.150842,0.028621,-0.071954,-0.013866,-0.017999,0.077719,0.037905,0.006496,-0.013188,0.032705,-0.000275,-0.014929,0.008486,-0.000913,-0.007728,-0.013575,0.012381,-0.009982,0.01014,0.002958,0.003012,-0.001916
    CHN_Tianyuan,-0.027318,-0.260991,-0.075424,0.071383,0.033545,-0.018407,-0.00799,-0.003,0.040291,0.021322,-0.006333,-0.005995,-0.003568,-0.00523,-0.000407,-0.000663,0.008084,0.002407,-0.001131,0.027263,-0.001747,0.008037,-0.008874,-0.010845,0.011256
    Yamnaya_UKR,0.119514,0.088351,0.044123,0.110144,-0.032006,0.038487,0.00799,0.002308,-0.05788,-0.076721,-0.002761,-0.002398,0.000743,-0.021056,0.033387,0.01485,0.004955,-0.008235,-0.002263,0.015007,0.002121,0.003462,0.002958,0.023 256,0.002874
    Anatolia_Barcin_N,0.1175998,0.180118,0.0035312,-0.101158,0.0510443,-0.0483875,-0.0043582,-0.0069334,0.0362287,0.0807473,0.0079718,0.0118803,-0.0234545,0.0004691,-0.0419807,-0.0101913,0.0233091,0.0019866,0.0136954,-0.0097489,-0.0142249,0.0057723,-0.0041232,-0.0031658,-0.0043437
    Levant_Natufian,0.020488,0.1431895,-0.0377125,-0.1387295,0.030775,-0.079484,-0.025616,-0.0175375,0.114329,0.002005,0.0332085,-0.0222555,0.076486,0.002133,0.0153365,0.009016,-0.0154505,-0.001014,-0.02206,0.040832,0.001497,0.0001235,-0.003636,-0.0044585,0.006287
    Yoruba,-0.6300625,0.0625011,0.022113,0.0167079,0.0005035,0 .0124741,-0.044417,0.0477673,-0.0488813,0.0327694,0.0046205,0.0007904,0.0230561, 0.0009509,0.0125232,-0.0096067,0.0070763,0.0004491,0.006022,-0.00299,0.0015542,0.0023156,-0.0017592,-0.0004711,-0.0004246
    Dinka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995
    Ju_hoan_North,-0.616466,0.0601194,0.0211942,0.028424,0.0025852,-0.0038486,0.2541404,-0.199192,0.0240112,0.007909,0.0032478,-0.0723558,-0.0255104,0.00867,0.0283928,-0.0321662,0.0461558,0.4102178,-0.1364076,0.003877,-0.0556018,-0.0051686,0.0126206,-0.0044826,0.0028978
    Mbuti,-0.6493608,0.0578852,0.0250785,0.038437,-0.001077,0.0054385,0.3631505,-0.291911,0.0193278,0.0323013,-0.0090938,0.2169692,0.1242805,3.45E-05,0.0080072,0.0017568,0.000717,-0.049567,0.015901,0.004471,0.0049288,-0.0020402,-0.002465,0.0057838,0.000389
    IRN_Wezmeh_N,0.037562,0.072103,-0.165556,-0.016473,-0.11756,0.01506,0.017861,-0.003231,-0.071583,-0.046835,0.003085,-0.003147,0.00669,0.000688,0.022122,0.053036,-0.011735,0.001014,0.014581,-0.035267,0.009358,-0.023741,-0.006655,-0.032896,0.019998
    IRN_Ganj_Dareh_N,0.0455292,0.0660095,-0.1518855,0.0026648,-0.1250232,0.0204982,0.0170972,-0.0017305,-0.0814005,-0.0579968,0.0004465,-0.001611,0.0072845,-0.0087735,0.0294512,0.0567152,-0.005248,0.0084882,0.007259,-0.037018,0.0075492,-0.0286258,-0.010322,-0.0404578,0.0265842
    ITA_Villabruna,0.121791,0.114755,0.18592,0.184111, 0.156337,0.060798,0.020211,0.035998,0.092445,0.018 041,-0.016239,-0.016186,0.016947,-0.010046,0.054017,0.067356,0.000782,0.005448,-0.008422,0.053526,0.100073,0.010758,-0.048313,-0.163517,0.01928
    GEO_CHG,0.091058,0.102568,-0.083344,-0.00323,-0.08617,0.020638,0.024911,-0.001846,-0.128236,-0.074717,-0.006333,0.023979,-0.054856,0.004404,0.026601,-0.03275,0.02386,-0.013429,-0.022249,0.034767,0.033815,-0.007048,0.006532,-0.025787,-0.002036
    MAR_LN,0.021626,0.148267,0.003394,-0.095285,0.047393,-0.054384,-0.027731,0.008769,0.083855,0.054124,0.020136,0.001 798,0.002973,-0.028901,0.004343,0.009944,0.032726,-0.014062,-0.033938,-5.00E-04,-0.018343,-0.02201,0.011709,-0.009881,-0.004191
    MAR_EN,-0.1735805,0.0919055,-0.0258325,-0.083657,0.0283125,-0.0596825,-0.079316,0.021461,0.1500185,0.0043735,0.0222475,-0.0264515,0.075148,-0.0461725,0.069353,-0.03381,0.0171455,-0.05549,-0.1487635,0.0340785,-0.038245,-0.118212,0.0826995,-0.009941,0.021615
    MAR_Iberomaurusian,-0.189857,0.0814452,-0.0242866,-0.085595,0.027636,-0.0552202,-0.0705968,0.0184146,0.155397,0.003499,0.0209156,-0.0318316,0.0747168,-0.0513334,0.0711988,-0.0363032,0.0052676,-0.066106,-0.1424162,0.0389938,-0.0376836,-0.1255322,0.0730118,-0.0137606,0.0164534
    Last edited by Angoliga; 03-29-2020 at 05:25 AM.
    .... .. I have spoken."

  2. The Following 2 Users Say Thank You to Angoliga For This Useful Post:

     Amhas (04-21-2020),  TonyScaletta (03-30-2020)

  3. #322
    Registered Users
    Posts
    56
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    Y-DNA (P)
    E-M78

    Quote Originally Posted by Angoliga View Post
    ...[/img]

    Could you add these two.


     

    ITA_Sardinia_C_o:I15940,-0.086506,0.136081,-0.012068,-0.097869,0.035083,-0.041834,-0.039717,0.003461,0.109011,0.035718,0.008282,-0.010341,0.027205,-0.018441,0.024294,-0.030761,-0.014473,-0.032939,-0.058324,0.012506,-0.013351,-0.045628,0.024526,-0.008676,0.00467


    Iberia_Central_CA_Afr:I4246,-0.05122,0.140143,-0.002263,-0.091086,0.0397,-0.047133,-0.036192,0.007384,0.091013,0.044283,0.012179,-0.000899,0.006987,-0.018029,0.020087,-0.016309,0.000652,-0.016596,-0.033561,0.003001,-0.011729,-0.018548,0.013064,-0.009399,0.005987



  4. The Following User Says Thank You to Amhas For This Useful Post:

     TonyScaletta (05-24-2020)

  5. #323
    Know this isnt the right place strictly but is there anyway to get David to upload more African samples to the G25? How do ya'll get your hands on samples anyway? I've checked the repositories but can't find Baganda, Basoga, Lugbara, Ivorian, Ghanaian, Efik, Guinean samples that have been used recently. Are they not always accessible?

  6. The Following User Says Thank You to ThaYamamoto For This Useful Post:

     drobbah (05-28-2020)

  7. #324
    Anyone have any African American coordinates or Caribbeans? Please share if so.

  8. The Following User Says Thank You to ThaYamamoto For This Useful Post:

     drobbah (05-28-2020)

  9. #325
    Registered Users
    Posts
    77
    Sex
    Location
    None Ya
    Ethnicity
    Multi-ethnic Belizean
    Nationality
    Belizean/American
    Y-DNA (P)
    E1b1a1g1, Q1a3a1
    mtDNA (M)
    L2b2, L3e2b

    Belize CARICOM United States of America African Union Belize
    Quote Originally Posted by ThaYamamoto View Post
    Anyone have any African American coordinates or Caribbeans? Please share if so.
    I'd offer to use myself. I'm not sure how I would impact the PCA, since I also have significant indigenous Central American and Northeastern South American/Southeastern Caribbean ancestry at +/- 10%. This would differentiate me from 95% of African-Americans or Afro-Caribbeans (I might be similar to a very SSA Puerto Rican though).

  10. The Following 2 Users Say Thank You to pgbk87 For This Useful Post:

     drobbah (05-28-2020),  ThaYamamoto (05-28-2020)

  11. #326
    Registered Users
    Posts
    749
    Sex
    Omitted
    Ethnicity
    Somali
    Nationality
    Canadian
    Y-DNA (P)
    E-V32
    mtDNA (M)
    L0a1d
    Y-DNA (M)
    T-FGC92488

    Somaliland Ethiopia Adal Sultanate Yemen Canada
    Quote Originally Posted by ThaYamamoto View Post
    Anyone have any African American coordinates or Caribbeans? Please share if so.
    I wished we had New World samples from admixed groups in Latin America and the Caribbean (African admixed groups) on the G25 sheet aswell. It would be cool to see who they plot closest with and which ethnic groups they derive their African ancestry from

    Target: Mother_scaled
    Distance: 5.4903% / 0.05490334
    50.8 Dinka
    35.8 Levant_Natufian
    9.0 Yemenite_Al_Jawf
    4.0 ETH_4500BP
    0.4 MAR_Taforalt

    Target: Drobbah_scaled
    Distance: 5.1638% / 0.05163817
    44.8 Dinka
    36.0 Levant_Natufian
    11.6 ETH_4500BP
    6.2 Yemenite_Al_Jawf
    1.4 MAR_EN

    Target: Father_scaled
    Distance: 5.5604% / 0.05560439
    48.0 Dinka
    42.0 Levant_Natufian
    8.6 ETH_4500BP
    1.0 MAR_EN
    0.4 Yemenite_Al_Jawf


  12. The Following User Says Thank You to drobbah For This Useful Post:

     ThaYamamoto (05-28-2020)

  13. #327
    Quote Originally Posted by pgbk87 View Post
    I'd offer to use myself. I'm not sure how I would impact the PCA, since I also have significant indigenous Central American and Northeastern South American/Southeastern Caribbean ancestry at +/- 10%. This would differentiate me from 95% of African-Americans or Afro-Caribbeans (I might be similar to a very SSA Puerto Rican though).
    Yeah man - new world/diaspora populations are of interest to me, have you modeled yourself? What are your closest pops and whats your admixture profile like?

    Quote Originally Posted by drobbah View Post
    I wished we had New World samples from admixed groups in Latin America and the Caribbean (African admixed groups) on the G25 sheet aswell. It would be cool to see who they plot closest with and which ethnic groups they derive their African ancestry from
    Bro, same. I'm sceptical of the Nigerian/Yoruba dominance for most of the new world from commercial tests and some of the newer papers.

  14. The Following User Says Thank You to ThaYamamoto For This Useful Post:

     drobbah (05-28-2020)

  15. #328
    Registered Users
    Posts
    77
    Sex
    Location
    None Ya
    Ethnicity
    Multi-ethnic Belizean
    Nationality
    Belizean/American
    Y-DNA (P)
    E1b1a1g1, Q1a3a1
    mtDNA (M)
    L2b2, L3e2b

    Belize CARICOM United States of America African Union Belize
    Quote Originally Posted by ThaYamamoto View Post
    Yeah man - new world/diaspora populations are of interest to me, have you modeled yourself? What are your closest pops and whats your admixture profile like?
    My closest matches are Afro-Caribbeans (particularly Anglophone islands), African-Americans, Mestizo Mexicans and Colombians.

    I'm approximately 77% West and Central African, 13% (mostly northwest) European, and 10% Indigenous (a mix from Central and northern South American/Caribbean natives)
    Last edited by pgbk87; 05-28-2020 at 11:26 PM.

  16. The Following 3 Users Say Thank You to pgbk87 For This Useful Post:

     drobbah (05-29-2020),  Hurricane (05-29-2020),  ThaYamamoto (05-29-2020)

  17. #329
    Quote Originally Posted by pgbk87 View Post
    My closest matches are Afro-Caribbeans (particularly Anglophone islands), African-Americans, Mestizo Mexicans and Colombians.

    I'm approximately 77% West and Central African, 13% (mostly northwest) European, and 10% Indigenous (a mix from Central and northern South American/Caribbean natives)
    Interesting, do you get Nigerian groups as your dominant component? Would love to see your coords when/if you get em

  18. #330
    Registered Users
    Posts
    77
    Sex
    Location
    None Ya
    Ethnicity
    Multi-ethnic Belizean
    Nationality
    Belizean/American
    Y-DNA (P)
    E1b1a1g1, Q1a3a1
    mtDNA (M)
    L2b2, L3e2b

    Belize CARICOM United States of America African Union Belize
    Quote Originally Posted by ThaYamamoto View Post
    Interesting, do you get Nigerian groups as your dominant component? Would love to see your coords when/if you get em
    It averages out like that, but it's a mix which just leans towards Yoruba+Igbo. The same happens with my native ancestry. I have no ancestry from what is now Colombia, it's just that Arawak, Carib and Maya ancestry that averages out to "Colombia" on modern Oracles.

  19. The Following 2 Users Say Thank You to pgbk87 For This Useful Post:

     drobbah (05-29-2020),  ThaYamamoto (05-29-2020)

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