Page 47 of 48 FirstFirst ... 3745464748 LastLast
Results 461 to 470 of 473

Thread: An nMonte and 4mix Guide for the Participants of the Basal-rich K7 and/or Global 10 T

  1. #461
    Registered Users
    Posts
    4,410
    Sex

    Just take out PC6 from the Global 10 and off you go.

    I have no idea why that works, because PC6 is such an informative dimension, but I think it might be heavily skewed by modern drift in Northern Europe.

    By the way, Iron Age models with England_IA, Nordic_IA, Altai_IA, etc. look awesome for Europeans.

  2. The Following 4 Users Say Thank You to Generalissimo For This Useful Post:

     Agamemnon (09-16-2017),  anglesqueville (09-16-2017),  Helgenes50 (09-19-2017),  randwulf (09-16-2017)

  3. #462
    Registered Users
    Posts
    924
    Sex
    Location
    Netherlands
    Ethnicity
    South-Dutch
    Nationality
    Dutch
    Y-DNA (P)
    I2a2a1b2-CTS1977
    mtDNA (M)
    H13a1a1

    Netherlands Belgium
    Quote Originally Posted by Generalissimo View Post
    Just take out PC6 from the Global 10 and off you go. ...
    I have no idea why that works, because PC6 is such an informative dimension, but I think it might be heavily skewed by modern drift in Northern Europe.
    Another possible cause might be because on a PC4/PC6 plot the crowded cline from Yamnaya to modern Europeans is not parallel to the PC6 dimension but some 30 degrees tilted. In that direction it projects some 15 percent on the PC4 dimension, which may not be very helpful.

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

     anglesqueville (09-16-2017),  randwulf (09-16-2017)

  5. #463
    Registered Users
    Posts
    924
    Sex
    Location
    Netherlands
    Ethnicity
    South-Dutch
    Nationality
    Dutch
    Y-DNA (P)
    I2a2a1b2-CTS1977
    mtDNA (M)
    H13a1a1

    Netherlands Belgium
    Quote Originally Posted by Huijbregts View Post
    Another possible cause might be because on a PC4/PC6 plot the crowded cline from Yamnaya to modern Europeans is not parallel to the PC6 dimension but some 30 degrees tilted. In that direction it projects some 15 percent on the PC4 dimension, which may not be very helpful.
    I just found that in the dataset 'Central & West Eurasia3' (without East-Eurasians) the corresponding clines are parallel to the corresponding dimensions PC1,PC2

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

     randwulf (09-16-2017)

  7. #464
    Gold Class Member
    Posts
    2,766
    Sex
    Location
    Pennsylvania
    Ethnicity
    West European
    Nationality
    USA
    Y-DNA (P)
    R1b-U152-Z36+FGC6511
    mtDNA (M)
    H11a2a

    United States of America Germany England France Scotland Ireland
    My results from earlier were decent nMonte models as far as distances. I wasn't too happy that PC1/PC2/PC3 weren't some of the closer matches in the nine dimensions (minus PC6, as it was removed). I was interested in the earlier conversation in this thread about the "variations" within the population. So, I decided to allow some controlled overfitting/correlation to let nMonte pick out the Yamnaya Samara, Barcin, and WHG-SHG populations (and Levant, which wasn't selected for any of us) that best worked for each person, with out groups. I used this spreadsheet:

    Code:
    ,PC1,PC2,PC3,PC4,PC5,PC7,PC8,PC9,PC10
    Hungary_HG,0.0185,0.0219,6.00E-04,-0.0922,-0.0196,0.0629,-0.0053,-0.0439,-0.0064
    Iberia_HG:I0585,0.0166,0.016,0,-0.0762,-0.0158,0.0604,-0.006,-0.0439,-0.0031
    Loschbour:Loschbour,0.0189,0.0206,0.0012,-0.0975,-0.0216,0.0706,-0.0036,-0.0535,-0.0045
    Bichon:Bichon,0.0166,0.0188,0.0003,-0.0933,-0.0204,0.0705,-0.0079,-0.0511,-0.0047
    Motala_HG:I0014,0.0189,0.0169,0.005,-0.0971,-0.0199,0.0595,-0.0009,-0.0345,-0.0086
    Villabruna:I9030,0.0147,0.0213,0,-0.0915,-0.0197,0.0688,-0.0071,-0.0501,-0.0057
    Yamnaya_Samara:I0231,0.0181,0.0168,0.0034,-0.0549,-0.0075,0.0349,0.0049,0.0123,-0.0077
    Yamnaya_Samara:I0357,0.018,0.0187,0.0019,-0.0513,-0.0043,0.0322,-0.0049,0.0046,-0.0049
    Yamnaya_Samara:I0370,0.0174,0.018,0.0038,-0.055,-0.0053,0.0327,0.0043,0.0144,-0.0072
    Yamnaya_Samara:I0429,0.0188,0.0178,0.0033,-0.0591,-0.005,0.0396,0.0025,0.0143,-0.0049
    Yamnaya_Samara:I0438,0.0178,0.0171,0.0036,-0.0583,-0.0071,0.0351,0.0047,0.0129,-0.0053
    Yamnaya_Samara:I0439,0.0173,0.0181,-0.0003,-0.0545,-0.0051,0.032,0.0011,0.0127,-0.0035
    Yamnaya_Samara:I0441,0.0178,0.0179,0.0035,-0.053,-0.0021,0.039,0.0037,0.0088,-0.003
    Yamnaya_Samara:I0443,0.0182,0.0196,0.0018,-0.0527,-0.0048,0.0337,0.0041,0.0172,-0.0053
    Yamnaya_Samara:I0444,0.0185,0.0189,0.0031,-0.0555,-0.0072,0.0364,0.0013,0.0074,-0.0085
    Barcin_N:Bar31,0.0139,0.0348,-0.0026,0.0223,0.0036,-0.011,-0.0039,-0.0021,0.0039
    Barcin_N:Bar8,0.0153,0.0338,0.0001,0.02,0.0015,-0.0093,-0.0015,-0.0008,0.0037
    Barcin_N:I0707,0.0172,0.0358,-0.0012,0.0272,0.0059,-0.0151,0.0003,-0.0007,0.0038
    Barcin_N:I0708,0.0168,0.0331,-0.0026,0.0236,0.0054,-0.0126,0.0024,0.007,0.0069
    Barcin_N:I0709,0.0165,0.0365,-0.001,0.0244,0.0043,-0.0125,0.0011,-0.0019,0.005
    Barcin_N:I0736,0.0164,0.0355,-0.0029,0.0236,0.0053,-0.0155,-0.0032,-0.0025,0.0014
    Barcin_N:I0744,0.0164,0.0359,-0.0037,0.0289,0.0049,-0.0145,-0.0023,0.0013,0.0052
    Barcin_N:I0745,0.0159,0.035,-0.0034,0.0241,0.0016,-0.014,0.0017,-0.002,0.0049
    Barcin_N:I0746,0.0165,0.0346,-0.0016,0.0229,0.0022,-0.0161,0.0002,-0.0007,0.0033
    Barcin_N:I1096,0.0167,0.0363,0.0005,0.0223,0.0012,-0.0122,-0.0033,-0.0025,0.0089
    Barcin_N:I1097,0.0169,0.0349,-0.0017,0.0271,0.0035,-0.0111,0.0015,-0.0035,0.0035
    Barcin_N:I1098,0.0159,0.0355,-0.0035,0.0218,0.0056,-0.0157,-0.0017,0.0009,0.0037
    Barcin_N:I1099,0.0159,0.0359,-0.0017,0.0215,0.0037,-0.0117,-0.0058,-0.0013,0.0059
    Barcin_N:I1100,0.0162,0.034,-0.0053,0.0213,0.0032,-0.0141,-0.0018,-0.0068,0.0067
    Barcin_N:I1101,0.0158,0.0352,-0.0027,0.0242,0.0045,-0.0135,0.0048,-0.0044,0.0022
    Barcin_N:I1103,0.0156,0.0336,-0.0034,0.0227,0.0049,-0.016,0.0008,-0.0003,0.0061
    Barcin_N:I1579,0.0168,0.0362,-0.0022,0.0232,0.0029,-0.0123,0.001,-0.0025,0.007
    Barcin_N:I1580,0.0165,0.0357,-0.0029,0.0253,0.0033,-0.014,-0.0003,0.0048,0.0018
    Barcin_N:I1581,0.0156,0.0348,-0.0035,0.0268,0.0044,-0.0179,-0.0038,-0.0039,0.0062
    Barcin_N:I1583,0.0157,0.0354,-0.0036,0.025,0.0047,-0.019,0.0009,-0.0064,0.0066
    Barcin_N:I1585,0.0165,0.035,-0.0018,0.0246,0.0035,-0.0103,-0.0013,-0.0006,0.0059
    Levant_N:I0867,0.0097,0.0339,-0.0046,0.0527,0.0055,-0.0404,0.0009,-0.013,0.0049
    Levant_N:I1699,0.01,0.0327,-0.0048,0.049,0.0059,-0.0421,0.003,-0.0096,0.0052
    Levant_N:I1704,0.0101,0.0313,-0.0064,0.0494,0.0029,-0.037,0.0024,-0.0167,0.0014
    Anatolia_BA:I2495,0.013,0.0309,-0.0024,0.0231,0.0056,-0.0105,0.0025,0.0134,-0.0001
    Anatolia_BA:I2499,0.0138,0.0299,-0.0034,0.0225,0.0086,-0.0062,0.0014,0.0151,0.0012
    Anatolia_BA:I2683,0.0132,0.0314,-0.002,0.0239,0.0055,-0.0101,-0.0006,0.0188,0.0016
    Ami,0.0084,-0.0826,0.0277,0.0438,0.0144,0.0473,0.0008,0.0177,-0.003
    Biaka,-0.1228,0.0048,0.0047,-0.0462,0.1389,-0.0122,-0.0006,0.0032,0.0067
    Bougainville,-0.0011,-0.0615,-0.1605,-0.0041,-0.0024,0.0011,0.1985,-0.0045,0.0064
    Chukchi,0.0116,-0.0636,0.0342,-0.0553,-0.0216,-0.075,0.0072,-0.007,0.0013
    Eskimo_Sireniki,0.0115,-0.0623,0.0325,-0.0579,-0.0217,-0.0751,0.0063,-0.0108,0.0025
    Han,0.009,-0.0807,0.0315,0.0239,0.0048,0.004,-0.0079,0.0092,0.0001
    Karitiana,0.0119,-0.0536,0.0236,-0.0493,-0.0123,-0.0292,0.0025,-0.0046,-0.0001
    Austroasiatic_Kharia,0.0037,-0.0431,-0.0141,0.0203,0.0141,0.0492,-0.0023,-0.0586,0.0056
    Andamanese_Onge,0.0013,-0.0453,-0.0257,0.012,0.0071,0.0272,0.0002,-0.0424,0.0009
    Papuan,-0.0037,-0.0578,-0.2166,-0.0239,-0.0121,-0.0246,-0.0794,0.0107,-0.0034
    She,0.0085,-0.0814,0.0322,0.0259,0.0055,0.0084,-0.0075,0.0094,-0.0013
    Ulchi,0.0098,-0.0761,0.0351,-0.0247,-0.014,-0.0623,-0.0004,-0.0001,0.0006
    Yoruba,-0.1169,0.006,0.0071,0.0004,-0.0461,0.0124,-0.0002,0.0078,-0.0155
    Hadza,-0.0882,0.0041,-0.0003,0.0047,0.0212,-0.0115,0.002,-0.028,-0.0271
    Bantu_SA_Tswana,-0.1167,0.0053,0.005,-0.0093,-0.0002,0.0021,0.0036,0.0007,-0.0238
    Pima,0.0114,-0.0514,0.025,-0.0466,-0.012,-0.0311,0.0023,-0.0057,-0.0005
    Piramalai,0.0072,-0.0156,-0.0152,0.011,0.0133,0.0358,-0.0028,-0.0497,0.0062
    Nganasan,0.01116,-0.06922,0.04114,-0.0641,-0.02772,-0.10372,0.01248,-0.00556,0.00258
    The models weren't too wild given the many options and correlation. I grouped the types for easier interpretation:

    Me:

    [1] "distance%=0.2447 / distance=0.002447"

    Barcin_N:I1096 33.90
    Barcin_N:I0707 12.45
    Yamnaya_Samara:I0444 24.60
    Yamnaya_Samara:I0441 8.65
    Loschbour:Loschbour 10.90
    Motala_HG:I0014 8.35
    Ami 1.15

    Dad:

    [1] "distance%=0.1131 / distance=0.001131"

    Barcin_N:I1096 43.30
    Yamnaya_Samara:I0357 19.15
    Yamnaya_Samara:I0429 10.85
    Yamnaya_Samara:I0444 7.70
    Motala_HG:I0014 7.15
    Hungary_HG 5.95
    Loschbour:Loschbour 4.30
    Ulchi 1.45
    Han 0.15

    Mom:

    [1] "distance%=0.3419 / distance=0.003419"

    Barcin_N:I1099 30.9
    Barcin_N:I1096 8.3
    Barcin_N:I1585 2.8
    Yamnaya_Samara:I0441 39.2
    Loschbour:Loschbour 11.5
    Bichon:Bichon 7.3

    Wife:

    [1] "distance%=0.2326 / distance=0.002326"

    Barcin_N:I1096 43.55
    Yamnaya_Samara:I0444 15.20
    Yamnaya_Samara:I0443 13.85
    Yamnaya_Samara:I0439 6.10
    Yamnaya_Samara:I0357 4.05
    Motala_HG:I0014 9.95
    Hungary_HG 7.30

    Father in law:

    [1] "distance%=0.2746 / distance=0.002746"

    Barcin_N:I1096 47.80
    Yamnaya_Samara:I0429 16.05
    Yamnaya_Samara:I0357 4.45
    Motala_HG:I0014 30.30
    Yoruba 0.85
    She 0.55

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

     Agamemnon (09-19-2017),  jortita (09-19-2017)

  9. #465
    Registered Users
    Posts
    245
    Sex
    Location
    Sevilla, Spain
    Ethnicity
    Italo-Celtic
    Nationality
    Spain
    Y-DNA (P)
    U152>L2>BY3485
    mtDNA (M)
    H65

    Italy Spain Andalucia
    Quote Originally Posted by randwulf View Post
    My results from earlier were decent nMonte models as far as distances. I wasn't too happy that PC1/PC2/PC3 weren't some of the closer matches in the nine dimensions (minus PC6, as it was removed). I was interested in the earlier conversation in this thread about the "variations" within the population. So, I decided to allow some controlled overfitting/correlation to let nMonte pick out the Yamnaya Samara, Barcin, and WHG-SHG populations (and Levant, which wasn't selected for any of us) that best worked for each person, with out groups. I used this spreadsheet:
    Me

    [1] "distance%=0.1243 / distance=0.001243"

    Ravai:Son

    Barcin_N:I1096 46.95
    Bichon:Bichon 21.10
    Barcin_N:I1099 19.00
    Yamnaya_Samara:I0357 9.95
    Han 3.00

    Father:

    [1] "distance%=0.2078 / distance=0.002078"

    Ravai_father

    Barcin_N:I1096 62.90
    Hungary_HG 9.55
    Yamnaya_Samara:I0444 9.40
    Yamnaya_Samara:I0357 7.60
    Motala_HG:I0014 6.65
    Han 2.65
    Yoruba 1.25
    Bichon:Bichon 0.00
    Paternal: R1b-U152+ L2+ BY4245+ BY3485+ BY3478+ , Giovanni Domenicus Rabai, b. 1609, Savona, Italy
    Maternal: Haplogroup H65, María García Martínez, b. 1746, Cuenca, Spain

    Manuel David Rabaez 1974, Manuel Rabaez 1948, Manuel Rabaez 1912, Antonio Rabay 1868, Antonio Rabay 1833, Manuel Rabay 1791, Manuel Rabay 1764, Pedro Rabai 1727, Pedro Joseph Rabai 1691, Giovanni Battista Rabai 1647, Jo. Domenicus Rabai 1609, Pietrus Rabai (work in progress...)

  10. The Following 3 Users Say Thank You to Ravai For This Useful Post:

     Agamemnon (09-19-2017),  Camulogène Rix (09-26-2017),  randwulf (09-19-2017)

  11. #466
    Gold Class Member
    Posts
    2,573
    Sex
    Location
    Brittany
    Ethnicity
    NW European
    Y-DNA (P)
    I-L813 >Y36690
    mtDNA (M)
    H3s
    mtDNA (P)
    H3s

    Normandie France Bretagne
    Quote Originally Posted by Ravai View Post
    Me

    [1] "distance%=0.1243 / distance=0.001243"

    Ravai:Son

    Barcin_N:I1096 46.95
    Bichon:Bichon 21.10
    Barcin_N:I1099 19.00
    Yamnaya_Samara:I0357 9.95
    Han 3.00

    Father:

    [1] "distance%=0.2078 / distance=0.002078"

    Ravai_father

    Barcin_N:I1096 62.90
    Hungary_HG 9.55
    Yamnaya_Samara:I0444 9.40
    Yamnaya_Samara:I0357 7.60
    Motala_HG:I0014 6.65
    Han 2.65
    Yoruba 1.25
    Bichon:Bichon 0.00
    You'll probably get best results and a best fit by using the BBC or the IA samples
    Recent Ancestry, full Normand. Known Genealogy 7/8 of the Cotentin peninsula 1/8 region of Coutances. Unfortunately, there are many missing branches on the maternal side.

  12. The Following User Says Thank You to Helgenes50 For This Useful Post:

     Ravai (09-27-2017)

  13. #467
    Gold Class Member
    Posts
    2,573
    Sex
    Location
    Brittany
    Ethnicity
    NW European
    Y-DNA (P)
    I-L813 >Y36690
    mtDNA (M)
    H3s
    mtDNA (P)
    H3s

    Normandie France Bretagne
    Quote Originally Posted by Ravai View Post
    Ravai

    With these populations you get probably a best result, closer to the truth.

    You get African in the first version, before restricted
    On the advice of David this one is the best if the African is real,
    As Spanish, this African makes sense



    [1] "distance%=0.5015 / distance=0.005015"

    Ravai

    Iberia_BA 63.0
    Iberia_ChL 26.6
    Anatolia_BA 9.8
    Yoruba 0.6



    [1] "distance%=0.5084 / distance=0.005084"

    Ravai

    Iberia_BA 64.8
    Iberia_ChL 25.1
    Anatolia_BA 10.2


    With these populations your steppe is boosted
    Recent Ancestry, full Normand. Known Genealogy 7/8 of the Cotentin peninsula 1/8 region of Coutances. Unfortunately, there are many missing branches on the maternal side.

  14. The Following User Says Thank You to Helgenes50 For This Useful Post:

     Ravai (09-27-2017)

  15. #468
    Suspended Account
    Posts
    31
    Sex
    Location
    South Carolina
    Ethnicity
    Italian x2
    Nationality
    American
    Y-DNA (P)
    R1b - L23 R-CTS 9219
    mtDNA (M)
    H30a

    Italy Italy Sicily

    Need some re-created plots

    Hello,

    The results I have from a PCA plot really do not Jive with the first-hand knowledge I have of my family's historical background.

    Would some kind, practiced and willing soul care to re-run this? I hope this is complete data.
    Thanks

    Global 10 coordinates

    ,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10
    0.0156,0.0283,-0.0016,0.0114,-0.0007,0.0144,-0.0024,-0.0077,0.0033,0.0028


    Global 10 Model A (modern-day)

    Italian_CentralSicilian 98.4
    Lebanese_Muslim 0.9
    Moroccan 0.7

    distance%=0.689 / distance=0.00689

    Global 10 Model B (ancient)

    LBK_EN 64.15
    Iran_Neolithic 22.60
    Yamnaya_Samara 5.15
    Western_HG 5.10
    Jordan_EBA 2.40
    Yoruba 0.60

    distance%=0.8214 / distance=0.008214


    K7
    Ancient_North_Eurasian 10.57
    Basal-rich 50.87
    East_Eurasian 0
    Oceanian 0
    Southeast_Asian 0
    Sub-Saharan 0.07
    Villabruna-related 38.48
    Last edited by Lancer; 06-28-2020 at 09:37 PM.

  16. #469
    Registered Users
    Posts
    4,410
    Sex

    Quote Originally Posted by Lancer View Post
    The results I have from a PCA plot really do not Jive with the first-hand knowledge I have of my family's historical background.

    Global 10 Model A (modern-day)

    Italian_CentralSicilian 98.4
    Lebanese_Muslim 0.9
    Moroccan 0.7

    distance%=0.689 / distance=0.00689
    These results are typical for someone of South Italian/Sicilian origin, and your profile says Italian x2. So it seems that they do make sense.

    In any case, if you have Global10 results then you can request the new Global25 coordinates for free.

  17. #470
    Suspended Account
    Posts
    31
    Sex
    Location
    South Carolina
    Ethnicity
    Italian x2
    Nationality
    American
    Y-DNA (P)
    R1b - L23 R-CTS 9219
    mtDNA (M)
    H30a

    Italy Italy Sicily
    Anybody care to model these with percentiles?

    Here are your G25 coordinates...

    ,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
    L_scaled,0.108132,0.142174,-0.008674,-0.044897,0.015387,-0.020638,-0.00329,0.004846,0.007363,0.022233,0.001461,0.0026 98,-0.003122,-0.004404,-0.000271,0.000663,0.000652,0.000127,-0.00088,0.000375,-0.001373,0.001237,-0.006409,0.003494,0.000838

    ,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
    L_,0.0095,0.014,-0.0023,-0.0139,0.005,-0.0074,-0.0014,0.0021,0.0036,0.0122,0.0009,0.0018,-0.0021,-0.0032,-0.0002,0.0005,0.0005,0.0001,-0.0007,0.0003,-0.0011,0.001,-0.0052,0.0029,0.0007
    Last edited by Lancer; 06-30-2020 at 09:57 PM.

  18. The Following User Says Thank You to Lancer For This Useful Post:

     Greekscholar (07-01-2020)

Page 47 of 48 FirstFirst ... 3745464748 LastLast

Similar Threads

  1. Replies: 1
    Last Post: 03-24-2019, 05:32 AM
  2. Replies: 337
    Last Post: 05-29-2018, 08:07 PM
  3. Do Northeast Europeans have Basal rich ancestry?
    By Sorcelow in forum Autosomal (auDNA)
    Replies: 5
    Last Post: 03-10-2018, 09:06 PM
  4. Davidski's Basal-rick K7 + Global 10 Genetic Map Results
    By khanabadoshi in forum Autosomal (auDNA)
    Replies: 831
    Last Post: 12-02-2017, 08:41 PM
  5. Replies: 17
    Last Post: 08-27-2017, 01:54 PM

Posting Permissions

  • You may not post new threads
  • You may not post replies
  • You may not post attachments
  • You may not edit your posts
  •