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Thread: Comprehensive qpgraph of ancient Eurasia

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    Comprehensive qpgraph of ancient Eurasia

    For the past few weeks I've been working on creating a qpgraph that fits every phylogenically unique/important/cornerstone ancient Eurasian population.
    I'm looking for suggestions as to how to improve this graph and requests for any other populations to add.
    Here is the result so far. It is quite a large graph with many edges and mixtures so it's too large for a single image.
    To view it paste the contents of the dotfile spoiler at http://viz-js.com/ it will render the image of the graph there where you can zoom and scroll and such.
    Worst outlier z-score is 3.626, generally you want under 3, but given the complexity of this graph, I don't think that's too bad at all. Overlapping snp count is a healthy 360k.

    The populations included in this current rendition are...
    Mbuti.DG (to act as the root)
    Taforalt
    Ust_Ishim
    Barcin_N
    Andaman_100BP
    GoyetQ116-1
    Kostenki14
    XiongNu (the ones that are basically identical to modern Han)
    Brazil_Sumidouro_10100BP
    EHG (I0061 & UzOO77 - Karelia_HG, I0124 - Samara_HG, Sidelkino)
    Sunghir
    Gravettian (Vestonice16, Ostuni1, KremsWA3)
    Loschbour
    Baikal_EN
    Iran_N
    CHG

    Some samples that were omitted and why...
    AG3
    Is low coverage and single handedly cuts the snp overlap count in 1/3.
    Was included in earlier stages of making this graph and it's removal has not changed the ANE node substantially.
    With AG3: ANE was 34% East 66% West, the drift length was about 110, and the mixture into America was 33%.
    Without AG3: ANE is 43% East 57% West, the drift length is 118, and the mixture into America is 34%.

    MA1
    Is almost certainly not pure/proto-ANE. When AG3 was also in graph MA1 fit as a mix of ANE and West5.
    Because ANE seems well enough anchored by the higher quality populations included, I don't think the snp loss MA1 would cause is necessary.

    Australian/Papuan
    Denisovan would be necessary which would mean using Chimp instead of Mbuti.DG as the outpop.
    Could be a whole bunch of subtle issues with doing that, and it takes a very long time to run even a single graph on my computersaurus.

    Tianyuan
    Something looks a bit weird about this sample, it's just not related enough to other pops as it should be, excess archaic mixture? Different technique for calling the genotype?

    DOTFILE
     

    digraph G {
    size = "7.5,10" ;
    labelloc = "t" ;
    label = "41319a :: Ust And Kos Los 0.001805 0.011829 0.010024 0.002765 3.626
    " ;

    Mbuti_DG [ label = "Mbuti_DG" ] ;
    Taforalt [ label = "Taforalt" ] ;
    Ust_Ishim [ label = "Ust_Ishim" ] ;
    Barcin_N [ label = "Barcin_N" ] ;
    Andaman_100BP [ label = "Andaman_100BP" ] ;
    GoyetQ116_1 [ label = "GoyetQ116_1" ] ;
    Kostenki14 [ label = "Kostenki14" ] ;
    XiongNu [ label = "XiongNu" ] ;
    Brazil_Sumidouro_10100BP [ label = "Brazil_Sumidouro_10100BP" ] ;
    EHG [ label = "EHG" ] ;
    Sunghir [ label = "Sunghir" ] ;
    Gravettian [ label = "Gravettian" ] ;
    Loschbour [ label = "Loschbour" ] ;
    Baikal_EN [ label = "Baikal_EN" ] ;
    Iran_N [ label = "Iran_N" ] ;
    CHG [ label = "CHG" ] ;
    Root -> Mbuti_DG [ label = "63" ] ;
    Root -> NodeA [ label = "63" ] ;
    NodeA -> Eurasia [ label = "18" ] ;
    Eurasia -> West1 [ label = "10" ] ;
    pre_IBM1 -> pre_IBM0 [ label = "93" ] ;
    West1 -> West3 [ label = "59" ] ;
    East0 -> East1 [ label = "17" ] ;
    pre_IBM0 -> Taforalt [ label = "116" ] ;
    West3 -> West5 [ label = "10" ] ;
    West3 -> West4 [ label = "0" ] ;
    NE0 -> NE1 [ label = "57" ] ;
    East1 -> Ust_Ishim [ label = "13" ] ;
    East1 -> East1a [ label = "22" ] ;
    AHG2 -> Barcin_N [ label = "39" ] ;
    East1a -> Andaman_100BP [ label = "460" ] ;
    East1a -> East2 [ label = "28" ] ;
    NE1 -> NE2 [ label = "22" ] ;
    West5 -> Aurignacian [ label = "226" ] ;
    West4 -> West6 [ label = "14" ] ;
    West4 -> West7 [ label = "26" ] ;
    pre_ANE -> ANE [ label = "118" ] ;
    NE3 -> NE4 [ label = "29" ] ;
    West6 -> West8 [ label = "37" ] ;
    West6 -> Kostenki14 [ label = "436" ] ;
    Aurignacian -> GoyetQ116_1 [ label = "224" ] ;
    East2 -> East3 [ label = "9" ] ;
    East3 -> East4 [ label = "5" ] ;
    East3 -> XiongNu [ label = "108" ] ;
    America -> Brazil_Sumidouro_10100BP [ label = "190" ] ;
    pre_BKN -> Baikal_EN [ label = "48" ] ;
    WHG4a -> Loschbour [ label = "66" ] ;
    pre_EHG2 -> EHG [ label = "122" ] ;
    pre_Sunghir -> Sunghir [ label = "58" ] ;
    pre_GRV -> Gravettian [ label = "289" ] ;
    WHG2 -> WHG3 [ label = "14" ] ;
    WHG3 -> WHG4 [ label = "21" ] ;
    WHG3 -> WHG5 [ label = "23" ] ;
    pre_Ganj2 -> Iran_N [ label = "57" ] ;
    pre_CHG2 -> CHG [ label = "265" ] ;
    WHG5 -> WHG6 [ label = "6" ] ;
    WHG5 -> WHG7 [ label = "30" ] ;
    NodeA -> pre_IBM1 [ style=dotted, label = "72%" ] ;
    pre_IBM2 -> pre_IBM1 [ style=dotted, label = "28%" ] ;
    Eurasia -> East0 [ style=dotted, label = "49%" ] ;
    West5 -> East0 [ style=dotted, label = "51%" ] ;
    West1 -> NE0 [ style=dotted, label = "66%" ] ;
    East1a -> NE0 [ style=dotted, label = "34%" ] ;
    AHG1 -> AHG2 [ style=dotted, label = "92%" ] ;
    pre_IBM0 -> AHG2 [ style=dotted, label = "8%" ] ;
    East2 -> pre_ANE [ style=dotted, label = "43%" ] ;
    West3 -> pre_ANE [ style=dotted, label = "57%" ] ;
    NE1 -> NE3 [ style=dotted, label = "94%" ] ;
    West8 -> NE3 [ style=dotted, label = "6%" ] ;
    ANE -> America [ style=dotted, label = "34%" ] ;
    East4 -> America [ style=dotted, label = "66%" ] ;
    ANE -> pre_BKN [ style=dotted, label = "7%" ] ;
    East4 -> pre_BKN [ style=dotted, label = "93%" ] ;
    WHG4 -> WHG4a [ style=dotted, label = "96%" ] ;
    Aurignacian -> WHG4a [ style=dotted, label = "4%" ] ;
    ANE -> pre_EHG1 [ style=dotted, label = "50%" ] ;
    WHG4a -> pre_EHG1 [ style=dotted, label = "50%" ] ;
    pre_EHG1 -> pre_EHG2 [ style=dotted, label = "86%" ] ;
    NE2 -> pre_EHG2 [ style=dotted, label = "14%" ] ;
    West7 -> pre_Sunghir [ style=dotted, label = "13%" ] ;
    West8 -> pre_Sunghir [ style=dotted, label = "87%" ] ;
    West7 -> pre_GRV [ style=dotted, label = "67%" ] ;
    West8 -> pre_GRV [ style=dotted, label = "33%" ] ;
    ANE -> WHG2 [ style=dotted, label = "20%" ] ;
    West7 -> WHG2 [ style=dotted, label = "80%" ] ;
    WHG6 -> pre_IBM2 [ style=dotted, label = "93%" ] ;
    Aurignacian -> pre_IBM2 [ style=dotted, label = "7%" ] ;
    ANE -> pre_Ganj1 [ style=dotted, label = "15%" ] ;
    NE4 -> pre_Ganj1 [ style=dotted, label = "85%" ] ;
    NE2 -> AHG1 [ style=dotted, label = "37%" ] ;
    WHG7 -> AHG1 [ style=dotted, label = "63%" ] ;
    ANE -> pre_CHG1 [ style=dotted, label = "21%" ] ;
    NE4 -> pre_CHG1 [ style=dotted, label = "79%" ] ;
    pre_Ganj1 -> pre_Ganj2 [ style=dotted, label = "82%" ] ;
    WHG7 -> pre_Ganj2 [ style=dotted, label = "18%" ] ;
    pre_CHG1 -> pre_CHG2 [ style=dotted, label = "67%" ] ;
    WHG7 -> pre_CHG2 [ style=dotted, label = "33%" ] ;
    }


    TERMINAL OUTPUT - further details
     

    user@debian:~/AdmixTools-master/bin$ ./qpGraph -p parqpgraph -g 41319a -o outgraph -d dotfile
    parameter file: parqpgraph
    ### THE INPUT PARAMETERS
    ##PARAMETER NAME: VALUE
    DIR: /scratch/root/AdmixTools/bin
    S1: dataset19b
    indivname: /scratch/root/AdmixTools/bin/dataset19b.ind
    snpname: /scratch/root/AdmixTools/bin/dataset19b.snp
    genotypename: /scratch/root/AdmixTools/bin/dataset19b.geno
    outpop: Mbuti.DG
    blgsize: 0.05
    lsqmode: YES
    diag: .0001
    hires: YES
    initmix: 1000
    precision: .0001
    zthresh: 3.0
    terse: NO
    useallsnps: NO
    ## qpGraph version: 6450
    outpop: Mbuti.DG
    seed: 1646999042
    simple lsqmode
    Mbuti.DG
    Ust_Ishim
    GoyetQ116-1
    XiongNu
    Brazil_Sumidouro_10100BP
    EHG
    Kostenki14
    Sunghir
    Gravettian
    Loschbour
    Taforalt
    Iran_N
    Barcin_N
    CHG
    Baikal_EN
    Andaman_100BP

    graph: 41319a


    numedge: 41 numancestor: 1
    0 Mbuti.DG
    1 Ust_Ishim
    2 GoyetQ116-1
    3 XiongNu
    4 Brazil_Sumidouro_10100BP
    5 EHG
    6 Kostenki14
    7 Sunghir
    8 Gravettian
    9 Loschbour
    10 Taforalt
    11 Iran_N
    12 Barcin_N
    13 CHG
    14 Baikal_EN
    15 Andaman_100BP
    root label: :Mbuti.DG
    nodata: rs61780219
    nodata: rs71629813
    nodata: rs12077803
    nodata: Affx-50004616
    nodata: Affx-50006276
    nodata: rs2799108
    nodata: rs17159675
    nodata: rs61816207
    nodata: Affx-50009874
    nodata: Affx-50009924
    nodata: Affx-50009932
    nodata: Affx-50009934
    nodata: rs4500359
    nodata: Affx-50009936
    nodata: Affx-50009937
    nodata: Affx-50014408
    nodata: Affx-50018257
    nodata: Affx-50020800
    nodata: Affx-50066782
    nodata: rs142953672
    nodata: Affx-50066783
    nodata: Affx-50069379
    nodata: Affx-50069565
    nodata: Affx-50066086
    nodata: Affx-50066092
    nodata: rs451002
    nodata: rs78333154
    nodata: rs62162900
    nodata: rs71224406
    nodata: rs55821748
    nodata: Affx-50066302
    nodata: Affx-50066353
    nodata: Affx-50070296
    nodata: Affx-50070298
    nodata: Affx-50070299
    nodata: rs1347870
    nodata: Affx-50070300
    nodata: rs62164875
    nodata: Affx-50070303
    nodata: rs3874273
    nodata: Affx-50086450
    nodata: rs138840766
    nodata: Affx-50086444
    nodata: rs141141725
    nodata: rs7698283
    nodata: Affx-50099670
    nodata: Affx-50099671
    nodata: rs150428
    nodata: Affx-50099676
    nodata: rs62386983
    nodata: rs1061581
    nodata: Affx-50112420
    nodata: rs148349653
    nodata: rs17201511
    nodata: rs139740532
    nodata: rs201647933
    nodata: rs77335078
    nodata: Affx-50119664
    nodata: rs2311899
    nodata: rs2109936
    nodata: rs801050
    nodata: Affx-50120102
    nodata: Affx-50120105
    nodata: rs34472859
    nodata: Affx-50120106
    nodata: rs1637142
    nodata: rs186407955
    nodata: rs139851927
    nodata: rs75647144
    nodata: Affx-50116060
    nodata: Affx-50116077
    nodata: Affx-50116081
    nodata: Affx-50116682
    nodata: Affx-50124647
    nodata: rs201166293
    nodata: Affx-50122316
    nodata: Affx-50122318
    nodata: rs11545441
    nodata: Affx-50122419
    nodata: Affx-50127044
    nodata: Affx-50127888
    nodata: rs61843996
    nodata: rs10508545
    nodata: Affx-50001783
    nodata: rs71497203
    nodata: rs145676940
    nodata: Affx-50001784
    nodata: rs71497209
    nodata: rs3858193
    nodata: Affx-50001788
    nodata: rs35701218
    nodata: Affx-50001790
    nodata: Affx-50001799
    nodata: rs45470101
    nodata: Affx-50001801
    nodata: Affx-50001803
    nodata: rs61844042
    nodata: Affx-50002744
    nodata: rs2942947
    nodata: Affx-50002746
    nodata: rs146410326
    nodata: rs201539751
    nodata: Affx-50002770
    nodata: Affx-50002771
    nodata: rs202183815
    nodata: Affx-50004046
    nodata: rs147158483
    nodata: rs150050324
    nodata: Affx-50011536
    nodata: rs79351613
    nodata: Affx-50032931
    nodata: rs71473119
    nodata: Affx-50036749
    nodata: Affx-50036772
    nodata: Affx-50036775
    nodata: Affx-50036779
    nodata: Affx-50037259
    nodata: rs145128593
    nodata: Affx-50037264
    nodata: Affx-50037270
    nodata: rs145771210
    nodata: Affx-50038810
    nodata: Affx-50040402
    nodata: rs62039661
    nodata: Affx-50040413
    nodata: rs76539946
    nodata: rs200703873
    nodata: Affx-50040139
    nodata: Affx-50047810
    nodata: Affx-50047802
    nodata: Affx-50047800
    nodata: Affx-50051857
    nodata: Affx-50064549
    nodata: Affx-50064552
    nodata: snp_24_3221179
    nodata: snp_24_3709585
    nodata: snp_24_3882879
    nodata: L381
    nodata: L1231
    nodata: rs186809987
    nodata: rs182663965
    nodata: snp_24_5423058
    nodata: 92R7_1
    nodata: snp_24_6424628
    nodata: Z3177
    nodata: Z3223
    nodata: 92R7_2
    nodata: rs201194017
    nodata: P68
    nodata: rs7892898
    nodata: P9.2
    nodata: V58
    nodata: rs199952688
    nodata: L353_1
    nodata: P16_1
    nodata: P16_2
    nodata: L353_2
    nodata: P112
    nodata: rs76320386
    nodata: Z3467
    nodata: Z3468
    nodata: snp_24_22272938
    nodata: Z3474
    nodata: rs200889326
    nodata: P19_1
    nodata: P34_1
    nodata: P19_2
    nodata: P34_2
    nodata: rs55880099
    nodata: P8_2
    nodata: P19_3
    nodata: P34_3
    nodata: P8_3
    nodata: P19_4
    nodata: P18_1
    nodata: P7_1
    nodata: rs150173
    nodata: P12_1
    nodata: P65_1
    nodata: P66_1
    nodata: P67_1
    nodata: P35_1
    nodata: P33_1
    nodata: P21_1
    nodata: P18_2
    nodata: P7_2
    nodata: P12_2
    nodata: P65_2
    nodata: P66_2
    nodata: P67_2
    nodata: P35_2
    nodata: P33_2
    nodata: P21_2
    nodata: P21_3
    nodata: P33_3
    nodata: P35_3
    nodata: P67_3
    nodata: P66_3
    nodata: P65_3
    nodata: P12_3
    nodata: P7_3
    nodata: P18_3
    outpop: Mbuti.DG
    population: 0 Mbuti.DG 5
    population: 1 Ust_Ishim 1
    population: 2 GoyetQ116-1 1
    population: 3 XiongNu 3
    population: 4 Brazil_Sumidouro_10100BP 4
    population: 5 EHG 4
    population: 6 Kostenki14 1
    population: 7 Sunghir 4
    population: 8 Gravettian 3
    population: 9 Loschbour 1
    population: 10 Taforalt 5
    population: 11 Iran_N 7
    population: 12 Barcin_N 10
    population: 13 CHG 2
    population: 14 Baikal_EN 13
    population: 15 Andaman_100BP 1
    before setwt numsnps: 1233013 outpop: Mbuti.DG
    setwt numsnps: 360139
    number of blocks for moving block jackknife: 711
    snps: 360139 indivs: 65
    lambdascale: 0.462
    fst:
    M U G X B E K S G L T I B C B A
    M 0 146 530 269 331 273 528 242 409 252 272 206 195 372 221 528
    U 146 0 512 184 262 200 514 150 360 164 250 127 108 330 125 512
    G 530 512 0 669 745 659 1000 612 837 615 694 594 566 798 607 1000
    X 269 184 669 0 359 335 669 306 517 314 390 267 253 470 184 651
    B 331 262 745 359 0 383 746 377 591 378 460 336 322 543 286 737
    E 273 200 659 335 383 0 660 281 497 250 384 248 219 452 266 670
    K 528 514 1000 669 746 660 0 598 835 623 695 590 566 797 609 1000
    S 242 150 612 306 377 281 598 0 424 233 350 225 192 426 242 636
    G 409 360 837 517 591 497 835 424 0 445 546 438 403 642 456 848
    L 252 164 615 314 378 250 623 233 445 0 351 227 177 426 249 642
    T 272 250 694 390 460 384 695 350 546 351 0 315 280 507 335 699
    I 206 127 594 267 336 248 590 225 438 227 315 0 144 355 207 594
    B 195 108 566 253 322 219 566 192 403 177 280 144 0 347 193 580
    C 372 330 798 470 543 452 797 426 642 426 507 355 347 0 410 801
    B 221 125 607 184 286 266 609 242 456 249 335 207 193 410 0 590
    A 528 512 1000 651 737 670 1000 636 848 642 699 594 580 801 590 0

    f2:
    M U G X B E K S G L T I B C B A
    M 0 194 674 349 425 355 665 311 520 327 347 268 256 475 288 664
    U 194 0 495 180 255 198 496 146 350 161 261 127 109 329 122 494
    G 674 495 0 658 718 622 915 559 761 557 711 585 543 775 591 969
    X 349 180 658 0 320 327 657 300 508 306 408 264 252 463 161 607
    B 425 255 718 320 0 353 720 363 568 361 476 328 315 524 251 688
    E 355 198 622 327 353 0 623 264 464 222 395 238 208 427 255 653
    K 665 496 915 657 720 623 0 525 748 571 712 573 540 767 593 981
    S 311 146 559 300 363 264 525 0 370 212 359 218 183 408 235 618
    G 520 350 761 508 568 464 748 370 0 398 555 426 381 616 444 826
    L 327 161 557 306 361 222 571 212 398 0 358 219 163 402 240 622
    T 347 261 711 408 476 395 712 359 555 358 0 326 282 522 349 727
    I 268 127 585 264 328 238 573 218 426 219 326 0 137 328 203 584
    B 256 109 543 252 315 208 540 183 381 163 282 137 0 325 191 573
    C 475 329 775 463 524 427 767 408 616 402 522 328 325 0 402 787
    B 288 122 591 161 251 255 593 235 444 240 349 203 191 402 0 548
    A 664 494 969 607 688 653 981 618 826 622 727 584 573 787 548 0

    ff3:
    M U G X B E K S G L T I B C B A
    M 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
    U 0 194 187 182 182 176 182 180 183 180 140 168 171 170 181 183
    G 0 187 674 183 190 204 212 213 216 222 155 179 193 187 186 185
    X 0 182 183 349 227 189 179 180 180 185 144 177 176 180 238 203
    B 0 182 190 227 425 213 185 187 189 195 148 183 183 188 231 201
    E 0 176 204 189 213 355 198 201 206 230 153 192 202 201 194 183
    K 0 182 212 179 185 198 665 225 219 210 149 180 190 186 180 174
    S 0 180 213 180 187 201 225 311 231 213 150 181 192 189 182 179
    G 0 183 216 180 189 206 219 231 520 225 156 181 197 189 182 179
    L 0 180 222 185 195 230 210 213 225 327 158 188 209 200 187 184
    T 0 140 155 144 148 153 149 150 156 158 347 144 160 149 143 142
    I 0 168 179 177 183 192 180 181 181 188 144 268 193 207 177 174
    B 0 171 193 176 183 202 190 192 197 209 160 193 256 203 176 173
    C 0 170 187 180 188 201 186 189 189 200 149 207 203 475 181 176
    B 0 181 186 238 231 194 180 182 182 187 143 177 176 181 288 202
    A 0 183 185 203 201 183 174 179 179 184 142 174 173 176 202 664

    ff3sig*10:
    M U G X B E K S G L T I B C B A
    M 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
    U 0 54 30 25 26 25 30 25 27 28 22 23 23 26 24 27
    G 0 30 28 25 27 26 33 27 28 29 24 23 23 27 25 29
    X 0 25 25 25 24 23 26 22 23 25 20 21 21 24 23 25
    B 0 26 27 24 27 24 27 23 24 26 21 21 21 24 23 26
    E 0 25 26 23 24 25 26 23 24 26 22 21 21 24 22 24
    K 0 30 33 26 27 26 28 28 29 29 24 23 24 27 25 28
    S 0 25 27 22 23 23 28 27 25 25 21 20 21 24 21 24
    G 0 27 28 23 24 24 29 25 26 27 22 21 22 25 22 26
    L 0 28 29 25 26 26 29 25 27 46 23 23 23 27 24 27
    T 0 22 24 20 21 22 24 21 22 23 25 19 20 22 19 22
    I 0 23 23 21 21 21 23 20 21 23 19 21 20 22 20 22
    B 0 23 23 21 21 21 24 21 22 23 20 20 21 22 20 22
    C 0 26 27 24 24 24 27 24 25 27 22 22 22 27 22 25
    B 0 24 25 23 23 22 25 21 22 24 19 20 20 22 23 24
    A 0 27 29 25 26 24 28 24 26 27 22 22 22 25 24 27

    starting analysis
    number of initial random trials: 2050
    initmixwts: :: NE0 West1 East1a 0.671 0.329
    initmixwts: : NE3 NE1 West8 0.960 0.040
    initmixwts: ::Ust_Ishim East0 Eurasia West5 0.439 0.561
    initmixwts: : pre_ANE East2 West3 0.459 0.541
    initmixwts: :Brazil_Sumidouro_10100BP America ANE East4 0.418 0.582
    initmixwts: :Baikal_EN pre_BKN ANE East4 0.066 0.934
    initmixwts: pre_EHG1 ANE WHG4a 0.451 0.549
    initmixwts: :EHG pre_EHG2 pre_EHG1 NE2 0.866 0.134
    initmixwts: :Sunghir pre_Sunghir West7 West8 0.145 0.855
    initmixwts: :Gravettian pre_GRV West7 West8 0.675 0.325
    initmixwts: :: WHG2 ANE West7 0.190 0.810
    initmixwts: :Loschbour WHG4a WHG4 Aurignacian 0.841 0.159
    initmixwts: pre_IBM2 WHG6 Aurignacian 0.777 0.223
    initmixwts: ::Taforalt pre_IBM1 NodeA pre_IBM2 0.677 0.323
    initmixwts: pre_Ganj1 ANE NE4 0.196 0.804
    initmixwts: :Iran_N pre_Ganj2 pre_Ganj1 WHG7 0.849 0.151
    initmixwts: AHG1 NE2 WHG7 0.366 0.634
    initmixwts: :Barcin_N AHG2 AHG1 pre_IBM0 0.919 0.081
    initmixwts: pre_CHG1 ANE NE4 0.217 0.783
    initmixwts: :CHG pre_CHG2 pre_CHG1 WHG7 0.663 0.337


    initial score: 22611.435
    init vg:
    0.671 0.960 0.439 0.459 0.418 ...
    0.066 0.451 0.866 0.145 0.675 ...
    0.190 0.841 0.777 0.677 0.196 ...
    0.849 0.366 0.919 0.217 0.663
    gslsetup called
    gslans: 4112 17978.796942
    0.658 0.942 0.493 0.432 0.345 ...
    0.070 0.505 0.856 0.132 0.667 ...
    0.196 0.959 0.928 0.719 0.151 ...
    0.821 0.368 0.924 0.214 0.673
    final vg:
    0.658 0.942 0.493 0.432 0.345 ...
    0.070 0.505 0.856 0.132 0.667 ...
    0.196 0.959 0.928 0.719 0.151 ...
    0.821 0.368 0.924 0.214 0.673

    final score: 17978.797 dof: 59 nominal p-val 0.000000
    ff3fit:
    M U G X B E K S G L T I B C B A
    M 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
    U 0 194 185 182 181 178 180 180 180 180 142 167 170 170 182 182
    G 0 185 674 185 190 204 214 214 214 221 155 180 191 187 186 185
    X 0 182 185 349 228 190 180 180 180 184 143 176 176 179 238 204
    B 0 181 190 228 425 212 186 186 186 197 146 183 183 189 231 199
    E 0 178 204 190 212 355 199 200 205 230 153 192 201 201 194 184
    K 0 180 214 180 186 199 664 226 219 211 150 179 190 186 181 180
    S 0 180 214 180 186 200 226 311 231 214 151 181 192 188 181 180
    G 0 180 214 180 186 205 219 231 520 224 154 182 199 191 181 180
    L 0 180 221 184 197 230 211 214 224 326 159 187 210 199 187 182
    T 0 142 155 143 146 153 150 151 154 159 347 144 160 149 143 142
    I 0 167 180 176 183 192 179 181 182 187 144 268 193 207 177 174
    B 0 170 191 176 183 201 190 192 199 210 160 193 256 203 177 174
    C 0 170 187 179 189 201 186 188 191 199 149 207 203 474 181 176
    B 0 182 186 238 231 194 181 181 181 187 143 177 177 181 288 203
    A 0 182 185 204 199 184 180 180 180 182 142 174 174 176 203 664

    ff3diff:
    M U G X B E K S G L T I B C B A
    M 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
    U 0 0 -2 0 -1 2 -2 0 -3 0 1 0 0 0 1 -1
    G 0 -2 0 2 0 1 2 1 -3 0 0 1 -2 0 0 0
    X 0 0 2 0 0 1 1 0 -1 0 -1 -1 -1 -2 0 1
    B 0 -1 0 0 0 -1 1 -1 -2 2 -2 0 0 1 0 -1
    E 0 2 1 1 -1 0 1 -1 -1 0 0 0 0 0 0 0
    K 0 -2 2 1 1 1 -1 1 0 1 1 -1 0 0 1 6
    S 0 0 1 0 -1 -1 1 0 0 1 1 0 0 -1 -1 1
    G 0 -3 -3 -1 -2 -1 0 0 0 0 -2 1 1 1 -1 1
    L 0 0 0 0 2 0 1 1 0 0 1 -1 0 0 -1 -2
    T 0 1 0 -1 -2 0 1 1 -2 1 0 0 0 -1 0 0
    I 0 0 1 -1 0 0 -1 0 1 -1 0 0 0 0 1 0
    B 0 0 -2 -1 0 0 0 0 1 0 0 0 0 0 1 1
    C 0 0 0 -2 1 0 0 -1 1 0 -1 0 0 0 0 1
    B 0 1 0 0 0 0 1 -1 -1 -1 0 1 1 0 0 1
    A 0 -1 0 1 -1 0 6 1 1 -2 0 0 1 1 1 -1

    mix: :: NE0 West1 East1a 0.658 0.342
    mix: : NE3 NE1 West8 0.942 0.058
    mix: ::Ust_Ishim East0 Eurasia West5 0.493 0.507
    mix: : pre_ANE East2 West3 0.432 0.568
    mix: :Brazil_Sumidouro_10100BP America ANE East4 0.345 0.655
    mix: :Baikal_EN pre_BKN ANE East4 0.070 0.930
    mix: pre_EHG1 ANE WHG4a 0.505 0.495
    mix: :EHG pre_EHG2 pre_EHG1 NE2 0.856 0.144
    mix: :Sunghir pre_Sunghir West7 West8 0.132 0.868
    mix: :Gravettian pre_GRV West7 West8 0.667 0.333
    mix: :: WHG2 ANE West7 0.196 0.804
    mix: :Loschbour WHG4a WHG4 Aurignacian 0.959 0.041
    mix: pre_IBM2 WHG6 Aurignacian 0.928 0.072
    mix: ::Taforalt pre_IBM1 NodeA pre_IBM2 0.719 0.281
    mix: pre_Ganj1 ANE NE4 0.151 0.849
    mix: :Iran_N pre_Ganj2 pre_Ganj1 WHG7 0.821 0.179
    mix: AHG1 NE2 WHG7 0.368 0.632
    mix: :Barcin_N AHG2 AHG1 pre_IBM0 0.924 0.076
    mix: pre_CHG1 ANE NE4 0.214 0.786
    mix: :CHG pre_CHG2 pre_CHG1 WHG7 0.673 0.327

    Mbuti.DG NodeA Eurasia West1 West3 NE1 NE4 NE2 West5 West4 West6 West7 West8 Aurignacian GoyetQ116-1 East1 Ust_Ishim East1a Andaman_100BP East2 East3 East4 XiongNu ANE Baikal_EN Brazil_Sumidouro_10100BP EHG Kostenki14 Sunghir Gravettian WHG3 WHG4 WHG5 WHG6 WHG7 Loschbour pre_IBM0 Taforalt Iran_N Barcin_N CHG
    0.0632 0.0632 0.0182 0.0102 0.0591 0.0567 0.0294 0.0215 0.0096 0.0000 0.0141 0.0258 0.0374 0.2262 0.2239 0.0168 0.0127 0.0223 0.4597 0.0276 0.0093 0.0047 0.1081 0.1181 0.0479 0.1903 0.1219 0.4362 0.0581 0.2887 0.0142 0.0207 0.0234 0.0063 0.0296 0.0655 0.0927 0.1164 0.0569 0.0388 0.2649


    fst: fitted estim diff std. err Z score
    Mbu Ust f2: 0.194439 0.194454 0.000015 0.005388 0.003
    Mbu Goy f2: 0.673709 0.673981 0.000272 0.002801 0.097
    Mbu Xio f2: 0.348985 0.349116 0.000131 0.002547 0.052
    Mbu Bra f2: 0.424983 0.425214 0.000231 0.002702 0.086
    Mbu EHG f2: 0.354876 0.355024 0.000148 0.002515 0.059
    Mbu Kos f2: 0.664194 0.664725 0.000530 0.002828 0.187
    Mbu Sun f2: 0.311285 0.311356 0.000071 0.002658 0.027
    Mbu Gra f2: 0.519865 0.520216 0.000351 0.002574 0.136
    Mbu Los f2: 0.326467 0.326546 0.000080 0.004579 0.017
    Mbu Taf f2: 0.346554 0.346696 0.000142 0.002476 0.057
    Mbu Ira f2: 0.267814 0.267883 0.000069 0.002088 0.033
    Mbu Bar f2: 0.255615 0.255662 0.000047 0.002121 0.022
    Mbu CHG f2: 0.474187 0.474509 0.000322 0.002658 0.121
    Mbu Bai f2: 0.288217 0.288275 0.000058 0.002288 0.025
    Mbu And f2: 0.663638 0.664196 0.000559 0.002718 0.206
    Ust Goy f2: 0.498857 0.495406 -0.003451 0.006252 -0.552
    Ust Xio f2: 0.179991 0.180444 0.000453 0.004884 0.093
    Ust Bra f2: 0.256753 0.254935 -0.001818 0.005268 -0.345
    Ust EHG f2: 0.194250 0.198084 0.003834 0.005122 0.748
    Ust Kos f2: 0.499104 0.496174 -0.002929 0.005820 -0.503
    Ust Sun f2: 0.146194 0.146344 0.000150 0.005151 0.029
    Ust Gra f2: 0.354774 0.349506 -0.005268 0.005296 -0.995
    Ust Los f2: 0.160658 0.161099 0.000440 0.006477 0.068
    Ust Taf f2: 0.257947 0.260881 0.002933 0.005367 0.547
    Ust Ira f2: 0.127448 0.127027 -0.000421 0.004831 -0.087
    Ust Bar f2: 0.109070 0.108828 -0.000242 0.004818 -0.050
    Ust CHG f2: 0.327726 0.328573 0.000847 0.005315 0.159
    Ust Bai f2: 0.119378 0.121638 0.002261 0.004824 0.469
    Ust And f2: 0.494644 0.493502 -0.001142 0.005662 -0.202
    Goy Xio f2: 0.653403 0.657908 0.004505 0.003486 1.292
    Goy Bra f2: 0.717942 0.718288 0.000345 0.004036 0.086
    Goy EHG f2: 0.619587 0.621820 0.002232 0.003501 0.638
    Goy Kos f2: 0.910073 0.914558 0.004484 0.005523 0.812
    Goy Sun f2: 0.557164 0.558646 0.001482 0.003724 0.398
    Goy Gra f2: 0.765744 0.761332 -0.004412 0.004404 -1.002
    Goy Los f2: 0.557717 0.557220 -0.000498 0.005649 -0.088
    Goy Taf f2: 0.710097 0.710581 0.000484 0.003561 0.136
    Goy Ira f2: 0.581868 0.584688 0.002820 0.002968 0.950
    Goy Bar f2: 0.546522 0.543375 -0.003146 0.002881 -1.092
    Goy CHG f2: 0.774043 0.774561 0.000518 0.004043 0.128
    Goy Bai f2: 0.590323 0.590957 0.000634 0.003242 0.196
    Goy And f2: 0.968056 0.968998 0.000943 0.004429 0.213
    Xio Bra f2: 0.318870 0.320208 0.001338 0.002320 0.577
    Xio EHG f2: 0.324554 0.326692 0.002138 0.002280 0.938
    Xio Kos f2: 0.653650 0.656654 0.003004 0.003328 0.903
    Xio Sun f2: 0.300740 0.300158 -0.000583 0.002401 -0.243
    Xio Gra f2: 0.509320 0.508456 -0.000865 0.002688 -0.322
    Xio Los f2: 0.307115 0.306368 -0.000747 0.004477 -0.167
    Xio Taf f2: 0.410292 0.408402 -0.001890 0.002598 -0.727
    Xio Ira f2: 0.265125 0.263718 -0.001408 0.001768 -0.796
    Xio Bar f2: 0.253342 0.251816 -0.001525 0.001761 -0.866
    Xio CHG f2: 0.465711 0.463027 -0.002683 0.002647 -1.014
    Xio Bai f2: 0.160782 0.160555 -0.000227 0.001229 -0.185
    Xio And f2: 0.604691 0.607070 0.002380 0.003029 0.786
    Bra EHG f2: 0.355231 0.353469 -0.001763 0.002492 -0.707
    Bra Kos f2: 0.716278 0.719724 0.003446 0.004021 0.857
    Bra Sun f2: 0.363369 0.362550 -0.000819 0.002787 -0.294
    Bra Gra f2: 0.571949 0.567952 -0.003996 0.003305 -1.209
    Bra Los f2: 0.357273 0.360856 0.003584 0.004782 0.749
    Bra Taf f2: 0.479155 0.475803 -0.003352 0.002972 -1.128
    Bra Ira f2: 0.327147 0.327746 0.000599 0.002153 0.278
    Bra Bar f2: 0.314000 0.314683 0.000684 0.002083 0.328
    Bra CHG f2: 0.522059 0.524135 0.002076 0.003025 0.686
    Bra Bai f2: 0.250357 0.251119 0.000762 0.001971 0.387
    Bra And f2: 0.690163 0.688248 -0.001915 0.003482 -0.550
    EHG Kos f2: 0.620925 0.622878 0.001952 0.003492 0.559
    EHG Sun f2: 0.265788 0.263923 -0.001865 0.002242 -0.832
    EHG Gra f2: 0.465329 0.464069 -0.001260 0.002694 -0.468
    EHG Los f2: 0.221420 0.222020 0.000600 0.004364 0.138
    EHG Taf f2: 0.395287 0.395497 0.000210 0.002714 0.078
    EHG Ira f2: 0.237698 0.237909 0.000211 0.001737 0.122
    EHG Bar f2: 0.208081 0.207558 -0.000523 0.001450 -0.360
    EHG CHG f2: 0.426311 0.426556 0.000245 0.002398 0.102
    EHG Bai f2: 0.254641 0.255275 0.000634 0.001883 0.337
    EHG And f2: 0.651415 0.652571 0.001156 0.003060 0.378
    Kos Sun f2: 0.523253 0.525217 0.001964 0.003381 0.581
    Kos Gra f2: 0.746865 0.747747 0.000882 0.004149 0.213
    Kos Los f2: 0.568370 0.570918 0.002548 0.005462 0.467
    Kos Taf f2: 0.710295 0.712489 0.002195 0.003430 0.640
    Kos Ira f2: 0.574080 0.573230 -0.000850 0.002650 -0.321
    Kos Bar f2: 0.539361 0.540338 0.000977 0.002653 0.368
    Kos CHG f2: 0.766207 0.766784 0.000578 0.003644 0.159
    Kos Bai f2: 0.590184 0.592997 0.002813 0.003118 0.902
    Kos And f2: 0.968303 0.980757 0.012454 0.004321 2.882
    Sun Gra f2: 0.369011 0.369709 0.000698 0.002653 0.263
    Sun Los f2: 0.210206 0.211686 0.001481 0.004456 0.332
    Sun Taf f2: 0.355955 0.358600 0.002645 0.002761 0.958
    Sun Ira f2: 0.217709 0.218145 0.000436 0.002021 0.216
    Sun Bar f2: 0.183141 0.182636 -0.000505 0.001889 -0.267
    Sun CHG f2: 0.409622 0.408388 -0.001235 0.002694 -0.458
    Sun Bai f2: 0.237275 0.235048 -0.002227 0.002149 -1.036
    Sun And f2: 0.615393 0.617532 0.002138 0.003187 0.671
    Gra Los f2: 0.397461 0.397565 0.000105 0.004864 0.022
    Gra Taf f2: 0.558732 0.555199 -0.003533 0.003027 -1.167
    Gra Ira f2: 0.424540 0.426489 0.001949 0.002255 0.864
    Gra Bar f2: 0.378285 0.380987 0.002702 0.002066 1.308
    Gra CHG f2: 0.612629 0.615863 0.003234 0.003084 1.049
    Gra Bai f2: 0.445855 0.443865 -0.001989 0.002411 -0.825
    Gra And f2: 0.823973 0.826195 0.002222 0.003758 0.591
    Los Taf f2: 0.355670 0.358047 0.002377 0.004793 0.496
    Los Ira f2: 0.220120 0.218722 -0.001398 0.004216 -0.332
    Los Bar f2: 0.162855 0.163365 0.000511 0.004046 0.126
    Los CHG f2: 0.401773 0.401508 -0.000265 0.004802 -0.055
    Los Bai f2: 0.241133 0.239947 -0.001186 0.004390 -0.270
    Los And f2: 0.626248 0.622023 -0.004225 0.005272 -0.801
    Taf Ira f2: 0.325435 0.326240 0.000806 0.002333 0.345
    Taf Bar f2: 0.281455 0.282413 0.000958 0.002184 0.439
    Taf CHG f2: 0.523146 0.522286 -0.000860 0.002986 -0.288
    Taf Bai f2: 0.348085 0.348856 0.000772 0.002421 0.319
    Taf And f2: 0.726164 0.727479 0.001315 0.003381 0.389
    Ira Bar f2: 0.137129 0.137167 0.000038 0.001076 0.035
    Ira CHG f2: 0.327059 0.327927 0.000868 0.001843 0.471
    Ira Bai f2: 0.201538 0.202740 0.001203 0.001557 0.772
    Ira And f2: 0.583583 0.583782 0.000199 0.002595 0.077
    Bar CHG f2: 0.324444 0.324885 0.000441 0.001914 0.230
    Bar Bai f2: 0.189479 0.191144 0.001665 0.001486 1.120
    Bar And f2: 0.570818 0.573373 0.002555 0.002574 0.993
    CHG Bai f2: 0.400978 0.401637 0.000659 0.002338 0.282
    CHG And f2: 0.785331 0.787376 0.002046 0.003662 0.559
    Bai And f2: 0.545835 0.548306 0.002472 0.002637 0.937


    outliers:
    Fit Obs Diff Std. error Z
    Mbu And Bra Kos -0.019464 -0.026499 -0.007035 0.002314 -3.040
    Mbu And Kos Los 0.002163 0.010277 0.008114 0.002559 3.171
    Ust Bar EHG Gra -0.004840 -0.011003 -0.006163 0.001933 -3.189
    Ust And EHG Kos -0.006017 -0.015047 -0.009031 0.002501 -3.611
    Ust And Kos Los 0.001805 0.011829 0.010024 0.002765 3.626
    Ust And Kos Taf 0.000491 0.008992 0.008501 0.002797 3.039
    Goy Kos Ira And -0.004017 -0.011608 -0.007591 0.002444 -3.105
    Goy Gra Xio Bar 0.012077 0.006468 -0.005609 0.001862 -3.012
    Goy Bar Xio Gra -0.006302 -0.012873 -0.006572 0.002130 -3.085
    Goy Bar Xio Bai 0.000392 -0.003139 -0.003531 0.001104 -3.198
    Goy CHG Xio Gra -0.017289 -0.024706 -0.007417 0.002415 -3.071
    Xio Bai EHG Bar -0.003025 -0.005372 -0.002348 0.000777 -3.023
    Xio Bai Sun Bar 0.000199 -0.002219 -0.002417 0.000774 -3.125
    Bra Kos Ira And -0.015603 -0.023513 -0.007909 0.002258 -3.503
    Bra Kos Bar And -0.026389 -0.033427 -0.007038 0.002278 -3.090
    Bra Ira Gra Los -0.005128 0.000335 0.005463 0.001773 3.082
    Bra Bai Los Taf 0.007466 0.003019 -0.004446 0.001468 -3.029
    Bra And Kos Los -0.008476 -0.000067 0.008408 0.002566 3.276
    Bra And Gra Los -0.008476 -0.001462 0.007013 0.002216 3.165
    EHG Kos Ira And 0.009747 0.003568 -0.006180 0.002025 -3.052
    Kos Gra Ira And -0.002605 0.003911 0.006516 0.002158 3.019
    Kos Los Sun And 0.014504 0.022601 0.008097 0.002695 3.004
    Kos Los Taf And -0.006285 0.002146 0.008430 0.002690 3.134
    Kos Los Ira And -0.005953 0.002113 0.008066 0.002373 3.398
    Kos Los Bar And -0.017226 -0.009120 0.008106 0.002325 3.486
    Kos Ira Ira And -0.094680 -0.088128 0.006553 0.002094 3.130
    Sun Gra Taf Bar 0.003816 -0.000876 -0.004693 0.001316 -3.566
    Sun Gra Taf CHG -0.000115 -0.005438 -0.005323 0.001686 -3.157


    worst f-stat: Ust And Kos Los 0.001805 0.011829 0.010024 0.002765 3.626

    ## end of qpGraph time: 3844.374 seconds memory: 1289.937 Mbytes
    Last edited by Kale; 04-16-2019 at 03:47 AM.
    Collection of 14,000 d-stats: Hidden Content Part 2: Hidden Content Part 3: Hidden Content PM me for d-stats, qpadm, qpgraph, or f3-outgroup nmonte models.

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  3. #2
    There's something strange about the way ANE is placed under the East branch. It looks like it would have existed near Southeast Asia as opposed to Siberia.

  4. #3
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    Sorry, does that mean you think ANE's East-Eurasian ancestry comes from South-East Asia or that the graph suggests that?
    The graph shows ANE's East-Eurasian ancestry sharing drift with XiongNu (basically Han) and Baikal_EN (also, not included, but the ancient Nepal samples and Jomon as well) to the exclusion of Onge, but branching off before XiongNu and Baikal_EN (and ancient Nepal and Jomon) split from each other. Sort of a generalized/undifferentiated East-Asian.

    Some F3 values...
    AG3 Onge.SG Mbuti.DG 0.2288
    AG3 Nepal_ancient Mbuti.DG 0.2365
    AG3 Jomon Mbuti.DG 0.2371
    AG3 XiongNu Mbuti.DG 0.2384

    EHG Onge.SG Mbuti.DG 0.2322
    EHG Nepal_ancient Mbuti.DG 0.2383
    EHG Jomon Mbuti.DG 0.2389
    EHG XiongNu Mbuti.DG 0.2393

    Sunghir Onge.SG Mbuti.DG 0.2284
    Sunghir Nepal_ancient Mbuti.DG 0.2287
    Sunghir Jomon Mbuti.DG 0.2297
    Sunghir XiongNu Mbuti.DG 0.2299
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  6. #4
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    What's the significance of solid lines vs dotted lines in qpGraph? There's only one solid line branch downstream of Eurasia leading to different Wests, with East0 being a near split between West5 and a branch stemming directly from Eurasia, but both those lines are dotted and not solid. Likewise with the 72% path directly from NodeA to IBM.

  7. #5
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    Normandie Wallonia
    Quote Originally Posted by Kale View Post
    Sorry, does that mean you think ANE's East-Eurasian ancestry comes from South-East Asia or that the graph suggests that?
    The graph shows ANE's East-Eurasian ancestry sharing drift with XiongNu (basically Han) and Baikal_EN (also, not included, but the ancient Nepal samples and Jomon as well) to the exclusion of Onge, but branching off before XiongNu and Baikal_EN (and ancient Nepal and Jomon) split from each other. Sort of a generalized/undifferentiated East-Asian.

    Some F3 values...
    AG3 Onge.SG Mbuti.DG 0.2288
    AG3 Nepal_ancient Mbuti.DG 0.2365
    AG3 Jomon Mbuti.DG 0.2371
    AG3 XiongNu Mbuti.DG 0.2384

    EHG Onge.SG Mbuti.DG 0.2322
    EHG Nepal_ancient Mbuti.DG 0.2383
    EHG Jomon Mbuti.DG 0.2389
    EHG XiongNu Mbuti.DG 0.2393

    Sunghir Onge.SG Mbuti.DG 0.2284
    Sunghir Nepal_ancient Mbuti.DG 0.2287
    Sunghir Jomon Mbuti.DG 0.2297
    Sunghir XiongNu Mbuti.DG 0.2299
    I don't understand
    I supposed AG3(an ANE lineage) had got an East Eurasian fraction almost inexisting in EHG and Sunghir. Therefore I waited for a f3 value welll stronger for AG3 than for EHG and Sunghir. Slightly stronger for AG3 compared to Sunghir, but not at all for AG3 and EHG.

  8. #6
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    Quote Originally Posted by TuaMan View Post
    What's the significance of solid lines vs dotted lines in qpGraph? There's only one solid line branch downstream of Eurasia leading to different Wests, with East0 being a near split between West5 and a branch stemming directly from Eurasia, but both those lines are dotted and not solid. Likewise with the 72% path directly from NodeA to IBM.
    Solid means drift (no mixture), dotted means mixture. Notice there are never two solid lines leading to a node/bubble, and never just one dotted line.

    Quote Originally Posted by palamede View Post
    I don't understand
    I supposed AG3(an ANE lineage) had got an East Eurasian fraction almost inexisting in EHG and Sunghir. Therefore I waited for a f3 value welll stronger for AG3 than for EHG and Sunghir. Slightly stronger for AG3 compared to Sunghir, but not at all for AG3 and EHG.
    Those stats were meant to illustrate the differential relationship that Sunghir EHG and AG3 have towards Onge and East-Asians, relative rather than absolute.
    Keeping in mind the std. error for a high snp count F3 is around 0.003, Sunghir's preference for East-Asians over Onge (0.0003 - 0.0015) is effectively nil.
    On the other hand AG3 has high relative preference for East-Asians over Onge (0.0077 - 0.0096).
    AG3's low coverage could explain the lower than expected absolute affinity (I've seen it before in other samples, not sure the technical reason, maybe during genotyping having a lower threshold for what passes to try and get more snps?)
    EHG being intermediate has an intermediate preference (0.0061 - 0.0071) as would be expected.

    EDIT: A question for any passers by who may happen to know the answer...
    Why is the greatest F4 outlier kind of the 'standard' for measuring the success/failure of a graph?
    With any sort of statistical analysis, there is noise/std. error. In this case, the more relationships there are, the more likely there are to be incidents of higher standard deviations just by chance.
    e.x. F4: A B C D with a z-score of 3. This could be the result of B underfit to D, A underfit to C, B overfit to C, or A overfit to D.
    With enough populations in the graph, eventually by chance you could happen upon a situation in which ALL of those conditions are met.
    Hypothetically this could fail a graph even if the individual relations between any two of the four populations are not really that far off.
    I know for a fact this is occurring in one of the other outliers... F4: Sun Gra Taf Bar = -3.566.
    Taforalt is too close to Sunghir and not close enough to Gravettians. Barcin_N is too close to Gravettians and not close enough to Sunghir, see the relevant F2's in the spoiler, the worst of which is only 1.308
     

    Sun Taf f2: 0.355955 0.358600 0.002645 0.002761 0.958
    Sun Bar f2: 0.183141 0.182636 -0.000505 0.001889 -0.267
    Gra Taf f2: 0.558732 0.555199 -0.003533 0.003027 -1.167
    Gra Bar f2: 0.378285 0.380987 0.002702 0.002066 1.308

    Unless I'm missing something the F2's seem more direct and informative.
    Last edited by Kale; Yesterday at 02:21 AM.
    Collection of 14,000 d-stats: Hidden Content Part 2: Hidden Content Part 3: Hidden Content PM me for d-stats, qpadm, qpgraph, or f3-outgroup nmonte models.

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