Georgian qpAdm: 4-way inconsistency, advice appreciated.

[kingmob]

Georgian (Reich dataset 1240K) is easily modelled with qpAdm:

38.4% Turkey_N + 16.6% Russia_Samara_EBA_Yamnaya + 18.3% Georgia_Kotias.SG + 26.8 Iran_GanjDareh_N.




qpAdm: parameter file: parqpadm.txt
### THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
fstatsname: fstatsa.txt
popleft: left.txt
popright: right.txt
details: YES
## qpAdm version: 1520
seed: 1828706265
*** recommended that inbreed be explicitly set ***
inbreed set NO

left pops:
Georgian.DG
Turkey_N.SG
Russia_Samara_EBA_Yamnaya
Georgia_Kotias.SG
Iran_GanjDareh_N

right pops:
Mbuti.DG
Russia_Ust_Ishim.DG
China_Tianyuan
Goyet_Neanderthal.SG
Russia_Sunghir3.SG
Russia_Kostenki14.SG
Russia_MA1_HG.SG
Georgia_Satsurblia.SG
Russia_DevilsCave_N.SG
Papuan.DG
Switzerland_Bichon.SG
Israel_Natufian_published
Russia_Steppe_Eneolithic
ONG.SG

codimension 1
f4info:
f4rank: 3 dof: 10 chisq: 15.717 tail: 0.108015561 dofdiff: 12 chisqdiff: -15.717 taildiff: 1
B:
scale 1.000 1.000 1.000
Russia_Ust_Ishim.DG 0.422 0.302 -0.015
China_Tianyuan 0.638 0.144 -0.719
Goyet_Neanderthal.SG 0.097 0.103 0.168
Russia_Sunghir3.SG 0.796 0.766 0.891
Russia_Kostenki14.SG 0.671 0.651 0.311
Russia_MA1_HG.SG 1.867 0.566 -1.487
Georgia_Satsurblia.SG 1.227 -2.574 1.441
Russia_DevilsCave_N.SG 0.707 -0.017 -0.195
Papuan.DG 0.459 0.104 -0.559
Switzerland_Bichon.SG 1.387 1.412 0.967
Israel_Natufian_published -0.323 1.690 2.162
Russia_Steppe_Eneolithic 1.823 -0.141 -1.112
ONG.SG 0.519 0.194 -0.278
A:
scale 579.928 641.726 1164.165
Turkey_N.SG -0.385 0.872 0.877
Russia_Samara_EBA_Yamnaya 1.573 0.599 -0.682
Georgia_Kotias.SG 0.730 -1.616 0.859
Iran_GanjDareh_N -0.919 -0.520 -1.424


full rank
f4info:
f4rank: 4 dof: 0 chisq: 0.000 tail: 1 dofdiff: 10 chisqdiff: 15.717 taildiff: 0.108015561
B:
scale 577.372 315.913 351.888 496.479
Russia_Ust_Ishim.DG 0.175 0.521 0.030 -0.348
China_Tianyuan -0.225 0.843 0.137 0.106
Goyet_Neanderthal.SG 0.162 0.100 -0.005 -0.173
Russia_Sunghir3.SG 0.745 0.793 -0.025 -1.407
Russia_Kostenki14.SG 0.686 0.876 0.043 -0.748
Russia_MA1_HG.SG -0.609 2.185 0.189 -0.527
Georgia_Satsurblia.SG -1.751 0.096 3.345 -0.716
Russia_DevilsCave_N.SG -0.419 0.631 0.278 -0.436
Papuan.DG -0.555 0.437 -0.137 -0.287
Switzerland_Bichon.SG 0.883 1.410 -0.442 -2.335
Israel_Natufian_published 2.302 -0.159 -1.021 -1.754
Russia_Steppe_Eneolithic -1.349 1.709 0.646 -0.766
ONG.SG -0.210 0.551 0.009 -0.350
A:
scale 2.000 2.000 2.000 2.000
Turkey_N.SG 2.000 0.000 0.000 0.000
Russia_Samara_EBA_Yamnaya 0.000 2.000 0.000 0.000
Georgia_Kotias.SG 0.000 0.000 2.000 0.000
Iran_GanjDareh_N 0.000 0.000 0.000 2.000


best coefficients: 0.384 0.166 0.183 0.268
totmean: 0.384 0.166 0.183 0.268
boot mean: 0.384 0.165 0.183 0.268
std. errors: 0.034 0.033 0.030 0.049

error covariance (* 1,000,000)
1142 -367 229 -1004
-367 1105 -252 -486
229 -252 917 -893
-1004 -486 -893 2383


summ: Georgian.DG 4 0.108016 0.384 0.165 0.183 0.268 1142 -367 229 -1004 1105 ...
-252 -486 917 -893 2383

fixed pat wt dof chisq tail prob
0000 0 10 15.717 0.108016 0.384 0.166 0.183 0.268
0001 1 11 45.498 3.96519e-06 0.489 0.212 0.299 0.000
0010 1 11 52.596 2.12535e-07 0.347 0.198 0.000 0.455
0100 1 11 40.572 2.85485e-05 0.433 0.000 0.232 0.335
1000 1 11 137.604 5.00013e-24 0.000 0.249 0.078 0.673
0011 2 12 178.506 0 0.618 0.382 0.000 0.000
0101 2 12 81.011 2.64612e-12 0.586 0.000 0.414 0.000
0110 2 12 91.274 2.79687e-14 0.388 0.000 0.000 0.612
1001 2 12 285.747 0 0.000 0.273 0.727 0.000
1010 2 12 141.059 3.66123e-24 0.000 0.261 0.000 0.739
1100 2 12 178.349 0 0.000 0.000 0.114 0.886
0111 3 13 298.987 0 1.000 0.000 0.000 0.000
1011 3 13 500.496 0 0.000 1.000 0.000 0.000
1101 3 13 300.376 0 0.000 0.000 1.000 0.000
1110 3 13 185.022 0 0.000 0.000 0.000 1.000
best pat: 0000 0.108016 - -
best pat: 0100 2.85485e-05 chi(nested): 24.855 p-value for nested model: 6.18192e-07
best pat: 0101 2.64612e-12 chi(nested): 40.439 p-value for nested model: 2.02815e-10
best pat: 1110 1.60033e-32 not nested

coeffs: 0.384 0.166 0.183 0.268

## dscore:: f_4(Base, Fit, Rbase, right2)
## genstat:: f_4(Base, Fit, right1, right2)

details: Turkey_N.SG Russia_Ust_Ishim.DG 0.000302 0.796048
details: Russia_Samara_EBA_Yamnaya Russia_Ust_Ishim.DG 0.001650 4.593210
details: Georgia_Kotias.SG Russia_Ust_Ishim.DG 0.000085 0.165907
details: Iran_GanjDareh_N Russia_Ust_Ishim.DG -0.000701 -1.818194
dscore: Russia_Ust_Ishim.DG f4: 0.000217 Z: 0.696908

details: Turkey_N.SG China_Tianyuan -0.000390 -0.992027
details: Russia_Samara_EBA_Yamnaya China_Tianyuan 0.002669 7.142844
details: Georgia_Kotias.SG China_Tianyuan 0.000389 0.694707
details: Iran_GanjDareh_N China_Tianyuan 0.000213 0.501668
dscore: China_Tianyuan f4: 0.000420 Z: 1.278265

details: Turkey_N.SG Goyet_Neanderthal.SG 0.000280 1.073947
details: Russia_Samara_EBA_Yamnaya Goyet_Neanderthal.SG 0.000318 1.246144
details: Georgia_Kotias.SG Goyet_Neanderthal.SG -0.000014 -0.039833
details: Iran_GanjDareh_N Goyet_Neanderthal.SG -0.000348 -1.175086
dscore: Goyet_Neanderthal.SG f4: 0.000065 Z: 0.297877

details: Turkey_N.SG Russia_Sunghir3.SG 0.001290 2.993695
details: Russia_Samara_EBA_Yamnaya Russia_Sunghir3.SG 0.002511 6.314184
details: Georgia_Kotias.SG Russia_Sunghir3.SG -0.000071 -0.129822
details: Iran_GanjDareh_N Russia_Sunghir3.SG -0.002834 -6.652933
dscore: Russia_Sunghir3.SG f4: 0.000140 Z: 0.414717

details: Turkey_N.SG Russia_Kostenki14.SG 0.001189 2.820787
details: Russia_Samara_EBA_Yamnaya Russia_Kostenki14.SG 0.002773 7.345817
details: Georgia_Kotias.SG Russia_Kostenki14.SG 0.000122 0.215924
details: Iran_GanjDareh_N Russia_Kostenki14.SG -0.001506 -3.447597
dscore: Russia_Kostenki14.SG f4: 0.000535 Z: 1.548392

details: Turkey_N.SG Russia_MA1_HG.SG -0.001055 -2.326802
details: Russia_Samara_EBA_Yamnaya Russia_MA1_HG.SG 0.006916 16.212671
details: Georgia_Kotias.SG Russia_MA1_HG.SG 0.000538 0.864543
details: Iran_GanjDareh_N Russia_MA1_HG.SG -0.001061 -2.263585
dscore: Russia_MA1_HG.SG f4: 0.000555 Z: 1.496394

details: Turkey_N.SG Georgia_Satsurblia.SG -0.003033 -7.163521
details: Russia_Samara_EBA_Yamnaya Georgia_Satsurblia.SG 0.000304 0.777786
details: Georgia_Kotias.SG Georgia_Satsurblia.SG 0.009507 14.201534
details: Iran_GanjDareh_N Georgia_Satsurblia.SG -0.001442 -3.241630
dscore: Georgia_Satsurblia.SG f4: 0.000236 Z: 0.677736

details: Turkey_N.SG Russia_DevilsCave_N.SG -0.000726 -2.065916
details: Russia_Samara_EBA_Yamnaya Russia_DevilsCave_N.SG 0.001998 6.031731
details: Georgia_Kotias.SG Russia_DevilsCave_N.SG 0.000790 1.644829
details: Iran_GanjDareh_N Russia_DevilsCave_N.SG -0.000878 -2.413530
dscore: Russia_DevilsCave_N.SG f4: -0.000039 Z: -0.132276

details: Turkey_N.SG Papuan.DG -0.000962 -2.860010
details: Russia_Samara_EBA_Yamnaya Papuan.DG 0.001384 4.523398
details: Georgia_Kotias.SG Papuan.DG -0.000389 -0.927276
details: Iran_GanjDareh_N Papuan.DG -0.000579 -1.662466
dscore: Papuan.DG f4: -0.000366 Z: -1.329549

details: Turkey_N.SG Switzerland_Bichon.SG 0.001530 3.613412
details: Russia_Samara_EBA_Yamnaya Switzerland_Bichon.SG 0.004464 10.795952
details: Georgia_Kotias.SG Switzerland_Bichon.SG -0.001255 -2.136870
details: Iran_GanjDareh_N Switzerland_Bichon.SG -0.004703 -10.901563
dscore: Switzerland_Bichon.SG f4: -0.000160 Z: -0.456438

details: Turkey_N.SG Israel_Natufian_published 0.003988 8.541429
details: Russia_Samara_EBA_Yamnaya Israel_Natufian_published -0.000504 -1.170499
details: Georgia_Kotias.SG Israel_Natufian_published -0.002900 -4.548156
details: Iran_GanjDareh_N Israel_Natufian_published -0.003532 -7.557682
dscore: Israel_Natufian_published f4: -0.000026 Z: -0.070274

details: Turkey_N.SG Russia_Steppe_Eneolithic -0.002337 -7.015012
details: Russia_Samara_EBA_Yamnaya Russia_Steppe_Eneolithic 0.005409 16.908710
details: Georgia_Kotias.SG Russia_Steppe_Eneolithic 0.001836 3.985277
details: Iran_GanjDareh_N Russia_Steppe_Eneolithic -0.001542 -4.741622
dscore: Russia_Steppe_Eneolithic f4: -0.000079 Z: -0.294754

details: Turkey_N.SG ONG.SG -0.000363 -1.081269
details: Russia_Samara_EBA_Yamnaya ONG.SG 0.001744 5.719163
details: Georgia_Kotias.SG ONG.SG 0.000025 0.060155
details: Iran_GanjDareh_N ONG.SG -0.000706 -2.063323
dscore: ONG.SG f4: -0.000035 Z: -0.129732

gendstat: Mbuti.DG Russia_Ust_Ishim.DG 0.697
gendstat: Mbuti.DG China_Tianyuan 1.278
gendstat: Mbuti.DG Goyet_Neanderthal.SG 0.298
gendstat: Mbuti.DG Russia_Sunghir3.SG 0.415
gendstat: Mbuti.DG Russia_Kostenki14.SG 1.548
gendstat: Mbuti.DG Russia_MA1_HG.SG 1.496
gendstat: Mbuti.DG Georgia_Satsurblia.SG 0.678
gendstat: Mbuti.DG Russia_DevilsCave_N.SG -0.132
gendstat: Mbuti.DG Papuan.DG -1.330
gendstat: Mbuti.DG Switzerland_Bichon.SG -0.456
gendstat: Mbuti.DG Israel_Natufian_published -0.070
gendstat: Mbuti.DG Russia_Steppe_Eneolithic -0.295
gendstat: Mbuti.DG ONG.SG -0.130
gendstat: Russia_Ust_Ishim.DG China_Tianyuan 0.517
gendstat: Russia_Ust_Ishim.DG Goyet_Neanderthal.SG -0.429
gendstat: Russia_Ust_Ishim.DG Russia_Sunghir3.SG -0.202
gendstat: Russia_Ust_Ishim.DG Russia_Kostenki14.SG 0.791
gendstat: Russia_Ust_Ishim.DG Russia_MA1_HG.SG 0.798
gendstat: Russia_Ust_Ishim.DG Georgia_Satsurblia.SG 0.046
gendstat: Russia_Ust_Ishim.DG Russia_DevilsCave_N.SG -0.740
gendstat: Russia_Ust_Ishim.DG Papuan.DG -1.836
gendstat: Russia_Ust_Ishim.DG Switzerland_Bichon.SG -0.949
gendstat: Russia_Ust_Ishim.DG Israel_Natufian_published -0.548
gendstat: Russia_Ust_Ishim.DG Russia_Steppe_Eneolithic -0.858
gendstat: Russia_Ust_Ishim.DG ONG.SG -0.778
gendstat: China_Tianyuan Goyet_Neanderthal.SG -0.939
gendstat: China_Tianyuan Russia_Sunghir3.SG -0.717
gendstat: China_Tianyuan Russia_Kostenki14.SG 0.294
gendstat: China_Tianyuan Russia_MA1_HG.SG 0.326
gendstat: China_Tianyuan Georgia_Satsurblia.SG -0.455
gendstat: China_Tianyuan Russia_DevilsCave_N.SG -1.436
gendstat: China_Tianyuan Papuan.DG -2.421
gendstat: China_Tianyuan Switzerland_Bichon.SG -1.529
gendstat: China_Tianyuan Israel_Natufian_published -1.009
gendstat: China_Tianyuan Russia_Steppe_Eneolithic -1.467
gendstat: China_Tianyuan ONG.SG -1.441
gendstat: Goyet_Neanderthal.SG Russia_Sunghir3.SG 0.192
gendstat: Goyet_Neanderthal.SG Russia_Kostenki14.SG 1.159
gendstat: Goyet_Neanderthal.SG Russia_MA1_HG.SG 1.194
gendstat: Goyet_Neanderthal.SG Georgia_Satsurblia.SG 0.419
gendstat: Goyet_Neanderthal.SG Russia_DevilsCave_N.SG -0.290
gendstat: Goyet_Neanderthal.SG Papuan.DG -1.278
gendstat: Goyet_Neanderthal.SG Switzerland_Bichon.SG -0.549
gendstat: Goyet_Neanderthal.SG Israel_Natufian_published -0.216
gendstat: Goyet_Neanderthal.SG Russia_Steppe_Eneolithic -0.421
gendstat: Goyet_Neanderthal.SG ONG.SG -0.300
gendstat: Russia_Sunghir3.SG Russia_Kostenki14.SG 1.122
gendstat: Russia_Sunghir3.SG Russia_MA1_HG.SG 1.067
gendstat: Russia_Sunghir3.SG Georgia_Satsurblia.SG 0.239
gendstat: Russia_Sunghir3.SG Russia_DevilsCave_N.SG -0.496
gendstat: Russia_Sunghir3.SG Papuan.DG -1.452
gendstat: Russia_Sunghir3.SG Switzerland_Bichon.SG -0.805
gendstat: Russia_Sunghir3.SG Israel_Natufian_published -0.389
gendstat: Russia_Sunghir3.SG Russia_Steppe_Eneolithic -0.667
gendstat: Russia_Sunghir3.SG ONG.SG -0.522
gendstat: Russia_Kostenki14.SG Russia_MA1_HG.SG 0.050
gendstat: Russia_Kostenki14.SG Georgia_Satsurblia.SG -0.743
gendstat: Russia_Kostenki14.SG Russia_DevilsCave_N.SG -1.588
gendstat: Russia_Kostenki14.SG Papuan.DG -2.638
gendstat: Russia_Kostenki14.SG Switzerland_Bichon.SG -1.799
gendstat: Russia_Kostenki14.SG Israel_Natufian_published -1.311
gendstat: Russia_Kostenki14.SG Russia_Steppe_Eneolithic -1.796
gendstat: Russia_Kostenki14.SG ONG.SG -1.673
gendstat: Russia_MA1_HG.SG Georgia_Satsurblia.SG -0.750
gendstat: Russia_MA1_HG.SG Russia_DevilsCave_N.SG -1.548
gendstat: Russia_MA1_HG.SG Papuan.DG -2.445
gendstat: Russia_MA1_HG.SG Switzerland_Bichon.SG -1.761
gendstat: Russia_MA1_HG.SG Israel_Natufian_published -1.281
gendstat: Russia_MA1_HG.SG Russia_Steppe_Eneolithic -1.944
gendstat: Russia_MA1_HG.SG ONG.SG -1.545
gendstat: Georgia_Satsurblia.SG Russia_DevilsCave_N.SG -0.728
gendstat: Georgia_Satsurblia.SG Papuan.DG -1.582
gendstat: Georgia_Satsurblia.SG Switzerland_Bichon.SG -0.932
gendstat: Georgia_Satsurblia.SG Israel_Natufian_published -0.595
gendstat: Georgia_Satsurblia.SG Russia_Steppe_Eneolithic -0.945
gendstat: Georgia_Satsurblia.SG ONG.SG -0.755
gendstat: Russia_DevilsCave_N.SG Papuan.DG -1.215
gendstat: Russia_DevilsCave_N.SG Switzerland_Bichon.SG -0.331
gendstat: Russia_DevilsCave_N.SG Israel_Natufian_published 0.033
gendstat: Russia_DevilsCave_N.SG Russia_Steppe_Eneolithic -0.138
gendstat: Russia_DevilsCave_N.SG ONG.SG 0.014
gendstat: Papuan.DG Switzerland_Bichon.SG 0.576
gendstat: Papuan.DG Israel_Natufian_published 0.855
gendstat: Papuan.DG Russia_Steppe_Eneolithic 0.956
gendstat: Papuan.DG ONG.SG 1.358
gendstat: Switzerland_Bichon.SG Israel_Natufian_published 0.311
gendstat: Switzerland_Bichon.SG Russia_Steppe_Eneolithic 0.244
gendstat: Switzerland_Bichon.SG ONG.SG 0.355
gendstat: Israel_Natufian_published Russia_Steppe_Eneolithic -0.145
gendstat: Israel_Natufian_published ONG.SG -0.024
gendstat: Russia_Steppe_Eneolithic ONG.SG 0.153

##end of qpAdm: 21.334 seconds cpu 1.491 Mbytes in use



The same model with G25:



Target: Georgian_Imer
Distance: 3.0576% / 0.03057601
55.2 GEO_CHG
38.4 TUR_Barcin_N
6.4 IRN_Ganj_Dareh_N


Why such big incosistency? What is the issue here?

[FinalFlash]

Georgian (Reich dataset 1240K) is easily modelled with qpAdm:

38.4% Turkey_N + 16.6% Russia_Samara_EBA_Yamnaya + 18.3% Georgia_Kotias.SG + 26.8 Iran_GanjDareh_N.




qpAdm: parameter file: parqpadm.txt
### THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
fstatsname: fstatsa.txt
popleft: left.txt
popright: right.txt
details: YES
## qpAdm version: 1520
seed: 1828706265
*** recommended that inbreed be explicitly set ***
inbreed set NO

left pops:
Georgian.DG
Turkey_N.SG
Russia_Samara_EBA_Yamnaya
Georgia_Kotias.SG
Iran_GanjDareh_N

right pops:
Mbuti.DG
Russia_Ust_Ishim.DG
China_Tianyuan
Goyet_Neanderthal.SG
Russia_Sunghir3.SG
Russia_Kostenki14.SG
Russia_MA1_HG.SG
Georgia_Satsurblia.SG
Russia_DevilsCave_N.SG
Papuan.DG
Switzerland_Bichon.SG
Israel_Natufian_published
Russia_Steppe_Eneolithic
ONG.SG

codimension 1
f4info:
f4rank: 3 dof: 10 chisq: 15.717 tail: 0.108015561 dofdiff: 12 chisqdiff: -15.717 taildiff: 1
B:
scale 1.000 1.000 1.000
Russia_Ust_Ishim.DG 0.422 0.302 -0.015
China_Tianyuan 0.638 0.144 -0.719
Goyet_Neanderthal.SG 0.097 0.103 0.168
Russia_Sunghir3.SG 0.796 0.766 0.891
Russia_Kostenki14.SG 0.671 0.651 0.311
Russia_MA1_HG.SG 1.867 0.566 -1.487
Georgia_Satsurblia.SG 1.227 -2.574 1.441
Russia_DevilsCave_N.SG 0.707 -0.017 -0.195
Papuan.DG 0.459 0.104 -0.559
Switzerland_Bichon.SG 1.387 1.412 0.967
Israel_Natufian_published -0.323 1.690 2.162
Russia_Steppe_Eneolithic 1.823 -0.141 -1.112
ONG.SG 0.519 0.194 -0.278
A:
scale 579.928 641.726 1164.165
Turkey_N.SG -0.385 0.872 0.877
Russia_Samara_EBA_Yamnaya 1.573 0.599 -0.682
Georgia_Kotias.SG 0.730 -1.616 0.859
Iran_GanjDareh_N -0.919 -0.520 -1.424


full rank
f4info:
f4rank: 4 dof: 0 chisq: 0.000 tail: 1 dofdiff: 10 chisqdiff: 15.717 taildiff: 0.108015561
B:
scale 577.372 315.913 351.888 496.479
Russia_Ust_Ishim.DG 0.175 0.521 0.030 -0.348
China_Tianyuan -0.225 0.843 0.137 0.106
Goyet_Neanderthal.SG 0.162 0.100 -0.005 -0.173
Russia_Sunghir3.SG 0.745 0.793 -0.025 -1.407
Russia_Kostenki14.SG 0.686 0.876 0.043 -0.748
Russia_MA1_HG.SG -0.609 2.185 0.189 -0.527
Georgia_Satsurblia.SG -1.751 0.096 3.345 -0.716
Russia_DevilsCave_N.SG -0.419 0.631 0.278 -0.436
Papuan.DG -0.555 0.437 -0.137 -0.287
Switzerland_Bichon.SG 0.883 1.410 -0.442 -2.335
Israel_Natufian_published 2.302 -0.159 -1.021 -1.754
Russia_Steppe_Eneolithic -1.349 1.709 0.646 -0.766
ONG.SG -0.210 0.551 0.009 -0.350
A:
scale 2.000 2.000 2.000 2.000
Turkey_N.SG 2.000 0.000 0.000 0.000
Russia_Samara_EBA_Yamnaya 0.000 2.000 0.000 0.000
Georgia_Kotias.SG 0.000 0.000 2.000 0.000
Iran_GanjDareh_N 0.000 0.000 0.000 2.000


best coefficients: 0.384 0.166 0.183 0.268
totmean: 0.384 0.166 0.183 0.268
boot mean: 0.384 0.165 0.183 0.268
std. errors: 0.034 0.033 0.030 0.049

error covariance (* 1,000,000)
1142 -367 229 -1004
-367 1105 -252 -486
229 -252 917 -893
-1004 -486 -893 2383


summ: Georgian.DG 4 0.108016 0.384 0.165 0.183 0.268 1142 -367 229 -1004 1105 ...
-252 -486 917 -893 2383

fixed pat wt dof chisq tail prob
0000 0 10 15.717 0.108016 0.384 0.166 0.183 0.268
0001 1 11 45.498 3.96519e-06 0.489 0.212 0.299 0.000
0010 1 11 52.596 2.12535e-07 0.347 0.198 0.000 0.455
0100 1 11 40.572 2.85485e-05 0.433 0.000 0.232 0.335
1000 1 11 137.604 5.00013e-24 0.000 0.249 0.078 0.673
0011 2 12 178.506 0 0.618 0.382 0.000 0.000
0101 2 12 81.011 2.64612e-12 0.586 0.000 0.414 0.000
0110 2 12 91.274 2.79687e-14 0.388 0.000 0.000 0.612
1001 2 12 285.747 0 0.000 0.273 0.727 0.000
1010 2 12 141.059 3.66123e-24 0.000 0.261 0.000 0.739
1100 2 12 178.349 0 0.000 0.000 0.114 0.886
0111 3 13 298.987 0 1.000 0.000 0.000 0.000
1011 3 13 500.496 0 0.000 1.000 0.000 0.000
1101 3 13 300.376 0 0.000 0.000 1.000 0.000
1110 3 13 185.022 0 0.000 0.000 0.000 1.000
best pat: 0000 0.108016 - -
best pat: 0100 2.85485e-05 chi(nested): 24.855 p-value for nested model: 6.18192e-07
best pat: 0101 2.64612e-12 chi(nested): 40.439 p-value for nested model: 2.02815e-10
best pat: 1110 1.60033e-32 not nested

coeffs: 0.384 0.166 0.183 0.268

## dscore:: f_4(Base, Fit, Rbase, right2)
## genstat:: f_4(Base, Fit, right1, right2)

details: Turkey_N.SG Russia_Ust_Ishim.DG 0.000302 0.796048
details: Russia_Samara_EBA_Yamnaya Russia_Ust_Ishim.DG 0.001650 4.593210
details: Georgia_Kotias.SG Russia_Ust_Ishim.DG 0.000085 0.165907
details: Iran_GanjDareh_N Russia_Ust_Ishim.DG -0.000701 -1.818194
dscore: Russia_Ust_Ishim.DG f4: 0.000217 Z: 0.696908

details: Turkey_N.SG China_Tianyuan -0.000390 -0.992027
details: Russia_Samara_EBA_Yamnaya China_Tianyuan 0.002669 7.142844
details: Georgia_Kotias.SG China_Tianyuan 0.000389 0.694707
details: Iran_GanjDareh_N China_Tianyuan 0.000213 0.501668
dscore: China_Tianyuan f4: 0.000420 Z: 1.278265

details: Turkey_N.SG Goyet_Neanderthal.SG 0.000280 1.073947
details: Russia_Samara_EBA_Yamnaya Goyet_Neanderthal.SG 0.000318 1.246144
details: Georgia_Kotias.SG Goyet_Neanderthal.SG -0.000014 -0.039833
details: Iran_GanjDareh_N Goyet_Neanderthal.SG -0.000348 -1.175086
dscore: Goyet_Neanderthal.SG f4: 0.000065 Z: 0.297877

details: Turkey_N.SG Russia_Sunghir3.SG 0.001290 2.993695
details: Russia_Samara_EBA_Yamnaya Russia_Sunghir3.SG 0.002511 6.314184
details: Georgia_Kotias.SG Russia_Sunghir3.SG -0.000071 -0.129822
details: Iran_GanjDareh_N Russia_Sunghir3.SG -0.002834 -6.652933
dscore: Russia_Sunghir3.SG f4: 0.000140 Z: 0.414717

details: Turkey_N.SG Russia_Kostenki14.SG 0.001189 2.820787
details: Russia_Samara_EBA_Yamnaya Russia_Kostenki14.SG 0.002773 7.345817
details: Georgia_Kotias.SG Russia_Kostenki14.SG 0.000122 0.215924
details: Iran_GanjDareh_N Russia_Kostenki14.SG -0.001506 -3.447597
dscore: Russia_Kostenki14.SG f4: 0.000535 Z: 1.548392

details: Turkey_N.SG Russia_MA1_HG.SG -0.001055 -2.326802
details: Russia_Samara_EBA_Yamnaya Russia_MA1_HG.SG 0.006916 16.212671
details: Georgia_Kotias.SG Russia_MA1_HG.SG 0.000538 0.864543
details: Iran_GanjDareh_N Russia_MA1_HG.SG -0.001061 -2.263585
dscore: Russia_MA1_HG.SG f4: 0.000555 Z: 1.496394

details: Turkey_N.SG Georgia_Satsurblia.SG -0.003033 -7.163521
details: Russia_Samara_EBA_Yamnaya Georgia_Satsurblia.SG 0.000304 0.777786
details: Georgia_Kotias.SG Georgia_Satsurblia.SG 0.009507 14.201534
details: Iran_GanjDareh_N Georgia_Satsurblia.SG -0.001442 -3.241630
dscore: Georgia_Satsurblia.SG f4: 0.000236 Z: 0.677736

details: Turkey_N.SG Russia_DevilsCave_N.SG -0.000726 -2.065916
details: Russia_Samara_EBA_Yamnaya Russia_DevilsCave_N.SG 0.001998 6.031731
details: Georgia_Kotias.SG Russia_DevilsCave_N.SG 0.000790 1.644829
details: Iran_GanjDareh_N Russia_DevilsCave_N.SG -0.000878 -2.413530
dscore: Russia_DevilsCave_N.SG f4: -0.000039 Z: -0.132276

details: Turkey_N.SG Papuan.DG -0.000962 -2.860010
details: Russia_Samara_EBA_Yamnaya Papuan.DG 0.001384 4.523398
details: Georgia_Kotias.SG Papuan.DG -0.000389 -0.927276
details: Iran_GanjDareh_N Papuan.DG -0.000579 -1.662466
dscore: Papuan.DG f4: -0.000366 Z: -1.329549

details: Turkey_N.SG Switzerland_Bichon.SG 0.001530 3.613412
details: Russia_Samara_EBA_Yamnaya Switzerland_Bichon.SG 0.004464 10.795952
details: Georgia_Kotias.SG Switzerland_Bichon.SG -0.001255 -2.136870
details: Iran_GanjDareh_N Switzerland_Bichon.SG -0.004703 -10.901563
dscore: Switzerland_Bichon.SG f4: -0.000160 Z: -0.456438

details: Turkey_N.SG Israel_Natufian_published 0.003988 8.541429
details: Russia_Samara_EBA_Yamnaya Israel_Natufian_published -0.000504 -1.170499
details: Georgia_Kotias.SG Israel_Natufian_published -0.002900 -4.548156
details: Iran_GanjDareh_N Israel_Natufian_published -0.003532 -7.557682
dscore: Israel_Natufian_published f4: -0.000026 Z: -0.070274

details: Turkey_N.SG Russia_Steppe_Eneolithic -0.002337 -7.015012
details: Russia_Samara_EBA_Yamnaya Russia_Steppe_Eneolithic 0.005409 16.908710
details: Georgia_Kotias.SG Russia_Steppe_Eneolithic 0.001836 3.985277
details: Iran_GanjDareh_N Russia_Steppe_Eneolithic -0.001542 -4.741622
dscore: Russia_Steppe_Eneolithic f4: -0.000079 Z: -0.294754

details: Turkey_N.SG ONG.SG -0.000363 -1.081269
details: Russia_Samara_EBA_Yamnaya ONG.SG 0.001744 5.719163
details: Georgia_Kotias.SG ONG.SG 0.000025 0.060155
details: Iran_GanjDareh_N ONG.SG -0.000706 -2.063323
dscore: ONG.SG f4: -0.000035 Z: -0.129732

gendstat: Mbuti.DG Russia_Ust_Ishim.DG 0.697
gendstat: Mbuti.DG China_Tianyuan 1.278
gendstat: Mbuti.DG Goyet_Neanderthal.SG 0.298
gendstat: Mbuti.DG Russia_Sunghir3.SG 0.415
gendstat: Mbuti.DG Russia_Kostenki14.SG 1.548
gendstat: Mbuti.DG Russia_MA1_HG.SG 1.496
gendstat: Mbuti.DG Georgia_Satsurblia.SG 0.678
gendstat: Mbuti.DG Russia_DevilsCave_N.SG -0.132
gendstat: Mbuti.DG Papuan.DG -1.330
gendstat: Mbuti.DG Switzerland_Bichon.SG -0.456
gendstat: Mbuti.DG Israel_Natufian_published -0.070
gendstat: Mbuti.DG Russia_Steppe_Eneolithic -0.295
gendstat: Mbuti.DG ONG.SG -0.130
gendstat: Russia_Ust_Ishim.DG China_Tianyuan 0.517
gendstat: Russia_Ust_Ishim.DG Goyet_Neanderthal.SG -0.429
gendstat: Russia_Ust_Ishim.DG Russia_Sunghir3.SG -0.202
gendstat: Russia_Ust_Ishim.DG Russia_Kostenki14.SG 0.791
gendstat: Russia_Ust_Ishim.DG Russia_MA1_HG.SG 0.798
gendstat: Russia_Ust_Ishim.DG Georgia_Satsurblia.SG 0.046
gendstat: Russia_Ust_Ishim.DG Russia_DevilsCave_N.SG -0.740
gendstat: Russia_Ust_Ishim.DG Papuan.DG -1.836
gendstat: Russia_Ust_Ishim.DG Switzerland_Bichon.SG -0.949
gendstat: Russia_Ust_Ishim.DG Israel_Natufian_published -0.548
gendstat: Russia_Ust_Ishim.DG Russia_Steppe_Eneolithic -0.858
gendstat: Russia_Ust_Ishim.DG ONG.SG -0.778
gendstat: China_Tianyuan Goyet_Neanderthal.SG -0.939
gendstat: China_Tianyuan Russia_Sunghir3.SG -0.717
gendstat: China_Tianyuan Russia_Kostenki14.SG 0.294
gendstat: China_Tianyuan Russia_MA1_HG.SG 0.326
gendstat: China_Tianyuan Georgia_Satsurblia.SG -0.455
gendstat: China_Tianyuan Russia_DevilsCave_N.SG -1.436
gendstat: China_Tianyuan Papuan.DG -2.421
gendstat: China_Tianyuan Switzerland_Bichon.SG -1.529
gendstat: China_Tianyuan Israel_Natufian_published -1.009
gendstat: China_Tianyuan Russia_Steppe_Eneolithic -1.467
gendstat: China_Tianyuan ONG.SG -1.441
gendstat: Goyet_Neanderthal.SG Russia_Sunghir3.SG 0.192
gendstat: Goyet_Neanderthal.SG Russia_Kostenki14.SG 1.159
gendstat: Goyet_Neanderthal.SG Russia_MA1_HG.SG 1.194
gendstat: Goyet_Neanderthal.SG Georgia_Satsurblia.SG 0.419
gendstat: Goyet_Neanderthal.SG Russia_DevilsCave_N.SG -0.290
gendstat: Goyet_Neanderthal.SG Papuan.DG -1.278
gendstat: Goyet_Neanderthal.SG Switzerland_Bichon.SG -0.549
gendstat: Goyet_Neanderthal.SG Israel_Natufian_published -0.216
gendstat: Goyet_Neanderthal.SG Russia_Steppe_Eneolithic -0.421
gendstat: Goyet_Neanderthal.SG ONG.SG -0.300
gendstat: Russia_Sunghir3.SG Russia_Kostenki14.SG 1.122
gendstat: Russia_Sunghir3.SG Russia_MA1_HG.SG 1.067
gendstat: Russia_Sunghir3.SG Georgia_Satsurblia.SG 0.239
gendstat: Russia_Sunghir3.SG Russia_DevilsCave_N.SG -0.496
gendstat: Russia_Sunghir3.SG Papuan.DG -1.452
gendstat: Russia_Sunghir3.SG Switzerland_Bichon.SG -0.805
gendstat: Russia_Sunghir3.SG Israel_Natufian_published -0.389
gendstat: Russia_Sunghir3.SG Russia_Steppe_Eneolithic -0.667
gendstat: Russia_Sunghir3.SG ONG.SG -0.522
gendstat: Russia_Kostenki14.SG Russia_MA1_HG.SG 0.050
gendstat: Russia_Kostenki14.SG Georgia_Satsurblia.SG -0.743
gendstat: Russia_Kostenki14.SG Russia_DevilsCave_N.SG -1.588
gendstat: Russia_Kostenki14.SG Papuan.DG -2.638
gendstat: Russia_Kostenki14.SG Switzerland_Bichon.SG -1.799
gendstat: Russia_Kostenki14.SG Israel_Natufian_published -1.311
gendstat: Russia_Kostenki14.SG Russia_Steppe_Eneolithic -1.796
gendstat: Russia_Kostenki14.SG ONG.SG -1.673
gendstat: Russia_MA1_HG.SG Georgia_Satsurblia.SG -0.750
gendstat: Russia_MA1_HG.SG Russia_DevilsCave_N.SG -1.548
gendstat: Russia_MA1_HG.SG Papuan.DG -2.445
gendstat: Russia_MA1_HG.SG Switzerland_Bichon.SG -1.761
gendstat: Russia_MA1_HG.SG Israel_Natufian_published -1.281
gendstat: Russia_MA1_HG.SG Russia_Steppe_Eneolithic -1.944
gendstat: Russia_MA1_HG.SG ONG.SG -1.545
gendstat: Georgia_Satsurblia.SG Russia_DevilsCave_N.SG -0.728
gendstat: Georgia_Satsurblia.SG Papuan.DG -1.582
gendstat: Georgia_Satsurblia.SG Switzerland_Bichon.SG -0.932
gendstat: Georgia_Satsurblia.SG Israel_Natufian_published -0.595
gendstat: Georgia_Satsurblia.SG Russia_Steppe_Eneolithic -0.945
gendstat: Georgia_Satsurblia.SG ONG.SG -0.755
gendstat: Russia_DevilsCave_N.SG Papuan.DG -1.215
gendstat: Russia_DevilsCave_N.SG Switzerland_Bichon.SG -0.331
gendstat: Russia_DevilsCave_N.SG Israel_Natufian_published 0.033
gendstat: Russia_DevilsCave_N.SG Russia_Steppe_Eneolithic -0.138
gendstat: Russia_DevilsCave_N.SG ONG.SG 0.014
gendstat: Papuan.DG Switzerland_Bichon.SG 0.576
gendstat: Papuan.DG Israel_Natufian_published 0.855
gendstat: Papuan.DG Russia_Steppe_Eneolithic 0.956
gendstat: Papuan.DG ONG.SG 1.358
gendstat: Switzerland_Bichon.SG Israel_Natufian_published 0.311
gendstat: Switzerland_Bichon.SG Russia_Steppe_Eneolithic 0.244
gendstat: Switzerland_Bichon.SG ONG.SG 0.355
gendstat: Israel_Natufian_published Russia_Steppe_Eneolithic -0.145
gendstat: Israel_Natufian_published ONG.SG -0.024
gendstat: Russia_Steppe_Eneolithic ONG.SG 0.153

##end of qpAdm: 21.334 seconds cpu 1.491 Mbytes in use



The same model with G25:



Target: Georgian_Imer
Distance: 3.0576% / 0.03057601
55.2 GEO_CHG
38.4 TUR_Barcin_N
6.4 IRN_Ganj_Dareh_N


Why such big incosistency? What is the issue here?

Georgians aren't a monolith. Where is the Georgian from in the qpAdm run?

[kingmob]

Georgians aren't a monolith. Where is the Georgian from in the qpAdm run?


Ι don't know, it's the one in the Reich Dataset 1240K which was probably also used in G25 before user/regional references were added.

However, the inconsistency still remains huge, even if someone also accounts for regional variance.

Armenians also show such inconsistency, although not as big, if you are interested.

[kingmob]

qpAdm Armenian (1240K) 4-way:

44.4% Turkey_N + 6.3% Russia_Samara_EBA_Yamnaya + 4.9% Georgia_Kotias.SG + 44.4% Iran_GanjDareh_N.





qpAdm: parameter file: parqpadm.txt
### THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
fstatsname: fstatsa.txt
popleft: left.txt
popright: right.txt
details: YES
## qpAdm version: 1520
seed: 1832362274
*** recommended that inbreed be explicitly set ***
inbreed set NO

left pops:
Armenian.DG
Turkey_N.SG
Russia_Samara_EBA_Yamnaya
Georgia_Kotias.SG
Iran_GanjDareh_N

right pops:
Mbuti.DG
Russia_Ust_Ishim.DG
China_Tianyuan
Goyet_Neanderthal.SG
Russia_Sunghir3.SG
Russia_Kostenki14.SG
Russia_MA1_HG.SG
Georgia_Satsurblia.SG
Russia_DevilsCave_N.SG
Papuan.DG
Switzerland_Bichon.SG
Israel_Natufian_published
Russia_Steppe_Eneolithic
ONG.SG

codimension 1
f4info:
f4rank: 3 dof: 10 chisq: 15.399 tail: 0.118166287 dofdiff: 12 chisqdiff: -15.399 taildiff: 1
B:
scale 1.000 1.000 1.000
Russia_Ust_Ishim.DG 0.346 0.372 -0.005
China_Tianyuan 0.593 0.286 -0.730
Goyet_Neanderthal.SG 0.091 0.122 0.154
Russia_Sunghir3.SG 0.594 0.944 0.906
Russia_Kostenki14.SG 0.490 0.755 0.336
Russia_MA1_HG.SG 1.694 0.944 -1.462
Georgia_Satsurblia.SG 1.800 -2.212 1.400
Russia_DevilsCave_N.SG 0.695 0.134 -0.195
Papuan.DG 0.393 0.226 -0.555
Switzerland_Bichon.SG 1.105 1.738 0.938
Israel_Natufian_published -0.641 1.496 2.198
Russia_Steppe_Eneolithic 1.831 0.317 -1.129
ONG.SG 0.447 0.298 -0.281
A:
scale 491.448 643.468 1156.039
Turkey_N.SG -0.089 0.743 1.123
Russia_Samara_EBA_Yamnaya 1.515 0.955 -0.480
Georgia_Kotias.SG 1.275 -1.420 1.063
Iran_GanjDareh_N -0.268 -0.721 -1.174


full rank
f4info:
f4rank: 4 dof: 0 chisq: 0.000 tail: 1 dofdiff: 10 chisqdiff: 15.399 taildiff: 0.118166287
B:
scale 664.430 290.594 310.376 532.238
Russia_Ust_Ishim.DG 0.107 0.438 -0.017 -0.448
China_Tianyuan -0.283 0.765 0.110 0.095
Goyet_Neanderthal.SG 0.261 0.125 0.031 -0.125
Russia_Sunghir3.SG 0.866 0.734 -0.018 -1.501
Russia_Kostenki14.SG 0.382 0.628 -0.152 -1.128
Russia_MA1_HG.SG -0.632 2.040 0.199 -0.509
Georgia_Satsurblia.SG -1.276 0.412 3.296 -0.175
Russia_DevilsCave_N.SG -0.266 0.675 0.346 -0.295
Papuan.DG -0.739 0.359 -0.167 -0.388
Switzerland_Bichon.SG 1.790 1.636 -0.028 -1.884
Israel_Natufian_published 2.251 -0.321 -1.086 -2.199
Russia_Steppe_Eneolithic -0.945 1.838 0.854 -0.334
ONG.SG -0.366 0.452 -0.051 -0.476
A:
scale 2.000 2.000 2.000 2.000
Turkey_N.SG 2.000 0.000 0.000 0.000
Russia_Samara_EBA_Yamnaya 0.000 2.000 0.000 0.000
Georgia_Kotias.SG 0.000 0.000 2.000 0.000
Iran_GanjDareh_N 0.000 0.000 0.000 2.000


best coefficients: 0.444 0.063 0.049 0.444
totmean: 0.444 0.063 0.049 0.444
boot mean: 0.444 0.063 0.049 0.444
std. errors: 0.035 0.035 0.032 0.048

error covariance (* 1,000,000)
1240 -492 134 -881
-492 1222 -220 -510
134 -220 1014 -928
-881 -510 -928 2319


summ: Armenian.DG 4 0.118166 0.444 0.063 0.049 0.444 1240 -492 134 -881 1222 ...
-220 -510 1014 -928 2319

fixed pat wt dof chisq tail prob
0000 0 10 15.399 0.118166 0.444 0.063 0.049 0.444
0001 1 11 93.848 2.92653e-15 0.624 0.126 0.249 0.000
0010 1 11 18.280 0.0753076 0.440 0.070 0.000 0.490
0100 1 11 19.081 0.0596492 0.466 0.000 0.064 0.470
1000 1 11 153.219 3.27489e-27 0.000 0.163 -0.097 0.933 infeasible
0011 2 12 169.162 7.08515e-30 0.745 0.255 0.000 0.000
0101 2 12 106.010 3.67102e-17 0.697 0.000 0.303 0.000
0110 2 12 24.664 0.0164998 0.460 0.000 0.000 0.540
1001 2 12 391.185 0 0.000 -0.217 1.217 0.000 infeasible
1010 2 12 158.788 9.27214e-28 0.000 0.141 0.000 0.859
1100 2 12 168.425 1.00225e-29 0.000 0.000 -0.093 1.093 infeasible
0111 3 13 216.189 0 1.000 0.000 0.000 0.000
1011 3 13 657.147 0 0.000 1.000 0.000 0.000
1101 3 13 395.774 0 0.000 0.000 1.000 0.000
1110 3 13 171.156 1.07462e-29 0.000 0.000 0.000 1.000
best pat: 0000 0.118166 - -
best pat: 0010 0.0753076 chi(nested): 2.881 p-value for nested model: 0.0896516
best pat: 0110 0.0164998 chi(nested): 6.384 p-value for nested model: 0.0115176
best pat: 1110 1.07462e-29 chi(nested): 146.492 p-value for nested model: 1.01334e-33

coeffs: 0.444 0.063 0.049 0.444

## dscore:: f_4(Base, Fit, Rbase, right2)
## genstat:: f_4(Base, Fit, right1, right2)

details: Turkey_N.SG Russia_Ust_Ishim.DG 0.000161 0.435561
details: Russia_Samara_EBA_Yamnaya Russia_Ust_Ishim.DG 0.001509 4.071985
details: Georgia_Kotias.SG Russia_Ust_Ishim.DG -0.000056 -0.110802
details: Iran_GanjDareh_N Russia_Ust_Ishim.DG -0.000842 -2.190011
dscore: Russia_Ust_Ishim.DG f4: -0.000209 Z: -0.664783

details: Turkey_N.SG China_Tianyuan -0.000425 -1.021752
details: Russia_Samara_EBA_Yamnaya China_Tianyuan 0.002634 6.795804
details: Georgia_Kotias.SG China_Tianyuan 0.000354 0.639475
details: Iran_GanjDareh_N China_Tianyuan 0.000178 0.426229
dscore: China_Tianyuan f4: 0.000074 Z: 0.211553

details: Turkey_N.SG Goyet_Neanderthal.SG 0.000393 1.454099
details: Russia_Samara_EBA_Yamnaya Goyet_Neanderthal.SG 0.000430 1.651377
details: Georgia_Kotias.SG Goyet_Neanderthal.SG 0.000099 0.269949
details: Iran_GanjDareh_N Goyet_Neanderthal.SG -0.000235 -0.812104
dscore: Goyet_Neanderthal.SG f4: 0.000102 Z: 0.452876

details: Turkey_N.SG Russia_Sunghir3.SG 0.001304 2.819711
details: Russia_Samara_EBA_Yamnaya Russia_Sunghir3.SG 0.002525 6.216838
details: Georgia_Kotias.SG Russia_Sunghir3.SG -0.000057 -0.105292
details: Iran_GanjDareh_N Russia_Sunghir3.SG -0.002820 -6.323039
dscore: Russia_Sunghir3.SG f4: -0.000516 Z: -1.369370

details: Turkey_N.SG Russia_Kostenki14.SG 0.000576 1.355747
details: Russia_Samara_EBA_Yamnaya Russia_Kostenki14.SG 0.002160 5.606173
details: Georgia_Kotias.SG Russia_Kostenki14.SG -0.000491 -0.835894
details: Iran_GanjDareh_N Russia_Kostenki14.SG -0.002119 -4.738923
dscore: Russia_Kostenki14.SG f4: -0.000572 Z: -1.554632

details: Turkey_N.SG Russia_MA1_HG.SG -0.000951 -2.012332
details: Russia_Samara_EBA_Yamnaya Russia_MA1_HG.SG 0.007020 16.020977
details: Georgia_Kotias.SG Russia_MA1_HG.SG 0.000642 1.060553
details: Iran_GanjDareh_N Russia_MA1_HG.SG -0.000957 -1.971142
dscore: Russia_MA1_HG.SG f4: -0.000372 Z: -0.925404

details: Turkey_N.SG Georgia_Satsurblia.SG -0.001921 -4.299080
details: Russia_Samara_EBA_Yamnaya Georgia_Satsurblia.SG 0.001416 3.436008
details: Georgia_Kotias.SG Georgia_Satsurblia.SG 0.010619 15.762360
details: Iran_GanjDareh_N Georgia_Satsurblia.SG -0.000329 -0.710970
dscore: Georgia_Satsurblia.SG f4: -0.000386 Z: -1.015336

details: Turkey_N.SG Russia_DevilsCave_N.SG -0.000401 -1.138777
details: Russia_Samara_EBA_Yamnaya Russia_DevilsCave_N.SG 0.002322 7.227428
details: Georgia_Kotias.SG Russia_DevilsCave_N.SG 0.001115 2.388670
details: Iran_GanjDareh_N Russia_DevilsCave_N.SG -0.000554 -1.480915
dscore: Russia_DevilsCave_N.SG f4: -0.000222 Z: -0.736037

details: Turkey_N.SG Papuan.DG -0.001112 -3.326106
details: Russia_Samara_EBA_Yamnaya Papuan.DG 0.001234 3.989281
details: Georgia_Kotias.SG Papuan.DG -0.000539 -1.272019
details: Iran_GanjDareh_N Papuan.DG -0.000729 -2.156908
dscore: Papuan.DG f4: -0.000765 Z: -2.690050

details: Turkey_N.SG Switzerland_Bichon.SG 0.002694 6.143189
details: Russia_Samara_EBA_Yamnaya Switzerland_Bichon.SG 0.005628 13.359654
details: Georgia_Kotias.SG Switzerland_Bichon.SG -0.000091 -0.153256
details: Iran_GanjDareh_N Switzerland_Bichon.SG -0.003539 -8.243028
dscore: Switzerland_Bichon.SG f4: -0.000023 Z: -0.063306

details: Turkey_N.SG Israel_Natufian_published 0.003388 6.951119
details: Russia_Samara_EBA_Yamnaya Israel_Natufian_published -0.001104 -2.534432
details: Georgia_Kotias.SG Israel_Natufian_published -0.003500 -5.505296
details: Iran_GanjDareh_N Israel_Natufian_published -0.004132 -8.845269
dscore: Israel_Natufian_published f4: -0.000571 Z: -1.468084

details: Turkey_N.SG Russia_Steppe_Eneolithic -0.001423 -4.088226
details: Russia_Samara_EBA_Yamnaya Russia_Steppe_Eneolithic 0.006323 19.620722
details: Georgia_Kotias.SG Russia_Steppe_Eneolithic 0.002751 6.027452
details: Iran_GanjDareh_N Russia_Steppe_Eneolithic -0.000628 -1.758288
dscore: Russia_Steppe_Eneolithic f4: -0.000375 Z: -1.267211

details: Turkey_N.SG ONG.SG -0.000552 -1.677360
details: Russia_Samara_EBA_Yamnaya ONG.SG 0.001556 5.218206
details: Georgia_Kotias.SG ONG.SG -0.000163 -0.382171
details: Iran_GanjDareh_N ONG.SG -0.000894 -2.685632
dscore: ONG.SG f4: -0.000551 Z: -2.025528

gendstat: Mbuti.DG Russia_Ust_Ishim.DG -0.665
gendstat: Mbuti.DG China_Tianyuan 0.212
gendstat: Mbuti.DG Goyet_Neanderthal.SG 0.453
gendstat: Mbuti.DG Russia_Sunghir3.SG -1.369
gendstat: Mbuti.DG Russia_Kostenki14.SG -1.555
gendstat: Mbuti.DG Russia_MA1_HG.SG -0.925
gendstat: Mbuti.DG Georgia_Satsurblia.SG -1.015
gendstat: Mbuti.DG Russia_DevilsCave_N.SG -0.736
gendstat: Mbuti.DG Papuan.DG -2.690
gendstat: Mbuti.DG Switzerland_Bichon.SG -0.063
gendstat: Mbuti.DG Israel_Natufian_published -1.468
gendstat: Mbuti.DG Russia_Steppe_Eneolithic -1.267
gendstat: Mbuti.DG ONG.SG -2.026
gendstat: Russia_Ust_Ishim.DG China_Tianyuan 0.775
gendstat: Russia_Ust_Ishim.DG Goyet_Neanderthal.SG 0.824
gendstat: Russia_Ust_Ishim.DG Russia_Sunghir3.SG -0.786
gendstat: Russia_Ust_Ishim.DG Russia_Kostenki14.SG -0.904
gendstat: Russia_Ust_Ishim.DG Russia_MA1_HG.SG -0.403
gendstat: Russia_Ust_Ishim.DG Georgia_Satsurblia.SG -0.430
gendstat: Russia_Ust_Ishim.DG Russia_DevilsCave_N.SG -0.039
gendstat: Russia_Ust_Ishim.DG Papuan.DG -1.698
gendstat: Russia_Ust_Ishim.DG Switzerland_Bichon.SG 0.487
gendstat: Russia_Ust_Ishim.DG Israel_Natufian_published -0.843
gendstat: Russia_Ust_Ishim.DG Russia_Steppe_Eneolithic -0.506
gendstat: Russia_Ust_Ishim.DG ONG.SG -1.101
gendstat: China_Tianyuan Goyet_Neanderthal.SG 0.070
gendstat: China_Tianyuan Russia_Sunghir3.SG -1.493
gendstat: China_Tianyuan Russia_Kostenki14.SG -1.601
gendstat: China_Tianyuan Russia_MA1_HG.SG -1.080
gendstat: China_Tianyuan Georgia_Satsurblia.SG -1.103
gendstat: China_Tianyuan Russia_DevilsCave_N.SG -0.887
gendstat: China_Tianyuan Papuan.DG -2.605
gendstat: China_Tianyuan Switzerland_Bichon.SG -0.248
gendstat: China_Tianyuan Israel_Natufian_published -1.470
gendstat: China_Tianyuan Russia_Steppe_Eneolithic -1.277
gendstat: China_Tianyuan ONG.SG -1.894
gendstat: Goyet_Neanderthal.SG Russia_Sunghir3.SG -1.471
gendstat: Goyet_Neanderthal.SG Russia_Kostenki14.SG -1.564
gendstat: Goyet_Neanderthal.SG Russia_MA1_HG.SG -1.041
gendstat: Goyet_Neanderthal.SG Georgia_Satsurblia.SG -1.121
gendstat: Goyet_Neanderthal.SG Russia_DevilsCave_N.SG -0.877
gendstat: Goyet_Neanderthal.SG Papuan.DG -2.363
gendstat: Goyet_Neanderthal.SG Switzerland_Bichon.SG -0.295
gendstat: Goyet_Neanderthal.SG Israel_Natufian_published -1.554
gendstat: Goyet_Neanderthal.SG Russia_Steppe_Eneolithic -1.310
gendstat: Goyet_Neanderthal.SG ONG.SG -1.871
gendstat: Russia_Sunghir3.SG Russia_Kostenki14.SG -0.147
gendstat: Russia_Sunghir3.SG Russia_MA1_HG.SG 0.342
gendstat: Russia_Sunghir3.SG Georgia_Satsurblia.SG 0.286
gendstat: Russia_Sunghir3.SG Russia_DevilsCave_N.SG 0.802
gendstat: Russia_Sunghir3.SG Papuan.DG -0.721
gendstat: Russia_Sunghir3.SG Switzerland_Bichon.SG 1.256
gendstat: Russia_Sunghir3.SG Israel_Natufian_published -0.121
gendstat: Russia_Sunghir3.SG Russia_Steppe_Eneolithic 0.382
gendstat: Russia_Sunghir3.SG ONG.SG -0.100
gendstat: Russia_Kostenki14.SG Russia_MA1_HG.SG 0.460
gendstat: Russia_Kostenki14.SG Georgia_Satsurblia.SG 0.432
gendstat: Russia_Kostenki14.SG Russia_DevilsCave_N.SG 0.950
gendstat: Russia_Kostenki14.SG Papuan.DG -0.553
gendstat: Russia_Kostenki14.SG Switzerland_Bichon.SG 1.412
gendstat: Russia_Kostenki14.SG Israel_Natufian_published 0.002
gendstat: Russia_Kostenki14.SG Russia_Steppe_Eneolithic 0.541
gendstat: Russia_Kostenki14.SG ONG.SG 0.060
gendstat: Russia_MA1_HG.SG Georgia_Satsurblia.SG -0.033
gendstat: Russia_MA1_HG.SG Russia_DevilsCave_N.SG 0.387
gendstat: Russia_MA1_HG.SG Papuan.DG -1.039
gendstat: Russia_MA1_HG.SG Switzerland_Bichon.SG 0.821
gendstat: Russia_MA1_HG.SG Israel_Natufian_published -0.417
gendstat: Russia_MA1_HG.SG Russia_Steppe_Eneolithic -0.009
gendstat: Russia_MA1_HG.SG ONG.SG -0.483
gendstat: Georgia_Satsurblia.SG Russia_DevilsCave_N.SG 0.432
gendstat: Georgia_Satsurblia.SG Papuan.DG -1.024
gendstat: Georgia_Satsurblia.SG Switzerland_Bichon.SG 0.848
gendstat: Georgia_Satsurblia.SG Israel_Natufian_published -0.391
gendstat: Georgia_Satsurblia.SG Russia_Steppe_Eneolithic 0.030
gendstat: Georgia_Satsurblia.SG ONG.SG -0.437
gendstat: Russia_DevilsCave_N.SG Papuan.DG -1.997
gendstat: Russia_DevilsCave_N.SG Switzerland_Bichon.SG 0.552
gendstat: Russia_DevilsCave_N.SG Israel_Natufian_published -0.859
gendstat: Russia_DevilsCave_N.SG Russia_Steppe_Eneolithic -0.505
gendstat: Russia_DevilsCave_N.SG ONG.SG -1.199
gendstat: Papuan.DG Switzerland_Bichon.SG 2.107
gendstat: Papuan.DG Israel_Natufian_published 0.484
gendstat: Papuan.DG Russia_Steppe_Eneolithic 1.278
gendstat: Papuan.DG ONG.SG 0.836
gendstat: Switzerland_Bichon.SG Israel_Natufian_published -1.218
gendstat: Switzerland_Bichon.SG Russia_Steppe_Eneolithic -1.017
gendstat: Switzerland_Bichon.SG ONG.SG -1.481
gendstat: Israel_Natufian_published Russia_Steppe_Eneolithic 0.486
gendstat: Israel_Natufian_published ONG.SG 0.050
gendstat: Russia_Steppe_Eneolithic ONG.SG -0.582

##end of qpAdm: 21.727 seconds cpu 1.491 Mbytes in use

[FinalFlash]

Ι don't know, it's the one in the Reich Dataset 1240K which was probably also used in G25 before user/regional references were added.

However, the inconsistency still remains huge, even if someone also accounts for regional variance.

Armenians also show such inconsistency, although not as big, if you are interested.

qpAdm I believe uses more SNPs and is more accurate when determining actual ancestry compared to G25. G25 tends to suffer from calculator effect where you can replace a certain ancient population with a similar ancient population without it affecting fit distances. qpAdm is also the tool of choice for pro geneticists so I'd wager it's probably a better choice.

As for the Georgian run, I think it's possible that it may be a Northeastern Georgian(Tusheti or Khevsur) given the excess Yamnaya. Imeretians score almost none in G25 runs.

You'd be surprised how different Georgians can be. Make some runs on G25 for all subgroups and you'll see.

[Zoro]

Georgian (Reich dataset 1240K) is easily modelled with qpAdm:


Why such big incosistency? What is the issue here?

Congrats on learning to use qpAdm! Looks like you have a pretty solid model. Your standard errors are low at about 3% and p-value is decent at 0.18. Your one to one results show Georgians a little closer to Iran-N than the rest and a little further from Yamnaya than the rest.

As far as your question. G25 or PCA coordinates are hugely affected by which samples he uses. Looks like Davidski finally came out recently and said you shouldn’t take G25 disrances too seriously. You can google all the papers written which talk about PCA coordinates problems.

It also seems that the nMonte program maker also posted the issue with the nMonte program people use with G25 for modeling (below). QpAdm on the other hand isn’t affected by all those issues. That’s why it is used in scientific papers and not G25 PCA !!


January 23, 2022 at 2:15 AM
Blogger huijbregts said...
I was surprised to find Matt yesterday explaining the place of nMonte in genetic history. I was not aware of this all.
Hopefully David will permit me a few supplementary remarks.
I wrote nMonte as an experiment because I was curious whether a simple random walk algorithm could identify relevant groups.
I was pleasantly surprises when it did. Actually it identified a single set of non-unique samples; next it used the naming labels within this set to infer distances to well known predefined groups.
I am still surprised that the simple trick worked so well.
By then (about 2015) I knew next to nothing about mathematical genetics.
By now I better understand the problems with this kind of algorithms.
In the first place there is the problem of overfitting. The ancients division of Global25 contains some five thousand samples. This permits no more 12 binary choices (because 2^12 = 4096).
And if you select a subset, the number is still smaller. So if you use 25 dimensions, you are are heavily overfitting.
Many guys have tried to repair this by by what they call "scaling" the data, but which is really an anti-scaling and does not solve the problem of too many dimensions. It is much better to truncate the dimensions at a much lower value than 25.
In nMonte3 I have limited the damage of overfitting by applying a penalty on larger distances. Unfortunately I also offered the opportunity to switch off this penalizing by using the option pen=0. In spite of my repeated warning not to use this, if you do not perfectly understand what you are doing, many users interpreted this as an opportunity to prove there expert status :(

If I were younger, I might try to improve nMonte by using a Bayesian algorithm.
As it is, I incidentally use nMonte as a quick and dirty simple method.
But mostly I am content with visualizing the data with algorithms like UMAP, which I think is underestimated, especially at this forum.

[kingmob]

qpAdm I believe uses more SNPs and is more accurate when determining actual ancestry compared to G25. G25 tends to suffer from calculator effect where you can replace a certain ancient population with a similar ancient population without it affecting fit distances. qpAdm is also the tool of choice for pro geneticists so I'd wager it's probably a better choice.

As for the Georgian run, I think it's possible that it may be a Northeastern Georgian(Tusheti or Khevsur) given the excess Yamnaya. Imeretians score almost none in G25 runs.

You'd be surprised how different Georgians can be. Make some runs on G25 for all subgroups and you'll see.


https://i.ibb.co/48Ppzh8/Screenshot-2022-02-06-at-14-14-50-Vahaduo-Admixture-JS-21-01.png


It doesn't look like it.


Also, I looked up the Georgian details in the Reich .anno file and it states: Zugdidi in Megrelia.

[kingmob]

Congrats on learning to use qpAdm! Looks like you have a pretty solid model. Your standard errors are low at about 3% and p-value is decent at 0.18. Your one to one results show Georgians a little closer to Iran-N than the rest and a little further from Yamnaya than the rest.

As far as your question. G25 or PCA coordinates are hugely affected by which samples he uses. Looks like Davidski finally came out recently and said you shouldn’t take G25 disrances too seriously. You can google all the papers written which talk about PCA coordinates problems.

It also seems that the nMonte program maker also posted the issue with the nMonte program people use with G25 for modeling (below). QpAdm on the other hand isn’t affected by all those issues. That’s why it is used in scientific papers and not G25 PCA !!



Thank you for the good post, very informative.

A couple of my ponticgreek runs have std. errors of 6.3%ish, I don't seem to be able to be able to bring it down further. What do you think it's a threshold for an acceptable model?

[Zoro]

qpAdm Armenian (1240K) 4-way:

44.4% Turkey_N + 6.3% Russia_Samara_EBA_Yamnaya + 4.9% Georgia_Kotias.SG + 44.4% Iran_GanjDareh_N.


1.491 Mbytes in use[/code][/spoiler]

P-value a little on the lower side at 0.11 but still a pass

You can test if your models are solid by modeling both Georgians and Armenians using

Iran-N
Kotias
ENF
EHG
WHG

for starters with and without WHG or CHG

[Zoro]

Thank you for the good post, very informative.

A couple of my ponticgreek runs have std. errors of 6.3%ish, I don't seem to be able to be able to bring it down further. What do you think it's an acceptable threshold for an acceptable model?

Yeah that’s acceptable. Std errors can be lowered by introducing an outgroup that is more related to some outgroups than others but that may or may not lower your p-value to below passing 0.05

[Sterling Archer]

Thank you for the good post, very informative.

A couple of my ponticgreek runs have std. errors of 6.3%ish, I don't seem to be able to be able to bring it down further. What do you think it's a threshold for an acceptable model?

Sorry for off topic. Does that database have Azerbaijani samples? What do you get when you run them?
I'm interested to see how they differ from G25. Can't use qpAdm unfortunately (are there any good tutorials? :))

[kingmob]

P-value a little on the lower side at 0.11 but still a pass

You can test if your models are solid by modeling both Georgians and Armenians using

Iran-N
Kotias
ENF
EHG
WHG

for starters with and without WHG or CHG


How many populations would you use on left? 4 or more?

And what would you aim for p-value? I thought 0.5 < p-value < 0.05 was enough?

[Petalpusher]

Imo this effect also appears because all three, CHG, Iran and Samara share too much, despite the different proportions, which is ANE and CHG (in itself some Basal mixed with ANE) and Samara has some CHG too and ANE through the EHG. You need to remove at least one of those. The two closest are defo Iran_N and CHG.

[kingmob]

Sorry for off topic. Does that database have Azerbaijani samples? What do you get when you run them?
I'm interested to see how they differ from G25. Can't use qpAdm unfortunately (are there any good tutorials? :))


No modern Azeri in 1240K.

[Zoro]

How many populations would you use on left? 4 or more?

And what would you aim for p-value? I thought 0.5 < p-value < 0.05 was enough?

You have the correct number of outgroups. I would use 8-14. Passing p is considered 0.05 to 1 but higher p means harder to reject model

[Sterling Archer]

No modern Azeri in 1240K.

And ain't that typical :) I took a test through FTDNA and even there Azerbaijan has less tests than Armenia and Georgia. And we are by far the largest group in the region :)
Thanks anyway!

[Zoro]

Sorry for off topic. Does that database have Azerbaijani samples? What do you get when you run them?
I'm interested to see how they differ from G25. Can't use qpAdm unfortunately (are there any good tutorials? :))

IMO Azeris should be similar to Kurds so something like the qpAdm models for Kurds at https://eurasiandna.com/2659-2/

[Sterling Archer]

IMO Azeris should be similar to Kurds so something like the qpAdm models for Kurds at https://eurasiandna.com/2659-2/

Maybe, but there should be differences. Not to mention heterogeneity in the Republic, which we have both seen.

[Human10101]

As far as your question. G25 or PCA coordinates are hugely affected by which samples he uses. Looks like Davidski finally came out recently and said you shouldn’t take G25 disrances too seriously. You can google all the papers written which talk about PCA coordinates problems.


For those interested in learning more about the problems associated with PCA, here is a paper which does an in-depth analysis on PCAs : “Why most Principal Component Analyses (PCA) in population genetic studies are wrong“

https://www.biorxiv.org/content/10.1101/2021.04.11.439381v4.full

[Lemminkäinen]

Low coverage in all tests? If you have distant admixtures in qpAdm you get high chisq and low tail, but still good std errors. Conversely if you get low chisq and high tail you get higher std errors, because admixture groups are relatively close each other.

G25 doesn't give coverage at all.

[Leto]

How much Steppe do North Caucasians such as Chechens and Dagestanis (Avars, Dargins, Laks, Lezgins, Tabasarans) get from that calculation?

[kingmob]

How much Steppe do North Caucasians such as Chechens and Dagestanis (Avars, Dargins, Laks, Lezgins, Tabasarans) get from that calculation?


There is a Chechen.DG and Lezgin.DG in the Reich 1240k file. Unfortunately, the above model for Georgians and Armenians doesn't seem to work for either of them as the tail prob. comes out too low. If anyone has any idea for a working model for those too, I can give it a shot, but I don't have much time to trial and error, atm.