An attempt at deep West Eurasian phylogeny

[Chad]

Iran N has West Eurasian that is for sure. It cannot be solely ANE because unlike ANE Iran N prefers WHG over every other Upper Paleolithic European just like Anatolian does. Iran N also prefers Neolithic Anatolians over Kotias UP so it is very late. It also prefers Anatolian Neolithic more than Anatolia Epipaleolithic, but this could be Iran Neolithic ancestry in Neolithic Anatolians too. I just think Iran N is a very late genotype and this is also backed up by the fact the Mesolithic samples from the Caspian are more ANE heavy than Zagrosian Neolithic people. I think the genotype formed during the Zarzian but finalized during the Neolithic.
Chimp.REF Georgia_Kotias_UP Italy_Mesolithic.SG Czech_Vestonice16 -0.00357 0.000681 -5.25 0.000000156
Chimp.REF Russia_MA1_HG.SG Italy_Mesolithic.SG Czech_Vestonice16 -0.0000764 0.000716 -0.107 0.915
Chimp.REF Iran_GanjDareh_N Georgia_Kotias_UP Turkey_N 0.00331 0.000435  7.62 2.59e-14
Chimp.REF Iran_GanjDareh_N Georgia_Kotias_UP Turkey_Epipaleolithic 0.00170 0.000535  3.17 0.00150

Also here's Tutkaulian exhibiting it's near pure ANE behavior, I seriously would consider adding it to your graphs to see what happens.
Chimp.REF Russia_Yana_UP.SG Russia_MA1_HG.SG Tajikistan_Tutkaul_N -0.000767 0.000790 -0.971 0.332
Chimp.REF Russia_Sunghir3.SG Russia_MA1_HG.SG Tajikistan_Tutkaul_N -0.000509 0.000849 -0.600 0.548
Chimp.REF China_Tianyuan Russia_MA1_HG.SG Tajikistan_Tutkaul_N -0.000528 0.000880 -0.600 0.549
Afontova Gora seems to work best as a mix of Tutkaulian and Mal'Ta
Chimp.REF Russia_AfontovaGora3 Russia_MA1_HG.SG Tajikistan_Tutkaul_N 0.00199 0.00119  1.66 0.0962
Chimp.REF Russia_MA1_HG.SG Russia_AfontovaGora3 Tajikistan_Tutkaul_N -0.00521 0.00106 -4.91 0.000000910
Chimp.REF Tajikistan_Tutkaul_N Russia_AfontovaGora3 Russia_MA1_HG.SG -0.00719 0.00115 -6.27 3.61e-10
EHG and Yamnaya both prefer Tutkaul over Malta, which could be the CHG related ancestry but also could be linked to their ANE origin.
Chimp.REF Russia_Karelia_HG Russia_MA1_HG.SG Tajikistan_Tutkaul_N 0.00244 0.000863  2.83 0.00467
Chimp.REF Russia_Samara_EBA_Yamnaya Russia_MA1_HG.SG Tajikistan_Tutkaul_N 0.00361 0.000704  5.13 0.000000290
Iran N and Anatolia Neolithic prefer Tutkaulian over Malta, but Anatolia Epipaleolithic and Kotias UP do not, at least not significantly enough.
Chimp.REF Iran_Wezmeh_N.SG Russia_MA1_HG.SG Tajikistan_Tutkaul_N 0.00376 0.000846  4.44 0.00000881
Chimp.REF Turkey_N Russia_MA1_HG.SG Tajikistan_Tutkaul_N 0.00259 0.000658  3.94 0.0000812
Chimp.REF Turkey_Epipaleolithic Russia_MA1_HG.SG Tajikistan_Tutkaul_N 0.000716 0.000871 0.822 0.411
Chimp.REF Georgia_Kotias_UP Russia_MA1_HG.SG Tajikistan_Tutkaul_N 0.00152 0.000949  1.60 0.109

That's because Iranian related ancestry is in whg via its Anatolian ancestry.