An attempt at deep West Eurasian phylogeny

[Kale]

1) If middle East was just populated by basal eurasians,how do they explain Haplogroups G-M201,H-P69 in middle east?
These are clearly west eurasian Haplogroups and formed around 47,000 BC when GHIJK started to differentiate and west and east eurasians started to split from each other.
These haplogroups aren't found in any UP european sample and so they can't be from there either.

2) Everybody would think that Taforalt had European UP Ancestry from aurignacians,if we didn't have the pinarbasi, natufian and dzudzuana samples.

3) It's clear that WHG isnt just post LGM 'post LGM bottlenecked drifted gravettian'.
Rather it's gravettians that are a mix of something CWE/WHG and aurignacian kind of Ancestry.
(Fu et al modelling)
The F4 runs by norfern ostrobothnia on kotias UP have already shown that,that Kotias Up can't just be gravettian/muierii and have something different,more related to WHG than to gravettians.
And dzudzuana is 5000 years before LGM and 10,000 years before WHG samples in europe and it already has WHG kind of Ancestry,much before.
I think pre LGM UP samples from Aegean/Bulgaria/Balkans will reveal WHGs without the need to model them as bottlenecked gravettians.
WHG/CWE kind of Ancestry arrived much earlier,around 30,000 BC,at this see you start seeing I in vestonice/krems and southern Balkans/aegean from this time will reveal WHGs.

1) 
G = Basal
H-P96 & K1 = East-Eurasian input into Near-East

2) If you look at the graph, I actually have Taforalt with Goyet-related ancestry on top of 'proto-Pinarbasi'. Levantine Aurignacian maybe?

3) Sketch the graph, I'll run it. That is a primary function of this thread.

[Jerome]

The utility of qpGraph is its ability to infer deep histories even with unsampled phases. The fact that you find Dzudzuana (not to mention Kotias UP) “uninformative” is quite odd. 

Anatolia was also uninhabited before the LGM, with no Gravettian sites, , so your “full of I-J” theory doesn’t work.
Pinarbasi ~ 15000 calBP is properly called Epipaleolithic, or post-LGM 

Obviously not true, given that WHG draw much of their ancestry from Vestonice, and there is a clear link of the 2 via Yhg I, mtDNA U5

Uniparentals aren't a source.
It's vestonice that has some WHG/CWE admixture(Fu et al) from where it gets its I and U5, and not WHG that is just vestonice.

If WHG is just vestonice,the wheres the C1a2 in WHG?
Around 40-60% of vestonice samples were C1a2,and had mtdna which wasn't U5,how do do you explain their absence in WHG?

WHGs simply lost all non-U5 and C1a2 from bottlenecking leaving only I and U5?

If you don't force fit WHGs as vestonice/krems on qpGraph then WHGs always tend to take another branch which is sibling to the west eurasian branch of dzudzuana.
Lazaridis and Fu call this branch 'CWE'.
Fu et al modelled krems and vestonice as 40-50% CWE and 50-60% kostenki-like.


It's wrong to reject simple hypothesis and rather focus on theories which make up WHGs as 'post LGM bottlenecked/drifted vestonice' when dzudzuana already has WHG kind of Ancestry much before the LGM and much before WHG samples appear in europe around 16,000 BC.

Dzudzuana is almost contemporary to vestonice samples.

[PopGenist82]

Y'all are trying to trace the phylogeny of Eurasians without any Middle Eastern UP samples (except for the relatively unhelpful Dzudzuana). Seems like an excercise in futility.

The utility of qpGraph is its ability to infer deep histories even with unsampled phases. The fact that you find Dzudzuana (not to mention Kotias UP) “uninformative” is quite odd. 

What makes you think that Anatolia was NOT occupied in the UP by the J's? Or I's? Anatolia seems to have been largely depopulated during the LGM. Pinarbasi might be a purely Mesolithic population with no deeper roots in Anatolia,

Anatolia was also uninhabited before the LGM, with no Gravettian sites, , so your “full of I-J” theory doesn’t work.
Pinarbasi ~ 15000 calBP is properly called Epipaleolithic, or post-LGM 

much like WHG's in most of Europe.

Obviously not true, given that WHG draw much of their ancestry from Vestonice, and there is a clear link of the 2 via Yhg I, mtDNA U5

Uniparentals aren't a source.
It's vestonice that has some WHG/CWE admixture(Fu et al) from where it gets its I and U5, and not WHG that is just vestonice.

If WHG is just vestonice,the wheres the C1a2 in WHG?
Around 40-60% of vestonice samples were C1a2,and had mtdna which wasn't U5,how do do you explain their absence in WHG?

WHGs simply lost all non-U5 and C1a2 from bottlenecking leaving only I and U5?

If you don't force fit WHGs as vestonice/krems on qpGraph then WHGs always tend to take another branch which is sibling to the west eurasian branch of dzudzuana.
Lazaridis and Fu call this branch 'CWE'.
Fu et al modelled krems and vestonice as 40-50% CWE and 50-60% kostenki-like.


It's wrong to reject simple hypothesis and rather focus on theories which make up WHGs as 'post LGM bottlenecked/drifted vestonice' when dzudzuana already has WHG kind of Ancestry much before the LGM and much before WHG samples appear in europe around 16,000 BC.

Dzudzuana is almost contemporary to vestonice samples.

You haven’t managed to make much sense there, so I’ll stick with my explanation.

[Jerome]

What makes you think that Anatolia was NOT occupied in the UP by the J's? Or I's? Anatolia seems to have been largely depopulated during the LGM. Pinarbasi might be a purely Mesolithic population with no deeper roots in Anatolia,

Anatolia was also uninhabited before the LGM, with no Gravettian sites, , so your “full of I-J” theory doesn’t work.
Pinarbasi ~ 15000 calBP is properly called Epipaleolithic, or post-LGM 

Absolutely wrong.
Human inhabitation in anatolia has been from since OOA.


And there's conirmed upper paleolithic human inhabitation in Anatolia predating the LGM


"In Anatolia. Karain B shows one site with human inhabitation dated to 31,000 bp, with bladelet cores, carinated burins and endscrapers, retouched blades and bladelets (Yalçinkaya & Otte 2000).

(Otte etl al 2007 Arguments for Population Movement of Anatomically Modern Humans) "



"Upper Paleolithic cultures have only been observed in the deposits of Karain B and Üçağızlı cave.
Runnels and Özdoğan had pointed out the existence of Aurignacien of the Upper Paleolithic Period in the coastline of the Black Sea (Runnels&Özdoğan 2001). dated in 40.000 and 28.000 BP. The Karain B Upper Paleolithic Industry shows common characteristics with some of the industries in Europe. 

(Taskiran et al 2016)"

[PopGenist82]

What makes you think that Anatolia was NOT occupied in the UP by the J's? Or I's? Anatolia seems to have been largely depopulated during the LGM. Pinarbasi might be a purely Mesolithic population with no deeper roots in Anatolia,

Anatolia was also uninhabited before the LGM, with no Gravettian sites, , so your “full of I-J” theory doesn’t work.
Pinarbasi ~ 15000 calBP is properly called Epipaleolithic, or post-LGM 

Absolutely wrong.
Human inhabitation in anatolia has been from since OOA.


And there's conirmed upper paleolithic human inhabitation in Anatolia predating the LGM


"In Anatolia. Karain B shows one site with human inhabitation dated to 31,000 bp, with bladelet cores, carinated burins and endscrapers, retouched blades and bladelets (Yalçinkaya & Otte 2000).

(Otte etl al 2007 Arguments for Population Movement of Anatomically Modern Humans) "



"Upper Paleolithic cultures have only been observed in the deposits of Karain B and Üçağızlı cave.
Runnels and Özdoğan had pointed out the existence of Aurignacien of the Upper Paleolithic Period in the coastline of the Black Sea (Runnels&Özdoğan 2001). dated in 40.000 and 28.000 BP. The Karain B Upper Paleolithic Industry shows common characteristics with some of the industries in Europe. 

(Taskiran et al 2016)"

The problem is none of those are properly dated or even from secure contexts. They could be back migrations from BK-1653, or they could be Mesolithic for all we know. 
The other issue is you’re obviously unfamiliar with Y phylogeny, which is why you claim it’s irrelevant. The non G2a Anatolian  Y DNA such as I2c and C1a2 is phylogenetically nested within European UP clades, so that doesn’t lend support for Anatolia being a source for I / J lineages, unless we appeal to some unprecedented level of turnover. 

Given that the Gravettian is known to be a periglacial culture of big hame hunters, its absence in Anatolia is hardly surprising. We see same issue in Greece (“ Looking out for the Gravettian in Greece”)- a sparsity of Gravettian sites, and those which do exist are in the northwest.

[Jerome]

What makes you think that Anatolia was NOT occupied in the UP by the J's? Or I's? Anatolia seems to have been largely depopulated during the LGM. Pinarbasi might be a purely Mesolithic population with no deeper roots in Anatolia, much like WHG's in most of Europe.

You are actually pretty right about this.

Almarri et al 2021 showed that natufians and AHG/anatolians split around
18,000 BC using sardinians and levantines/gulf arabs as a proxy.
I am sure same results can be gotten using the Pinarbasi and Natufian throug Globetrotter,etc.


The earlier pre-LGM sites in Anatolia don't show much similarities to the Levant,but after the LGM we see a s sudden change.
New assemblages appear which show affinities and smilarities with the Levantine early epi-paleolithic.
 
I figured out from this that anatolia was depopulated during the LGM and when the LGM ended,it was settled by pre-geometric kebarans from the levant.
 

"Belbaşı industry of central west anatolia shows indications of an early connection to the Kebaran industry assemblages of Palestine."


"At central Anatolia Pınarbaşı exavations here yielded a geometric microlithic assemblage with technological features comparable to Early Natufian and  industries, offering sig- nificant insights into Late Pleistocene forager lifeways on the Anatolian Plateau from ca. 15,000–12,000 CAL B.C. (Baird 2012)"

-Cilingrioglu et al 2021

Whem I stumbled on these studies I took it as a clear Indication that Anatolia was repopulated after the LGM from Levant

[Jerome]

Btw,Kamm et al 2018 showed that the Basal Eurasian Ancestry mixed with west eurasian to create Anatolian_HG/Natufian Ancestry around 32,000 BC.

This predates the dzudzuana/Kotias_UP samples by 7000 years and also predates the gravettian by 1000-2000 years.

And we do know that WHG has some deep special relationship with AHG/Natufians,which other west eurasians don't have.
I think this gives a light that WHG/CWE has deep roots in west asia,even older than dzudzuana.

Samples from Karain B site will clear up everything though Turkish archaeogenetics field is a bit slow so it would take time.
I hope that Reich lab is holding something about this and will release it into the near future...

[Kale]

I'm determined to give the WHG/CWE model a concerted effort, but I need to know what exactly the perception of CWE is in relation to WHG. I guess to start, does WHG = 100% CWE, or is WHG considered/allowed to be mixed in any way at all?

[PopGenist82]

I'm determined to give the WHG/CWE model a concerted effort, but I need to know what exactly the perception of CWE is in relation to WHG. I guess to start, does WHG = 100% CWE, or is WHG considered/allowed to be mixed in any way at all?

What do you mean by ”CWE model” ?

[TanTin]

I'm determined to give the WHG/CWE model a concerted effort, but I need to know what exactly the perception of CWE is in relation to WHG. I guess to start, does WHG = 100% CWE, or is WHG considered/allowed to be mixed in any way at all?

Common West Eurasian (CWE)
It seems CWE was introduced by Lazaridis back in 2018.
"Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry"

According to this model, a common population contributed ancestry to Gravettians (represented by Vestonice16) and to a “Common West Eurasian” population that contributed all the ancestry of Villabruna and most of the ancestry of Dzudzuana which also had 28.4±4.2% Basal Eurasian ancestry21 (Supplementary Information section 2).

[Norfern-Ostrobothnian]

I'm determined to give the WHG/CWE model a concerted effort, but I need to know what exactly the perception of CWE is in relation to WHG. I guess to start, does WHG = 100% CWE, or is WHG considered/allowed to be mixed in any way at all?

I think you should treat CWE as the West Eurasian side of Kotias UP and Dzudzuana. They show no affinity for any UP Europeans aside from a slight affinity for Pestera Muierii and Gravettians. So I suggest the following:
Make a CWE edge that branches off before, ANE, GoyetQ116-1, BK1653 and Kostenki-Sunghir does. Then let Gravettians and Pestera Muierii contribute to the west Eurasian in Dzudzuana. Let the edge contribute to WHG and compensate for affinities through admixtures, while giving Dzudzuana a Basal Eurasian edge instead. An alternative is to forgo the Basal Eurasian edge entirely, which seems possible but is contradicted by some fstats. 

What bothers me the most is the fact that Dzudzuana is equally related to Pinarbasi and WHG. I think giving a later edge from CWE that is more related to WHG pre admixture to Dzudzuana and then letting actual WHG contribute to Pinarbasi would work out for this stat. However, if you have any other solutions feel free to test them out. 

Also look into the possibility of Malta1 having some relationship with Dzudzuana/EEF. They seem to have something that Yana doesn't. And for good measure try and fit TTK1 and AfontovaGora3 in too, those two have a lot of affinity for EEF for some reason as well, could be bidirectional geneflow for all I know.

[PopGenist82]

I'm determined to give the WHG/CWE model a concerted effort, but I need to know what exactly the perception of CWE is in relation to WHG. I guess to start, does WHG = 100% CWE, or is WHG considered/allowed to be mixed in any way at all?

Common West Eurasian (CWE)
It seems CWE was introduced by Lazaridis back in 2018.
"Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry"

According to this model, a common population contributed ancestry to Gravettians (represented by Vestonice16) and to a “Common West Eurasian” population that contributed all the ancestry of Villabruna and most of the ancestry of Dzudzuana which also had 28.4±4.2% Basal Eurasian ancestry21 (Supplementary Information section 2).

 

I can’t see this model as accurate, as Goyet-Q116 has pseudo-east Asian/ BK affinities
It’s also not historically plausible as uniparentals and archaeology documents at least 2 or more UP waves into Europe instead of a monolithic dispersal.

[Kale]

I'm determined to give the WHG/CWE model a concerted effort, but I need to know what exactly the perception of CWE is in relation to WHG. I guess to start, does WHG = 100% CWE, or is WHG considered/allowed to be mixed in any way at all?

1) I think you should treat CWE as the West Eurasian side of Kotias UP and Dzudzuana. They show no affinity for any UP Europeans aside from a slight affinity for Pestera Muierii and Gravettians. So I suggest the following:
2) Make a CWE edge that branches off before, ANE, GoyetQ116-1, BK1653 and Kostenki-Sunghir does. Then let Gravettians and Pestera Muierii contribute to the west Eurasian in Dzudzuana. Let the edge contribute to WHG and compensate for affinities through admixtures, while giving Dzudzuana a Basal Eurasian edge instead. An alternative is to forgo the Basal Eurasian edge entirely, which seems possible but is contradicted by some fstats. 

3) What bothers me the most is the fact that Dzudzuana is equally related to Pinarbasi and WHG. I think giving a later edge from CWE that is more related to WHG pre admixture to Dzudzuana and then letting actual WHG contribute to Pinarbasi would work out for this stat. However, if you have any other solutions feel free to test them out. 

4) Also look into the possibility of Malta1 having some relationship with Dzudzuana/EEF. They seem to have something that Yana doesn't. And for good measure try and fit TTK1 and AfontovaGora3 in too, those two have a lot of affinity for EEF for some reason as well, could be bidirectional geneflow for all I know.

1) In the current graph the affinity of Georgia_UP to Gravettians is mediated by a geneflow from Muierii > BK1653 > Gravettians.

2) So to make sure I'm understanding you right...
Georgia_UP = Muierii (and maybe Gravettian) + CWE + Basal
WHG = CWE, but are you saying WHG is to receive admixtures to compensate or give them?

3) That is the least of the problems, all we'd need is to have Pinarbasi and Georgia_UP be the same product of a 'WHG-ish' line and Basal, then diverged shortly enough after that to not to accrue too much drift with each other.

4) Yana has a little extra Tianyuan which pulls them slightly away from all West Eurasians relative to MA1. AG3 is really close to the extant ANE line, and forget not EEF does have actual ANE via Iran_N and (if you'd like) WHG. TTK has ~25% Iran_N ancestry which pulls it towards the Near East.

The biggest problem I see with trying to model WHG as unmixed is WHG are more related to East-Asians than to Ust-Ishim whilst paleo-Europeans are not.

Show Content

Spoiler
1 Congo_Mbuti.DG Sunghir.SG                  Ust_Ishim.DG Jomon.SG                      0.000653658  0.000505231  1.29378  0.195741  1146798
2 Congo_Mbuti.DG Sunghir.SG                  Ust_Ishim.DG RUS_Primorsky_DevilsCave_N.SG  0.000329417  0.000513573  0.641422 0.521249  1146527
3 Congo_Mbuti.DG Muierii1                    Ust_Ishim.DG Jomon.SG                      -0.000298181  0.000634969 -0.469600 0.638641  1145964
4 Congo_Mbuti.DG Muierii1                    Ust_Ishim.DG RUS_Primorsky_DevilsCave_N.SG -0.000236223  0.000631803 -0.373887 0.708488  1145718
5 Congo_Mbuti.DG Gravettian_KremsVestonice    Ust_Ishim.DG Jomon.SG                      0.0000617202 0.000534533  0.115466 0.908076  1028506
6 Congo_Mbuti.DG Gravettian_KremsVestonice    Ust_Ishim.DG RUS_Primorsky_DevilsCave_N.SG  0.000210763  0.000540606  0.389865 0.696637  1028300
7 Congo_Mbuti.DG GoyetQ116_1                  Ust_Ishim.DG Jomon.SG                      0.000193737  0.000725384  0.267083 0.789406    763445
8 Congo_Mbuti.DG GoyetQ116_1                  Ust_Ishim.DG RUS_Primorsky_DevilsCave_N.SG -0.000604925  0.000687789 -0.879521 0.379119    763343
9 Congo_Mbuti.DG Italy_AreneCandide_HG        Ust_Ishim.DG Jomon.SG                      0.00202123  0.000639478  3.16075  0.00157362  828736
10 Congo_Mbuti.DG Italy_AreneCandide_HG        Ust_Ishim.DG RUS_Primorsky_DevilsCave_N.SG  0.00193012  0.000631330  3.05723  0.00223396  828569
11 Congo_Mbuti.DG Italy_GrottaContinenza_HG.SG Ust_Ishim.DG Jomon.SG                      0.00170467  0.000594608  2.86688  0.00414544 1138149
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1 Congo_Mbuti.DG Jomon.SG                      Sunghir.SG                Italy_AreneCandide_HG        0.000789996  0.000473427  1.66868  0.0951817    830426
2 Congo_Mbuti.DG Jomon.SG                      Sunghir.SG                Italy_GrottaContinenza_HG.SG  0.00115690  0.000400604  2.88790  0.00387828  1140526
3 Congo_Mbuti.DG Jomon.SG                      Muierii1                  Italy_AreneCandide_HG        0.00124816  0.000562626  2.21846  0.0265237    829874
4 Congo_Mbuti.DG Jomon.SG                      Muierii1                  Italy_GrottaContinenza_HG.SG  0.00156549  0.000488518  3.20457  0.00135266  1139781
5 Congo_Mbuti.DG Jomon.SG                      Gravettian_KremsVestonice Italy_AreneCandide_HG        0.00100986  0.000483733  2.08765  0.0368298    783111
6 Congo_Mbuti.DG Jomon.SG                      Gravettian_KremsVestonice Italy_GrottaContinenza_HG.SG  0.00121981  0.000392316  3.10925  0.00187563  1023025
7 Congo_Mbuti.DG Jomon.SG                      GoyetQ116_1              Italy_AreneCandide_HG        -0.000907888  0.000595058 -1.52571  0.127081    614206
8 Congo_Mbuti.DG Jomon.SG                      GoyetQ116_1              Italy_GrottaContinenza_HG.SG -0.000490716  0.000560660 -0.875247 0.381439    759741
9 Congo_Mbuti.DG RUS_Primorsky_DevilsCave_N.SG Sunghir.SG                Italy_AreneCandide_HG        0.00103801  0.000450330  2.30499  0.0211669    830262
10 Congo_Mbuti.DG RUS_Primorsky_DevilsCave_N.SG Sunghir.SG                Italy_GrottaContinenza_HG.SG  0.00131303  0.000398223  3.29722  0.000976484 1140302
11 Congo_Mbuti.DG RUS_Primorsky_DevilsCave_N.SG Muierii1                  Italy_AreneCandide_HG        0.00118815  0.000548736  2.16526  0.0303679    829719
12 Congo_Mbuti.DG RUS_Primorsky_DevilsCave_N.SG Muierii1                  Italy_GrottaContinenza_HG.SG  0.00142919  0.000483509  2.95586  0.00311798  1139575
13 Congo_Mbuti.DG RUS_Primorsky_DevilsCave_N.SG Gravettian_KremsVestonice Italy_AreneCandide_HG        0.000650354  0.000457142  1.42265  0.154837    782955
14 Congo_Mbuti.DG RUS_Primorsky_DevilsCave_N.SG Gravettian_KremsVestonice Italy_GrottaContinenza_HG.SG  0.000881678  0.000384966  2.29027  0.0220055  1022857
15 Congo_Mbuti.DG RUS_Primorsky_DevilsCave_N.SG GoyetQ116_1              Italy_AreneCandide_HG        0.0000758159 0.000577775  0.131220 0.895601    614128
16 Congo_Mbuti.DG RUS_Primorsky_DevilsCave_N.SG GoyetQ116_1              Italy_GrottaContinenza_HG.SG  0.000264391  0.000538274  0.491183 0.623297    759659
17 Congo_Mbuti.DG Ust_Ishim.DG                  Sunghir.SG                Italy_AreneCandide_HG        -0.000395833  0.000545114 -0.726147 0.467749    828747
18 Congo_Mbuti.DG Ust_Ishim.DG                  Sunghir.SG                Italy_GrottaContinenza_HG.SG  0.000128569  0.000472953  0.271844 0.785742    1138161
19 Congo_Mbuti.DG Ust_Ishim.DG                  Muierii1                  Italy_AreneCandide_HG        -0.000936378  0.000645183 -1.45134  0.146686    828192
20 Congo_Mbuti.DG Ust_Ishim.DG                  Muierii1                  Italy_GrottaContinenza_HG.SG -0.000376910  0.000567782 -0.663829 0.506800    1137414
21 Congo_Mbuti.DG Ust_Ishim.DG                  Gravettian_KremsVestonice Italy_AreneCandide_HG        -0.000865684  0.000529302 -1.63552  0.101941    781484
22 Congo_Mbuti.DG Ust_Ishim.DG                  Gravettian_KremsVestonice Italy_GrottaContinenza_HG.SG -0.000366342  0.000439393 -0.833745 0.404425    1020820
23 Congo_Mbuti.DG Ust_Ishim.DG                  GoyetQ116_1              Italy_AreneCandide_HG        -0.00215897  0.000720888 -2.99487  0.00274562  612812
24 Congo_Mbuti.DG Ust_Ishim.DG                  GoyetQ116_1              Italy_GrottaContinenza_HG.SG -0.00166473  0.000642301 -2.59183  0.00954681  757939

Then you have a problem tree that descends from that.
 A) Are WHG mixed with East Asians?
     1) Yes
         A) Directly? If so how?
         B) Indirectly (the OP graph uses a bit of option 1 and 2)
             1) Via ANE?
                A) Why is ANE slightly less related to WHG than to Paleo-Euros, and why are paleo-Euros more related to WHG than to ANE? 
             2) Via Near East (think Iran_N)
     2) No, how to account for the affinity?

[Norfern-Ostrobothnian]

1) I don't think that is enough considering Georgia_UP prefers Pestera Muierii over Bacho Kiro MUP
2) Georgia_UP = CWE+Basal+Muierii+Gravettian
WHG = CWE+ANE+Gravettian+BK1653 is what has worked for me quite well, but the amount of ANE they receive is surprisingly low usually. Some Aurignacian might work too.
3) Sure
4) That doesn't seem to be true. Tutkaulian forms a near perferct clade with AG3 against all populations except Malta1 and Iran Neolithic. I think the PCA position is simply compensating for the affinity they have with the Basal Eurasian heavy Iran Neolithic population.
1 Chimp.REF Iran_GanjDareh_N Tajikistan_Tutkaul_N Russia_AfontovaGora3 -0.00183 0.000755 -2.43 0.0151
2 Chimp.REF Georgia_Kotias.SG Tajikistan_Tutkaul_N Russia_AfontovaGora3 -0.00139 0.000934 -1.48 0.138
3 Chimp.REF Romania_PesteraMuierii_EUP Tajikistan_Tutkaul_N Russia_AfontovaGora3 0.00112 0.000901 1.24 0.215
4 Chimp.REF Russia_Kostenki14.SG Tajikistan_Tutkaul_N Russia_AfontovaGora3 -0.0000423 0.000885 -0.0478 0.962
5 Chimp.REF Russia_Sunghir3.SG Tajikistan_Tutkaul_N Russia_AfontovaGora3 0.000807 0.000946 0.853 0.394
6 Chimp.REF Turkey_N Tajikistan_Tutkaul_N Russia_AfontovaGora3 -0.000950 0.000725 -1.31 0.190
7 Chimp.REF Turkey_Epipaleolithic Tajikistan_Tutkaul_N Russia_AfontovaGora3 0.000229 0.000925 0.248 0.804
8 Chimp.REF Russia_Yana_UP.SG Tajikistan_Tutkaul_N Russia_AfontovaGora3 0.000105 0.000807 0.130 0.897
9 Chimp.REF Russia_MA1_HG.SG Tajikistan_Tutkaul_N Russia_AfontovaGora3 0.00521 0.00106 4.91 0.000000910
10 Chimp.REF China_Tianyuan Tajikistan_Tutkaul_N Russia_AfontovaGora3 0.000445 0.000925 0.481 0.630
11 Chimp.REF Czechia_Bohemia_UP_HG Tajikistan_Tutkaul_N Russia_AfontovaGora3 -0.00131 0.000915 -1.43 0.153

As for the latter part
ANE, and specifically Yana is less related because WHG is predominantly descending from CWE which splits off before ANE's West Eurasian side does, whatever this may be.
They seem to have some weird affinities for GoyetQ116-1 and Fournoul, but don't seem to prefer Muierii or Sunghir. However, a slight pull toward Kostenki exists and they all seem to harbor a connection with some Gravettians.
Iran_N is too late of a mixture I think, it is essentially just very late ANE, specifically related to TTK, ANF and Basal Eurasian/Zagrosian.
Besides Anatolians are in the way and so is CHG, not to mention EHG.

Also, I think Zlaty Kun might be paraphyletic to Basal Eurasian

1 Chimp.REF China_YR_LN Turkey_N Iran_Wezmeh_N.SG -0.000611 0.000398 -1.54 0.125
2 Chimp.REF China_Tianyuan Turkey_N Iran_Wezmeh_N.SG -0.000929 0.000478 -1.94 0.0520
3 Chimp.REF Czechia_Bohemia_UP_HG Turkey_N Iran_Wezmeh_N.SG 0.000360 0.000478 0.752 0.452
4 Chimp.REF Russia_Ust_Ishim_HG.DG Turkey_N Iran_Wezmeh_N.SG -0.00110 0.000475 -2.31 0.0209
5 Chimp.REF Bulgaria_BachoKiro_LatePleistocene Turkey_N Iran_Wezmeh_N.SG -0.00103 0.000398 -2.59 0.00947

[Kale]

I think damage/noise quality issues are greatly underappreciated in aDNA, the most common effect being dampening affinities across the board, and that both BK1653 and AG3 suffer from this.

In F4 stats Tarim_EMBA1 shows a similar pattern to Tutkaul, but Tarim has a huge surplus of Northeast Asian ENA (~20%), so why isn't it's affinity to Yana and other West Eurasians dampened relative to AG3?
1 Chimp.REF Iran_GanjDareh_N Tarim_EMBA1 AG3 -0.000960558 0.000518937 -1.85101 6.41678e-2 250594
2 Chimp.REF CHG.SG Tarim_EMBA1 AG3 -0.000887562 0.000564142 -1.57330 1.15650e-1 253442
3 Chimp.REF Muierii1 Tarim_EMBA1 AG3 -0.0000883525 0.000650566 -0.135809 8.91973e-1 253330
4 Chimp.REF Kostenki14.SG Tarim_EMBA1 AG3 -0.000804984 0.000655654 -1.22776 2.19538e-1 238665
5 Chimp.REF Sunghir.SG Tarim_EMBA1 AG3 -0.000416471 0.000540782 -0.770128 4.41224e-1 253504
6 Chimp.REF Anatolia_Barcin_N Tarim_EMBA1 AG3 -0.000787757 0.000501720 -1.57011 1.16389e-1 253495
7 Chimp.REF Anatolia_Epipaleolithic Tarim_EMBA1 AG3 -0.000451219 0.000659449 -0.684237 4.93826e-1 214690
8 Chimp.REF Yana_UP.SG Tarim_EMBA1 AG3 -0.000534715 0.000558463 -0.957478 3.38326e-1 253496
9 Chimp.REF MA1.SG Tarim_EMBA1 AG3 0.00292411 0.000799371 3.65802 2.54170e-4 185393
10 Chimp.REF China_UP Tarim_EMBA1 AG3 -0.00272282 0.000582481 -4.67453 2.94628e-6 250395
11 Chimp.REF ZlatyKun.SG Tarim_EMBA1 AG3 -0.00186521 0.000641267 -2.90864 3.63008e-3 251231

Also direct comparison between Tutkaul and Tarim
1 Chimp.REF Iran_GanjDareh_N Tarim_EMBA1 Tajikistan_Tutkaul_N 0.00257993 0.000534724 4.82480 1.40147e-6 214731
2 Chimp.REF CHG.SG Tarim_EMBA1 Tajikistan_Tutkaul_N 0.00243433 0.000636191 3.82642 1.30021e-4 218520
3 Chimp.REF Muierii1 Tarim_EMBA1 Tajikistan_Tutkaul_N 0.000798176 0.000633468 1.26001 2.07666e-1 218410
4 Chimp.REF Kostenki14.SG Tarim_EMBA1 Tajikistan_Tutkaul_N 0.00110063 0.000687103 1.60185 1.09190e-1 204753
5 Chimp.REF Sunghir.SG Tarim_EMBA1 Tajikistan_Tutkaul_N 0.000376060 0.000557097 0.675036 4.99653e-1 218558
6 Chimp.REF Anatolia_Barcin_N Tarim_EMBA1 Tajikistan_Tutkaul_N 0.00172296 0.000502070 3.43172 5.99772e-4 218462
7 Chimp.REF Anatolia_Epipaleolithic Tarim_EMBA1 Tajikistan_Tutkaul_N 0.000752320 0.000665427 1.13058 2.58231e-1 183692
8 Chimp.REF Yana_UP.SG Tarim_EMBA1 Tajikistan_Tutkaul_N -0.000182068 0.000578292 -0.314837 7.52885e-1 218553
9 Chimp.REF MA1.SG Tarim_EMBA1 Tajikistan_Tutkaul_N -0.00131569 0.000744083 -1.76820 7.70274e-2 158385
10 Chimp.REF China_UP Tarim_EMBA1 Tajikistan_Tutkaul_N -0.00130099 0.000592188 -2.19691 2.80267e-2 212051
11 Chimp.REF ZlatyKun.SG Tarim_EMBA1 Tajikistan_Tutkaul_N 0.000101988 0.000660986 0.154297 8.77375e-1 216602

Also qpadm
Tajikistan_Tutkaul_N
AG3 0.697467 0.0317748 21.9503
Iran_GanjDareh_N 0.255216 0.0336011 7.59547
Andaman_100BP.SG 0.0473169 0.0297302 1.59154
Tail: 0.23
right = c('Chimp.REF', 'ZlatyKun.SG', 'Ust_Ishim.DG', 'BachoKiro_IUP', 'China_UP', 'Kostenki14', 'Muierii1', 'GoyetQ116_1', 'Sunghir.SG', 'BachoKiro_BK1653', 'Gravettian_KremsVestonice', 'Yana_UP.SG', 'MA1.SG', 'Italy_GrottaContinenza_HG.SG', 'Papuan.DG', 'Jomon.SG', 'RUS_Primorsky_DevilsCave_N.SG', 'Peru_RioUncallane_1800BP.SG', 'Iran_Wezmeh_N.SG', 'CHG.SG', 'Anatolia_Epipaleolithic')
allsnps=TRUE

If pressed I'm sure I could dig up some examples of something really uncontroversial, like EEF samples from the same or nearby sites or Native American samples with some showing 'dampening damage' compared to others.
EDIT: Here's an example.
1 Chimp.REF Iran_GanjDareh_N Argentina_BeagleChannel_Yamana_1500BP Argentina_LagunaChica_1600BP 0.00121005 0.000527364 2.29452 0.0217604 472625
2 Chimp.REF CHG.SG Argentina_BeagleChannel_Yamana_1500BP Argentina_LagunaChica_1600BP 0.000615622 0.000571536 1.07714 0.281420 473505
3 Chimp.REF Muierii1 Argentina_BeagleChannel_Yamana_1500BP Argentina_LagunaChica_1600BP 0.00124880 0.000628117 1.98817 0.0467934 473254
4 Chimp.REF Kostenki14.SG Argentina_BeagleChannel_Yamana_1500BP Argentina_LagunaChica_1600BP 0.00118757 0.000638993 1.85851 0.0630967 449656
5 Chimp.REF Sunghir.SG Argentina_BeagleChannel_Yamana_1500BP Argentina_LagunaChica_1600BP 0.00114738 0.000511030 2.24523 0.0247537 473616
6 Chimp.REF Anatolia_Barcin_N Argentina_BeagleChannel_Yamana_1500BP Argentina_LagunaChica_1600BP 0.00112030 0.000483547 2.31683 0.0205131 473634
7 Chimp.REF Anatolia_Epipaleolithic Argentina_BeagleChannel_Yamana_1500BP Argentina_LagunaChica_1600BP 0.00130419 0.000655547 1.98946 0.0466504 412518
8 Chimp.REF Yana_UP.SG Argentina_BeagleChannel_Yamana_1500BP Argentina_LagunaChica_1600BP 0.000735844 0.000571647 1.28723 0.198013 473606
9 Chimp.REF MA1.SG Argentina_BeagleChannel_Yamana_1500BP Argentina_LagunaChica_1600BP 0.00146578 0.000720385 2.03472 0.0418786 349301
10 Chimp.REF China_UP Argentina_BeagleChannel_Yamana_1500BP Argentina_LagunaChica_1600BP 0.00112895 0.000566869 1.99156 0.0464197 472119
11 Chimp.REF ZlatyKun.SG Argentina_BeagleChannel_Yamana_1500BP Argentina_LagunaChica_1600BP 0.000412921 0.000610963 0.675853 0.499134 469823