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An attempt at deep West Eurasian phylogeny

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An attempt at deep West Eurasian phylogeny
Kale Offline
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#271
12-20-2023, 05:21 AM
(12-19-2023, 06:57 PM)old europe Wrote: at Anthrogenica you modeled also the western side of ANS/ANE with Muierii too. Here are your models:

MA1.SG
Muierii1 0.657092 0.0226929 28.9559
Andaman_100BP.SG 0.309727 0.0544981 5.68326
AR33K 0.0331809 0.0482626 0.687508
Tail: 0.55
right = c('Congo_Mbuti.DG', 'ZlatyKun.SG', 'Ust_Ishim.DG', 'BachoKiro_IUP', 'Papuan.DG', 'Tianyuan', 'Kostenki14', 'Sunghir.SG', 'Gravettian', 'GoyetQ116_1', 'Jomon.SG', 'RUS_Primorsky_Boisman_MN', 'Taiwan_Hanben_IA')

Yana_UP.SG
Muierii1 0.632288 0.0188614 33.5228
Andaman_100BP.SG 0.218551 0.0424194 5.15215
AR33K 0.149161 0.0376843 3.95818
Tail: 0.30
right = c('Congo_Mbuti.DG', 'ZlatyKun.SG', 'Ust_Ishim.DG', 'BachoKiro_IUP', 'Papuan.DG', 'Tianyuan', 'Kostenki14', 'Sunghir.SG', 'Gravettian', 'GoyetQ116_1', 'Jomon.SG', 'RUS_Primorsky_Boisman_MN', 'Taiwan_Hanben_IA')
allsnps=TRUE

Yana_UP.SG
MA1.SG 0.933781 0.0259009 36.0521
AR33K 0.0662188 0.0259009 2.55662
Tail: 0.86
right = c('Congo_Mbuti.DG', 'ZlatyKun.SG', 'Ust_Ishim.DG', 'BachoKiro_IUP', 'Papuan.DG', 'Tianyuan', 'Kostenki14', 'Sunghir.SG', 'Gravettian', 'GoyetQ116_1', 'Jomon.SG', 'RUS_Primorsky_Boisman_MN', 'Taiwan_Hanben_IA')

Any toughts or changes?

Muierii for Georgia_UP and for ANE is representing 2 different things. For Georgia_UP, the Muierii could be pretty proximate/literal, as it works with the full suite of paleo-Euro right pops, and Georgia_UP do have elevated affinity to Muierii vis-a-vis say Kostenki/Sunghir. On the other hand, ANE don't, and it shows if BK1653 (Muierii's closest relative) is added to the right in the above models by killing the tail prob. Instead, for ANE, Muierii is standing in for something more generic.
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Norfern-Ostrobothnian Offline
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#272
12-20-2023, 02:35 PM (This post was last modified: 12-20-2023, 02:36 PM by Norfern-Ostrobothnian.)
An interesting possibility for the problem of continuity with Baradostian and Zarzian is the Baradostians moving away from the Zagros to Caspian and further to the Plateau suich as Garm Roud 2. Garm Roud 2 actually seems to share most with Dzudzuana and Kotias Klde type Caucasus EUP sites than Baradostian or Kulbulakian ones. They all may however share some common ancestry.

Quote:Finally, it may be with some Early Upper Palaeolithic assemblages from the northern region of the Caucasus that the techno-typological similarities seem most obvious. In 2012, Y. E. Demidenko proposed connections between “Southern Caucasus Early Upper Paleolithic” industries and some assemblages of the Southern Zagros (e.g. Ghār-e Boof Cave AH IV-III) and the Alborz region such as Garm Roud 2 (Demidenko 2014). The majority of the “southern Caucasus EUP” assemblages, including those of the Dzudzuana cave Units D (35-32 ka cal BP) and Ortval Klde rock-shelter layers 4d-4c (40-26 ka cal BP) in the south and Mezmaiskaya cave (35-34 ka BP) in the north, share similar technical traits based on fine or narrow bladelet and microbladelet production mainly from unidirectional – prismatic or pyramidal – cores and narrow-flake bladelet cores on flakes (e.g. Meshveliani et al. 2004; Bar-Yosef et al. 2006; Adler et al. 2008; Golovanova & Doronichev 2012; Demidenko 2014). In all these assemblages, the most distinctive tool types are small finely retouched bladelets (or microliths) about 2-4 mm in width, fine backed bladelets and light points with fine bilateral retouches. In the eastern part of the southern Caucasus, the assemblage of Aghitu 3 cave AH VI-III (36-24 ka cal BP) (Kandel et al. 2014, 2017) also has close typo-technological affinities with the assemblages mentioned above (e.g. Dzudzuana cave) and offer perhaps the best comparison to Garm Roud 2. Throughout the sequence, the industry shows an emphasis on small or narrow bladelet production mainly from unidirectional platform cores. The tool types are mainly represented by laterally finely retouched bladelets (on one or both edges) while other tool types, including a variety of backed bladelets, burins and carinated scrapers, are rare, as are cores. Additionally, the presence of narrow and often twisted bladelets can be highlighted here (Kandel et al. 2014).

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9977010/
The supplementary of paper below mentions dates from all the way to 23 ka calBP.
https://mnhn.hal.science/mnhn-03431530/document
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Kale Offline
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#273
12-20-2023, 04:53 PM (This post was last modified: 12-20-2023, 04:54 PM by Kale.)
https://genarchivist.com/showthread.php?...60#pid6760
"Accurate detection of identity-by-descent segments in human ancient DNA"

It seems pretty noisy/lots of false positives, especially with segments <~3000 positions or so, so looking for consistency is key.
A few things relevant to the time depth discussed here.
- No real hits for CHG surprisingly
- Doesn't look like Dzudzuana, Kotias_UP, Goyet, ElMiron, were included (or they just didn't even have noise hits with anybody)

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#274
12-24-2023, 10:45 PM
(12-20-2023, 04:53 PM)Kale Wrote: https://genarchivist.com/showthread.php?...60#pid6760
"Accurate detection of identity-by-descent segments in human ancient DNA"

It seems pretty noisy/lots of false positives, especially with segments <~3000 positions or so, so looking for consistency is key.
A few things relevant to the time depth discussed here.
- No real hits for CHG surprisingly
- Doesn't look like Dzudzuana, Kotias_UP, Goyet, ElMiron, were included (or they just didn't even have noise hits with anybody)

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I was looking at the supplements for hours until I found the full file is under Data availability. Seems like it's really only useful for close relatives and the older ancients aren't sampled densely enough for this but there still might be something interesting.
Zlaty Kun shares 3 segments with Ust-Ishim and that's the only one she shares multiple segments with. Ust-Ishim also shares 2 with Tianyuan, who shares 3 with NE20 (Amur river 33k).
The Yana samples share multiple segments only with each other, just like the Taforalt guys. Pinarbasi also doesn't have any interesting connections, one Boncuklu individual and a few way later European farmers.
After that you get more connections. Villabruna shares a lot with different WHGs. PES001, the earliest EHG, shares multiple segments with Iron Gates, Ukraine and Swedish HGs. UKY001 shares so much with Bronze Age Siberians that I think there might be something wrong there.



(12-18-2023, 11:05 PM)Chad Wrote: Kale, here is one qpAdm model, just as a reference...

So do we think the Iberomaurusian is something real African/Basal or is it just compensating for the other too Eastern references? Because I would think this question was the main reason the Dzudzuana paper never got released.
The ANE relations are also not clear to me. With Y-haplogroup P in Yana, the R2 in Iran is surely a sign of ANE ancestry. But when would it arrive, ~26k BC when it formed, or ~14k BC which is the TMRCA? With the former Iran_N could act as a real source for Dzudzuana/Kotias but I don't think it's really plausible.
I would also expect some geneflow from EHG to the Caucasus after the LGM (when I think ANE arrived in Eastern Europe) but it isn't obvious from the f4s I ran. Is it something like Dzudzuana being closer to ANE's West or more Basal in CHG/Anatolia so it evens out the stat? I know we've modelled CHG with EHG.
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#275
12-24-2023, 11:58 PM (This post was last modified: 12-25-2023, 12:10 AM by pkchu.)
(12-20-2023, 02:35 PM)Norfern-Ostrobothnian Wrote: An interesting possibility for the problem of continuity with Baradostian and Zarzian is the Baradostians moving away from the Zagros to Caspian and further to the Plateau suich as Garm Roud 2. Garm Roud 2 actually seems to share most with Dzudzuana and Kotias Klde type Caucasus EUP sites than Baradostian or Kulbulakian ones. They all may however share some common ancestry.

Quote:Finally, it may be with some Early Upper Palaeolithic assemblages from the northern region of the Caucasus that the techno-typological similarities seem most obvious. In 2012, Y. E. Demidenko proposed connections between “Southern Caucasus Early Upper Paleolithic” industries and some assemblages of the Southern Zagros (e.g. Ghār-e Boof Cave AH IV-III) and the Alborz region such as Garm Roud 2 (Demidenko 2014). The majority of the “southern Caucasus EUP” assemblages, including those of the Dzudzuana cave Units D (35-32 ka cal BP) and Ortval Klde rock-shelter layers 4d-4c (40-26 ka cal BP) in the south and Mezmaiskaya cave (35-34 ka BP) in the north, share similar technical traits based on fine or narrow bladelet and microbladelet production mainly from unidirectional – prismatic or pyramidal – cores and narrow-flake bladelet cores on flakes (e.g. Meshveliani et al. 2004; Bar-Yosef et al. 2006; Adler et al. 2008; Golovanova & Doronichev 2012; Demidenko 2014). In all these assemblages, the most distinctive tool types are small finely retouched bladelets (or microliths) about 2-4 mm in width, fine backed bladelets and light points with fine bilateral retouches. In the eastern part of the southern Caucasus, the assemblage of Aghitu 3 cave AH VI-III (36-24 ka cal BP) (Kandel et al. 2014, 2017) also has close typo-technological affinities with the assemblages mentioned above (e.g. Dzudzuana cave) and offer perhaps the best comparison to Garm Roud 2. Throughout the sequence, the industry shows an emphasis on small or narrow bladelet production mainly from unidirectional platform cores. The tool types are mainly represented by laterally finely retouched bladelets (on one or both edges) while other tool types, including a variety of backed bladelets, burins and carinated scrapers, are rare, as are cores. Additionally, the presence of narrow and often twisted bladelets can be highlighted here (Kandel et al. 2014).

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9977010/
The supplementary of paper below mentions dates from all the way to 23 ka calBP.
https://mnhn.hal.science/mnhn-03431530/document

"mentioned" but no raw data, serial #s or references are offered. Makes is difficult to assess the authenticity of the claims.
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#276
Thumbs Up  12-24-2023, 11:59 PM (This post was last modified: 12-25-2023, 12:11 AM by pkchu.)
(12-21-2023, 10:33 AM)zocram Wrote: https://www.researchgate.net/publication...rwasi_Iran

in this rockshelter we have Early Zagros Aurignacian, Late Zagros Aurignacian, and Zarzian:
there are several important differences beetwen zarzian and upper paleolithic

Interestingly, there is not a single C14 date in that paper. 
In fact, some of those excavators saw ‘direct continuity’ in the Zagros since the middle Paleolithic, so does that mean modern humans evolved out of Iranian Neanderthals? They even suggested so, but this is obviously not a credible position. Even with neat layering of strata, there could be thousands of years time separation between each layer.
These kind of arguments just doesn’t cut it in the modern scientific age.

Quote:.Even in the Caucasus mountains there was a gap but it was only 5000 years and perhaps not so genetically relevant: a very different thing if it had been 15000 years as perhaps in the Zagros.
In the Caucasus there is also a demonstrated cultural filiation, evolution between the two different periods (pre and post lgm paleolithic) even if they are different cultures, a sign that perhaps the population during the lgm did not go very far.
https://www.sciencedirect.com/science/ar...9X19302688

That's not correct- there’s no 5000 year gap. Dzudzuana and Bondi cave (e.g. section B4 & C3) were continuously populated during the LGM, with dates existing between 26,000 and 20,000 calBP. There was a technological shift in the Caucasus after 20,000 calBP, and archaeologists have this coming from the Levant (late Ahmarian), not Iran.
So the Caucasus region has a series of C14 continuity that the Zagros region can only dream of. Combining the fact that Zagros groups belong to G2a, whilst Kotias_UP and later CHG both belong to Y-hg J, it becomes fairly clear that CHG don’t come from the Zagros region.
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Chad Offline
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#277
12-25-2023, 04:57 AM (This post was last modified: 12-25-2023, 05:00 AM by Chad.)
(12-24-2023, 11:59 PM)pkchu Wrote:
(12-21-2023, 10:33 AM)zocram Wrote: https://www.researchgate.net/publication...rwasi_Iran

in this rockshelter we have Early Zagros Aurignacian, Late Zagros Aurignacian, and Zarzian:
there are several important differences beetwen zarzian and upper paleolithic

Interestingly, there is not a single C14 date in that paper. 
In fact, some of those excavators saw ‘direct continuity’ in the Zagros since the middle Paleolithic, so does that mean modern humans evolved out of Iranian Neanderthals? They even suggested so, but this is obviously not a credible position. Even with neat layering of strata, there could be thousands of years time separation between each layer.
These kind of arguments just doesn’t cut it in the modern scientific age.

Quote:.Even in the Caucasus mountains there was a gap but it was only 5000 years and perhaps not so genetically relevant: a very different thing if it had been 15000 years as perhaps in the Zagros.
In the Caucasus there is also a demonstrated cultural filiation, evolution between the two different periods (pre and post lgm paleolithic) even if they are different cultures, a sign that perhaps the population during the lgm did not go very far.
https://www.sciencedirect.com/science/ar...9X19302688

That's not correct- there’s no 5000 year gap. Dzudzuana and Bondi cave (e.g. section B4 & C3) were continuously populated during the LGM, with dates existing between 26,000 and 20,000 calBP. There was a technological shift in the Caucasus after 20,000 calBP, and archaeologists have this coming from the Levant (late Ahmarian), not Iran.
So the Caucasus region has a series of C14 continuity that the Zagros region can only dream of. Combining the fact that Zagros groups belong to G2a, whilst Kotias_UP and later CHG both belong to Y-hg J, it becomes fairly clear that CHG don’t come from the Zagros region.

Kotias UP is female. How did you not know this?
Check line 143 of Supplement 1.
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pkchu Offline
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#278
12-25-2023, 06:54 AM (This post was last modified: 12-25-2023, 07:10 AM by pkchu.)
(12-25-2023, 04:57 AM)Chad Wrote:
(12-24-2023, 11:59 PM)pkchu Wrote:
(12-21-2023, 10:33 AM)zocram Wrote: https://www.researchgate.net/publication...rwasi_Iran

in this rockshelter we have Early Zagros Aurignacian, Late Zagros Aurignacian, and Zarzian:
there are several important differences beetwen zarzian and upper paleolithic

Interestingly, there is not a single C14 date in that paper. 
In fact, some of those excavators saw ‘direct continuity’ in the Zagros since the middle Paleolithic, so does that mean modern humans evolved out of Iranian Neanderthals? They even suggested so, but this is obviously not a credible position. Even with neat layering of strata, there could be thousands of years time separation between each layer.
These kind of arguments just doesn’t cut it in the modern scientific age.

Quote:.Even in the Caucasus mountains there was a gap but it was only 5000 years and perhaps not so genetically relevant: a very different thing if it had been 15000 years as perhaps in the Zagros.
In the Caucasus there is also a demonstrated cultural filiation, evolution between the two different periods (pre and post lgm paleolithic) even if they are different cultures, a sign that perhaps the population during the lgm did not go very far.
https://www.sciencedirect.com/science/ar...9X19302688

That's not correct- there’s no 5000 year gap. Dzudzuana and Bondi cave (e.g. section B4 & C3) were continuously populated during the LGM, with dates existing between 26,000 and 20,000 calBP. There was a technological shift in the Caucasus after 20,000 calBP, and archaeologists have this coming from the Levant (late Ahmarian), not Iran.
So the Caucasus region has a series of C14 continuity that the Zagros region can only dream of. Combining the fact that Zagros groups belong to G2a, whilst Kotias_UP and later CHG both belong to Y-hg J, it becomes fairly clear that CHG don’t come from the Zagros region.

Kotias UP is female. How did you not know this?
Check line 143 of Supplement 1.

yep that's true, the younger Kotias is J2b2. , theyre adjacent in suppl. table.
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#279
12-25-2023, 05:46 PM (This post was last modified: 12-25-2023, 05:51 PM by Chad.)
Still stands to reason that Baradostian or another UP West Asian pop will be like Ganj Dareh. They are just too good of a statistical fit as the core, root population of West Asia. They have to have a very deep origin.

I have as much faith in this as I did in calling ENA to ANE, Anatolian in KO1 and when I called that epipaleolithic Anatolia would be like Boncuklu.
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#280
12-25-2023, 09:51 PM (This post was last modified: 12-25-2023, 09:55 PM by Kale.)
(12-24-2023, 10:45 PM)kolompar Wrote: UKY001 shares so much with Bronze Age Siberians that I think there might be something wrong there.

Yes there is. There is a mix up in all AADR datasets starting with I believe v44.3, that 'UKY001' is actually a wrongfully labeled duplicate of KPT002 (a bronze age Siberian). I e-mailed Dr. Reich a while ago about this, and he said he was aware of the mix-up. Just sent a follow up e-mail to make sure he hasn't forgotten.
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#281
12-25-2023, 11:12 PM (This post was last modified: 12-25-2023, 11:17 PM by pkchu.)
(12-25-2023, 05:46 PM)Chad Wrote: Still stands to reason that Baradostian or another UP West Asian pop will be like Ganj Dareh. They are just too good of a statistical fit as the core, root population of West Asia. They have to have a very deep origin.

I have as much faith in this as I did in calling ENA to ANE, Anatolian in KO1 and when I called that epipaleolithic Anatolia would be like Boncuklu.

Boncuklu being like Pinarbasi isn't rocket science. An impresive prediction would have been calling the obvious back-migration from Europe to the Near East, something which some people still struggle to admit, despite its now self-evident nature. 


It's one thing suggesting that the Gulf or Zagros region being refugial for a 'basal-like'population, and its another thing in proposing that Iran_N is a major source. Iran_N itself underwent significant modification/ admixture. After the LGM in West Asia, we see differentiated populations, with 'European like' west-central Anatolia, north African -like Natufians and differentiation between the Zagros and Caucasus-Caspian variety of the CHG-Iran cline
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#282
12-28-2023, 01:28 AM
(12-05-2023, 04:37 AM)Kale Wrote:
(12-05-2023, 04:13 AM)CJC Wrote: Archaeologically, East Eurasian ancestral population probably spread from the steppe, specifically the Tianyuan-related branch has material evidence connecting it to Upper Paleolithic Altai industries about 40.000 years ago.

I find your model about Yana and East Asians interesting, but are Northern East Asian groups such as Primorsky or DevilsGateCave_N closer to Yana than Tianyuan to Yana? Or closer to Yana than Onge? Usually they appear equal related in stats I have seen.

However, Yang et al. (2020) in the paper "Ancient DNA indicates human population shifts and admixture in northern and southern China" (also co-authored by Fu Qiaomei) suggest some presence of ANE ancestry in northern East Asian populations such as Yumin or Boshan in their qpAdm runs (proxied by Kolyma-related "Paleosiberian" ancestry). Perhaps this evidence for the Yana-related gene flow.

Yana and Salkhit (who is Tianyuan-heavy in ancestry) seem to have some bidrectional flow. You can see MA1 prefers the East-Asians over China_UP, but Yana doesn't. That is because China_UP is closer to Yana, not that East-Asians are closer to MA1.
Mbuti.DG Yana_UP.SG China_UP Jomon 0.00024 0.53 918598
Mbuti.DG Yana_UP.SG China_UP RUS_Primorsky_Boisman_MN 0.00000 -0.01 962533
Mbuti.DG Yana_UP.SG China_UP Taiwan_Hanben_IA -0.00035 -0.96 1028933
Mbuti.DG MA1.SG China_UP Jomon 0.00144 2.57 661818
Mbuti.DG MA1.SG China_UP RUS_Primorsky_Boisman_MN 0.00127 2.60 690766
Mbuti.DG MA1.SG China_UP Taiwan_Hanben_IA 0.00120 2.61 733082
Mbuti.DG China_UP Yana_UP.SG MA1.SG -0.00139 -2.67 734005
Mbuti.DG Onge.DG Yana_UP.SG MA1.SG 0.00007 0.13 787129
Mbuti.DG Jomon Yana_UP.SG MA1.SG 0.00001 0.03 683539
Mbuti.DG RUS_Primorsky_Boisman_MN Yana_UP.SG MA1.SG 0.00006 0.12 721979
Mbuti.DG Taiwan_Hanben_IA Yana_UP.SG MA1.SG 0.00022 0.50 799607

I am a bit confused sorry, does this mean that East Asians not closer to MA1? Then how to explain affinity between Kostenki and DevilsGate_N relative to Tianyuan? 

How can f4(Mbuti, Boisman;Yana,MA1) be not significant like f4(Mbuti, Onge;Yana,MA1) but f4(Chimp,Kostenki;China_UP,DevilsGate) be positive indicating affinity Kostenki-DevilsGate?

It is furthermore interesting the paper "Accurate detection of identity-by-descent segments in human ancient DNA" by Ringbauer et al (2023) indicate shared IBD between Boisman_MN and DevilsGateN therefore it is likely both population groups expand in similar timeframe. 

There are also IBD connections between some Jomon specimens but hard to interpret, separated by more than 1000 year across site but in some cases, no sharing within site. 

Finally, what Desdonas say about Denisovan ancestry in East Asians seem to hold true, there is shared Denisovan across all East Eurasian populations and then specific admixture to the following groups:
D0= East Asians and Jomon, Tibet
D3=Australian, Papuan groups
DAeta=Aeta Negrito populations see: "Philippine Ayta possess the highest level of Denisovan ancestry in the world" by Larena et al (2021)
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#283
12-28-2023, 07:25 AM (This post was last modified: 12-28-2023, 07:29 AM by Norfern-Ostrobothnian.)
yeah I think the unique component in Iran N would be unmixed in form during the Baradostian and even the early Zarzian, since the ANE and EEF related ancestries in Iran N seem very late, probably post-LGM if not fully Epipaleolithic. I think CHG and Iran N might have formed through a cline between EEF and Baradostian with an incursion of ANE discreetly influencing the both remaining populations to various degrees. I think Tutkaulian might be on a Baradostian-ANE cline without EEF so the question of when each component entered this area might depend on the region, with the Tutkaulian being largely ANE with some Kulbulakian related ancestry linking them to the Baradostians and thus Iran Neolithic. Although I still hold onto the possibility that Tutkaul N is fully ANE without any other admixture as Yana doesn't seem to prefer MA1 over Tutkaul which shouldn't be if either have any other ancestry components besides ANE, unless MA1 has something that pulls it away from Yana at an equal degree as the Iran N related ancestry in Tutkaulian. I guess what I am saying is that Iran N has some very deep ancestry but I don't think Iran N itself represents a pure Paleolithic population as it, due to it having affinity to later ANE and EEF.
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#284
12-28-2023, 04:30 PM
(12-28-2023, 01:28 AM)CJC Wrote: I am a bit confused sorry, does this mean that East Asians not closer to MA1? Then how to explain affinity between Kostenki and DevilsGate_N relative to Tianyuan? 
How can f4(Mbuti, Boisman;Yana,MA1) be not significant like f4(Mbuti, Onge;Yana,MA1) but f4(Chimp,Kostenki;China_UP,DevilsGate) be positive indicating affinity Kostenki-DevilsGate?
That was only addressing Yana and MA1 compared to each other, not either compared to Kostenki.
F4 uses 4 populations, call them W X Y Z. A positive score means a relationship between X&Z or W&Y. Negative score means relationship between X&Y or W&Z. Outgroups like Mbuti/Chimp are used to help narrow things down, so if your outgroup is truly an outgroup, positive score means relationship between X&Z, negative between X&Y.
f4(Mbuti, Boisman;Yana,MA1) being 0 says nothing in absolute value about how related Boisman is to Yana, or to MA1, only that Boisman is no more related to one than the other.
Here's some outgroup F3 values which do show absolute value
F3: Mbuti Boisman Yana = 0.2534
F3: Mbuti China_UP Yana = 0.2528
F3: Mbuti Boisman MA1 = 0.2531
F3: Mbuti China_UP MA1 = 0.2468
F3: Mbuti Boisman Kostenki14 = 0.2428
F3: Mbuti China_UP Kostenki14 = 0.2385
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#285
12-28-2023, 08:37 PM
(12-28-2023, 07:25 AM)Norfern-Ostrobothnian Wrote: yeah I think the unique component in Iran N would be unmixed in form during the Baradostian and even the early Zarzian, since the ANE and EEF related ancestries in Iran N seem very late, probably post-LGM if not fully Epipaleolithic. I think CHG and Iran N might have formed through a cline between EEF and Baradostian with an incursion of ANE discreetly influencing the both remaining populations to various degrees. I think Tutkaulian might be on a Baradostian-ANE cline without EEF so the question of when each component entered this area might depend on the region, with the Tutkaulian being largely ANE with some Kulbulakian related ancestry linking them to the Baradostians and thus Iran Neolithic. Although I still hold onto the possibility that Tutkaul N is fully ANE without any other admixture as Yana doesn't seem to prefer MA1 over Tutkaul which shouldn't be if either have any other ancestry components besides ANE, unless MA1 has something that pulls it away from Yana at an equal degree as the Iran N related ancestry in Tutkaulian. I guess what I am saying is that Iran N has some very deep ancestry but I don't think Iran N itself represents a pure Paleolithic population as it, due to it having affinity to later ANE and EEF.

Yes, Ganj Dareh has some ANE and possibly some Anatolian, but I'm not sold on the latter. It's not necessary.  I think, in my graphs, Iran only has 12% ANE, after being the root of West Asia. You can simply create Anatolians and Dzudzuana/Kotias as a geographic and genetic mix of something UP Europe and something very close to Iran. It works, and makes sense.
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