Basal Eurasian discussion

[TanTin]

I am glad we checked here for Iran Mesolithic . ( Iran_Mesolithic_HotuIIIb )
It is only 1 individual: I1293_noUDG_d
dated: 9100-8600 BCE
Very_High_Contamination [0.004,0.114]

Despite low coverage for this sample: I can tell: it seems to be earlier than other Iranian samples. We see it has influence on later Caucasian groups: armenian, kumyks, lezgin, abkhazian.
( It may also have some influence to bulgarian and kalash, but I have to do other tests to validate on that. )

[TanTin]

Here I will show you there are 2 different types of Iranian components.
1.  Iran_Mesolithic_HotuIIIb  . Related to this type is Iran_Mesolithic_BeltCave_noUDG  . Due to the lower coverage or contamination the second individual is projected between Loschbour and MA1  while the first one is after Israel and Egypt, more Basal.

2. The second type is the well known KK1  - Kotias / Georgia_Satsurblia or CHG.
This is also a good distinction between Iranian / CHG.

You may also notice that  Iran_Mesolithic_HotuIIIb is somehow related to Malawi Hora.  Apparently he inherited some genes along this line.

[TanTin]

.. And finally, to confirm the connection between Iran_Mesolitic and Malawi I run another test:

"F4 (  Primate_Chimp Malawi_Hora_LSA_8500BP Yoruba TEST )"

BTW, I should advise also , that here I used the other dataset v52 HO which is only 590 k snips.  ( I can rerun it on the full dataset, but I needed some extra groups for validation).
The results with Malawi  are just beautiful:

So we may see Malawi highly contributed to the future Mesolithic population of Iran.

[TanTin]

Rerunning the Malawi test by using  v52.2_1240K dataset.
(Unfortunately this Malawi individual is low coverage - more than 0.9 missingness. )

[Kale]

It seems to be an interesting concept combined with Haplogroup G in iran_n(First split in GHIJK,Formed 47K BC),I don't know why Kale stopped exploring this likely ancestry in iran_n.

The primary intent behind that line of inquiry was to consolidate the Western and Basal ancestries in Iran_N. That was accomplished by effectively shifting Basal to East-Eurasia; All East Eurasians (of which Ust-Ishim was counted also) were then a mix of an 'Eastern Basal' and a Paleolithic European source typified by Goyet.
The implications of that would be best visualized on a graph...
Green = Basal East Eurasian
Black = East Eurasians
Blue = First people in West Asia
Red = First people in Europe

   
The problem is ZlatyKun is one of the first people in Europe, and is completely off where would be expected, and not even on the cline, suggesting she'd be mixed or something even more complicated. The hypothetical Zagros Paleolithic is what would happen if the 'known quantities' of ANE and Southern-ENA are subtracted from Iran_N.

I did some thinking today though, starting with the most recent graph on my Deep phylogeny thread...
https://genarchivist.com/showthread.php?...7#pid15547
I found a 3rd way of accounting for Basal...
Stage 1) A (late Middle Paleolithic?) migration from Levant to Zagros/Iran, staying put for the time being ('Super-basal' in my most recent modeling)
Stage 2) A second (IUP?) expansion from Levant, 1 way goes North to Europe as ZlatyKun, another to Zagros/Iran again, mixing with the first wave / super-basal, and spreads further becoming Crown Eurasians in Central-Asia.
... I think that makes more sense from a geographic perspective because it eliminates the need for the Basal Eurasian (as maximized in Iran_N) to have some unique interaction with ZlatyKun (where and when could that have happened?). It also has the fun implication of making ZlatyKun the only sample without 'Basal Eurasian'! The only problem at the moment is that, since everybody (except ZlatyKun) has Zagrosian-super Basal, there is nothing to constrain when it branched off, or what % it contributed. For that I'll have to wait until Ranis comes out.

[Jerome]

It seems to be an interesting concept combined with Haplogroup G in iran_n(First split in GHIJK,Formed 47K BC),I don't know why Kale stopped exploring this likely ancestry in iran_n.

That was a long time ago. ZlatyKun was the main reason I stopped that line of inquiry. Up until that sample, I didn't see a need for Basal Eurasian. Not sure how ZlatyKun would fit in a graph where Iran_N has no Basal. I'll give it some thought on the road today.

Thinking of this,I think it would be interesting to see how IRAN_n models on QpAdm if Kostenki14+Zlaty Kun/Ust ishim+ANE/MA1 are used in left pops alongwith Dinka and Onge added in left pops to see if there's still any contribution from Dinka(Deep/Basal proxy) and Onge if Zlaty/Ust and Kostenki are used in left pops to account for the archaic west Eurasian affinities that can't be provided by dzudzuana/WHG.
Best outgroup for this model would Be SA_2000BP and the other usual list of right pops.

Iran_Wezmeh_N.SG
ZlatyKun.SG            0.325104  0.0881079 3.68984
Kostenki14.SG          0.275399  0.0391516 7.03417
AG3                    0.139199  0.0215189 6.46866
Andaman_100BP.SG        0.189066  0.0520910 3.62953
Mota.SG 0.0712322 0.0176885 4.02704
Tail: 0.13
right = c('SouthAfrica_2000BP.SG', 'Ust_Ishim.DG', 'BachoKiro_IUP', 'Papuan.DG', 'China_UP', 'RUS_Primorsky_DevilsCave_N.SG', 'Muierii1', 'BachoKiro_BK1653', 'Yana_UP.SG', 'MA1.SG', 'Peru_RioUncallane_1800BP.SG')
allsnps=TRUE
Goyet, Fournol, or Sunghir in right kill the model.

Thanks!
The results are interesting,onge is still present,in greater quantities than before but I think this is a case of Wezmeh in particular who seems to be pretty different compared to other iran_n samples like the GanjDareh_N.
Could you model that sample similarly?

Also,now mota/mbuti/deep ancestry takes a major hit,and it seems it's not needed anymore In that large amounts,this does cast a doubt on the basalness of iranN,if only 6% mota/deep Ancestry is needed.

Zlaty Kun is a bit more of an early crown Eurasian so it may eating up a bit of deep ancestry, I wonder what the results will be if bacho Kiro IUP is used instead of Zlaty Kun.
Ust ishim could work too but he has a bit more eastern affinity.

A minor request,could you try this model with BachoKiro_IUP instead of Zlaty Kun,and MA1 instead of AG3?(since MA1 is more eastern than AG3 and the ANE in iranN could be more AG3 and using AG3 may be inflating the Onge).
Also,GanjDareh instead of Wezmeh as the target so the results could be compared a bit to lazaridis' 2018 modelling with Dzudzuana.

[Jerome]

It seems to be an interesting concept combined with Haplogroup G in iran_n(First split in GHIJK,Formed 47K BC),I don't know why Kale stopped exploring this likely ancestry in iran_n.

That was a long time ago. ZlatyKun was the main reason I stopped that line of inquiry. Up until that sample, I didn't see a need for Basal Eurasian. Not sure how ZlatyKun would fit in a graph where Iran_N has no Basal. I'll give it some thought on the road today.

Thinking of this,I think it would be interesting to see how IRAN_n models on QpAdm if Kostenki14+Zlaty Kun/Ust ishim+ANE/MA1 are used in left pops alongwith Dinka and Onge added in left pops to see if there's still any contribution from Dinka(Deep/Basal proxy) and Onge if Zlaty/Ust and Kostenki are used in left pops to account for the archaic west Eurasian affinities that can't be provided by dzudzuana/WHG.
Best outgroup for this model would Be SA_2000BP and the other usual list of right pops.

Iran_Wezmeh_N.SG
ZlatyKun.SG            0.325104  0.0881079 3.68984
Kostenki14.SG          0.275399  0.0391516 7.03417
AG3                    0.139199  0.0215189 6.46866
Andaman_100BP.SG        0.189066  0.0520910 3.62953
Mota.SG 0.0712322 0.0176885 4.02704
Tail: 0.13
right = c('SouthAfrica_2000BP.SG', 'Ust_Ishim.DG', 'BachoKiro_IUP', 'Papuan.DG', 'China_UP', 'RUS_Primorsky_DevilsCave_N.SG', 'Muierii1', 'BachoKiro_BK1653', 'Yana_UP.SG', 'MA1.SG', 'Peru_RioUncallane_1800BP.SG')
allsnps=TRUE
Goyet, Fournol, or Sunghir in right kill the model.

Btw,here's your graph from the dotfile you pasted on that anthrogenica thread about NE0/,NE1

   

It's a bit blurry so would have to click on it to view the details

[Jerome]

Here I will show you there are 2 different types of Iranian components.
1.  Iran_Mesolithic_HotuIIIb  . Related to this type is Iran_Mesolithic_BeltCave_noUDG  . Due to the lower coverage or contamination the second individual is projected between Loschbour and MA1  while the first one is after Israel and Egypt, more Basal.

2. The second type is the well known KK1  - Kotias / Georgia_Satsurblia or CHG.
This is also a good distinction between Iranian / CHG.

You may also notice that  Iran_Mesolithic_HotuIIIb is somehow related to Malawi Hora.  Apparently he inherited some genes along this line.

Couldn't this be resolved by minor iranN/hotu input in malawai 6500 BP? Through PPNB/Levant_N?
Considering that malawi_15500BP or malwai_8500BP don't show this affinity.

Could be just contamination too or low SNPs or some other reason.
Otherwise other malawis will have showed some connection too.

[Desdonas]

It seems to be an interesting concept combined with Haplogroup G in iran_n(First split in GHIJK,Formed 47K BC),I don't know why Kale stopped exploring this likely ancestry in iran_n.

The primary intent behind that line of inquiry was to consolidate the Western and Basal ancestries in Iran_N. That was accomplished by effectively shifting Basal to East-Eurasia; All East Eurasians (of which Ust-Ishim was counted also) were then a mix of an 'Eastern Basal' and a Paleolithic European source typified by Goyet.
The implications of that would be best visualized on a graph...
Green = Basal East Eurasian
Black = East Eurasians
Blue = First people in West Asia
Red = First people in Europe


The problem is ZlatyKun is one of the first people in Europe, and is completely off where would be expected, and not even on the cline, suggesting she'd be mixed or something even more complicated. The hypothetical Zagros Paleolithic is what would happen if the 'known quantities' of ANE and Southern-ENA are subtracted from Iran_N.

I did some thinking today though, starting with the most recent graph on my Deep phylogeny thread...
https://genarchivist.com/showthread.php?...7#pid15547
I found a 3rd way of accounting for Basal...
Stage 1) A (late Middle Paleolithic?) migration from Levant to Zagros/Iran, staying put for the time being ('Super-basal' in my most recent modeling)
Stage 2) A second (IUP?) expansion from Levant, 1 way goes North to Europe as ZlatyKun, another to Zagros/Iran again, mixing with the first wave / super-basal, and spreads further becoming Crown Eurasians in Central-Asia.
... I think that makes more sense from a geographic perspective because it eliminates the need for the Basal Eurasian (as maximized in Iran_N) to have some unique interaction with ZlatyKun (where and when could that have happened?). It also has the fun implication of making ZlatyKun the only sample without 'Basal Eurasian'! The only problem at the moment is that, since everybody (except ZlatyKun) has Zagrosian-super Basal, there is nothing to constrain when it branched off, or what % it contributed. For that I'll have to wait until Ranis comes out.

If C* and mt-M* formed on the green line/basal east eurasian, it will fit the haplogroup distribution better. Then a geneflow from proto-ENA to Goyet is needed.

I am always thinking that haplogroup C and K2 are not native to the Near East, and they represent CWE/ANE backflow. If M1 is also from CWE or even Goyet-related backflow, then mt-M would be the same situation as C/K2. In these new ideas of Eurasian phylogeny, C and mt-M may leave "Near East-core" first, then was K2. Their origin may be eastern Iran Plateau or South Central Asia.

[Kale]

Thanks!
The results are interesting,onge is still present,in greater quantities than before but I think this is a case of Wezmeh in particular who seems to be pretty different compared to other iran_n samples like the GanjDareh_N.
Could you model that sample similarly?

Also,now mota/mbuti/deep ancestry takes a major hit,and it seems it's not needed anymore In that large amounts,this does cast a doubt on the basalness of iranN,if only 6% mota/deep Ancestry is needed.

Zlaty Kun is a bit more of an early crown Eurasian so it may eating up a bit of deep ancestry, I wonder what the results will be if bacho Kiro IUP is used instead of Zlaty Kun.
Ust ishim could work too but he has a bit more eastern affinity.

A minor request,could you try this model with BachoKiro_IUP instead of Zlaty Kun,and MA1 instead of AG3?(since MA1 is more eastern than AG3 and the ANE in iranN could be more AG3 and using AG3 may be inflating the Onge).
Also,GanjDareh instead of Wezmeh as the target so the results could be compared a bit to lazaridis' 2018 modelling with Dzudzuana.

Iran_N's ANE is more related to AG3 than to MA1, and I would argue that AG3/MA1 are about equally East/West, if there is any Eastern leaning, it would be from AG3 due to a trifle of UKY/Kolyma stuff.

Iran_GanjDareh_N
BachoKiro_IUP 0.232202 0.128585 1.80582
Kostenki14 0.275729 0.0478508 5.76226
AG3 0.191370 0.0177896 10.7574
Andaman_100BP.SG 0.198286 0.0799078 2.48144
Mota.SG 0.102413 0.0158679 6.45410
Tail: 0.07
right = c('SouthAfrica_2000BP.SG', 'Ust_Ishim.DG', 'Papuan.DG', 'China_UP', 'RUS_Primorsky_DevilsCave_N.SG', 'GoyetQ116_1', 'Muierii1', 'BachoKiro_BK1653', 'Yana_UP.SG', 'MA1.SG', 'Peru_RioUncallane_1800BP.SG')

It is a haaardddd fail if ZlatyKun is put in the right.

[Norfern-Ostrobothnian]

The Zarzians seem to simply be Iran Neolithic with some Tutkaulian
Target: Iran_HotuIIIb_Mesolithic
Distance: 3.2652% / 0.03265196
73.0 Iran_Wezmeh_N.SG
23.2 Tajikistan_Tutkaul_N
3.2 Georgia_Kotias.SG
0.6 Turkey_Barcin_LN.SG
0.0 Russia_AfontovaGora3

[Hammas]

Kind of interesting, Hotu has CHG ancestry, does anyone really know where does the CHG like signal or which is also present in Eneolithic Central Asians

[TanTin]

Couldn't this be resolved by minor iranN/hotu input in malawai 6500 BP? Through PPNB/Levant_N?
Considering that malawi_15500BP or malwai_8500BP don't show this affinity.

Could be just contamination too or low SNPs or some other reason.
Otherwise other malawis will have showed some connection too.

No, that's not the case. There is a mysterious archaic component . In this case we have a very good example where the old archaic component is present in both Malawi and later Iranian groups.
This old archaic component is mostly from North Africa .
------
I don't know. I did few more tests.
One issue is the low coverage.
Malawi 8000 are also low to middle coverage.

[Hammas]

Can you model Pinarbasi with the same model? I want to see if they have the same Onge related ancestry since they can be modeled with 30% Zarzian ancestry in your previous model

[Jerome]

Here I will show you there are 2 different types of Iranian components.
1.  Iran_Mesolithic_HotuIIIb  . Related to this type is Iran_Mesolithic_BeltCave_noUDG  . Due to the lower coverage or contamination the second individual is projected between Loschbour and MA1  while the first one is after Israel and Egypt, more Basal.

2. The second type is the well known KK1  - Kotias / Georgia_Satsurblia or CHG.
This is also a good distinction between Iranian / CHG.

You may also notice that  Iran_Mesolithic_HotuIIIb is somehow related to Malawi Hora.  Apparently he inherited some genes along this line.

Couldn't this be resolved by minor iranN/hotu input in malawai 6500 BP? Through PPNB/Levant_N?
Considering that malawi_15500BP or malwai_8500BP don't show this affinity.

Could be just contamination too or low SNPs or some other reason.
Otherwise other malawis will have showed some connection too.

Kind of interesting, Hotu has CHG ancestry, does anyone really know where does the CHG like signal or which is also present in Eneolithic Central Asians

Its present in tepe guran and nemrik9 PPN too who get modelled as half CHG and half Ganj Dareh.
Of course there wasn't a CHG migration as no evidence of imeretian lithics are found.
Rather I would say that Iran_N being ancestral to CHG(zarzian->imeretian movement to Caucasus from zagros after LGM),some regions of iranN like north zagros, Mesopotamia had more of a CHG affinity because they simply were the proximate node to the zarzian subtypes that contributed to CHG/Caucasus.

This affinity seems to peak in upper Mesopotamia/North Zagros which also seems to be the hotspot for basal J2a1 clades(found in CHG too) and the Cayonu cay007 sample from 8500 BC has a ratio of affinity of 70% CHG/30% GanjD which fits with the evidence that the Iran_Mesolithic people of Zarzian that migrated to Caucasus were from north zagros/NE Mesopotamia.

So,when people use Ganj dareh to denote IranN in models,the model simply splits the affinity towards CHG/Kotias because the Target has more affinity to CHG than Ganj dareh can provide.

Lazaridis in his 2018 study modelled CHG with 8% ENA and iran_N with 10.5% ENA.

So,both have ENA/Onge, however I saw some stats before on this affinity(can't find them currently) and the signal was stronger with Jomon and equidistant with NEA and Onge,so I am not sure if it's onge or something else.
The ENA gets reduced when MA1 vs AG3 is used,so it's not very clear currently.

Maybe the Y-Dna R2/mtdna R1a ANE types that mixed with iran_n had a slightly different ancestry than MA1/AG3?