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View Full Version : qpAdm runs in admixtools2 for Northwest/Northeast Europe


Russki
08-06-2023, 12:07 AM
target = c()
left = c('Russia_Samara_EBA_Yamnaya', 'Italy_North_Villabruna_HG', 'Turkey_Barcin_LN.SG', 'Nganasan.HO')
right = c('Mbuti.DG', 'Ethiopia_4500BP.SG', 'Russia_Ust_Ishim.DG', 'Czech_Vestonice16', 'Belgium_UP_GoyetQ116_1', 'Russia_Kostenki14.SG', 'Russia_AfontovaGora3', 'Han.DG', 'Papuan.DG', 'Karitiana.DG', 'Georgia_Satsurblia.SG', 'Iran_GanjDareh_N', 'Turkey_Epipaleolithic', 'Morocco_Iberomaurusian', 'Jordan_PPNB', 'Russia_Karelia_HG.SG', 'Czech_CordedWare', 'Armenia_LBA.SG', 'ONG.SG')
mypops = c('Mbuti.DG', 'Ethiopia_4500BP.SG', 'Russia_Ust_Ishim.DG', 'Czech_Vestonice16', 'Belgium_UP_GoyetQ116_1', 'Russia_Kostenki14.SG', 'Russia_AfontovaGora3', 'Italy_North_Villabruna_HG', 'Han.DG', 'Papuan.DG', 'Karitiana.DG', 'Georgia_Satsurblia.SG', 'Iran_GanjDareh_N', 'Turkey_Epipaleolithic', 'Morocco_Iberomaurusian', 'Jordan_PPNB', 'Russia_Karelia_HG.SG', 'Russia_Samara_EBA_Yamnaya', 'Czech_CordedWare', 'Armenia_LBA.SG', 'ONG.SG', 'Turkey_Barcin_LN.SG', 'Nganasan.HO')
results = qpadm(prefix, left, right, target, allsnps = TRUE)
results$weights
results$popdrop

Belarusian.HO
52.2% Russia_Samara_EBA_Yamnaya
11.7% Italy_North_Villabruna_HG
31.5% Turkey_Barcin_LN.SG
4.67% Nganasan.HO

Russian_Smolensk.HO
54.6% Russia_Samara_EBA_Yamnaya
9.6% Italy_North_Villabruna_HG
31.3% Turkey_Barcin_LN.SG
4.42% Nganasan.HO

Czech.HO
51% Russia_Samara_EBA_Yamnaya
9.25% Italy_North_Villabruna_HG
36.8% Turkey_Barcin_LN.SG
2.92% Nganasan.HO

English.HO
45.8% Russia_Samara_EBA_Yamnaya
15.3% Italy_North_Villabruna_HG
37.3% Turkey_Barcin_LN.SG
1.69% Nganasan.HO

Estonian.HO
53.4% Russia_Samara_EBA_Yamnaya
17.3% Italy_North_Villabruna_HG
24.5% Turkey_Barcin_LN.SG
4.89% Nganasan.HO

Finnish
52.6% Russia_Samara_EBA_Yamnaya
15.8% Italy_North_Villabruna_HG
21.8% Turkey_Barcin_LN.SG
9.85% Nganasan.HO

Hungarian.HO
45.1% Russia_Samara_EBA_Yamnaya
9.86% Italy_North_Villabruna_HG
40.8% Turkey_Barcin_LN.SG
4.18% Nganasan.HO

Icelandic.HO
50.9% Russia_Samara_EBA_Yamnaya
14.7% Italy_North_Villabruna_HG
32.2% Turkey_Barcin_LN.SG
2.22% Nganasan.HO

Karelian.HO
49.8% Russia_Samara_EBA_Yamnaya
17.3% Italy_North_Villabruna_HG
21.6% Turkey_Barcin_LN.SG
11.2% Nganasan.HO

Lithuanian.HO
56.4% Russia_Samara_EBA_Yamnaya
17.4% Italy_North_Villabruna_HG
23.6% Turkey_Barcin_LN.SG
2.61% Nganasan.HO

Mordovian.HO
53.5% Russia_Samara_EBA_Yamnaya
9.83% Italy_North_Villabruna_HG
26% Turkey_Barcin_LN.SG
10.6% Nganasan.HO

Norwegian.HO
51.6% Russia_Samara_EBA_Yamnaya
12% Italy_North_Villabruna_HG
33.5% Turkey_Barcin_LN.SG
2.93% Nganasan.HO

Orcadian.DG
51% Russia_Samara_EBA_Yamnaya
11.9% Italy_North_Villabruna_HG
34.8% Turkey_Barcin_LN.SG
2.29% Nganasan.HO

Russian_Arkhangelsk_HGDP.DG
52.3% Russia_Samara_EBA_Yamnaya
12.7% Italy_North_Villabruna_HG
23.8% Turkey_Barcin_LN.SG
11.2% Nganasan.HO

Russian_Arkhangelsk_Krasnoborsky.HO
47.8% Russia_Samara_EBA_Yamnaya
14% Italy_North_Villabruna_HG
25.9% Turkey_Barcin_LN.SG
12.3% Nganasan.HO

Russian_Arkhangelsk_Leshukonsky.HO
50.7% Russia_Samara_EBA_Yamnaya
14.8% Italy_North_Villabruna_HG
17.5% Turkey_Barcin_LN.SG
17% Nganasan.HO

Russian_Arkhangelsk_Pinezhsky.HO
52.1% Russia_Samara_EBA_Yamnaya
14% Italy_North_Villabruna_HG
19.6% Turkey_Barcin_LN.SG
14.3% Nganasan.HO

Russian_Kaluga.HO
53.7% Russia_Samara_EBA_Yamnaya
15.2% Italy_North_Villabruna_HG
27.1% Turkey_Barcin_LN.SG
4.05% Nganasan.HO

Russian_Kostroma.HO
53.1% Russia_Samara_EBA_Yamnaya
10.5% Italy_North_Villabruna_HG
29.6% Turkey_Barcin_LN.SG
6.87% Nganasan.HO

Russian_Kursk.HO
51.3% Russia_Samara_EBA_Yamnaya
13.7% Italy_North_Villabruna_HG
29.7% Turkey_Barcin_LN.SG
5.31% Nganasan.HO

Russian_Orel.HO
49.6% Russia_Samara_EBA_Yamnaya
12.7% Italy_North_Villabruna_HG
32.2% Turkey_Barcin_LN.SG
5.54% Nganasan.HO

Russian_Pskov.HO
51.3% Russia_Samara_EBA_Yamnaya
15.7% Italy_North_Villabruna_HG
28.4% Turkey_Barcin_LN.SG
4.6% Nganasan.HO

Russian_Ryazan.HO
51.8% Russia_Samara_EBA_Yamnaya
11.9% Italy_North_Villabruna_HG
29.7% Turkey_Barcin_LN.SG
6.66% Nganasan.HO

Scottish.HO
54.6% Russia_Samara_EBA_Yamnaya
8.64% Italy_North_Villabruna_HG
34.6% Turkey_Barcin_LN.SG
2.17% Nganasan.HO

Ukrainian.HO
50.2% Russia_Samara_EBA_Yamnaya
12.2% Italy_North_Villabruna_HG
33.2% Turkey_Barcin_LN.SG
4.41% Nganasan.HO

Russian_Belgorod.HO
50.1% Russia_Samara_EBA_Yamnaya
13.5% Italy_North_Villabruna_HG
31.9% Turkey_Barcin_LN.SG
4.54% Nganasan.HO

Veps.HO
51% Russia_Samara_EBA_Yamnaya
16.1% Italy_North_Villabruna_HG
20.4% Turkey_Barcin_LN.SG
12.5% Nganasan.HO



The results I received are very similar to this peer-reviewed study (https://www.researchgate.net/figure/Mixture-proportions-from-five-sources-estimated-using-qpAdm-Sources-used-were-Nganasan_fig4_329218949), although not exactly identical and they used LBK instead of proper ANF.


https://i.imgur.com/kUuThrj.png
ugochaves
08-06-2023, 05:00 AM
The results I received are very similar to this peer-reviewed study (https://www.researchgate.net/figure/Mixture-proportions-from-five-sources-estimated-using-qpAdm-Sources-used-were-Nganasan_fig4_329218949), although not exactly identical and they used LBK instead of proper ANF.


https://i.imgur.com/kUuThrj.png

All Europeans have an admixture of East Asia. Among Hungarians, it is clearly visible in these calculators. If everyone learns this, many interesting calculators will appear on the forum.
ugochaves
08-06-2023, 06:19 AM
Spanish.HO
30.8% Russia_Samara_EBA_Yamnaya
9.6% Italy_North_Villabruna_HG
56.2% Turkey_Barcin_LN.SG
3.4% Nganasan.HO
Grace O'Malley
08-06-2023, 06:23 AM
Can you do Irish?

Thanks
ugochaves
08-06-2023, 06:35 AM
Can you do Irish?

Thanks
I can't find the Irish in the database. And there are no Swedes either. Perhaps Russki knows?
Grace O'Malley
08-06-2023, 06:58 AM
I can't find the Irish in the database. And there are no Swedes either. Perhaps Russki knows?

No problems. That's most probably the reason why Russki didn't run them.
ugochaves
08-06-2023, 07:02 AM
We need to add SSA

Spanish.HO
31.8% Russia_Samara_EBA_Yamnaya
10.6% Italy_North_Villabruna_HG
53.2% Turkey_Barcin_LN.SG
3.1% Nganasan.HO
1.2% Yoruba

Belarusian.HO
52.1% Russia_Samara_EBA_Yamnaya
11.6% Italy_North_Villabruna_HG
31.3% Turkey_Barcin_LN.SG
4.6% Nganasan.HO
0.4% Yoruba.HO
Ibericus
08-06-2023, 12:16 PM
Basques can you do ? i want to see the Whg levels
Gallop
08-06-2023, 12:19 PM
We need to add SSA

Spanish.HO
31.8% Russia_Samara_EBA_Yamnaya
10.6% Italy_North_Villabruna_HG
53.2% Turkey_Barcin_LN.SG
3.1% Nganasan.HO
1.2% Yoruba

Belarusian.HO
52.1% Russia_Samara_EBA_Yamnaya
11.6% Italy_North_Villabruna_HG
31.3% Turkey_Barcin_LN.SG
4.6% Nganasan.HO
0.4% Yoruba.HO


It's amazing how an investment in two components makes the difference between being on top of the world and leaving a mark on humanity forever and going completely unnoticed.
Russki
08-06-2023, 12:32 PM
Basques can you do ? i want to see the Whg levels


I'm not quite sure yet how to model South Europe.

There were Neolithic Farmers with more East Eurasian affinity than Barcin_LN.SG.

If I apply the same model to South Europe, a lot of people will be protesting that South Europeans can't have these levels of East Eurasian admixture.
Sheppey
08-06-2023, 12:34 PM
All Europeans have an admixture of East Asia. Among Hungarians, it is clearly visible in these calculators. If everyone learns this, many interesting calculators will appear on the forum.

Perhaps but I fail to see how 1.69% Nganasan.HO , for English people , is mathematically significant compared to about 10% for the Finnish etc...
Ibericus
08-06-2023, 12:48 PM
I'm not quite sure yet how to model South Europe.

There were Neolithic Farmers with more East Eurasian affinity than Barcin_LN.SG.

If I apply the same model to South Europe, a lot of people will be protesting that South Europeans can't have these levels of East Eurasian admixture.

no, its ok for me the nganassan, im just curious abou the WHG
ugochaves
08-06-2023, 12:57 PM
no, its ok for me the nganassan, im just curious abou the WHG
This simulation is no more complicated than in g25 and vahaduo. There is a detailed instruction. I'm too lazy to understand modeling, there are enthusiasts here. We will wait for them.
Demirkazık
08-06-2023, 01:08 PM
How do I model myself with admixtools ?
Tried modelling but failed to do so.
Voskos
08-06-2023, 01:21 PM
Extra : CHG, Iran_N, SE_Asian and some Onge is not sufficient for South Euro? That's what i would try anyway, i tried by the way a few months ago but my pc would overheat and freeze.
Ibericus
08-06-2023, 01:50 PM
This simulation is no more complicated than in g25 and vahaduo. There is a detailed instruction. I'm too lazy to understand modeling, there are enthusiasts here. We will wait for them.

Yes, well.I imagine they would get around 15% Villabruna, similar to other models ive seen
rothaer
08-06-2023, 07:15 PM
(...)

Which type if file out of the four provided provided by the Reich lab do I need? And what kind of file do I need for my own raw data?

https://i.imgur.com/PXjVeCX.jpg

I hate not to understand things.
Russki
08-06-2023, 07:27 PM
Which type if file out of the four provided provided by the Reich lab do I need? And what kind of file do I need for my own raw data?

https://i.imgur.com/PXjVeCX.jpg

I hate not to understand things.


Download all 8 files and put them in two folders.

If you request eupator to add you and your family members raw data, he will send you a new dataset.


https://sun9-30.userapi.com/impg/sQPTjznVhGHRokcVZ8tw6nI-qdn95r3B5Sdkqw/Bo2kyZhZlTU.jpg?size=378x95&quality=95&sign=4d2af1952a13ccca9f5b53417b288933&type=album


Inside a folder you need 4 files with identical names.

You can also create a notepad file with prepared commands to run.


https://sun9-62.userapi.com/impg/65a0tsz-RZjHTF6X7MB4mPWBTYJQg5wGdQmt4A/AkhDhzCdhek.jpg?size=647x238&quality=95&sign=3e3d169cdb83437ff030b17d18a5a7db&type=album


.ind is the one where you can rename samples (giving two samples identical names will make them being used together whenever you put them - left, right or target).
ugochaves
08-06-2023, 07:43 PM
Which type if file out of the four provided provided by the Reich lab do I need? And what kind of file do I need for my own raw data?

https://i.imgur.com/PXjVeCX.jpg

I hate not to understand things.
You're German, aren't you? All Turks and Russians figured it out in half an hour) is the leopard the same? I'm sorry, I'm a very caustic user)
rothaer
08-06-2023, 09:16 PM
You're German, aren't you? All Turks and Russians figured it out in half an hour) is the leopard the same? I'm sorry, I'm a very caustic user)

And I figured it out in just 12 minutes that were between my question and Russki's answer, as you easily can see. :thumb001:
Russki
08-07-2023, 03:34 PM
no, its ok for me the nganassan, im just curious abou the WHG


Tell me which relevant sources I should put for Basques and I will make another run.



target = c('Basque.DG')
left = c('Russia_Samara_EBA_Yamnaya', 'Italy_North_Villabruna_HG', 'Turkey_Barcin_LN.SG', 'Nganasan.HO')
right = c('Mbuti.DG', 'Ethiopia_4500BP.SG', 'Russia_Ust_Ishim.DG', 'Czech_Vestonice16', 'Belgium_UP_GoyetQ116_1', 'Russia_Kostenki14.SG', 'Russia_AfontovaGora3', 'Han.DG', 'Papuan.DG', 'Karitiana.DG', 'Georgia_Satsurblia.SG', 'Iran_GanjDareh_N', 'Turkey_Epipaleolithic', 'Morocco_Iberomaurusian', 'Jordan_PPNB', 'Russia_Karelia_HG.SG', 'Czech_CordedWare', 'Armenia_LBA.SG', 'ONG.SG')
mypops = c('Mbuti.DG', 'Ethiopia_4500BP.SG', 'Russia_Ust_Ishim.DG', 'Czech_Vestonice16', 'Belgium_UP_GoyetQ116_1', 'Russia_Kostenki14.SG', 'Russia_AfontovaGora3', 'Italy_North_Villabruna_HG', 'Han.DG', 'Papuan.DG', 'Karitiana.DG', 'Georgia_Satsurblia.SG', 'Iran_GanjDareh_N', 'Turkey_Epipaleolithic', 'Morocco_Iberomaurusian', 'Jordan_PPNB', 'Russia_Karelia_HG.SG', 'Russia_Samara_EBA_Yamnaya', 'Czech_CordedWare', 'Armenia_LBA.SG', 'ONG.SG', 'Turkey_Barcin_LN.SG', 'Nganasan.HO', 'Basque.DG')
results = qpadm(prefix, left, right, target, allsnps = TRUE)
results$weights
results$popdrop

https://sun9-12.userapi.com/impg/UkXBPibIc_IjyCvyr29M26WNrBIaHEsYUPAN-w/LLgjl8hrzBk.jpg?size=500x134&quality=95&sign=d0b32b7295ee74af9ff27232b4087c9b&type=album


Basque.DG
31.6% Russia_Samara_EBA_Yamnaya
14% Italy_North_Villabruna_HG
52.4% Turkey_Barcin_LN.SG
2.01% Nganasan.HO
Eurafricanid
08-09-2023, 07:00 PM
I wonder what whould happen if you use Rochedane instead of Villabruna, I can't do that myself, the last time I tried, it took 6 hours to give me an error (the error was mine, while selecting the left and right groups), so I really can't do it, unfortunately.
Johnson Reed
07-31-2024, 09:10 AM
We need to add SSA

Spanish.HO
31.8% Russia_Samara_EBA_Yamnaya
10.6% Italy_North_Villabruna_HG
53.2% Turkey_Barcin_LN.SG
3.1% Nganasan.HO
1.2% Yoruba

Belarusian.HO
52.1% Russia_Samara_EBA_Yamnaya
11.6% Italy_North_Villabruna_HG
31.3% Turkey_Barcin_LN.SG
4.6% Nganasan.HO
0.4% Yoruba.HO

Why are you using modern Nganasan and Yoruba alongside ancient samples from thousands of years ago? Have Nganasan and Yoruba really stayed the same through all those thousands of years? That's really impressive, though I bet some European admixture would improve the Yoruba.