Mega QAPDM Models thread

Thanks for the info. Works best when i only change barcin . P value is now bit lower.

Attachment 142256

Quote:

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Originally Posted by Gannicus

Hey, Majevica have you admix modeled yourself with modern populations yet?

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Yea, this model has the best p-value so far

https://i.postimg.cc/1t37rRPx/IMG.jpg

https://i.postimg.cc/xCLWXJVy/image.png
https://i.postimg.cc/Gtr6GLc0/image.png

What References would fit better for these sources, or is p-value good enough?

Attachment 142314
I modeled myself as 83% ANF in qpadm with a pval of 0.6

Quote:

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Originally Posted by Fistora

https://i.postimg.cc/xCLWXJVy/image.png
https://i.postimg.cc/Gtr6GLc0/image.png

What References would fit better for these sources, or is p-value good enough?

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This is definitely an AndreiDNA question or someone who has more extensive experience than I. My suggestion would be to include some East Asian and Near Eastern References and see if that tightens the standard errors a bit.

Buenos dias Attachment 142339 Attachment 142340Attachment 142341Attachment 142342Attachment 142343

Quote:

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Originally Posted by AndreiDNA

Attachment 142314
I modeled myself as 83% ANF in qpadm with a pval of 0.6

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What should be inferred from this model?

This is one of my best fitting modern models yet.
Scottish + Central Italian:

Attachment 142363


References:

Attachment 142364
Attachment 142365

Edit: Realized that I forgot to add in Italian south and English into the references. Also added Papuan.HO.

P value went up slightly:

Attachment 142370

Here i did the same thing. With Barcin my p value was very low.
But changing it with the precursor of EEF i get very good P value!

Attachment 142372

Here the one with Barcin.

Attachment 142374

Scottish + South Italian Attachment 142376 These are the references I used: Attachment 142377Attachment 142378Attachment 142379Attachment 142380

Quote:

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Originally Posted by Gannicus

Scottish + South Italian Attachment 142376 These are the references I used: Attachment 142377Attachment 142378Attachment 142379Attachment 142380

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Do they have an Irish population? If not I won't be bothering paying for it.

Quote:

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Originally Posted by Grace O'Malley

Do they have an Irish population? If not I won't be bothering paying for it.

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In the .HO dataset I haven’t seen modern Irish. It also does not have German, Austrian, Danish, Welsh, Bretons etc. There is always an opportunity for IllustrativeDNA to add more genomes in the future. In the AADR dataset they have the medieval Irish from Kilteasheen and the Rathlin EBA Irish Genomes. Attachment 142381Attachment 142382

My fst distances with a slightly more extended list of countries
https://i.postimg.cc/K8TvvRb7/image.png
https://i.postimg.cc/c4p0j03v/image.png

Bueno

Attachment 142392

Adding Cypriot to the references further increased the p value.

Full references used:

Attachment 142393
Attachment 142394
Attachment 142395

My best model so far, using similar references as Gannicus
https://i.postimg.cc/mkt8FWhW/image.png

Attachment 142442

Attachment 142443

Attachment 142444

Similar to the reference list I used in post #94 Obviously with Sicilian removed from the rights. Spanish.HO is in the list, but Spanish North is not.

Attachment 142445

This one is with 26 references found in post #94 with French, Spanish, Cypriot, and Spanish North left out.

https://i.postimg.cc/9ffnJL2F/image.png

Quote:

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Originally Posted by Fistora

https://i.postimg.cc/9ffnJL2F/image.png

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Have you tried Modeling yourself with Polish yet?

Quote:

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Originally Posted by Gannicus

Have you tried Modeling yourself with Polish yet?

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Only a single modern Polish sample is available, which I presume comes from southern Poland. Unfortunately, it models me with a low p-value and frequently suggests false feasibility

Scottish + Sicilian

Attachment 142465


Scottish + North Italian

Attachment 142466



When modeling myself, the Scottish and North Italian run is the highest 2-way p-value so far. Even compared to Scottish and South French:

Attachment 142467

I've shared this model before, however, with this run I used a different set of references. P-value isn't as good as the previous model, but it's still comfortably above 0.05

Attachment 142473

References:

Attachment 142474
Attachment 142475

Quote:

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Originally Posted by Gannicus

I've shared this model before, however, with this run I used a different set of references. P-value isn't as good as the previous model, but it's still comfortably above 0.05

Attachment 142473

References:

Attachment 142474
Attachment 142475

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It might be a bit above 0,05 but it is still bad don't you think?

I might be to harsh but i would only take p values around 0,5 and above serious.

Quote:

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Originally Posted by Croatian Legend

It might be a bit above 0,05 but it is still bad don't you think?

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I was able to repeat this model earlier with a related Levant Neolithic population with different references:

Attachment 142476

This was the earlier run with a much higher p value:

Attachment 142477


Levant N populations have a significant Anatolian component. And Corded Ware is not 100% Western Steppe Herder.

Quote:

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Originally Posted by Croatian Legend

I might be to harsh but i would only take p values around 0,5 and above serious.

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That's not correct. https://www.nature.com/articles/s41586-025-09195-5

P-value for NUE001 that was modeled as ~80% Morocco MN and 20% Mesopotamia N yielded a p value of 0.12

"Ancestry of the Nuwayrat genome
We used the qpAdm42 framework to model the genetic ancestry components that best represent the Nuwayrat genome using a fully rotating model competition approach, in which a set of candidate populations are iteratively used as sources to construct one-source, two-source and three-source population ancestry models, whereas the remaining candidates are set as outgroup (right) populations43,44 (Supplementary Information section 4). We used a set of 13 populations from Neolithic and Chalcolithic West Asia, North Africa and the North Mediterranean region that predate the Nuwayrat individual as potential sources (Fig. 3c,d and Methods). No single-source model fitted the data (maximum P value observed = 2.39 × 10−6 for a model with Morocco_MN as a single source). Instead, a single two-source model (P = 0.12) met the significance criteria (P > 0.05), which consisted of a mixture of 77.6 ± 3.8% ancestry represented by genomes from the Middle Neolithic Moroccan site of Skhirat-Rouazi dated to 4780–4230 bce (Morocco_MN), and the remainder most closely related to genomes from 9000 to 8000 bce Neolithic Mesopotamia (22.4 ± 3.8%; Fig. 3a). In addition, two three-source models showed similar ancestry proportions but with a minor contribution of a third ancestry component represented by genomes from the Neolithic/Chalcolithic Levant (4.7 ± 8.2% at P = 0.11 and 1.1 ± 8.7% at P = 0.07, respectively; Supplementary Table 6)."

Quote:

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Originally Posted by Gannicus

That's not correct. https://www.nature.com/articles/s41586-025-09195-5

P-value for NUE001 that was modeled as ~80% Morocco MN and 20% Mesopotamia N yielded a p value of 0.12

"Ancestry of the Nuwayrat genome
We used the qpAdm42 framework to model the genetic ancestry components that best represent the Nuwayrat genome using a fully rotating model competition approach, in which a set of candidate populations are iteratively used as sources to construct one-source, two-source and three-source population ancestry models, whereas the remaining candidates are set as outgroup (right) populations43,44 (Supplementary Information section 4). We used a set of 13 populations from Neolithic and Chalcolithic West Asia, North Africa and the North Mediterranean region that predate the Nuwayrat individual as potential sources (Fig. 3c,d and Methods). No single-source model fitted the data (maximum P value observed = 2.39 × 10−6 for a model with Morocco_MN as a single source). Instead, a single two-source model (P = 0.12) met the significance criteria (P > 0.05), which consisted of a mixture of 77.6 ± 3.8% ancestry represented by genomes from the Middle Neolithic Moroccan site of Skhirat-Rouazi dated to 4780–4230 bce (Morocco_MN), and the remainder most closely related to genomes from 9000 to 8000 bce Neolithic Mesopotamia (22.4 ± 3.8%; Fig. 3a). In addition, two three-source models showed similar ancestry proportions but with a minor contribution of a third ancestry component represented by genomes from the Neolithic/Chalcolithic Levant (4.7 ± 8.2% at P = 0.11 and 1.1 ± 8.7% at P = 0.07, respectively; Supplementary Table 6)."

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It clear to me that everything above 0,05 can be looked at as valid. Still it is better to go for a higher p value if it is possible.

Quote:

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Originally Posted by Gannicus

I was able to repeat this model earlier with a related Levant Neolithic population with different references:

Attachment 142476

This was the earlier run with a much higher p value:

Attachment 142477


Levant N populations have a significant Anatolian component. And Corded Ware is not 100% Western Steppe Herder.

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Well they seem way better!

May i ask why you try to model yourself with natufian like components? Do you have ancestry from there? Just wondering, since i tried to create models with natufian in it for myself and it fails.

Quote:

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Originally Posted by Croatian Legend

It clear to me that everything above 0,05 can be looked at as valid. Still it is better to go for a higher p value if it is possible.

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Yes, I do aim for higher p values if I can. :)

There are other papers that publish models with p values of 0.06 too.

Lazaridis et al. 2022 paper on the southern arc: "The genetic history of the Southern Arc: A bridge between West Asia and Europe"

Quote:

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Originally Posted by Croatian Legend

May i ask why you try to model yourself with natufian like components? Do you have ancestry from there? Just wondering, since i tried to create models with natufian in it for myself and it fails.

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I'm glad you asked! It all started when I uploaded my DNA file to gedmatch a few years ago and was seeing results like this:

Eurogenes k13: North_Atlantic 50.78 Pct
Baltic 20.29 Pct
West_Med 14.55 Pct
West_Asian 5.04 Pct
East_Med 3.71 Pct
Red_Sea 3.71 Pct
South_Asian 0.55 Pct
East_Asian -
Siberian -
Amerindian 0.9 Pct
Oceanian 0.39 Pct
Northeast_African -
Sub-Saharan 0.09 Pct

# Primary Population (source) Secondary Population (source) Distance
1 95.9% Southwest_English + 4.1% Saudi @ 2.11
2 81.4% West_Scottish + 18.6% Spanish_Extremadura @ 2.32
3 96.3% Southwest_English + 3.7% Yemenite_Jewish @ 2.35
4 80% West_Scottish + 20% Spanish_Galicia @ 2.39
5 79.8% West_Scottish + 20.2% Spanish_Castilla_Y_Leon @ 2.43
6 80.5% West_Scottish + 19.5% Portuguese @ 2.46
7 95.9% Southwest_English + 4.1% Bedouin @ 2.48
8 81.3% West_Scottish + 18.7% Spanish_Murcia @ 2.51
9 81.4% West_Scottish + 18.6% Spanish_Castilla_La_Mancha @ 2.56
10 96.1% Southwest_English + 3.9% Egyptian @ 2.59
11 96.1% Southwest_English + 3.9% Palestinian @ 2.61
12 69.7% West_Scottish + 30.3% French @ 2.66
13 96.2% Southwest_English + 3.8% Jordanian @ 2.67
14 96.1% Southwest_English + 3.9% Syrian @ 2.69
15 95.7% Southwest_English + 4.3% Moroccan @ 2.69
16 95.6% Southwest_English + 4.4% Algerian @ 2.7
17 79.3% Irish + 20.7% Spanish_Castilla_Y_Leon @ 2.7
18 81.1% Irish + 18.9% Spanish_Extremadura @ 2.71
19 83.2% West_Scottish + 16.8% Spanish_Andalucia @ 2.71
20 96.4% Southwest_English + 3.6% Samaritan @ 2.72



And in G25:

Target: Gannicus_MergedFile_officialDavidski_scaled
Distance: 0.0171% / 0.01706667 | R5P
45.3 Irish
28.9 Icelandic
22.7 Spanish_Soria
3.1 Yemenite_Jew


Target: Gannicus_MergedFile_officialDavidski_scaled
Distance: 0.0175% / 0.01749323 | R3P
77.3 Irish
19.9 Spanish_Soria
2.8 Saudi

"World Countries Calculator" list:

Target: Gannicus_MergedFile_officialDavidski_scaled
Distance: 0.0193% / 0.01930650 | R5P
61.3 Ireland
13.6 Iceland
11.7 France
11.2 Spain
2.2 Yemen

Distance to: Gannicus_MergedFile_officialDavidski_scaled
0.01979896 23.20% Spain + 76.80% Ireland
0.01994210 32.40% France + 67.60% Ireland
0.02028329 20.40% Portugal + 79.60% Ireland
0.02041020 26.60% Switzerland + 73.40% Ireland
0.02056362 13.60% Spain + 86.40% Wales
0.02060842 12.00% Portugal + 88.00% Wales
0.02064201 4.40% Palestine + 95.60% Wales
0.02064660 3.60% Yemen + 96.40% Wales
0.02077307 3.40% Saudi_Arabia + 96.60% Wales
0.02077975 21.00% Spain + 79.00% Scotland
0.02078383 19.40% France + 80.60% Wales
0.02083812 4.20% Jordan + 95.80% Wales
0.02089739 29.80% France + 70.20% Scotland
0.02094917 15.00% Switzerland + 85.00% Wales
0.02096239 4.40% Lebanon + 95.60% Wales
0.02096458 4.60% Cyprus + 95.40% Wales
0.02098500 32.60% Spain + 67.40% Iceland
0.02099838 3.40% Tunisia + 96.60% Wales
0.02100424 4.60% Syria + 95.40% Wales
0.02100611 49.20% Belgium + 50.80% Ireland
0.02100744 3.60% United_Arab_Emirates + 96.40% Wales
0.02103141 8.00% Italy + 92.00% Wales
0.02103156 6.00% Israel + 94.00% Wales
0.02105459 3.20% Libya + 96.80% Wales
0.02107681 3.80% Egypt + 96.20% Wales



I'm rigorously testing now with qpAdm to correlate with these results and others.

Also, ANFs have Natufian or Natufian like admix too. Barcin is around 15% Natufian or Natufian like.

Quote:

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Originally Posted by Gannicus

I'm glad you asked! It all started when I uploaded my DNA file to gedmatch a few years ago and was seeing results like this:

Eurogenes k13: North_Atlantic 50.78 Pct
Baltic 20.29 Pct
West_Med 14.55 Pct
West_Asian 5.04 Pct
East_Med 3.71 Pct
Red_Sea 3.71 Pct
South_Asian 0.55 Pct
East_Asian -
Siberian -
Amerindian 0.9 Pct
Oceanian 0.39 Pct
Northeast_African -
Sub-Saharan 0.09 Pct

# Primary Population (source) Secondary Population (source) Distance
1 95.9% Southwest_English + 4.1% Saudi @ 2.11
2 81.4% West_Scottish + 18.6% Spanish_Extremadura @ 2.32
3 96.3% Southwest_English + 3.7% Yemenite_Jewish @ 2.35
4 80% West_Scottish + 20% Spanish_Galicia @ 2.39
5 79.8% West_Scottish + 20.2% Spanish_Castilla_Y_Leon @ 2.43
6 80.5% West_Scottish + 19.5% Portuguese @ 2.46
7 95.9% Southwest_English + 4.1% Bedouin @ 2.48
8 81.3% West_Scottish + 18.7% Spanish_Murcia @ 2.51
9 81.4% West_Scottish + 18.6% Spanish_Castilla_La_Mancha @ 2.56
10 96.1% Southwest_English + 3.9% Egyptian @ 2.59
11 96.1% Southwest_English + 3.9% Palestinian @ 2.61
12 69.7% West_Scottish + 30.3% French @ 2.66
13 96.2% Southwest_English + 3.8% Jordanian @ 2.67
14 96.1% Southwest_English + 3.9% Syrian @ 2.69
15 95.7% Southwest_English + 4.3% Moroccan @ 2.69
16 95.6% Southwest_English + 4.4% Algerian @ 2.7
17 79.3% Irish + 20.7% Spanish_Castilla_Y_Leon @ 2.7
18 81.1% Irish + 18.9% Spanish_Extremadura @ 2.71
19 83.2% West_Scottish + 16.8% Spanish_Andalucia @ 2.71
20 96.4% Southwest_English + 3.6% Samaritan @ 2.72



And in G25:

Target: Gannicus_MergedFile_officialDavidski_scaled
Distance: 0.0171% / 0.01706667 | R5P
45.3 Irish
28.9 Icelandic
22.7 Spanish_Soria
3.1 Yemenite_Jew


Target: Gannicus_MergedFile_officialDavidski_scaled
Distance: 0.0175% / 0.01749323 | R3P
77.3 Irish
19.9 Spanish_Soria
2.8 Saudi

"World Countries Calculator" list:

Target: Gannicus_MergedFile_officialDavidski_scaled
Distance: 0.0193% / 0.01930650 | R5P
61.3 Ireland
13.6 Iceland
11.7 France
11.2 Spain
2.2 Yemen

Distance to: Gannicus_MergedFile_officialDavidski_scaled
0.01979896 23.20% Spain + 76.80% Ireland
0.01994210 32.40% France + 67.60% Ireland
0.02028329 20.40% Portugal + 79.60% Ireland
0.02041020 26.60% Switzerland + 73.40% Ireland
0.02056362 13.60% Spain + 86.40% Wales
0.02060842 12.00% Portugal + 88.00% Wales
0.02064201 4.40% Palestine + 95.60% Wales
0.02064660 3.60% Yemen + 96.40% Wales
0.02077307 3.40% Saudi_Arabia + 96.60% Wales
0.02077975 21.00% Spain + 79.00% Scotland
0.02078383 19.40% France + 80.60% Wales
0.02083812 4.20% Jordan + 95.80% Wales
0.02089739 29.80% France + 70.20% Scotland
0.02094917 15.00% Switzerland + 85.00% Wales
0.02096239 4.40% Lebanon + 95.60% Wales
0.02096458 4.60% Cyprus + 95.40% Wales
0.02098500 32.60% Spain + 67.40% Iceland
0.02099838 3.40% Tunisia + 96.60% Wales
0.02100424 4.60% Syria + 95.40% Wales
0.02100611 49.20% Belgium + 50.80% Ireland
0.02100744 3.60% United_Arab_Emirates + 96.40% Wales
0.02103141 8.00% Italy + 92.00% Wales
0.02103156 6.00% Israel + 94.00% Wales
0.02105459 3.20% Libya + 96.80% Wales
0.02107681 3.80% Egypt + 96.20% Wales



I'm rigorously testing now with qpAdm to correlate with these results and others.

Also, ANFs have Natufian or Natufian like admix too. Barcin is around 15% Natufian or Natufian like.

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Ok i see where you are coming from. Well i can already asure you to completly ditch the breakdowns from G25 and the official Davdski files.
Vahaduo and the g25 coords is only trying to place you on a certain point in a pca nothing more nothing less. you being pretty much northwest european that maybe has some stong neolthic signal pushes you little south. That is why Vahaduo/g25 uses extreme points! Which is misleading!

Again Vahaduo is only good for general clustering nothing more. Gedmatch is the same and pretty outdated !

Also Vahaduo is also very bad at seperating EEF from CHG or rather it overastimtes EEF . Me being the perfect example looking at my QPADM results and also my other DNA rsults. I will never again take davdskis coords serious and any other amateur tool after what i have learned and read thru various actuall scientific papers!
I just find it funny how he pushes a certain agenda .

So don´t take it serious.

Quote:

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Originally Posted by Croatian Legend

Ok i see where you are coming from. Well i can already asure you to completly ditch the breakdowns from G25 and the official Davdski files.
Vahaduo and the g25 coords is only trying to place you on a certain point in a pca nothing more nothing less. you being pretty much northwest european that maybe has some stong neolthic signal pushes you little south. That is why Vahaduo/g25 uses extreme points! Which is misleading!

Again Vahaduo is only good for general clustering nothing more. Gedmatch is the same and pretty outdated !

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I have seen that idea before that it's just extra EEF/ANF. My hypothesis is that it's that plus a little extra dash of post neolithic geneflow from the MENA.

You are from Croatia right? And you haven't been able to model with Natufian heavy populations?

Quote:

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Originally Posted by Gannicus

I have seen that idea before that it's just extra EEF/ANF. My hypothesis is that it's that plus a little extra dash of post neolithic geneflow from the MENA.

You are from Croatia right? And you haven't been able to model with Natufian heavy populations?

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Yes i tried it and it fails. As i said in my previous post i will never take vahaduo or davdskis model serious!

Yes i am Croat by ethnicity.

Quote:

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Originally Posted by Croatian Legend

Yes i tried it and it fails. As i said in my previous post i will never take vahaduo or davdskis model serious!

Yes i am Croat by ethnicity.

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May need to experiment further with different reference populations and different sources. I would assume that your ANF admix would be higher than me. I shared my Steppe/ANF/WHG and I'm 40% Barcin ANF. I'm experimenting with Sintashta now.

Quote:

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Originally Posted by Gannicus

May need to experiment further with different reference populations and different sources. I would assume that your ANF admix would be higher than me. I shared my Steppe/ANF/WHG and I'm 40% Barcin ANF. I'm experimenting with Sintashta now.

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Well the Dinaric plain was actually a safe haven for CHG's that came thru various waves. looking at papers they can confim it as also my qpadm run confirms it in my case. Now before some people might wonder , why am i not then close Georgians and such is simple. CHG ≠ CHG the CHG that i seem to contain is an older form and not mixed with natufian or iran-n or very little it seems.

Quote:

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Originally Posted by Gannicus

May need to experiment further with different reference populations and different sources. I would assume that your ANF admix would be higher than me. I shared my Steppe/ANF/WHG and I'm 40% Barcin ANF. I'm experimenting with Sintashta now.

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And as you can see i only have 27- 30% EEF which places me at lowest among Europeans . The only explanation i have why i can be also modelt with AHG instead of EEF and still get excellent p-value is perhabs because i seem to have some old neolthic/anatolian line even tho small but still.

Quote:

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Originally Posted by Croatian Legend

And as you can see i only have 27- 30% EEF which places me at lowest among Europeans . The only explanation i have why i can be also modelt with AHG instead of EEF and still get excellent p-value is perhabs because i seem to have some old neolthic/anatolian line even tho small but still.

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Have you tried the simple 3-way: Russia_Samara_EBA_Yamnaya, Turkey_Marmara_Barcin_N, and Loschbour? Because if you are doing mesolithic like based admixture model, your CHG would be coming from the Western Steppe Herders.

Quote:

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Originally Posted by Gannicus

Have you tried the simple 3-way: Russia_Samara_EBA_Yamnaya, Turkey_Marmara_Barcin_N, and Loschbour? Because if you are doing mesolithic like based admixture model, your CHG would be coming from the Western Steppe Herders.

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yes i have tried it and the p value goes way below 0,05! Yes i certainly have CHG from Steppe herders but you had other influx of CHG that came to the dinaric plain via Anatolia from Caucasus and maybe around the black sea.