Mega QAPDM Models thread

[Xavier727]

England_LIA / Denmark_EarlyViking

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[Xavier727]

England_MIA / Norway_IA

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Playing around with the reference pops and managed to get the P value up slightly

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[Gannicus]

England_MIA / Norway_IA

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Here's what I get:

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I haven't tried it with your references.

[Xavier727]

Here's what I get:

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I haven't tried it with your references.


Yeah, you should try it out when you get a chance, I’d be interested to see what you get.

[Fistora]

this is what I get when using your NW populations as a source combined with Russia Sunghir, which seems to me to be one of the best proxies for Slavs

https://i.postimg.cc/wvnfCNY0/image.png

[Gannicus]

Yeah, you should try it out when you get a chance, I’d be interested to see what you get.

With your references:

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With the additional references, it does not improve the p value for me.

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[Xavier727]

With your references:

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With the additional references, it does not improve the p value for me.

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Interesting, that’s quite a solid amount of Germanic you’ve got there, how much do you normally get with these IA models.

[AnthrogenicaRefugee]

A guy from Russia ran my Ancestry kit.

Models that passed
https://i.postimg.cc/5HLD7gVg/IMG-20251102-103802-054.jpg (https://postimg.cc/5HLD7gVg)

https://i.postimg.cc/NymZJDcC/IMG-20251102-103807-159.jpg (https://postimg.cc/NymZJDcC)

https://i.postimg.cc/CZk9P7g2/IMG-20251102-103816-345.jpg (https://postimg.cc/CZk9P7g2)

Models with Thracian and Illyrian sources failed, only the Glinoe Scythian, which he said is actually Dacian worked.

[Gannicus]

Interesting, that’s quite a solid amount of Germanic you’ve got there, how much do you normally get with these IA models.

It varies based on the samples used:

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Not really sure that in most cases qpAdm can reliably distinguish between Celtic and Germanic populations.

I can model myself with just Celtic sources also:

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And then Modeling with just Germanic sources:

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[Xavier727]

It varies based on the samples used:

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Not really sure that in most cases qpAdm can reliably distinguish between Celtic and Germanic populations.

I can model myself with just Celtic sources also:

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And then Modeling with just Germanic sources:

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Yeah, I've noticed that as well, which is interesting given how people always say how much better qpAdm is to G25. Also, it seems that your choice of right populations can have quite a big impact on your results, which is annoying given that there doesn't seem to be any clear formula on what makes for an optimal reference set.

[Gannicus]

I'm going to be experimenting with this combination more and see if I can get these standard errors down:

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[Fistora]

https://i.postimg.cc/43Ky3cXK/kddjsfjsfjsjf.png

[Gannicus]

About the best I can do with this combination

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Tried VK579 instead

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Both were ran with the Gernarchivist references I think Opie linked in an earlier post.

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[Artzenlohe]

PCA vs. qpAdm: More Similar Than People Think

Fundamentally, autosomal PCA and qpAdm modeling operate on the same basic idea:
They both assess how populations are related based on genome-wide allele frequencies — just using different statistical approaches.


PCA uses principal components to reduce genetic variance into 2D/3D plots, revealing clustering patterns.
qpAdm estimates ancestry proportions by modeling a test population as a mix of chosen “left” sources, with “right” reference groups to anchor the model.


But in both cases, your results depend almost entirely on your inputs.
You can cherry-pick populations in either method — and get misleading results that still “look” scientific.

Why qpAdm Isn't Immune to Narrative Bias

There’s a tendency to treat qpAdm as more rigorous than PCA, and while it can be more formalized, it’s just as vulnerable to biased modeling choices.

That’s why so many published studies claim Ashkenazi Jews are “50%+ Levantine” — even though PCA consistently places them overlapping with Southern Italians.

Here’s why:
Most of these studies use deeply flawed European proxies — Northern Italians, French, Sardinians, or even Tuscans — while completely ignoring Southern Italians or Sicilians. This artificially inflates the Levantine component, because these proxies are genetically too distant and don't match PCA placement.

The qpAdm model still returns a “feasible” result — because qpAdm doesn't know your sources are bad.
It just fits whatever you give it.

In other words: Bad source selection in qpAdm doesn’t get corrected by the math — it gets rewarded. The tool will give you a p-value and ancestry breakdown that looks clean, but is fundamentally built on cherry-picked assumptions.

PCA-Informed qpAdm is the Solution

That’s why my models start with PCA — which clearly shows Ashkenazi Jews clustering directly on top of Southern Italians — and then use qpAdm to test models that reflect that structure.

Examples from my thread:
Stable qpAdm Models of Ashkenazi Jewish Ancestry – Ignoring PCA No More (https://www.theapricity.com/forum/showthread.php?397054-%26%23129516%3B-Stable-qpAdm-Models-of-Ashkenazi-Jewish-Ancestry-%96-Ignoring-PCA-No-More)

Models such as:

Italian_South.HO + Lebanese_Muslim.HO
Italian_South.HO + Israel_Ashkelon_LBA.AG
Italian_South.HO + Israel_C_o2.AG


All produce stable 2-way models with:

~75–78% Southern Italian–like ancestry
~22–25% Levantine
Strong p-values and standard errors
Full consistency with PCA and historical records


This matches not just the genetic structure, but also the well-documented Roman and Byzantine-era Jewish presence in Southern Italy.

Visual Results

https://i.ibb.co/M0ZfVqC/1.png
Modern Levantine Proxy model

https://i.ibb.co/S4FnRm4s/2.png
Bronze Age Coastal Levantine (Philistine-admixed)

https://i.ibb.co/G43Kn5wk/3.png
Inland Bronze Age Levantine (likely Israelite/Canaanite)

Don’t Let Narrative Modeling Skew the Data

You can go check nearly any study by Behar, Hammer, or Ostrer — they almost all use Northern Italians or French as the European side of the model.
Even YouTubers like Andrei DNA — who is also an Apricity forum member — repeat the same setup and get the same distorted results: Ashkenazi Jews as a “Middle Eastern” population.

But if Ashkenazi Jews sit right on top of Southern Italians in PCA — and they do — then they’re no more “Middle Eastern” than a Calabrian is.

That’s why PCA-aligned qpAdm is essential — and narrative-driven modeling needs to be called out.

https://www.youtube.com/watch?v=5gxr79HfpYQ

You need southern Italians, Levantines, and Northern Europeans to model Ashkenazi Jews.

[Gannicus]

Using AndreiDNA's right and left populations, I modeled my Basal Eurasian admixture.



https://www.youtube.com/watch?v=t59yXBo1MoI





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Mbuti is the proxy for Basal Eurasian.

[userNa]

Mbuti is the proxy for Basal Eurasian.

Bad proxy in my opinion.

Target: Israel_Natufian
Distance: 27.4820% / 0.27482024
97.4 Russia_Kostenki14
2.6 Mbuti

Target: Georgia_Kotias.SG
Distance: 28.6263% / 0.28626346
100.0 Russia_Kostenki14

Target: Iran_GanjDareh_N
Distance: 27.1517% / 0.27151689
99.8 Russia_Kostenki14
0.2 Mbuti

[Gannicus]

Bad proxy in my opinion.

Target: Israel_Natufian
Distance: 27.4820% / 0.27482024
97.4 Russia_Kostenki14
2.6 Mbuti

Target: Georgia_Kotias.SG
Distance: 28.6263% / 0.28626346
100.0 Russia_Kostenki14

Target: Iran_GanjDareh_N
Distance: 27.1517% / 0.27151689
99.8 Russia_Kostenki14
0.2 Mbuti

You can't use G25 like that. It has to do with the outgroups that Andrei selected in his video. He made that video on it 4 months ago. Perhaps he has changed his mind on the method. It'd be nice if he could comment on it.

[userNa]

-

I've seen his videos.

In my opinion what shows up as Mbuti in his model is just an out-of-africa wave that postdates the first Eurasian arrivals and not actual African admixture.

[Gannicus]

I've seen his videos.

In my opinion what shows up as Mbuti in his model is just an out-of-africa wave that postdates the first Eurasian arrivals and not actual African admixture.

Right, it's not African at all. It's his attempt to measure Basal Eurasian that's using Mbuti as a proxy. Using his model with his source populations and reference populations it's speculated that I have 24% basal eurasian admixture. I thought it was interesting. So, I decided to share it.

[Gannicus]

Anyways back to the more typical modeling. Using Xaviers references a few posts ago I modeled myself with 2 Iron age sources, Norway IA and Czechia IA Hallstatt.

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Target: Gannicus_MergedFile_officialDavidski_scaled
Distance: 0.0326% / 0.03258002
66.6 Czech_IA_Hallstatt
33.4 Norway_IA.SG

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Target: Gannicus_MergedFile_officialDavidski_scaled
Distance: 0.0326% / 0.03258002
66.6 Czech_IA_Hallstatt
33.4 Norway_IA.SG

[userNa]

Right, it's not African at all. It's his attempt to measure Basal Eurasian that's using Mbuti as a proxy. Using his model with his source populations and reference populations it's speculated that I have 24% basal eurasian admixture. I thought it was interesting. So, I decided to share it.

Andrei claims (unless I haven't understood his videos) that Basal Eurasian is a politically correct term for African admixture in Eurasians. Anyways, thanks for posting.

[Gannicus]

Andrei claims (unless I haven't understood his videos) that Basal Eurasian is a politically correct term for African admixture in Eurasians. Anyways, thanks for posting.

I think he has since changed his mind.

[Gannicus]

Anyways back to the more typical modeling. Using Xaviers references a few posts ago I modeled myself with 2 Iron age sources, Norway IA and Czechia IA Hallstatt.

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Target: Gannicus_MergedFile_officialDavidski_scaled
Distance: 0.0326% / 0.03258002
66.6 Czech_IA_Hallstatt
33.4 Norway_IA.SG

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Target: Gannicus_MergedFile_officialDavidski_scaled
Distance: 0.0326% / 0.03258002
66.6 Czech_IA_Hallstatt
33.4 Norway_IA.SG

Tried it with Austria IA La Tene with different references this time.

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And this is what it looks like in G25:

Target: Gannicus_MergedFile_officialDavidski_scaled
Distance: 0.0309% / 0.03092630
55.0 Norway_IA.SG
45.0 Austria_IA_LaTene

[userNa]

That's me:
p value: 0.0954|Feasibility: TRUE
Greece_Peloponnese_N.AG_I5427.AG 56.5 +/- 9.25%
Iran_GanjDareh_N.AG_I1954.AG 22.96 +/- 4.60 %
Russia_Samara_HG.AG_I0124.AG 8.43 +/- 4.67 %
Russia_Ekven_OldBeringSea.AG_I7333.AG 2.48 +/- 2.35%
Jordan_PPNC.AG_I1699.AG 9.62 +/- 8.62%

[Gannicus]

That's me:
p value: 0.0954|Feasibility: TRUE
Greece_Peloponnese_N.AG_I5427.AG 56.5 +/- 9.25%
Iran_GanjDareh_N.AG_I1954.AG 22.96 +/- 4.60 %
Russia_Samara_HG.AG_I0124.AG 8.43 +/- 4.67 %
Russia_Ekven_OldBeringSea.AG_I7333.AG 2.48 +/- 2.35%
Jordan_PPNC.AG_I1699.AG 9.62 +/- 8.62%

Have you tried IA, BA, and Medieval yet?

[Xavier727]

Austria_IA_LaTene.AG + Denmark_IA.SG

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slightly different reference set

[userNa]

Have you tried IA, BA, and Medieval yet?

I haven't managed to obtain a good model for BA and IA so far (standard error is too high).
I have a decent one for medieval though:


p value: 0.7524|Feasibility: TRUE|
Ukraine_Medieval_Rus.SG_VK541.SG 16.56 +/- 7.25%
Turkey_Marmara_Iznik_Basilica_Roman_Byzantine_A.AG _I8366.AG 79.06 +/- 11.67%
Egyptian.HO_Egypt7.HO 4.38 +/- 7.75%

[Gannicus]

Austria_IA_LaTene.AG + Denmark_IA.SG

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slightly different reference set

I used your previous two reference lists:

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[Gannicus]

I haven't managed to obtain a good model for BA and IA so far (standard error is too high).
I have a decent one for medieval though:


p value: 0.7524|Feasibility: TRUE|
Ukraine_Medieval_Rus.SG_VK541.SG 16.56 +/- 7.25%
Turkey_Marmara_Iznik_Basilica_Roman_Byzantine_A.AG _I8366.AG 79.06 +/- 11.67%
Egyptian.HO_Egypt7.HO 4.38 +/- 7.75%

might want to use ancient egyptians jk2134 and jk2911. Modern Egyptians have more SSA than their ancient ancestors.

Pooling the samples together might help too. Like this:

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[Gannicus]

More with England MIA LIA

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[Xavier727]

interesting, that's quite surprising it's more Germanic than I would have thought, given your known ancestry. Why do you think that is?

[Gannicus]

interesting, that's quite surprising it's more Germanic than I would have thought, given your known ancestry. Why do you think that is?

I feel like some of the Iron Age Germanic is soaking up some of the Celtic since both groups have similar proportions of Steppe/ANF/WHG. I've done models with Iron Age Gauls and it pukes when Iron Age Germanics are added. To me, that tells me that qpAdm sees the similar proportions of Steppe Pastoralist, Anatolian Farmer, and West European hunter-Gatherer and can't make up it's mind where its coming from: Celtic or Germanic.

This one isn't too bad:

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standard errors are higher than I'd like which feeds into my thoughts about Celtic and Germanic groups having similar admixtures.


Or I am wrong and I am more Germanic than Celtic. I wouldn't think so considering my known ancestry. On the whole average English are roughly 60/40 Celtic/Germanic. French are still mostly IA Gaulish and Scottish and Irish have picked up some Germanic but not as much as the English.

AncestryDNA:

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MyHeritage:

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23&Me:

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[drb234]

More with England MIA LIA

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you need a continental celtic pop for gallic ancestry (i used R2055.SG + NOR2B6.SG ). also I'd use Scotland_IA for insular celtic. definitely an overestimate


These were the right pops i used for a personal iron age model on myself:
Mbuti.DG, Czechia_IA_LaTene.AG, France_MN.AG, Germany_Tollense_BA.SG, Switzerland_EBA_1.AG, England_EIA.AG, France_Alsace_Lingolsheim_EBA.AG, France_N.AG, France_Occitanie_IA2.SG, Germany_BellBeaker.AG, Germany_Saxony_LBK_N.SG, Hungary_IA_LaTene.AG, Latvia_BA.AG, Sweden_IA.SG, England_IA.AG, England_MIA.AG, Sweden_IA_2.SG, Sweden_Viking.SG, Switzerland_LN.AG, Sweden_Mesolithic.SG, Norway_North_Pre_Viking.SG

[Gannicus]

you need a continental celtic pop for gallic ancestry (i used R2055.SG + NOR2B6.SG ). also I'd use Scotland_IA for insular celtic. definitely an overestimate


These were the right pops i used for a personal iron age model on myself:
Mbuti.DG, Czechia_IA_LaTene.AG, France_MN.AG, Germany_Tollense_BA.SG, Switzerland_EBA_1.AG, England_EIA.AG, France_Alsace_Lingolsheim_EBA.AG, France_N.AG, France_Occitanie_IA2.SG, Germany_BellBeaker.AG, Germany_Saxony_LBK_N.SG, Hungary_IA_LaTene.AG, Latvia_BA.AG, Sweden_IA.SG, England_IA.AG, England_MIA.AG, Sweden_IA_2.SG, Sweden_Viking.SG, Switzerland_LN.AG, Sweden_Mesolithic.SG, Norway_North_Pre_Viking.SG

It took quite a few attempts and basically, I had to use Scotland LIA instead of Scotland IA. This is my result with your references:

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[drb234]

It took quite a few attempts and basically, I had to use Scotland LIA instead of Scotland IA. This is my result with your references:

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germanic looks about right considering your ancestry but i think insular celtic is too low

[Xavier727]

I feel like some of the Iron Age Germanic is soaking up some of the Celtic since both groups have similar proportions of Steppe/ANF/WHG. I've done models with Iron Age Gauls and it pukes when Iron Age Germanics are added. To me, that tells me that qpAdm sees the similar proportions of Steppe Pastoralist, Anatolian Farmer, and West European hunter-Gatherer and can't make up it's mind where its coming from: Celtic or Germanic.

This one isn't too bad:

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standard errors are higher than I'd like which feeds into my thoughts about Celtic and Germanic groups having similar admixtures.


Or I am wrong and I am more Germanic than Celtic. I wouldn't think so considering my known ancestry. On the whole average English are roughly 60/40 Celtic/Germanic. French are still mostly IA Gaulish and Scottish and Irish have picked up some Germanic but not as much as the English.

AncestryDNA:

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MyHeritage:

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23&Me:

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Yeah, that makes sense. Celtic and Germanic both draw from very similar Steppe/ANF/WHG proportions, so it's likely that qpAdm might be struggling to cleanly separate them, unless you've got a really well chosen ref list. I would agree that broadly, the English average is probably somewhere around 30–50% Germanic, maybe slightly higher depending on region, so considering you have quite a sizable amount of English it’s possible for you to come out a bit more Germanic-shifted

[Gannicus]

germanic looks about right considering your ancestry but i think insular celtic is too low

I'm still experimenting with your references. Using Scotland EIA bumps up the Insular.

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[userNa]

Right, it's not African at all. It's his attempt to measure Basal Eurasian that's using Mbuti as a proxy. Using his model with his source populations and reference populations it's speculated that I have 24% basal eurasian admixture. I thought it was interesting. So, I decided to share it.

I just watched AndreiDNA's video (the one you posted). It's actually a very clever idea. My apologies for criticizing his method.

[Gannicus]

Here's a couple more:

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And this one is with French Bell Beakers. Different references though.

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[drb234]

Here's a couple more:

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And this one is with French Bell Beakers. Different references though.

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model with scotland_mia looks very solid

[userNa]

My grandmother's result. Her Slavic admixture is much higher than mine (around 30% higher), even though we're both from the same region.

p value: 0.1449|Feasibility: TRUE|
Ukraine_Medieval_Rus.SG_VK541.SG 22.23 +/- 7.37 %
Egyptian.HO_Egypt7.HO 9.41 +/- 10.69 %
Italy_Imperial.SG_R126.SG 68.37 +/- 14.84 %

[Xavier727]

Denmark IA, Scotland IA, France Grand est, Drb234's model

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[J. Ketch]

Denmark IA, Scotland IA, France Grand est, Drb234's model

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How much non-English Germanic ancestry do you have? That's quite high Germanic for an Englishman if true.