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
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
Modern Levantine Proxy model
Bronze Age Coastal Levantine (Philistine-admixed)
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.
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Originally Posted by Lard
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