A Vahaduo generated PCA model for Sardinians gives:
82.8% Barcin Neolithic
11.6% Loschbour
5.6% Yamnaya
Distance: 3.4303%
Ganj Dareh was included in the sources but gets a weight of zero. This seems to imply that Sardinians don’t have any eastern-Farmer related ancestry.
When Sardinians are modelled with qpAdm using Barcin Neolithic, Loschbour, Yamnaya, and Ganj Dareh, the model fits well:
68.6% Barcin Neolithic
11.9% Loschbour
10.2% Yamnaya
9.4% Ganj Dareh Neolithic
p = 0.769
When Ganj Dareh is dropped, the model fails:
p = 1.18 × 10⁻¹²
This does not neccesarily that Sardinians derive exactly 9.4% of their ancestry directly from Ganj Dareh. But it shows that, with Barcin Neolithic as the core Anatolian source, the other three populations do not reproduce the target’s allele-sharing relationships.
The Vahaduo result answers a different question. It finds the weighted combination lying closest to Sardinians in the PCA space.
The qpAdm result also changes when a more eastern-shifted Anatolian farmer source is used:
75.1% Çatalhöyük EN
12.8% Loschbour
12.1% Yamnaya
p = 0.685
There is no longer a requirement for a separate Ganj Dareh source. Due to its genetic profile, Çatalhöyük is able to incorporate the eastern farmer related signal that previously was represented by a mixture of Barcin and Ganj Dareh.
This example therefore distinguishes three separate questions:
Is an ancestry dimension missing from the proposed model?
Which sampled population is the best available proxy for it?
Which historical population was the actual source?
qpAdm can formally address the first question and can help with the second. It cannot, by itself, guarantee the third.
PCA distance minimisation does not even formally test the first question. Its zero coefficient means only that a source was unnecessary for obtaining the closest point in that particular PCA (used here: G25). It cannot definitely tell that the drift represented by that group is absent.
Hence, the closest PCA fit might look geometrically plausible while still being an inadequate admixture model.
Disclaimer: qpAdm results are always conditional on the chosen right populations. A different right set can change the result. That said, with a reasonable selection of right groups, the models should be revealing, especially at this time depth. The right set used here is:
right = [ "Chimp", "Turkey_Epipaleolithic", "Georgia_KotiasKlde_Mesolithic", "Russia_Vologda_Mesolithic", "Switzerland_Epipaleolithic", "Iran_BeltCave_Mesolithic", ]With decent right groups, qpAdm can detect when a proposed source combination is missing an ancestry dimension. Removing Belt Cave and Klde Mesolithic in this example specifically would be tuning the right groups around the wanted result. But even after removing Belt Cave Mesolithic and Kotias Klde Mesolithic, the three-source model still fails decisively .