Mega QAPDM Models thread

[Gannicus]

Another combination that works for Morocco_MN skh001:



references:





This makes it look more like there is an actual Anatolian component.

Then again, the p value is better if one just models him with Natufian:

[AndreiDNA]

i've seen folks on the illustrative subreddit post their Fst charts to various ancient groups with such extension as .SG or .AG
Im banned from reddit so I can't respond to them.
But I want to say here that Fst does not work the way you want it to (showing your genetic distance to some group) with haploid samples.
It works as intended only with diploid groups.
Here's a comparison of Fst of modern french vs some modern diploid ethnicities (Mbuti,Australian) vs Iron age Gauls who are basically identical to french on a PCA


Notice how the French end up closer to Mbuti than to Iron age Gauls? That's because the Gaul sample is non diploid.

It gets even more tricky when you compare yourself with haploid groups that consist of multiple samples. When you do that, essentially the more samples a group has the lower the Fst will be. That's because according to statistics, with more samples the allele frequency will be closer to the expected frequency in that population


Hopefully someone here can drop this in the illustrative subreddit so folks know how to interpret Fst the right way

[Gannicus]

i've seen folks on the illustrative subreddit post their Fst charts to various ancient groups with such extension as .SG or .AG
Im banned from reddit so I can't respond to them.
But I want to say here that Fst does not work the way you want it to (showing your genetic distance to some group) with haploid samples.
It works as intended only with diploid groups.
Here's a comparison of Fst of modern french vs some modern diploid ethnicities (Mbuti,Australian) vs Iron age Gauls who are basically identical to french on a PCA


Notice how the French end up closer to Mbuti than to Iron age Gauls? That's because the Gaul sample is non diploid.

It gets even more tricky when you compare yourself with haploid groups that consist of multiple samples. When you do that, essentially the more samples a group has the lower the Fst will be. That's because according to statistics, with more samples the allele frequency will be closer to the expected frequency in that population


Hopefully someone here can drop this in the illustrative subreddit so folks know how to interpret Fst the right way

I shared this model on another forum and one member said: "i highly doubt you have any natufian . let alone 8%". What do you think about that? I said: "If some of it does not come from Roman and Greek period interactions, then it's from ANF."
And I shared this qpAdm model of Barcin:

[AndreiDNA]

I shared this model on another forum and one member said: "i highly doubt you have any natufian . let alone 8%". What do you think about that? I said: "If some of it does not come from Roman and Greek period interactions, then it's from ANF."
And I shared this qpAdm model of Barcin:

I think the West Asian admix in ANF is from Iran N, not CHG. Since Iran N were farmers and such, that's likely where the tradition comes from in ANFs. Although I guess CHG being the source is also possible. Try to exchange CHG for Iran N in your model and see if the pval improves.

[Gannicus]

I think the West Asian admix in ANF is from Iran N, not CHG. Since Iran N were farmers and such, that's likely where the tradition comes from in ANFs. Although I guess CHG being the source is also possible. Try to exchange CHG for Iran N in your model and see if the pval improves.

P Value did improve. Natufian dropped a bit. I guess that could be from qpAdm's struggle with the basal Eurasian component in both Iran_N and Natufian?

[Opie]

Now that IllustrativeDNA introduced QAPDM service, I thought starting a thread where everyone shares QAPDM models would be resourceful.

As a start, I am sharing this model:

Sources

Turkey_Marmara_Barcin_N.AG (Anatolian Neolithic Farmer)

Russia_Sidelkino_HG.SG (Eastern European Hunter-Gatherer)

Luxembourg_Mesolithic.AG (Western European Hunter-Gatherer)

Georgia_Kotias_Mesolithic.SG (Caucasus Hunter-Gatherer)

Iran_GanjDareh_N.AG (Neolithic Iranian Farmer)

References

Mbuti.DG

Russia_AfontovaGora3_UP.AG

Italy_Epigravettian.SG

Russia_Kostenki14_UP.SG

Turkey_Central_Pinarbasi_Epipaleolithic.AG

Turkey_Central_Boncuklu_PPN.AG

Russia_Tyumen_HG.AG

Israel_Natufian.AG

Morocco_Iberomaurusian.AG

Georgia_Satsurblia_LateUP.SG

Iran_Wezmeh_N.SG

India_GreatAndaman_100BP.SG

I forgot to post my results with this model. Here it is.

[Opie]

I did this with your sources and references except India_GreatAndaman_100BP.SG and
Russia_Kostenki14_UP.SG


Attachment 141698

I've seen QAPDM models which don't make a distinction between CHG and ZNF. Maybe it's something about QAPDM. I think Iran both you and me is misinterpreted CHG for the most part.

[Opie]

Remove kostenki and Andaman from your rights. They're irrelevant to the model and will lead to worse pval

Here's the results of your suggestion. P value of this is better I guess.

[Opie]

A list of references suggested by a genarchivist.


References

Mbuti.DG, China_YR_MN.SG, Morocco_Iberomaurusian.AG, Israel_Natufian.AG, Iran_GanjDareh_N.AG, Turkey_Marmara_Barcin_N.AG, France_Mesolithic.AG, Russia_YuzhniyOleniyOstrov_Mesolithic.AG, Russia_Samara_EBA_Yamnaya.AG, Poland_GlobularAmphora.AG

[Gannicus]

A list of references suggested by a genarchivist.


References

Mbuti.DG, China_YR_MN.SG, Morocco_Iberomaurusian.AG, Israel_Natufian.AG, Iran_GanjDareh_N.AG, Turkey_Marmara_Barcin_N.AG, France_Mesolithic.AG, Russia_YuzhniyOleniyOstrov_Mesolithic.AG, Russia_Samara_EBA_Yamnaya.AG, Poland_GlobularAmphora.AG

Took you long enough Opie . A few posts ago (post #34), I shared a model with the references I used that measured my EHG, AHG, CHG, Natufian, WHG, and Iran Neolithic admixture. I’d like to see what you score with that model.