Closest modern pops to ANE?

[Token]

I C. Its formal stats that are used to test prehistoric samples right? Would be great if someone can teach people how to use formal stats though but I guess its too difficult and complicated for most.

That would be a complete waste of time considering that the vast majority can't even use Global25 properly.

Ok. Yamnaya are around 50% ANE?

No.

[Maguzanci]

Yes but the difference would be very small anyway.

I see.

Yes, but it is the only steppe population that works well for Europeans. If you want very precise figures, you wil have to break down the Yamnaya and Koros_HG in deeper components (EHG, EEF, WHG, etc), which is not hard to do if you have a calculator and some free time.

Right. Why doesn't other steppe group work well? I will try but Saami and Udmurt, Mari are still roughly around 10% EEF as you estimated earlier?

They are firmly in the West Eurasian clade. These populations are so old that it doesn't even make sense to compare them to present-day populations, but the closest would be the West Eurasians in the northern fringes of west Eurasia since they have the least amount of Basal Eurasian admixture, considering that Kostenki14 had none.

Would that be Finns and other Uralics like Saami, Udmurt, Mari or some group like Chuvash?

Yes. West Eurasian PCAs with qpAdm are quite common out there, but i've never seen an East Eurasian PCA. That is in consonance with the fact that i've never seen a person using qpAdm that is not West Eurasian by ancestry. As a person of European descent, i don't care enough about East Eurasians to waste my time on such a project.

That's strange. But I think it make sense as people of West Eurasian origin are much more interested in genetics than East Eurasians. In fact, most people of East Asian/any other ENA origin I know, barely know anything about genetics outside of 23andme and gedmatch calculators. Have you seen an African PCA based on qpAdm?

That's ok. Im wondering though that if a Global PCA based on qpAdm results is created, would it still be affected by drift or any other factors?

[Maguzanci]

That would be a complete waste of time considering that the vast majority can't even use Global25 properly.


No.

How much ANE does Yamanya have? I read somewhere that Steppe populations in general are around 50% CHG and 50% EHG. Oh wait I think I confused the EHG with ANE.

[Token]

Right. Why doesn't other steppe group work well?

Archeogenetics is still trying to figure that out.

I will try but Saami and Udmurt, Mari are still roughly around 10% EEF as you estimated earlier?

Yes.

Would that be Finns and other Uralics like Saami, Udmurt, Mari or some group like Chuvash?

No because these have substantial East Eurasian admixture.

Have you seen an African PCA based on qpAdm?

No.

That's ok. Im wondering though that if a Global PCA based on qpAdm results is created, would it still be affected by drift or any other factors?

qpAdm is much less affected by recent population-specific drift.

[Zoro]

That would be a complete waste of time considering that the vast majority can't even use Global25 properly.

Sadly I've come to realize this too.

Im wondering though that if a Global PCA based on qpAdm results is created, would it still be affected by drift or any other factors?

No not affected by drift since qpAdm uses outgroups to mitigate but you still would have to look at other PCs besides PC1 and PC2

So both AG3 and MA1 are HAPLOID genomes meaning that they're not accurate because any actual hetrozygous positions have been genotyped as homozygous. So they're about 30%+ wrong. To make things worse, MA1 has 1x coverage and AG3 something like 0.2x coverage if I remember. People here should familiarize themselves with the concept of coverage if they want to get serious about leaning some basics

It would be immensely more accurate to use DIPLOID genomes such as the 30kya Yana Ancient Siberian which has 25x coverage or the 10Kya Ancient PaleoSiberian Kolyma genome with 14x coverage !! Other DIPLOID ancients that are available are Yamnaya Karagash and Botai and Ust Ishim and Stuttgart and Loschbour.

When talking about genetic similarity you'll get wildly different results depending on the tool used. But more basic than than are you asking maximum IBS similarity or actual IBD decent ?

Luckily ANE is old enough so the confounding factor that occurs with more recent BA genomes is not there. Meaning having to worry about whether the SNP between ANE and test subject is the same due to common ancient origin vs direct decent. Being as old as they are also means that every Eurasian is descended from them to some degree. I think Mansi and Nenets should be up there.


Lastly, you'll get very different results whether you use WGS vs limited number of SNPs from commercial genotyping companies such as 23andMe

[Maguzanci]

Archeogenetics is still trying to figure that out.

I see.

Yes.

Thanks for confirming it. I will still try to break the components for fun.

No because these have substantial East Eurasian admixture.

Would it be Scandinavians like Norwegians, Swedes, etc then?

No.

Alright. Would be nice to see one though.

qpAdm is much less affected by recent population-specific drift.

I see. Would be nice if Davidski can create a Global PCA based on qpAdm.

[Token]

Would it be Scandinavians like Norwegians, Swedes, etc then?

Probably Balts since they have the least amount of Basal Eurasian admixture of West Eurasia. But as i said, it doesn't makes much sense to compare a 40k year old individual with moderns, they will always be drastically different.

[Narration]

If you try to utilize Uralics as the closest modern day proxy for West Eurasian ancestry in Amerindians, the fit will be very bad since Uralics have some WHG and Basal Eurasian which Amerindians lack.

[Maguzanci]

If you try to utilize Uralics as the closest modern day proxy for West Eurasian ancestry in Amerindians, the fit will be very bad since Uralics have some WHG and Basal Eurasian which Amerindians lack.

Would EHG be a better choice as they are mostly ANE derived (but with good amount of WHG)?

True. But Uralics seem to have really low Basal Eurasian compared to most modern West Eurasians.

[Token]

Maguzanci, why are you so insistent in NOT simply using ANE to model Amerindians, when people keep telling you that nothing else will work?