Basal Eurasian discussion

[kolompar]

The affinity for Zlaty Kun in Iranian HG's is likely from their Baradostian ancestry, which we don't have samples of, and which is not Zlaty Kun, just some early branch of Eurasians. Perhaps this is what those early researchers called "Basal Eurasian": a mixture of Baradostian (admixture calculators go for Zlaty Kun as a proxy in the absence of actual Baradostian samples) and "ANA" (quite possibly Emiran). Zlaty Kun had Neanderthal ancestry though, and probably so did Baradostian.

If I recall, even Iberomaurusians had higher than average Neanderthal ancestry, which doesn't make a lot of sense if operating under the assumption that ANA is really some sort of genuinely African type ancestry. I'm skeptical that the ANA-side of IBM is really some deeply rooted local Aterian relict and not just some very old Egyptian or Levantine (Emiran as you mentioned) reflux.

They clearly have European HG ancestry, maybe all of their non-ANA is simply WHG-like, so that's where their Neanderthal comes from. I also think Aterian is too old, haplogroup E probably came from East Africa less than 40 thousand years ago, and that should be most of the African part.

Aren't Nilote's y-hg A mostly/all A-M13? Y-full and FtDNA both have the TRMCA of M13 at ~10KBC. Probably a later incursion from the South.
Y-hg B seems to have most of it's diversity in Central Africa.
At some point in the past, it is possible East Africa may not have had y-hg A or B, just E (and D0).

Could be just a bottleneck? I used to think CT is Eurasian because it would be unlikely that C and F (and D?) all went extinct in Africa, but there really isn't all that much diversity in Africa, something like 10 branches at the OoA time depth with E and D0 both there from CT. So likely a lot went extinct, plus sampling is also way behind, maybe something could turn up eventually.

What kind of lame Basal Eurasian is that if it's not more related to populations with Basal Eurasian?

What I was trying to illustrate regarding point 3 was this.
Congo_Mbuti.DG Sunghir.SG      ZlatyKun.SG Ust_Ishim.DG  0.00278  4.44  1127764
Congo_Mbuti.DG MA1.SG          ZlatyKun.SG Ust_Ishim.DG  0.00285  3.89  791393
Congo_Mbuti.DG Andaman_100BP.SG ZlatyKun.SG Ust_Ishim.DG  0.00289  4.22  1111692
Congo_Mbuti.DG Iran_Wezmeh_N.SG ZlatyKun.SG Ust_Ishim.DG -0.00048 -0.75 1126449
If Iran_N is ~60% of it's ancestry from something in the neighborhood of Sunghir/MA1/Andaman, and there is no connection between ZlatyKun and Iran_N, shouldn't that last stat have 60% of the d-value of the first 3?

Well, what could be wrong there...

Code:

Mbuti.DG Iran_GanjDareh_N Czechia_Bohemia_UP_HG Russia_Ust_Ishim.DG -8.73E-05 0.000547693 -0.159441747 0.87332085 1024958
Mbuti.DG Iran_GanjDareh_N Czechia_Bohemia_UP_HG China_Tianyuan 0.001100443 0.000547264 2.010810096 0.044345519 841640
Mbuti.DG Iran_GanjDareh_N Czechia_Bohemia_UP_HG Russia_Kostenki14 0.004344356 0.000534625 8.125992513 4.44E-16 1003557
Mbuti.DG Iran_GanjDareh_N Czechia_Bohemia_UP_HG Russia_MA1_HG.SG 0.006491183 0.000560707 11.57679177 5.40E-31 729232
Mbuti.DG Iran_GanjDareh_N Czechia_Bohemia_UP_HG Indian_GreatAndaman_100BP.SG 0.001585569 0.000522755 3.033100144 0.002420553 1016556

It might be something in Ust-Ishim, the same thing that also makes him less related to East Eurasians than he should be.
The other option is this is proof there was Iran/Basal gene flow into West Eurasians.

Let me add something about this Z- requirement.
It is valid only when we do statistics for some group of individuals or for some population.
However we can run F-statistics for individuals only.
In our case: ZK - is one individual only.
BK are 4 or 5, but we may run Fstats for for whichever we like. 
Laos_Hoabinhian.SG  - is pretty much the same..
So to avoid this inconvenience with Z-requirement - the simple step to bypass it:  just select one individual  and run the F-test with it.
In such case F-stats will just count the number of shared alleles between these 4 individuals and it will provide results in the form of simple count and percentage.. 
Z-number doesn't matter in such case. More especially in the case where est  is near 0 .  
Dividing near 0 value with some small number is not much recommended.
If our test populations are a group with significant numbers, then we must take into account Z-value. however when working with individuals we may just ignore this.

Z is only a requirement to show there was gene flow. Maybe you can't prove a negative but if Z is close to zero you have no evidence of gene flow, that's how f-stats are usually used.
Don't really know about bias but f4 should be less affected by it if I go by this.
https://uqrmaie1.github.io/admixtools/ar...stats.html

F4( TEST, NA19012.SG ,  Vindija_snpAD.DG, Loschbour.DG )

For Africans that will be positive because Japan and Loschbour are both OoA bottlenecked. Will a simple PCA not work? First component should separate modern and archaic.

In fact, until now I still believe that BE split from other Eurasians before 55-60 kya. But if there is not much Neanderthal in Oceanians and Onge, then the Neanderthal pulse shared by all Eurasians at around 55 kya may be the similar size. The extra Neanderthal in Oase, Bacho Kiro and East Asians is secondary. Furthermore, BE may not be very basal, while Crown Eurasian may be more derived than expected.

It was Hoabinhian, Jomon, and maybe Longlin and AASI. For Oceanians I don't know because I can't really calculate their Neanderthal from just f-stats because of their Denisovan. For East Asians it might also be that their extra archaic affinity comes from the Denisovan that the Salkhit paper detected. I don't know how much the European ancients are considered for the usual suggestion that there was only one Neanderthal admixture event. Maybe all admixing Neanderthal was very similar, I think around the Altai they also got replaced by Vindija ones?