Basal Eurasian discussion

[Riverman]

I have some doubts about the phylogenetic position of ANA. Especially E1b1b is deeply nested in the diversity of E2, E1a, and E1b1a. In this situation, could the following three situations be considered?

1. ANA is a mixture of an East/West African related lineage and an unknown para-Eurasian lineage.

2. Some ANA-related populations contributed to East/West Africans.

3. Some lineages like A00 indicates a more ancient layer in West Africans.

I would venture to say mt-L3* and y-hg CT* formed in East Africa. The OOA group moved out, developing/retaining mt-L3m and L3n and y-hg CF*, pre-D1'2. Those that stay behind retain various other mt-L3 and y-hg pre-E and D0. This group later spreads within Africa giving arise to a large portion of the ancestry of extant East & West Africans, as well as ANA. Upon superficial examination East/West/North African ancestries don't seem to attract much to each other, but in test qpgraph runs, if you put a deep branch into each of them (South -> East, Deep A00 -> West, Aterian? -> ANA), you can flesh out a 'y-hg E' associated autosomal signature.

It is pretty obvious that we deal with different Basal African and Archaic African branches which form layers above each other and the ANA-like E-dominated group coming in later on top. Now the question is from where, and this should be fairly close to Basal Eurasian/the split from Eurasians plus more removed from those older layers, with which they didn't mix before the ANA - Basal Eurasian split.
Therefore one would have to prove or disprove who lived in say East Africa, because West Africa was settled later by the E-people anyway, before the supposed split. Was it that ancestral population, or a separate Basal African branch. The current sampling doesn't allow that, because its too shallow in time. Its however clear that the E-people spread their earlier than in West Africa and we have the separate Nilotic branches which being dominated by haplogroup A and B, not E:
https://en.wikipedia.org/wiki/Nilotic_peoples#Y_DNA

With E1b1b being mainly spread with Afro-Asiatic people, which origin in East Africa, North East Africa or West Asia is also a matter of debate.

The Hadza too being dominated by haplogroup B: https://en.wikipedia.org/wiki/Hadza_peop...ic_history

Therefore in Central-East Africa, all non-Afro-Asiatic and likely older, deeper rooted people (Pygmy, Nilotes, Hadza etc.) are dominated by haplogroup A and B.

The Mota sample in itself is fairly young and no real evidence for any sort of deeply rooted presence of E in East Africa.

That doesn't mean there wasn't one, but the current evidence is insufficient to directly prove it.

[Kale]

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).

[Norfern-Ostrobothnian]

Onge only appears in qpAdm if the non-West Eurasian ancestry in them doesn't have a good proxy. Usually if the proxy is Mbuti or Mota. Zlaty Kun mostly compensates in qpAdm.
In qpGraph I haven't seen a need for admixture from East Eurasians to Iran Neolithic as Basal Eurasian, ANE and AHG seems to be enough.

[Norfern-Ostrobothnian]

Most of East African E is either specific to Omotics with E1b1a2 or later Afro-Asiatic admixture. I suspect B2b1 is the proxy for Nilotic ancestry.

[Riverman]

At some point in the past, it is possible East Africa may not have had y-hg A or B, just E (and D0).

Highly unlikely in my opinion, but without ancient DNA I can't exclude it with certainty.

I think that the Nilotics and Hadza are the smoking gun, because the Afro-Asiatics from East Africa got lots of Natufian-like admixture pointing to how they acquired E1b1b. They got it from either North East Africa or the Levante/Near East/Southern Arabia imho. But that too is more conjecture without factual evidence from ancient DNA.

[kolompar]

The problem with these examples is that Z is below 3.. Many people will not accept this examples as statistically significant.  The requirement is to have Z> 3.

No, that's the point, there are several East Eurasian populations which don't have significantly more Neanderthal than Iran, so there's no need for a lower Neanderthal Basal, as long as you don't force high Neanderthal Europeans into them. And from those stats I would also guess that the Anatolian/Natufian parent population does actually have some European admixture.

I was skeptical of Basal Eurasian for a while, and decided I would be convinced of it's existence if a sample was found meeting the following criteria.
1) Equally related to East-Eurasians, Paleolithic Europeans, and Ust-Ishim
2) Less related to all of the above than they are to each other
3) More related to hypothesized Basal Eurasian carrying populations

ZlatyKun checks boxes 1 and 2, and gets partial credit on 3. She is not more related to ancient Near Easterners, but... ancient Near Easterners are equally related to her and Ust-Ishim, and that is despite the majority of their ancestry being derived from populations with significant preference for Ust-Ishim, meaning, the 'Basal' portion has to be more ZlatyKun related to counterbalance.

What's going on with IBM is probably a separate phenomenon than BE. However, there is the matter that ZlatyKun is more related to Ust-Ishim than Iran_N are, meaning Iran_N is more 'Basal'. There are 2 simple ways of resolving that. Either 1) ZK = BE + some undifferentiated 'crown Eurasian', or 2) Iran_N has ZK-like BE, plus something even more Basal (which could be IBM-related).

What kind of lame Basal Eurasian is that if it's not more related to populations with Basal Eurasian?
It is basal in a way, just not what we're looking for, more like the undifferentiated early Eurasian Ust'-Ishim was thought to be.
So rerunning the Basal f-stats with it:

Code:

pop1    pop2    pop3    pop4    est    se    z    p    n
Cameroon_SMA    Czechia_Bohemia_UP_HG    Bulgaria_BachoKiro_LatePleistocene    Morocco_Iberomaurusian    -0.011211485    0.000727954    -15.40135625    1.60E-53    495040
Cameroon_SMA    Czechia_Bohemia_UP_HG    Bulgaria_BachoKiro_LatePleistocene    Israel_Natufian_contam    -0.00307463    0.000854294    -3.599028348    0.000319408    254448
Cameroon_SMA    Czechia_Bohemia_UP_HG    Bulgaria_BachoKiro_LatePleistocene    Turkey_Epipaleolithic    -0.000292403    0.000792452    -0.368985631    0.712138435    417232
Cameroon_SMA    Czechia_Bohemia_UP_HG    Bulgaria_BachoKiro_LatePleistocene    Iran_GanjDareh_N    -0.001805539    0.000624155    -2.892772527    0.003818577    493867
Cameroon_SMA    Czechia_Bohemia_UP_HG    Russia_Kostenki14    Morocco_Iberomaurusian    -0.010603615    0.000751687    -14.10643125    3.47E-45    519216
Cameroon_SMA    Czechia_Bohemia_UP_HG    Russia_Kostenki14    Israel_Natufian_contam    -0.00248992    0.000899673    -2.767583596    0.005647356    262659
Cameroon_SMA    Czechia_Bohemia_UP_HG    Russia_Kostenki14    Turkey_Epipaleolithic    0.000303433    0.000800846    0.378890575    0.704769124    435022
Cameroon_SMA    Czechia_Bohemia_UP_HG    Russia_Kostenki14    Iran_GanjDareh_N    -0.001247553    0.000687364    -1.814981966    0.069526681    518137
Cameroon_SMA    Czechia_Bohemia_UP_HG    Laos_Hoabinhian.SG    Morocco_Iberomaurusian    -0.011393172    0.000830525    -13.71802839    7.92E-43    256781
Cameroon_SMA    Czechia_Bohemia_UP_HG    Laos_Hoabinhian.SG    Israel_Natufian_contam    -0.002366398    0.001081062    -2.188957071    0.02859996    133818
Cameroon_SMA    Czechia_Bohemia_UP_HG    Laos_Hoabinhian.SG    Turkey_Epipaleolithic    0.000301645    0.000968891    0.311330156    0.755549645    215485
Cameroon_SMA    Czechia_Bohemia_UP_HG    Laos_Hoabinhian.SG    Iran_GanjDareh_N    -0.001449651    0.000767333    -1.889207001    0.058864097    256042
Cameroon_SMA    Czechia_Bohemia_UP_HG    Russia_Ust_Ishim.DG    Morocco_Iberomaurusian    -0.011627461    0.000782028    -14.86835158    5.29E-50    521997
Cameroon_SMA    Czechia_Bohemia_UP_HG    Russia_Ust_Ishim.DG    Israel_Natufian_contam    -0.003146805    0.000936899    -3.358746331    0.000782969    263124
Cameroon_SMA    Czechia_Bohemia_UP_HG    Russia_Ust_Ishim.DG    Turkey_Epipaleolithic    -0.000272478    0.000874841    -0.311459822    0.755451083    436733
Cameroon_SMA    Czechia_Bohemia_UP_HG    Russia_Ust_Ishim.DG    Iran_GanjDareh_N    -0.002167952    0.00075457    -2.873095032    0.004064718    520831

Iberomaurusian and Natufian are obvious, Pinarbasi is ~0. Iran is very close to significant, as expected if it was just a slightly earlier split, with maybe a bit of Natufian admixture?
To keep some hopes alive, with closer, haplogroup E outgroups:

Code:

Ethiopia_4500BP    Czechia_Bohemia_UP_HG    Bulgaria_BachoKiro_LatePleistocene    Iran_GanjDareh_N    -0.002500162    0.000634907    -3.937837842    8.22E-05    594160
Ethiopia_4500BP    Czechia_Bohemia_UP_HG    Belgium_UP_GoyetQ116_1    Iran_GanjDareh_N    -0.002554129    0.000744764    -3.429445081    0.000604817    391027
Ethiopia_4500BP    Czechia_Bohemia_UP_HG    Laos_Hoabinhian.SG    Iran_GanjDareh_N    -0.001986818    0.000725395    -2.738948336    0.006163606    293441
Ethiopia_4500BP    Czechia_Bohemia_UP_HG    Russia_Ust_Ishim.DG    Iran_GanjDareh_N    -0.001940386    0.000767471    -2.528286968    0.011462062    622948
Yoruba.DG    Czechia_Bohemia_UP_HG    Bulgaria_BachoKiro_LatePleistocene    Iran_GanjDareh_N    -0.001964273    0.000556041    -3.532604444    0.000411488    927135
Yoruba.DG    Czechia_Bohemia_UP_HG    Belgium_UP_GoyetQ116_1    Iran_GanjDareh_N    -0.002474731    0.000630034    -3.927932564    8.57E-05    520514
Yoruba.DG    Czechia_Bohemia_UP_HG    Laos_Hoabinhian.SG    Iran_GanjDareh_N    -0.001540393    0.000554349    -2.778744424    0.005456944    514578
Yoruba.DG    Czechia_Bohemia_UP_HG    Russia_Ust_Ishim.DG    Iran_GanjDareh_N    -0.001452546    0.000653141    -2.223941437    0.026152385    1024983

Some significant Z but looks more like just Zlaty Kun connection with Europeans.

[TanTin]

The problem with these examples is that Z is below 3.. Many people will not accept this examples as statistically significant.  The requirement is to have Z> 3.

No, that's the point, there are several East Eurasian populations which don't have significantly more Neanderthal than Iran, so there's no need for a lower Neanderthal Basal, as long as you don't force high Neanderthal Europeans into them. And from those stats I would also guess that the Anatolian/Natufian parent population does actually have some European admixture.

Some significant Z but looks more like just Zlaty Kun connection with Europeans.

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.

[Kale]

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?

[Desdonas]

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?

OK. But does AHG and Zlaty Kun show a certain connection like this? If that's the case, ZK (and possibly Ranis) may enter Europe through Anatolia. If not, then ZK may come from the Caucasus.

Anyway, Ust Ishim is likely to originate from Sistan or northwestern South Asia and migrated northward through Central Asia. The TMRCA difference of K2a and K2a1 is only a few hundred years, while K2a1 has a epicenter on the southern route, and all these below is a rapid process.

K2a-M2308
    K2a*  Ust Ishim
    K2a*  Oase
    K2a1-M2335
        "K2a1b"-Y28394
            K-Y28299  South Asia
            K-F14963  SE Asia
        "K2a1a"-M2311
            K-MF106925  SE Asia
            NO  East Asia

Last, Kolompar mentioned that some East Eurasian populations do not have significantly more Neanderthal than Iran. Maybe Onge/Oceanians? In this case, there may be some independent Neanderthal geneflow that enter East Asia through the northern route, leading to higher Neanderthal level in East Asians?

[Ebizur]

The route by which Y-DNA haplogroup C2-M217 has reached eastern Asia is an utter mystery. There is quite a gap between the estimated TMRCA of C-M130 (TMRCA 46,886 [95% CI 53,605 - 41,009] ybp according to FTDNA) and the estimated TMRCA of C2-M217 (TMRCA 33,324 [95% CI 38,168 - 29,094] ybp according to FTDNA). No example of pre-C2 has been found anywhere as far as I know. Three subclades have emerged almost simultaneously from the MRCA of C2-M217, but each of these three subclades has a much more recent MRCA of its own, and their geographic distributions are quite different from one another:

C2a-L1373 (TMRCA 21,987 [95% CI 25,245 - 19,148] ybp): this subclade of C2-M217 is the one that contributes most greatly to the generally recognized distribution of C2-M217 (covering mainly Central Asia, Mongolia, the Russian Far East, and indigenous Americans)
C2b1-Z1312 (TMRCA 14,871 [95% CI 17,239 - 12,826] ybp): this subclade of C2-M217 accounts for most members of C2-M217 among "East Asians proper" (e.g. Han Chinese, Koreans, Japanese)
C2b2-CTS4660 (TMRCA 2,155 [95% CI 3,011 - 1,507] ybp according to FTDNA, but it should be noted that FTDNA's samples do not cover the entire extant diversity of this subclade; 23mofang's TMRCA estimate for C-CTS4660 is 4960 ybp): found mainly among Tai peoples and among Han Chinese from extremely southern parts of China (e.g. Guangdong, Hainan, Guangxi)

It seems plausible that the carriers of pre-C2 might have experienced a distinct episode of admixture with some group of Neanderthals, but there is no positive evidence for such a scenario to my knowledge, either.

[TanTin]

There are many ways how to check Neanderthal or Denisovan  components .
From my experience, by using F4 or PCA  I could claim that the highest levels of Neanderthal and Denisovan ancestry  are in Africa...

The statement for:
"East Eurasians have higher Neanderthal ancestry than West Eurasians" -  is not so obvious at all.

With the time the Denisovan  / Neanderthal  archaic markers are decreasing and this is true in all directions.
The highest levels of both Neanderthal and Denisovan are clearly  visible in Africans. The reason for it: simple: they are the most ancient as origin. Most of the other populations are descendants of these Africans.

However with the first OOA towards Asia we have some early populations where the levels of Neanderthal / Denisovan is comparable to that in Africa. In general these levels will drop with the time, except for some populations living in isolation.  Isolated populations especially on some islands tend to keep the archaic markers and we see higher levels of those markers.  Best examples are from Australia and Oceania, Japan and some Mediterranean islands.

[TanTin]

Here is another example:


You may reproduce such results by running the following F4 stats:

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

NA19012.SG - is Japan

TEST - is per individual, not per population. !!!

I am doing this graphic by using other calculation technique, because running F4 for 10k individuals will take significant time. 
Also as I explained: by running F4 for individuals you don't need to care for Z anymore.  F4 for individuals will give you the number of shared markers and the result is presented as a percentage.

In general depending on QC ( quality control) if you put any , you should get between 30k - 200k markers and the results are good. (including Z in most of the cases will show high numbers).
If you follow me, you will understand my idea: that Africa is the most Denisovan/Neanderthal compared to the rest of the World..  The Denisova/Neanderthal differences in some parts of the world are mostly result of isolation or other reasons.

[Desdonas]

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?

OK. But does AHG and Zlaty Kun show a certain connection like this? If that's the case, ZK (and possibly Ranis) may enter Europe through Anatolia. If not, then ZK may come from the Caucasus.

Anyway, Ust Ishim is likely to originate from Sistan or northwestern South Asia and migrated northward through Central Asia. The TMRCA difference of K2a and K2a1 is only a few hundred years, while K2a1 has a epicenter on the southern route, and all these below is a rapid process.

K2a-M2308
    K2a*  Ust Ishim
    K2a*  Oase
    K2a1-M2335
        "K2a1b"-Y28394
            K-Y28299  South Asia
            K-F14963  SE Asia
        "K2a1a"-M2311
            K-MF106925  SE Asia
            NO  East Asia

Last, Kolompar mentioned that some East Eurasian populations do not have significantly more Neanderthal than Iran. Maybe Onge/Oceanians? In this case, there may be some independent Neanderthal geneflow that enter East Asia through the northern route, leading to higher Neanderthal level in East Asians?

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.

[TanTin]

The ANS/ANE lineage derived between 32% to 40% of their ancestry from the Basal East Asian Tianyuan lineage, and between 60% to 68% from the Early West Eurasian Kostenki14/Sunghir lineage. Accordingly, the ANS/ANE samples carried the Y-chromosome haplogroups belonging or downstream to P-M45 (P1 and Q/R) and the Mt-chromosome U.

ANCIENT NORTH EURASIAN
Distance: 4.6414 / 0.04641380
Sources: 2 / Cycles: 1/ Time 0.004 s

70.0 EUR_ KOSTENKI14_ 38kya
30.0 ESEA_ Tyanyuan_40kya

 From the explanation of  Jacob Harringer. Thanks   old europe 
 for providing the link:
https://www.google.com/url?sa=t&rct=j&q=...i=89978449

Basal East Asian Tianyuan lineage is not the same as Basal Eurasian  . However the idea for "Basal" is still the same. 
Basal are low of Neanderthal markers.

[TanTin]

There are also basal East Eurasians (bEE).

This was introduced by Takashi Gakuhari .
https://doi.org/10.1038/s42003-020-01162-2

The basal East Eurasians (bEE) are an ancient population that had no divergence among the ancestors of East Asians, Northeast Asians/East Siberian, and Native Americans. NA-ES-NA presents another ancient population that had no split between the ancestors of Northeast Asians/East Siberian and Native Americans.