Basal Eurasian discussion

[TanTin]

In regards to the qpgraph model in the OP, it frustrates me to no end that authors do not conduct basic sanity checks when performing these. The 36 unit drift edge leading to Iran_N (~twice their OOA bottleneck!) is bogus, Iran_N are the least bottlenecked population in West Eurasia at that time. To correct that issue would change the whole structure of the graph.

I am afraid that  we will have  to change the  whole structure  and to find new some new terminology. 
Because the idea of Basal is not covering well the existing models and also by using this terminology we can't describe the existing migration lines, that we can see in the real data. 


I just notices another confusing term:   'northern route' .
There is OOA Northern route / OOA Southern route ( you may see it on the picture in the first post here).
And there is " Northern route" proposed to explain  postglacial migrations of modern humans into East Asia. The general term for  Northern route  is more related to the continental migrations inside Central and North Asia, than SW Asia.  

I will have to stop using "Basal" as it doesn't fit in my models with its current meaning.

[Norfern-Ostrobothnian]

Although maybe a bit presumptuous to say this yet but as I see it:
Ancient North African = Aterian
Basal Eurasian = Baradostian and Rostamian eg. Zagros Aurignacian

I suspect that Kulbulakian might also be linked through Zagros Aurignacian but my hot take is that it was actually one of many Ancient North Eurasian cultures as it allegedly gave rise to the ANE heavy Tutkaulian culture during the Neolithic.

[Horatio McCallister]

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.

[Horatio McCallister]

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).

We are sorely missing IUP genomes from the Middle East, it's really just that simple - a single sample from 40,000-50,000 years ago would really blow the doors wide open on untangling broader Eurasian (and probably African) population history. Just to elaborate further on your sense of why BE is still a valid construct, one thing to keep in mind is that Zlaty Kun is not that much older than Ust Ishim, but is clearly more basal. So just imagine if we had a 45k, let along 50k or older sample from the Near East, Egypt, Persian Gulf, etc you would surely expect that sample to be significantly more basal than ZK.

One other issue is with understanding how African ancestry relates to BE. You brought up IBM, but I'm not sure how much we can say how African their ANA side really is. One thing that I find extremely under-investigated is why the direct f4/D stats are so bad teasing out relationships within Africans. I've seen stats in the form Chimp Yoruba Han Esan that are barely significant, meanwhile something like Chimp French Yoruba Han (I'm making up these particular scenarios but you get the idea) gets a hugely positive Z score, and it can't be just due to the OOA bottleneck because most SSA groups like Yoruba/Esan aren't some distinct tens of thousands of years drifted groups comparable in separation to something like French/Han. So unless we understand how to properly identify actual African ancestry, there will questions regarding what we can identify as exactly BE too.

[Kale]

With Africans there is probably a few complicating factors...
1) Not enough African populations in the construction of the 1240k snp panel. I think there were only 2? (Yoruba and San?). You'd think it would pick out strong signals at least for Yoruba and related populations if this were the only problem, (it would be interesting as a test to see how strong of a signal 1st degree African relatives would have in F-stats)
2) Multiple layers of ancestry at varying depths, as evidenced by y-hg A00, A0, A1a, A1b, B, E.

[Desdonas]

In regards to the qpgraph model in the OP, it frustrates me to no end that authors do not conduct basic sanity checks when performing these. The 36 unit drift edge leading to Iran_N (~twice their OOA bottleneck!) is bogus, Iran_N are the least bottlenecked population in West Eurasia at that time. To correct that issue would change the whole structure of the graph.

I am afraid that  we will have  to change the  whole structure  and to find new some new terminology. 
Because the idea of Basal is not covering well the existing models and also by using this terminology we can't describe the existing migration lines, that we can see in the real data. 


I just notices another confusing term:   'northern route' .
There is OOA Northern route / OOA Southern route ( you may see it on the picture in the first post here).
And there is " Northern route" proposed to explain  postglacial migrations of modern humans into East Asia. The general term for  Northern route  is more related to the continental migrations inside Central and North Asia, than SW Asia.  

I will have to stop using "Basal" as it doesn't fit in my models with its current meaning.

If "OoA" refers to the migration from Africa to Southwest Asia, then there is only one, either through Sinai or through Bab-el-Mandeb. Anyway, this happened in a meta population between 65 and 55kya.

Regarding East Asians, it is evident that they form a meta population with Hoabinhian and Oceanians which can be traced back to approximately 47-40kya (long before LGM). At this point, we can discuss the "Northern Route" and "Southern Route" by placing the East Eurasian meta population in the eastern part of Iranian Plateau. But all of these happened long after the initial OoA expansion.

[Norfern-Ostrobothnian]

An actual "African" genotype doesn't actually exist, the grouping is entirely geographical and paraphyletic in regards to Eurasians. South Sudanese Nilo-Saharans without any additional admixture from West Asia are more related to Eurasians than they are to West Africans, and both are more related to Eurasians than either are to Central African Hunter-Gatherers or South Africans. Eurasians are not the first split among human clades on a Middle Paleolithic scale in regards to Homo Sapiens, they are one of the last ones of the big clades to be still extant. Arguably there's also the internal North and South divide of South Africans but according to some models that also predated Eurasian East African split. So by definition Ancient North African is African but also not since the term doesn't actually refer to any single monophyletic clade. Now if they had any West or East African ancestry or contributed to them that's a different question, but even so at some point there has to have been a clade more related to Eurasians than to East or West Africans that became the bulk of the ancestry in Ancient North African and subsequently the non-Anatolian part of Iberomaurusian and partially Natufian.

[Desdonas]

An actual "African" genotype doesn't actually exist, the grouping is entirely geographical and paraphyletic in regards to Eurasians. South Sudanese Nilo-Saharans without any additional admixture from West Asia are more related to Eurasians than they are to West Africans, and both are more related to Eurasians than either are to Central African Hunter-Gatherers or South Africans. Eurasians are not the first split among human clades on a Middle Paleolithic scale in regards to Homo Sapiens, they are one of the last ones of the big clades to be still extant. Arguably there's also the internal North and South divide of South Africans but according to some models that also predated Eurasian East African split. So by definition Ancient North African is African but also not since the term doesn't actually refer to any single monophyletic clade. Now if they had any West or East African ancestry or contributed to them that's a different question, but even so at some point there has to have been a clade more related to Eurasians than to East or West Africans that became the bulk of the ancestry in Ancient North African and subsequently the non-Anatolian part of Iberomaurusian and partially Natufian.

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.

[Norfern-Ostrobothnian]

My guess is that E is actually a panmixic haplogroup that was simply lost in Eurasians during OOA because it appears in West Africans, East Africans and Iberomaurusian. Another option is founder effect but I believe a panmixia would work better
E2 E1a and E1b1a1 probably became West African specific and the ancestors of East Africans, ANA and Eurasians only retained E1b1b and E1b1a2 latter of which remained only in East Africans. Then finally E1b1b was lost among Eurasians once they split away from ANA.

[Desdonas]

My guess is that E is actually a panmixic haplogroup that was simply lost in Eurasians during OOA because it appears in West Africans, East Africans and Iberomaurusian. Another option is founder effect but I believe a panmixia would work better
E2 E1a and E1b1a1 probably became West African specific and the ancestors of East Africans, ANA and Eurasians only retained E1b1b and E1b1a2 latter of which remained only in East Africans. Then finally E1b1b was lost among Eurasians once they split away from ANA.

The TMRCA of E1b1 is too late. According to Yfull, it is 41,400 BP.

https://www.yfull.com/tree/E-P177/

OoA, or the time when Eurasians split from ANA, is far before the born of E1b1. If we consider that 55kya (Razib Khan's chronology of Neanderthal admixture) as the lower limit of OoA, it may even be before E*.

[Riverman]

An actual "African" genotype doesn't actually exist, the grouping is entirely geographical and paraphyletic in regards to Eurasians. South Sudanese Nilo-Saharans without any additional admixture from West Asia are more related to Eurasians than they are to West Africans, and both are more related to Eurasians than either are to Central African Hunter-Gatherers or South Africans. Eurasians are not the first split among human clades on a Middle Paleolithic scale in regards to Homo Sapiens, they are one of the last ones of the big clades to be still extant. Arguably there's also the internal North and South divide of South Africans but according to some models that also predated Eurasian East African split. So by definition Ancient North African is African but also not since the term doesn't actually refer to any single monophyletic clade. Now if they had any West or East African ancestry or contributed to them that's a different question, but even so at some point there has to have been a clade more related to Eurasians than to East or West Africans that became the bulk of the ancestry in Ancient North African and subsequently the non-Anatolian part of Iberomaurusian and partially Natufian.

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.

Number 2 is correct since we already know that the foragers of Africa before the Niger-Kordofanian/Bantu and Afro-Asiatic expansions were completely dominated by yDNA A and B and we deal with a later expansion of these groups, which had a strong ANA contribution.

In my opinion we might deal with a back migration of ANA from West Asia or a development in situ, in North Eastern Africa. From there first the modern SSA lineages spread and they were followed by E1b1b which already had West Eurasian admixture and was no longer Basal Eurasian/ANA.

In my opinion the splits go like that:
Basal African <-> ANA
ANA <-> Basal Eurasian (presumably its here that E split into ancestral modern SSA which remained in North Africa and WANA branches, mainly E1b1b of E.
Basal Eurasian <-> Crown Eurasian (E1b1b remained in the refuge the others moved out and mixed with Neandertals)

[Horatio McCallister]

An actual "African" genotype doesn't actually exist, the grouping is entirely geographical and paraphyletic in regards to Eurasians. South Sudanese Nilo-Saharans without any additional admixture from West Asia are more related to Eurasians than they are to West Africans, and both are more related to Eurasians than either are to Central African Hunter-Gatherers or South Africans. 

Yeah, sorry but I don't believe this, that might be what the formal stats show but I think it just simply strains credulity to believe in these ultra inflated intra-African divergences (San and perhaps pygmies excluded). 

Look at the nearest phylogenetic relative to West Africans we have, Mota with E-M329, split from West African E-M2 40,000 ybp, and mtDNA L3x which is cladal with West African L3e, one of the most common WA mtDNA lineages. These splits are admittedly old but are comparable in age to the splits we see within East Eurasians between Tianyuan, Onge, Hoabhinian, Oceanian, etc. You really think the ancestors of South Sudanese living right next door would somehow be more related to Eurasians than their nearest neighbors? And the deep ancestors of WAs and SS surely remained more in contact with each other for thousands of years longer than all the different branches of the East Eurasian meta-population did.

The vast majority of living African variation stems exactly from this Ethiopian/Sudanese nexus in the Later Stone Age, formal stats can show what they show but when they contraindicate basic common sense then we need to take a step back and see if there's something wrong with the underlying methodology.

[Norfern-Ostrobothnian]

Mota is more related to South Sudanese but West Africans only arrived to the region with the Ubangian migrations in the past 3000 years. Obviously barring the Kordofanian groups of Nuba mountains which may be earlier incursions.
E1b1a2 may also be a founder effect considering that Mota is only 4500 years old with other Nilotic related peoples being mostly B2b1 instead. In fact I believe Mota may be the earliest E1b1a2 we have so far from the region.

[Kale]

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.

[Hammas]

I know this is kind of unrelated but is it really true that Iran N has 20% Onge related ancestry? I’ve seen other models with Zlaty Kun and the Onge admixture isn’t present. Which model is more accurate?