Basal Eurasian discussion

[Desdonas]

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.

1. The point isn't that IBM had any Neanderthal ancestry at all, it's that their Neanderthal levels were higher than you would expect being a half/half West Eurasian + ANA mix. I went back to the original IBM paper's supplements ( Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations | Science) to see what they had to say about this - "Considering the dual ancestry of the Taforalt individuals, we can explain the Altai affinity in Taforalt as a dilution of its Natufian-related ancestry with its significant proportion (~36.5%) of sub-Saharan African ancestry." However, when looking at the f4s they used to determine this, some things stood out as unusual:

Imgur: The magic of the Internet

IBM has comparable Z scores to Natufians and Levant_N, even though the latter obviously have proportionately much less ANA than IBM does, although to be fair they do have lowish SNP counts. Also Iran_N has lowest Neanderthal out of all the Eurasians in that test and even lower than some of the Africans. There are some other odd results too like the high scores for Mozabites and Ju_Huan North, I would be interested in seeing if someone here could possibly re-run these or similar tests as a sanity check.

2. There have been lots of papers over the last few years showing that the divergence between Eurasians and Africans is very deep, going back 100k years. I don't think there's any real reason to assume that this proto-Eurasian coalescence (CT and L3) needed to have taken place in Africa. The below paper makes the case that the proto-Eurasian population spent an extended period of time coalescing in the neighborhood of Arabia for tens of thousands of years before disseminating across Eurasia as a whole, which sounds a lot more likely to me than the conventional OoA scenario whereby a branch of humans leaves East Africa 55,000-60,000 years ago and rapidly colonizes and replaces Neanderthals and Denisovans from all parts of Eurasia.

pnas.2213061120

Anyway, the y-hg E related population seems to be outgroup of all Eurasian-proper. Although the deep divergence between Africans and Eurasians can be explained by deep ancestry like A00, A and B, but if there was an early back migration (E, D2) from Arabia to Africa, we may see the "Arabian Standstill" alleles in Africans significantly.

An alternative scenario is that, follow the conventional OoA theory but consider that the chronology of BT, CT, DE and D may be older than expected. The following graph shows that D2(D0) split from D1-M174 at about 71kya.