The mixed genetic origin of the first farmers of Europe

[Ryukendo]

One can quibble with the theoretical nature of the constructs produced in Lipson et. al., but until we get aDNA whatever estimate we get from models that have a solution for the "Iberomaurusian-attracting/Yoruba-repelling" problem would be better than models that don't. One could also introduce an admixture edge from Iberomaurusian to Yoruba in the context of Lipson et. al's models, which I guess would push the ANA divergence back a bit.

There can also both be migration back to Africa (from Neanderthal in Yoruba probably true), together with the fact that the overwhelming majority of ancestry of Africans (incl. the major parts of Yoruba-ANA, Mota, Dinka, etc.) are native to Africa, in fact this must be the case because demographic inference always finds that no classically "SSA" group shows a signal of the OoA bottleneck ~60-50kya like Eurasians do.

Riffing off your earlier comment regarding uniparentals, if Taforalt is really over 50% ANA, and ANA is basically just a highly diverged form of pre-OoA SSA, then this isn't reflected at all in what we see in the y-dna or mtdna of North Africans. The earliest samples we have from the region, Taforalt and IAM, are 100% E-M35 and M1/U6, which are conventional post-OoA lineages and not some 70 kya+ relics. It looks like we have around 14 samples between Taf and IAM, not one of them has some obviously super-old SSA-type lineage. If these people were really half pre-OoA ANA/SSA, what are the odds not a single one of 14 samples wouldn't have some obviously archaic y-dna like A or B or L0, L1, L2 mtdna?

Normally I don't place too much emphasis on uniparentals since they are single markers but thats a good point, did not know this before.

[Riverman]

are native to Africa, in fact this must be the case because demographic inference always finds that no classically "SSA" group shows a signal of the OoA bottleneck ~60-50kya like Eurasians do.

But you realise that this is the timing at which the supposed ANA-related/Neo-African back migration happened or already did happen? If, for example, the Southern Arabian habitat would have dried out, just as a hypothetical scenario, groups could have split up, one becoming Crown Eurasians, pushing into Neandertal territory, while mixing with them at a very low level, Basal Eurasian occupying the remaining more humid parts of Arabia, in which life could go on and ANA shortly before leaving for Africa again, where would either replace or mix with local more basal African lineages.
If they would have left before the actual bottle neck happened, that would just mean they migrated back somewhat earlier, not waiting it out, whereas those remaining in Arabia went through a bottle neck. I always wondered why there should have been such a bottle neck anyway, but if they were caught in a region which deteriorated, and they had to barely survive there or fight their way out of it, against strong competitors, like Neandertals, it would be the best kind of explanation. Rather than the OOA-even as such being necessarily the biggest bottle-neck in and by itself.

I mean I can't say it was like that with any certainty, but there are so many possible scenarios which can, at this point, hardly be refuted and with some a back migration right before the bottle neck being a possibility. Actually deteriorating conditions would be a good reason to move back and deeper into Africa from the North East.

[Echo]

I don't get why some here seem to talk about ANA as though it's Basal Eurasian or something. It is not a Eurasian component. It did not seemingly take any part in the Eurasian
bottleneck:

 

It is basically what people around these forums like to call "SSA". Just a unique "SSA" component that is closer to Eurasians than other SSA components are either due to much of its ancestry being a sister group to the Proto-Eurasians or it having some sort of ancient Eurasian admixture similar to what Mota shows or both. Whether or not it formed south of the Sahara is semantics as some of the other "SSA" components likely didn't entirely form south of the Sahara or Sahel anyway. I mean for God's sake, it's presence in Iberomaurusians which makes up about 45% of their ancestry pretty much makes them cluster like an ancient version of modern Horners:

 

It's even interesting how well the proportion of ANA Vs Eurasian (Dzudzuana-like ancestry) fits with where they cluster. They cluster just ahead of Tigrinyas in the direction of Eurasians which is exactly where you would expect a 55:45 Eurasian:SSA group to cluster. Even the rather impressive G25 simulation of ANA I've seen thrown around on this forum pretty much clusters like an "SSA" component that just has a downward shift toward something in the direction of ENAs and Ust-Ishim as you can see above. This is all in stark contrast to Neolithic Anatolians (mostly Dzudzuana-like derived) who still, despite the notable proposed Basal-Eurasian, still firmly cluster among Eurasians.

The results of our analysis using the All set, as well as the results of the analysis of ref.15 do suggest that Taforalt can be modeled as a mixture of a West Eurasian related population (represented by Dzudzuana in our case) and a Sub-Saharan African lineage. However, when one uses only a single African population as a source without using others as outgroups, this mixture can only be interpreted as evidence of ancestry from a lineage basal to members of the All set, rather than as evidence of ancestry specifically specifically 44 related to the chosen African population. No Sub-Saharan African populations appear to be good sources for the ancestry of Taforalt as described previously.

I think you're absolutely right and ANA is just further proof that Paleolithic Africa was quite diverse and housed a number of highly distinct groups who all shared in at least the fact that most of their ancestry did not partake in the Eurasian bottleneck. As for IBMs' craniofacial traits, they're interesting and might very well mark that, for whatever reason, they may have skewed toward one side of their ancestry far more than the other in this particular respect (similar to Somalis). Whatever the case, genetic data takes precedence and in that respect they seem to clearly be an intermediate population and not full Eurasians. It's interesting to note, for the record, that some Natufians clearly showed a shift in craniofacial features toward "SSA" groups like the Dahomey even though the Natufians have so far been shown to be less ANA than IBMs. This is precisely why Lazardis and co. noted in their very first paper that the original claim that there was nothing non-Eurasian in their ancestry was surprising:

A population without Neanderthal admixture, basal to other Eurasians, may have plausibly lived in Africa. Craniometric analyses have suggested an affinity between the Natufians and populations of north or sub-Saharan Africa24,25, a result that finds some support from Y chromosome analysis which shows that the Natufians and successor Levantine Neolithic populations carried haplogroup E, of likely ultimate African origin, which has not been detected in other ancient males from West Eurasia (Supplementary Information, section 6) 7,8. However, no affinity of Natufians to sub-Saharan Africans is evident in our genome-wide analysis, as present-day sub-Saharan Africans do not share more alleles with Natufians than with other ancient Eurasians (Extended Data Table 1).

It was expected that they were going to turn out admixed based on their craniofacial traits so the Lazaridis paper's findings back then were understandably surprising.

For all I have seen people have just been calling it ANA.

I have no idea where calling this component ANA is a problem.

The name is explicit yet.

Some people seem to have a problem with callin it ANA as opposed to SSA apparently. They are emotionally envolved into it.

I think some guys are very strongly emotionally entitled to it. That it just bother somehow when some people make theory of their own.

Some people made the theory it's Basal Eurasian well it's their own theory doesn't mean it's true. I'm no sure where the problem. There are always theories standing around.

Some other people have proposed that ANA is supposedly a migration back to Africa of an early non-bottlenecked OoA wave that offshooted yDNA DE both sides of the continents, into Africa and out of Africa (into Eurasia). As part of the 'multiple wave theory'.

We don't see how this hypothesis is wrong. It's a theory amongst many other theories that has been going on.

This theory existed long before ANA was found. For example Dienekes has long time argued modern Africans were Afro-Eurasian as opposed to relic-Paleolithic African isolates.

Some people should handle their emotions I think. Better rather arguement and find evidences against or for a theory.

[Awale]

But the graph is showing exactly what I was talking about, that ANA branched off from BEA-EA the latest of all other African components, by far. In this graph its ANA splits from all EA first, then BEA splits from EA. Still, its one pathway and the distance to for example Mota - I know it has basal African ancestry, is just immense. Going one step back and comparing with South Africa HG/San and you bring it into perspective, because the Basal African ancestry, even without archaic admixture, was on a completely different clade for that time. I mean that's a huge difference by all means. This doesn't answer where the split of ANA - EA happened, but most likely are, once more North East Africa or the Near East.

This is quite disconcerting, my man. I go out of my way to riddle my writings with caveats to avoid getting lost in semantics like the use of the term "SSA" and it seems you still manage to do it anyway. Here is the bottom line:

• Eurasians are characterized by the Eurasian bottleneck characterized by the "Main Eurasian" node here
• You can clearly see a PCA separation recognizing this bottleneck in any global PCA where all Eurasians including Neolithic Anatolians and HGs cluster off to the side
• Africa is genetically very diverse and not some sort of genetic monolith. Some components seemed closer phylogenetically to Eurasians than to each other by far
• But what all "SSA" (whatever you wish to call it) components share is that they clearly did not partake in the Eurasian bottleneck and they cluster off to the other side

ANA, whatever it is, clearly fits this same mold that characterizes what makes an "SSA" vs. a Eurasian component fundamentally. It is not Eurasian in the same way most of the ancestry in Mota, Dinkas, Mbutis and the San is not Eurasian, however differentiated these ancestries might be from each other. It could have geographically formed in Japan for all it matters. Doesn't change that it does not look to be genetically a "Eurasian" component in the way Ust-Ishim, ENAs, UP Europeans & Siberians and the theoretical Basal-Eurasians are.

Riffing off your earlier comment regarding uniparentals, if Taforalt is really over 50% ANA, and ANA is basically just a highly diverged form of pre-OoA SSA, then this isn't reflected at all in what we see in the y-dna or mtdna of North Africans. The earliest samples we have from the region, Taforalt and IAM, are 100% E-M35 and M1/U6, which are conventional post-OoA lineages and not some 70 kya+ relics. It looks like we have around 14 samples between Taf and IAM, not one of them has some obviously super-old SSA-type lineage. If these people were really half pre-OoA ANA/SSA, what are the odds not a single one of 14 samples wouldn't have some obviously archaic y-dna like A or B or L0, L1, L2 mtdna?

Are you suggesting that E-M35 entered the region with their Dzudzuana-related side? That doesn't make much sense. I think it seems likely that the pre-ANE & North-African admixture Y-DNA profile of West-Asia were lineages like G, J, T and L, no? E-M35 in these guys is likely owed to their ANA ancestry which then syncs fairly well with their autosomes. ANA Y-DNA and Eurasian mtDNA. I think ANAs probably had a lot to do with Y-DNA E. Can't be a coincidence that Mota who seems more closely related to whatever ANA might be than other "SSA" components was E-Y175024 which is a subclade of E-P177 just like E-M215, the ancestor of E-M35. And the split between E and D happened a long time ago. Around 65,000ybp which may very well fit with how, in terms of auDNA, ANA seems close to Eurasians compared to other non-Eurasian components. Am I missing something here?

[Keneki20]

So at this point we don't know if ANA is closer to West Africans or Eurasians just that it is somewhere in between? I'm also confused by Iberomarusians being y E if they were ~ 50% West Eurasian. Were the West Eurasian ydnas wiped out?

Also I wonder if ANA admixture in West Africans and Natufians blurring where ANA lied phenotypically.

Unfortunately, I don't think I can give you a satisfactory answer to your first and last questions right now. Although, as for Iberomaurusians samples so far yielding only E lineages (and the lack so far of native mtDNA lineages), I think that exogamy may be able to help explain that. Amongst the Ongota in Ethiopia, for example, Ongota men apparently tend to marry Ts'amakko women and not Ongota women. The same applies with respect to the neighboring Gawwada.

That, unfortunately, has apparently contributed to the moribund status of the language, as the children of these unions grow up speaking Ts'amakko or Gawwada rather than Ongota (i.e., the mothers speak to their children in their language, not the father's). I think that the reluctance toward teaching the children of the mixed marriages how to speak Ongota may be due to their ethnically marginalized status; they're apparently considered a largely social outcast group and have a connotation of being magicians amongst some of their neighbors. Then, most neighboring pastoralist groups apparently regard them with a great deal of scorn, since they don't own cattle/practice a pastoral lifestyle and speak a rather different language.

Also, amongst many peoples of the Vaupés basin in Northwestern Amazonia, a common phenomenon is that a man must find a wife who speaks a different language to his own. Kubeo speakers (of the Tukanoan family), for example, practice linguistic exogamy with the Baniwa, who are Arawakan speakers. Even Kubeo speakers are the result of originally Arawakan speakers moving into Tukanoan-speaking territory and adopted a Tukanoan language. Interestingly, this widespread phenomenon has caused there to be the sharing of many salient morphological features between the languages in the basin.

The sources I have that mention this don't explain exactly why this preference even exists for the Ongota or these Amazonians, but the fact that it does exist, I think, partly explains how there can be very large discrepancies in haplogroup frequencies in many populations both past and present worldwide. Then, when taking into account that population sizes were much smaller in the past, particularly amongst hunter-gatherers, which is what any group during the time of Iberomaurians or their ancestors must have been, then that may allow for stark shifts in haplogroup frequencies in some groups.

[davit]

[*]Africa is genetically very diverse and not some sort of genetic monolith. Some components seemed closer phylogenetically to Eurasians than to each other by far

I think this is the best point you made. But it also makes classifying every non Eurasian component as SSA when one might be closer to Eurasian than each other. This is same problem I have with people claiming Ust-Ishim is East Eurasian. I mean there is room for nuance.

[Riverman]

This is quite disconcerting, my man.

Not intentional. Sorry.

Here is the bottom line:

[*]Eurasians are characterized by the Eurasian bottleneck characterized by the "Main Eurasian" node here[*]You can clearly see a PCA separation recognizing this bottleneck in any global PCA where all Eurasians including Neolithic Anatolians and HGs cluster off to the side

That's correct, but my hypothetical alternative to the conventional intepretation is that this bottleneck was caused by detrimental effects working on the population AFTER the ANA had split and back migrated. It doesn't really make a big difference whether they were actually sitting in North East Africa or the Near East, the point is they lived together with ancestral Eurasians almost directly up to the bottle neck event and separated in a relatively short time span before, either by staying behind, or moving back - or both in an originally fluent border situation.
This is indeed not that new, there were various papers on the issue proposing that kind of back migration.

[*]Africa is genetically very diverse and not some sort of genetic monolith. Some components seemed closer phylogenetically to Eurasians than to each other by far

And the reason might have been they were one population for a longer period of time or direct neighbours. How can anyone say with certainty whether ANA separated in a back migration or Proto-Eurasians moved out that late? I don't think they moved out that late, we now have more than enough evidence for AMH living outside of Africa longer before and I think the bottleneck event being simply best explained by deteriorating conditions affecting the central group of early Proto-Eurasians, living in Arabia probably.

[*]But what all "SSA" (whatever you wish to call it) components share is that they clearly did not partake in the Eurasian bottleneck and they cluster off to the other side[/LIST]

Absolutely, just read my comment above, which I wrote before yours. Also, the Eurasian bottleneck is not the same as moving out of Africa. It just means that there was a serious shrinking event - somewhere, caused by unknown factors. And I say its unlikely to have been the migratoin as such, but rather the deteriorating conditions.
If you look at it like a tree with branches, its just that ANA is the latest branching event before the bottleneck and I suggest its POSSIBLE that this is because they migrated back, before the remaining Proto-Eurasians went through it. Just an alternative scenario, if you can tell me why its impossible, even though we seem to have evidence of human occupation much earlier, I'm listening.
Peace.

[JRD]

Taforalt's situation regarding ANA seems to be similar to ANE's situation regarding ENA. The mtDNAs (U6 and M1 in Taforalt's case; U* and U2'3'4'7'8'9 in ANE's case) come from the West Eurasian side, while the Y-DNAs (E-M35 in Taforalt's case and P1 in ANE's case) are from the non-West Eurasian side, despite the latter being present in lower amounts (~45% ANA in Taforalt and 24-29% ENA in ANE). R1, though, complicates the analogy in that it seems to have appeared within ANE, plus, there's C1.

Edit: C1 is an ENA mtDNA.

[Riverman]

Taforalt's situation regarding ANA seems to be similar to ANE's situation regarding ENA. The mtDNAs (U6 and M1 in Taforalt's case; U* and U2'3'4'7'8'9 in ANE's case) come from the West Eurasian side, while the Y-DNAs (E-M35 in Taforalt's case and P1 in ANE's case) are from the non-West Eurasian side, despite the latter being present in lower amounts (~45% ANA in Taforalt and 24-29% ENA in ANE). R1, though, complicates the analogy in that it seems to have appeared within ANE, plus, there's C1.

We still don't know where E came up and where E1b1b split from its more clearly African brothers. Actually a lot of the migration paths before the time of actual samples is totally unclear. Need I to remind people on the fact that just some years ago we could read about R1b coming from the Iberian refuge or something similar in some high brow articles and papers?

[Echo]

A notable problem of World Wide PCA Plot is that they are very sensible to drift.

It makes African populations look like they form a small tight kettle of fish. While Eurasian populations are established in a very wide place and occupies 2/3 of the space.

This situation by itself doesn't make sense. We should see rather the opposite or a situation where Africans and Eurasians occupy an equal share of spaces relative to their respective genetic diversity.