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Did the Y-Adam ventured outside Africa before coming back and expanding again ?
#1
(I don't think this interpretation of published data have already been proposed, if someone already raised these elements, please feel free to add a link toward the related discussion).


I think most people here are knowing very well the paper from Petr et al. 2020 (https://www.science.org/doi/10.1126/science.abb6460) that unveiled modern human Y-chr as more closely related to Neanderthal Y-chr and more distant to Denisovan Y-chr. Similar results were found for mtDNA (see e.g., Posth et al. 2017, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5500885/).
These results were in tension with autosomal DNA results showing that Denisovans and Neanderthalensis were sharing a common ancestor that already splitted from the Sapiens lineage.

The sequencing of the mtDNA of the Sima de los Huesos Neanderthal sample that unfolded as being more closely related to Denisovan than to modern Human led to the conclusion that Sapiens mtDNA came to replace Neanderthal mtDNA at some point after ~400 kyr BP.
In their paper, Petr et al. 2020 proposed that the same thing occured for Y-DNA, around the same epoch ~370 kyr BP.
However, there is no known Y-DNA from Neanderthals or Sapiens before the claimed replacement. Which in fact opens another possibility, what if it was the other way around and Sapiens Y-chr came to be replaced by a Neanderthal Y-chr that would became ultimately our Y-Adam ?

When we look closely at the results of Posth at al 2017 and Petr et al. 2020 we can notice that :
-Denisovans mtDNA separated from Sapiens mtDNA 1065 +/- 172 kyr ago (1 sigma interval, 68% confidence interval).
-Neanderthal mtDNA separated from Denisovan mtDNA ~785 +/- 137 kyr ago.
-The Sapiens related mtDNA that replaced Neanderthal mtDNA splitted from modern lineage ~414 +/- 27 kyr ago.
Whereas,
-Denisova Y-chr splitted ~707 +/- 50 kyr ago from the shared Y-chr of Sapiens and Neanderthals
-Sapiens and Neanderthal Y-chr splitted ~360 +/- 20 kyr ago.

The main issue with the results of Posth et al. 2017 is the large gap between mtDNA Neanderthal/Denisovan split and their proposed dating of the nDNA split between Neanderthal and Denisovan (~427 +/- 23 kyr ago).
Indeed, for this to work a ~358 +/- 140 kyr old diversity (~2.5 sigma tension with a ~0 kyr diversity hypothesis) for the mtDNA should have been carried by the "rather small" Neandersovan population when they splitted.
The same applied to the source population of Sapiens and Neandersovans split estimation from nDNA (~657 +/- 53 kyr ago), that should have conserved ~400 \pm 180 kyr old mtDNA diversity when they splitted (a ~2.2 sigma tension with a ~0 kyr diversity hypothesis).
By comparison, modern humans, despite being highly diffusive and spatially isolated, failed to conserve anything older than ~150kyr diversity for mtDNA up to modern days.
It is therefore hard to justify ~400 kyr diversity carriage by early human populations. Which cast doubts about the nDNA-based estimation of divergence times between Sapiens, Neanderthals, and Denisovans proposed in Posth et al. 2017 analysis. In particular, all sampled Neanderthals and Denisovans are exhibiting fairly short diversity "horizon", which disfavor the proposition of Neandersovan population carrying very old diversity since their root.





Let consider few hypotheses :
1) mtDNA, Y-chr, and autosomal separation between this three groups (Sapiens, Denisovan, Neanderthal) occurred from small populations carrying few ~kyr old diversity.
2) The events that produced the late mix-up between Sapiens and Neanderthal for mtDNA and Y-chr is a single admixture event.
3) We assume that Posth et al. 2017 mtDNA molecular-clock and Petr et al. 2020 Y-chr molecular clock are consistent.


Under these three hypotheses :
--> The dating from Posth et al. 2017 of the mtDNA splits favors the idea that Sapiens and Neandersovans splitted ~1065 +/- 172 kyr ago, and that Neanderthals and Denisovans splitted ~785 +/- 137 kyr ago. It is interesting to note that such early splitting times for Neanderthal and Denisovan are also proposed by Roger et al. 2020 (https://www.science.org/doi/10.1126/sciadv.aay5483) based on nDNA.
--> We can note a ~390 kyr split between Sapiens and late-Neanderthals mtDNA and Y-chr (assumed to derive from a single event in our hypothesis-2, that support similar molecular clocks calibration from Posth et al. 2017 and Petr et al. 2020), we however note that the two splits are separated by 54 +/- 33 kyr (at ~1.6 sigma from a simultaneous hypothesis).
--> The dating of the Y-Chr split between Sapiens and Denosivans in Petr et al. 2020 (~707 +/- 50) favors the idea that what we are seeing here is not the Sapiens/Neandersovans split (1065 +/- 172 kyr, ~2 sigma tension) but the Neanderthal/Denisovan split (785 +/- 137, ~0.5 sigma agreement). Which would imply that this Y-Chr originally transited by Neanderthal-population before introgressing into Sapiens population.
--> Sometimes around ~360 +/- 20 kyr ago Neanderthals and Sapiens came into contact and mtDNA and Y-chr got exchanged, Sapiens mtDNA introgressed into Neanderthal population and Neanderthal Y-chr introgressed into Sapiens population.




What could kill this interpretation ?

We have seen above that removing hypothesis (1) would cost a lot about the amount of diversity to be carried by the source populations of Sapiens, Neanderthals, and Denisovans. Therefore, I would considered hypothesis (1) as fairly secured grounds.
If we remove hypothesis (2), then we didn't need anymore to have Sapiens/late-Neanderthals split to occur at roughly the same time for mtDNA and Y-chr ... therefore, we can challenge the molecular clocks of Petr et al. 2020 (or Posth et al. 2017) to reconcile the Denisovan/Sapiens split from Y-chr with the same split from mtDNA.
However, removing hypothesis (2) would imply two independent introgression events from Sapiens to Neanderthals that would have ended in mtDNA replacement in one occurence and Y-chr replacement for the other. 
Hypothesis (3) is supported by the similar time of mtDNA and Y-chr splits for Sapiens and late-Neanderthals, therefore a miscalibration of the molecular clocks can only accounts for a ~50 kyr mismatch around ~400 kyr between the two datation systems, that remains small (at the order of ~0.5 sigma for the Sapiens/Denisovans split timing).




How could have happened such haplogroup-exchange ?

Here is a proposed scenario:
*A population from ~Sapiens-branch left the Great Rift Valley around ~414 +/- 27 kyr ago, splitting the mtDNA that will be introgressed into Neanderthals from the mtDNA line that will become Mitocondrial-Eve.
* Around ~360 +/- 20 kyr ago this population came into contact with a Neanderthal population. A minimal interaction between the two populations led to the introgression of Sapiens-related mtDNA into Neanderthal population and early Neanderthal Y-chr into the Sapiens-related population.
* These two populations later diffused the introgressed mtDNA (for Neanderthals) and Y-chr (for the Sapiens-related).
In this model, carriers of this Y-chr originating from Neanderthal population before 400 kyr BP would became our Y-Adam around ~236 kyr ago.

The main question that remains open under this model is about "where" to make these two populations interact ?
There is two main realistic options :
1) Around Western Asia
2) Gibraltar Straight (the low-likelyhood of crossing the straight would explain why no significant autosomal DNA signal was exchanged)

As of today, under such model, I would find Gibraltar as the best option. We know that by ~300 kyr modern-humans were around in Morocco at Djebel Irhoud.
In particular, 315 +/- 34 kyr Lellavois-technique tools are documented from this archeological site.
Also the diffusion of Acheulean tools might support the idea of an original Gibraltar-crossing ~700 kyr ago due to the lack of early-Acheulean tools in South-Eastern part of Europe. However, a fast coastal migration from Western Asia toward Iberian peninsula can not be completely ruled out.

The later point is important, as these claimed "contacts" and introgression events can be supported by potential cultural elements diffusion such as :
-Acheulean tools, who reached Europe fairly lately (~700 kyr BP) likely with Homo-Heidelbergensis when the Denisovans/Neanderthal split occurred. Which therefore favors again a high splitting time for Neanderthal and Denisovan around ~700 kyr ago (and thus a required higher dating of the Sapiens/Denisovans split, hard to reconcile with the low-datation of Modern-Sapiens/Denisovans Y-chr from Petr et al. 2020).
-The Levallois tecnique tools, that appears in Africa, Europe and Asia around MIS9 (~330 kyr). That might have been spread by the wave of humans responsible for the mtDNA and Y-chr exchange event. According to Moncel et al. 2020 (https://www.sciencedirect.com/science/ar...via%3Dihub), Levallois Technique tools elaboration is documented from MIS12 to MIS9 in Western Europe.
Therefore, we can propose that this technology spread from South-Western Europe and then the introgression event led to the a back diffusion of this technic in North Western Africa.



Could have the Y-chr of modern human transited among another human subgroup instead of Neanderthal ?

Such scenario would involve a ghost population, probably in North Africa, that was carrying the modern Y-chr line, and that would have splitted from Denisovan around ~700 kyr ago.
Around ~400 kyr ago, this population would have been overwhelmed by Sapiens demography (when Sapiens mtDNA diffused) but got its Y-chr becoming dominent inside the predominantly Sapiens population and introgressing into Neanderthal population.
Yet, traces of archaic population into modern humans genome mostly propose an extra archaic population who splitted away before Sapien/Neanderthal-split, therefore not fitting the needed hierarchy of having a closer relation with Neandersovans than Sapiens.
If such ghost population existed, we have yet to find genetic traces of its existence.



Conclusion :

As we have seen, mtDNA and cultural contacts are favoring an early dating for splits of the populations that would become Sapiens, Neanderthal, and Denisovans (~1Myr for Sapiens/Neandersovans split and ~700kyr for Neanderthals/Denisovans split).
Such early splits are hard to reconcile with the modern-Human/Denisovan Y-chr split that post date the said split by ~360 +/- 180 kyr,
Whereas it better corresponds (with a likelihood ratio of ~10) to the Neanderthal/Denisovan mtDNA split ~785 +/- 137 kyr ago.
The rapid diffusion around the world of Levallois-technique tools around ~330 kyr BP appears to be nearly concomitant with the MRCA of Modern-Humans and late-Neanderthal mtDNA and Y-chr, opening the possibility that the diffusion of this technology might, at least partially, explain the success of the associated lineages.

Interestingly, a careful analysis of the split dating might indicates that Y-Adam ancestor ventured outside Africa before coming back and diffusing again (inside and outside Africa with the ~50 kyr OoA event).
The ideal method to test such possibility would be to have access to a ~450 kyr old Y-chr from a Neanderthal individual (or a Sapiens, but considering sample conservation, this seems less likely to occur).
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#2
(05-09-2024, 12:47 PM)GHurier Wrote: Could have the Y-chr of modern human transited among another human subgroup instead of Neanderthal ?

Such scenario would involve a ghost population, probably in North Africa, that was carrying the modern Y-chr line, and that would have splitted from Denisovan around ~700 kyr ago.
Around ~400 kyr ago, this population would have been overwhelmed by Sapiens demography (when Sapiens mtDNA diffused) but got its Y-chr becoming dominent inside the predominantly Sapiens population and introgressing into Neanderthal population.
Yet, traces of archaic population into modern humans genome mostly propose an extra archaic population who splitted away before Sapien/Neanderthal-split, therefore not fitting the needed hierarchy of having a closer relation with Neandersovans than Sapiens.
If such ghost population existed, we have yet to find genetic traces of its existence.

I am rather a supporter of such a hypothesis.  However the initial split must be somewhere in South Africa or West Africa, as here we find the oldest A00 haplogroups.
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#3
(05-09-2024, 03:06 PM)TanTin Wrote:
(05-09-2024, 12:47 PM)GHurier Wrote: Could have the Y-chr of modern human transited among another human subgroup instead of Neanderthal ?

Such scenario would involve a ghost population, probably in North Africa, that was carrying the modern Y-chr line, and that would have splitted from Denisovan around ~700 kyr ago.
Around ~400 kyr ago, this population would have been overwhelmed by Sapiens demography (when Sapiens mtDNA diffused) but got its Y-chr becoming dominent inside the predominantly Sapiens population and introgressing into Neanderthal population.
Yet, traces of archaic population into modern humans genome mostly propose an extra archaic population who splitted away before Sapien/Neanderthal-split, therefore not fitting the needed hierarchy of having a closer relation with Neandersovans than Sapiens.
If such ghost population existed, we have yet to find genetic traces of its existence.

I am rather a supporter of such a hypothesis.  However the initial split must be somewhere in South Africa or West Africa, as here we find the oldest A00 haplogroups.

Africa maybe, but West or South Africa? Rather not.
I think the oldest A branches ended up where they are now, because they were the fringe groups from the start and that's where they ended up surviving, at the fringe, where other pulse migrations came in the latest and which had big refuges to survive them one way or another.
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#4
More recents studies place the mtdna Denisovians/Sima de Los Huesos vs LateNeandertal/Sapiens split closer to the Y-dna one instead of Posth2017 ~1Mya. My own estimations (for what it's worth) based on a fixed rate of 1.57x10e-8 mutations per site per year (which is the usual accepted one for human mtdna, even used by Posth2017) gives about ~650kya split between Denosovians and Sapiens mtdna.  That would make the Y-dna split consistent with the mtdna one and no need for an additionnal mix from Neandertal to early Sapiens. That is also consistent with an approximative Denisovians-Sapiens split autosomally (~600-800kya), leaving no space for a distinct Neandertal split at that time.

Some references:
Petr et al. 2020 The evolutionary history of Neanderthal and Denisovan Y chromosomes
Skov et al. 2022 Genetic insights into the social organization of Neanderthals
Zeberg et al. 2024 The genetic changes that shaped Neandertals, Denisovans, and modern humans
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#5
Excellent topic. Here's the little I have to contribute.
https://genarchivist.com/showthread.php?...28#pid5528
Also, maybe the technical limits of the 1240k have been reached regarding archaic ancestry, but what to make of this? The 'deeper' you go in Sapiens lineage, the more Denisovan/'Neandersovan' pull there is?
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#6
Mysterious ‘ghost' populations
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#7
(05-09-2024, 12:47 PM)GHurier Wrote: Conclusion :

As we have seen, mtDNA and cultural contacts are favoring an early dating for splits of the populations that would become Sapiens, Neanderthal, and Denisovans (~1Myr for Sapiens/Neandersovans split and ~700kyr for Neanderthals/Denisovans split).
Such early splits are hard to reconcile with the modern-Human/Denisovan Y-chr split that post date the said split by ~360 +/- 180 kyr,
Whereas it better corresponds (with a likelihood ratio of ~10) to the Neanderthal/Denisovan mtDNA split ~785 +/- 137 kyr ago.
The rapid diffusion around the world of Levallois-technique tools around ~330 kyr BP appears to be nearly concomitant with the MRCA of Modern-Humans and late-Neanderthal mtDNA and Y-chr, opening the possibility that the diffusion of this technology might, at least partially, explain the success of the associated lineages.

Interestingly, a careful analysis of the split dating might indicates that Y-Adam ancestor ventured outside Africa before coming back and diffusing again (inside and outside Africa with the ~50 kyr OoA event).
The ideal method to test such possibility would be to have access to a ~450 kyr old Y-chr from a Neanderthal individual (or a Sapiens, but considering sample conservation, this seems less likely to occur).

Considering that apes - including humans - are patriarchal, it makes sense that the common maternal lineage of Homo sapiens, Neandertals, and Denisovans would have an older coalescence date than the common paternal lineage of these three species.

The reason is that younger coalescence dates of paternal lineages reflect the replacement of a population's previous paternal lineages with those of invading, conquering males. This happened in Europe when the paternal lineage of Western Steppe Herders (R1b) replaced Europe's pre-Neolithic paternal lineages (I,C, and H) in most parts of the continent. This also happened in Africa when Bantus spread E-M2 via the Bantu expansion, thus replacing A1b1 and B-M60 in various parts of the continent. 


Therefore, the younger coalescence date for the common paternal lineage of Homo sapiens and Denisovans may reflect a conquest executed by Homo sapiens males over Denisovans - or vice versa.
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#8
At marker 19:32 for a few minutes.... great coverage about Modern Human, Neanderthal, and Denisovan Y-DNA extraction and analysis.

https://www.youtube.com/watch?v=jfLt5F7cyJw&t=11s

UPDATE: 29:44 Neanderthal ancestry in African genomes
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#9
The models from "A weakly structured stem for human origins in Africa" are relevant to this. Ancestors of modern humans split into Stem 1 and Stem 2 about a million years ago, with gene flow continuing between these groups afterward. Neanderthals split from Stem 1. In one version, there is a bottleneck in Stem 1 after the Neanderthal divergence, then Stem 1 split up into Eastern and Southern African branches 250-500 000 years ago; then 100-125 000 years ago both mixed with Stem 2 again in large proportions to form ancestral East and South Africans (non-Africans branching off the former), with additional recent Stem 2 gene flow into West Africans. 

While the authors put both stems in Africa, it seems to me you can have Stem 1 in Eurasia early on, provided there is enough gene flow between continents. Then after splitting from Neanderthals the other Stem 1 branch returns to Africa (this could be the cause of the bottleneck?) and mixes with the African humans, maybe at the beginning of the Middle Stone Age/Middle Palaeolithic. Presumably modern human uniparentals come from this Stem 1 branch. There are some problems with trying to fit all this together though. 

Unfortunately this paper didn't include any Denisovans, so don't know where they would have fit (or maybe they would have completely broken the model). I guess they would branch of Stem 1 earlier, but then continue to have gene flow with ancestral Neanderthals and probably eastern archaic humans too. The real history probably being quite complicated.

There was a recent preprint that proposed a different model along these same lines, but I can't find it any more.
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