Paleolithic DNA from the Caucasus

[bicicleur 2]

The asiatic population European HGs mixed with had affinities to both Ust'Ishim and Tianyuan, now what? Middle Eastern HGs need no 'Basal' or 'Deep' anything in that scenario. Assuming the Europeans are pure while the middle Easterns are mixed looks like a political statement rather than anything scientific.

nothing is pure, it all depends on how far you go back in time
but ancestral Villabruna was pure compared to Vestonice and El Miron and it is very usefull to use this component
ancestral Villabruna probably originated 35-40 ka in Eastern Europe, prior to the formation of the Vestonice cluster, and it is linked to the origins of the Gravettian

Basal Eurasian is a much older component

 

[bicicleur 2]

As to Taforalt...

"Our co-modeling of Epipaleolithic Natufians and Ibero-Maurusians from Taforalt confirmsthat the Taforalt population was mixed11 162 , but instead of specifying gene flow from the163 ancestors of Natufians into the ancestors of Taforalt as originally reported, we infer gene flow164 in the reverse direction (into Natufians). The Neolithic population from Morocco, closelyrelated to Taforalt17 165 is also consistent with being descended from the source of this gene flow,166 and appears to have no admixture from the Levantine Neolithic (Supplementary Information167 section 3). If our model is correct, Epipaleolithic Natufians trace part of their ancestry to168 North Africa, consistent with morphological and archaeological studies that indicate a spreadof morphological features22 169 and artifacts from North Africa into the Near East."

"Such a 170 scenario would also explain the presence of Y-chromosome haplogroup E in the Natufiansand Levantine farmers6171 , a common link between the Levant and Africa. Moreover, our model172 predicts that West Africans (represented by Yoruba) had 12.5±1.1% ancestry from a Taforalt173related group rather than Taforalt having ancestry from an unknown Sub-Saharan Africansource11 174 ; this may have mediated the limited Neanderthal admixture present in WestAfricans23 175 . An advantage of our model is that it allows for a local North African component176 in the ancestry of Taforalt, rather than deriving them exclusively from Levantine and Sub-Saharan sources."

WOW!

So much for this paper:
https://www.eupedia.com/forum/threa...ion-from-Levant-and-Europe?highlight=Taforalt

it confirms what I suspected when Tarofalt Y-DNA was published
it is E-M78, but a dead end of E-M78
the E-M78 branch split 13.3 ka in the Levant
it has been found in Ain Ghazal and it's E-L618 branch in Cardial Ware Croatia, ancestral to E-V13

Natufians were a mixture of E-Z830 and Tarofalt-like E-M78 with probably also some H2

 

[bicicleur 2]

Basal Eurasian of various populations:

[/IMG]

As we've speculated, was it perhaps around Mesopotamia?

I don't think so, BE is >50 ka.
But it has not been detected prior to the 26 ka Dzudzuana.
It was not in Siberia, northern China or Europe.
That's all we know.

My guess remains India or the Indus delta, and it was brought to the Near East by haplo G and H2.

Do you have any data of BE in Dravidians?

 

[halfalp]

Ok wow, so if i udnerstand the paper clearly, this new Caucasus genome is some kind of an ancestor to some modern middle-eastern and " the whole neolithic " and also related with the Villabruna Cluster, but Villabruna descend from AG3, so are Anatolian_Neolithic also partially coming from AG3?

What's the big difference of this HG and Satsurblia / Kotias? Can someone make some kind of resumé of all the genetic relation with the different party?

Btw, mtdna U6 is now probably the most interesting maternal lineage to study, looking at his ancient and modern distribution.

 

[halfalp]

Did you notice that now Samara_HG is now modeled roughly 20% Villabruna, 70% Afontova Gora 3, 10% Baikal Eneolithic... What is that change?

 

[bicicleur 2]

Ok wow, so if i udnerstand the paper clearly, this new Caucasus genome is some kind of an ancestor to some modern middle-eastern and " the whole neolithic " and also related with the Villabruna Cluster, but Villabruna descend from AG3, so are Anatolian_Neolithic also partially coming from AG3?

What's the big difference of this HG and Satsurblia / Kotias? Can someone make some kind of resumé of all the genetic relation with the different party?

Btw, mtdna U6 is now probably the most interesting maternal lineage to study, looking at his ancient and modern distribution.

How does Villabruna connect with AG3? Was this before or after 26 ka?

 

[bicicleur 2]

Did you notice that now Samara_HG is now modeled roughly 20% Villabruna, 70% Afontova Gora 3, 10% Baikal Eneolithic... What is that change?

Baikal Early Neolithic ..

Interesting. It coincides with first pottery in the eastern Pontic steppe .. 9 ka.

 

[bicicleur 2]

Extended Data Figure 6: Modeling present-day and ancient West-Eurasians. Mixture364 proportions computed with qpAdm (Supplementary Information section 4). The proportion of365 ‘Mbuti’ ancestry represents the total of ‘Deep’ ancestry from lineages that split prior to the366 split of Ust’Ishim, Tianyuan, and West Eurasians and can include both ‘Basal Eurasian’ and367 other (e.g., Sub-Saharan African) ancestry. (a) ‘Conservative’ estimates. Each population368 cannot be modeled with fewer admixture events than shown. (b) ‘Speculative’ estimates. The369 highest number of sources (≤5) with admixture estimates within [0,1] are shown for each370 population. Some of the admixture proportions are not significantly different from 0371 (Supplementary Information section 4).

I guess without a pure Basal Eurasian genome this is the best they can do...

[/IMG]

[/IMG]

this Mbuti component is confusing
Laziridis should have split between Mbuti and Ancestral North African as in the admixture graph
I suspect the Mbuti in Tarofalt is not Mbuti, but a proxy for Ancestral North African
he says himself that there was no Yoruba in Tarofalt, but it was the other way around ..
see also the admixture graph

 

[Regio X]

I don't think so, BE is >50 ka.
But it has not been detected prior to the 26 ka Dzudzuana.
It was not in Siberia, northern China or Europe.
That's all we know.
My guess remains India or the Indus delta, and it was brought to the Near East by haplo G and H2.
Do you have any data of BE in Dravidians?

bicicleur, why do you think G came from India? I mean, it could be, but I don't know of any evidence of that. In fact, the highest G-M201 diversity would be far from there (Armenia and surroundings?). Its TMRCA is abt. 26k ybp.

 

[halfalp]

How does Villabruna connect with AG3? Was this before or after 26 ka?

The way i understand it is that, Villabruna - Bichon Cluster is something El Miron + Dzudzuana Related and AG3 = WHG. How the relationship works... no idea. The " southern " part of Villabruna detected early is probably linking with Dzudzuana and the little " far east " detected in some Villabruna Cluster individuals is maybe AG3.

 

[halfalp]

Baikal Early Neolithic ..

Interesting. It coincides with first pottery in the eastern Pontic steppe .. 9 ka.

Oh yeah...
I dont understand how CHG wich is between EHG and Iran_Neolithic and is not at all related with Dzudzuana and was previously thought to be part of Samara. Is not anymore? And what is the Samara individual use as a reference?

 

[bicicleur 2]

bicicleur, why do you think G came from India? I mean, it could be, but I don't know of any evidence of that. In fact, the highest G-M201 diversity would be far from there (Armenia and surroundings?). Its TMRCA is abt. 26k ybp.

looking at the distribution of F, H and K, it's my guess that FGHIJK split in India or the Indus Valley
these splits happened in a very short time, between 48.8 and 45.4 ka
along the Narmada river in India, some 48 ka blade tools from cilindric core stones were found, maybe the oldest in the world

TMRCA of G is 26 ka, same time as Dzdzuana, maybe a coincidence?
where was G between 48 and 26 ka?

in the mean time, I see that CHG and Iran Neo have even more Basal Eurasian than Dzudzuana, so more Basal Eurasian was coming to this area, parallel with Dzudzuana
Basal Eurasian may have been in India 70 ka or more subsequent to the people in Jebel Faya, 129 ka

 

[epoch]

There's so much to think about in this paper that it's hard to focus.

"Outgroup f3-statistics10 108 show that Dzudzuana clusters with Near Eastern populations109 primarily from Anatolia and secondarily from the Levant, but not with the geographically110 proximate CHG (Extended Data Fig. 3). A genetic relationship between Dzudzuana and111 Neolithic Anatolians is also shown by principal components analysis (PCA) in the space of‘outgroup f4-statistics’16 112 of the form f4(Test, O1; O2, O3) where (O1; O2, O3) is a triple of113 outgroups (Fig. 1c; Methods); performing PCA on the space defined by these statistics has114 the advantage of not being affected by genetic drift peculiar to the Test populations. It also115 allows us to visualize genetic relationships between ancient populations alone, without116 projecting onto the variation of present-day people. European hunter-gatherers in our analysis117 form a cline with Villabruna/WHG samples on one end and ANE on the other. None of the118 PGNE populations other than the Neolithic Anatolians cluster with the Ice Age Caucasus119 population from Dzudzuana."

Contrary to the Felman paper from the Krause group on Anatolian farmers...

"These125 analyses show that ESHG share more alleles with Dzudzuana than with PGNE populations,126 except Neolithic Anatolians who form a clade with Dzudzuana to the exclusion of ESHG127 (Extended Data Fig. 5a). Thus, our results prove that the European affinity of NeolithicAnatolians6128 does not necessarily reflect any admixture into the Near East from Europe, as an129 Anatolian Neolithic-like population already existed in parts of the Near East by ~26kya.130 Furthermore, Dzudzuana shares more alleles with Villabruna-cluster groups than with other131 ESHG (Extended Data Fig. 5b), suggesting that this European affinity was specifically132 related to the Villabruna cluster, and indicating that the Villabruna affinity of PGNE133 populations from Anatolia and the Levant is not the result of a migration into the Near East134 from Europe."

So, if they weren't in Europe originally, where were they?

Remember that I pushed a theory of a very old remigration from Aurignacian Europe to the ME? The exchanges that pissed off MarkoZ? That obviously wasn't mine, it came from Ofer Bar-Yosef, one of the coauthors of this paper. It can be found in these articles:

http://www.patrimoniocultural.gov.pt/media/uploads/trabalhosdearqueologia/45/20.pdf
http://www.patrimoniocultural.gov.pt/media/uploads/trabalhosdearqueologia/45/19.pdf

For that matter, where were the BE people?

"The Dzudzuana population was not145 identical to the WHG, as it shared fewer alleles with both an early Upper Paleolithic Siberian(Ust’Ishim19) and an early Upper Paleolithic East Asian (Tianyuan20 146 ) (Extended Data Fig.5c), thus, it too—like the PGNE populations—had Basal Eurasian ancestry6,9147 . The detectionof this type of ancestry, twice as early as previously documented5,6148 and at the northern edge149 of the Near East, lends weight to the hypothesis that it represents a deep Near Eastern lineagerather than a recent arrival from Africa6."

Were they both in the Near East, one near the Caucasus originally and one closer to the Levant?

What do we know of the Middle-Eastern cultures of the Upper Paleolithic? There is the Zagros Aurignacian in Iran, there is Ahmarian in the Levent, apparently contemporaneous to the Levantine Aurignacian. What more do we know?

Also, the paper claims that there are *two* kinds of basal Eurasian, one that did go through the same bottleneck as current Eurasians went, and one that didn't. An approach to identifying the cultures associated with these two Basal Eurasian ancestries might be to figure what caused that bottleneck, where that happened and when.

 

[epoch]

Did anyone notice in that qpAdm output that Chan do Lindeiro (Iberia_Chan) sample is almost full blooded Magdalenian? It is 9000 years old. We see Magdalenian continuity into the Mesolithic.

 

[Regio X]

looking at the distribution of F, H and K, it's my guess that FGHIJK split in India or the Indus Valley
these splits happened in a very short time, between 48.8 and 45.4 ka
along the Narmada river in India, some 48 ka blade tools from cilindric core stones were found, maybe the oldest in the world
TMRCA of G is 26 ka, same time as Dzdzuana, maybe a coincidence?
where was G between 48 and 26 ka?
in the mean time, I see that CHG and Iran Neo have even more Basal Eurasian than Dzudzuana, so more Basal Eurasian was coming to this area, parallel with Dzudzuana
Basal Eurasian may have been in India 70 ka or more subsequent to the people in Jebel Faya, 129 ka

F is in fact ancestor of GHIJK. https://www.yfull.com/tree/CF/
As for G route, there is indeed a huge gap between the time of G formation and its TMRCA. GHIJK first split could have happened around the area you mentioned, or close to it, indeed. In the case of G, ok, it could have been a route from east to west, till the first split of G itself around Armenia. HIJK from west to east doesn't seem to work, since the clades involved don't present such gap, as you suggested. No time to HIJK "jump" from the area around Caucasus to South Asia.
Anyway, I guess I got your hypothesis. Correct me if I'm wrong. You speculate people related to an older wave from Africa, with a now extinct Y-DNA lineage(?), would have lived in South Asia and would have been the original Basal Eurasians. Then GHIJK - related to another wave - came without this component. Already separated, G and H would have gone south and mixed with this older pop, whereas IJK took another route. Later, G and H would have migrated west bringing BE. Is that right?

 

[epoch]

Ah. There is off course the Emiran culture.. Looked like it was a continuation on the Mousterien. Good candidate for a Basal Eurasian culture.

 

[Angela]

this Mbuti component is confusing
Laziridis should have split between Mbuti and Ancestral North African as in the admixture graph
I suspect the Mbuti in Tarofalt is not Mbuti, but a proxy for Ancestral North African
he says himself that there was no Yoruba in Tarofalt, but it was the other way around ..
see also the admixture graph

What he says is that " ‘Mbuti’ ancestry represents the total of ‘Deep’ ancestry from lineages that split prior to the366 split of Ust’Ishim, Tianyuan, and West Eurasians and can include both ‘Basal Eurasian’ and367 other (e.g., Sub-Saharan African) ancestry. "

So, there could be "extra" Basal in there, a lineage that split before Basal, as well as any modern SSA or East African in people. Remember the SSA that used to show up in ancient samples? If the algorithm spotted something really old it threw it in SSA perhaps.
He has no sample for these deep lineages that include not only Basal Eurasian but other lineages that split off before Basal. There's also the language about bottlenecked and non-bottlenecked lineages. Which one was which, the Basal or the pre-Basal? What was the bottleneck, what caused it, where?

Looking at this graph I'm struck by the Dzudzuana in the more "eastern" hunter-gatherers, like Ukraine, Norway, Sweden, Russian Mesolithic, Motala and Iron Gates. Movement westward from the Caucasus? Or straight from Anatolia?

Part of that is Basal Eurasian.

You can also see it in the graph of the amount of Basal Eurasian. According to that, the hunter gatherers had what looks like from 1 to 10%, which is just about what the Feldman et al (Krause) paper on Anatolian hunter-gatherer transition to farmer said would be in the ball park for the amount of Basal Eurasian that would need to be in Iron Gates if there had been movement from Anatolia to Europe at that period. Of course, they only found something like 1.6.

 

[markod]

I 100% agree with bicicleur about Y-DNA dispersals, but I think the BE in India is rather unlikely. East Eurasian components from India and surroundings show the typically Eurasian inflation of archaic human ancestry. There's also the similiarity of BE to the newly detected Ancestral North African component, as well as the peaks of BE ancestry in modern North Africans.

I find it more likely that early humans who migrated from South Asia to the West would have picked up BE ancestry in the Arabian peninsula or vicinity when they crossed the Persian Gulf. This would also explain the secondary peak of BE ancestry in ancient Western Iran, whence it migrated up the Zagros range into the Caucasus. BE and Ancestral North African likely existed in a continuum in North & East Africa as well as the Arabian peninsula, the Sinai etc. . Earlier human migrations mopped up archaic human populations so BE/ANA only acquired limited & indirect admixture with them.

It would be interesting to test whether haplogroup D like its sister clade is also at least to an extent associated with a reduction of archaic human ancestry, because its present distribution seems to be the result of a migration that went the opposite direction of most early Eurasian population movements that generally went from the East to the West.

The precise nature of these movements will be very difficult to figure out without DNA from India and South-East Asia in any case, as these places should be the primary homelands of Eurasian humans.

 

[berun]

What I have noticed is how it's possible to get easily Yamnaya ancestries if running a supervised admixture.

 

[epoch]

What he says is that " ‘Mbuti’ ancestry represents the total of ‘Deep’ ancestry from lineages that split prior to the366 split of Ust’Ishim, Tianyuan, and West Eurasians and can include both ‘Basal Eurasian’ and367 other (e.g., Sub-Saharan African) ancestry. "

So, there could be "extra" Basal in there, a lineage that split before Basal, as well as any modern SSA or East African in people. Remember the SSA that used to show up in ancient samples? If the algorithm spotted something really old it threw it in SSA perhaps.

Basal means that we see ancestral rather than derived SNP's. So, they split off very early, after which the rest shared mutations and drift. These changes in the rest will be shared among them but not with Basal. As Mbuti is the farthest from anybody else - It split the earliest - chances that it shares something *ancestral* - i.e. not mutated or otherwise changed - with Basal rather than with later Eurasian is greater. Hence the possibility to use Mbuti as proxy. However, if the affinity was due to later SSA admixture, than the part that admixted must share *other* drift and mutations with SSA. In other words, in that case it is not so much the ancestral that it shares but the derived. That should be clearly picked up with formal stats, but it doesn't.

EDIT: I don't think this is accurate anymore. Drift is by far a bigger changer of DNA than mutations.

From the SI: "It is clear that Sub Saharan African populations lack shared genetic drift between North African and West Eurasian populations, usually interpreted as the Out-of-Africa bottleneck."

He has no sample for these deep lineages that include not only Basal Eurasian but other lineages that split off before Basal. There's also the language about bottlenecked and non-bottlenecked lineages. Which one was which, the Basal or the pre-Basal? What was the bottleneck, what caused it, where?

Exactly. Also, we should take a look at the Emiran. It is considered ancestral to Ahmarian in the Levant as well as later UP cultures in North-Africa.

Looking at this graph I'm struck by the Dzudzuana in the more "eastern" hunter-gatherers, like Ukraine, Norway, Sweden, Russian Mesolithic, Motala and Iron Gates. Movement westward from the Caucasus? Or straight from Anatolia?

Part of that is Basal Eurasian.

You can also see it in the graph of the amount of Basal Eurasian. According to that, the hunter gatherers had what looks like from 1 to 10%, which is just about what the Feldman et al (Krause) paper on Anatolian hunter-gatherer transition to farmer said would be in the ball park for the amount of Basal Eurasian that would need to be in Iron Gates if there had been movement from Anatolia to Europe at that period. Of course, they only found something like 1.6.

Assuming that you refer to Extended Dat Fig. 7: I am quite curious which HG's that are. The only identified ones have 0% Basal.