Paleolithic DNA from the Caucasus

Angela

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See: Lazaridis et al:
"Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry"

https://www.biorxiv.org/content/biorxiv/early/2018/09/20/423079.full.pdf

All I can say is WOW!

"The earliest ancient DNA data of modern humans from Europe dates to ~40 thousand years ago, but that from the Caucasus and the Near East to only ~14 thousand years ago, from populations who lived long after the Last Glacial Maximum (LGM) ~26.5-19 thousand years ago. To address this imbalance and to better understand the relationship of Europeans and Near Easterners, we report genome-wide data from two ~26 thousand year old individuals from Dzudzuana Cave in Georgia in the Caucasus from around the beginning of the LGM. Surprisingly, the Dzudzuana population was more closely related to early agriculturalists from western Anatolia ~8 thousand years ago than to the hunter-gatherers of the Caucasus from the same region of western Georgia of ~13-10 thousand years ago. Most of the Dzudzuana population's ancestry was deeply related to the post-glacial western European hunter-gatherers of the 'Villabruna cluster', but it also had ancestry from a lineage that had separated from the great majority of non-African populations before they separated from each other, proving that such 'Basal Eurasians' were present in West Eurasia twice as early as previously recorded. We document major population turnover in the Near East after the time of Dzudzuana, showing that the highly differentiated Holocene populations of the region were formed by 'Ancient North Eurasian' admixture into the Caucasus and Iran and North African admixture into the Natufians of the Levant. We finally show that the Dzudzuana population contributed the majority of the ancestry of post-Ice Age people in the Near East, North Africa, and even parts of Europe, thereby becoming the largest single contributor of ancestry of all present-day West Eurasians."
 
Can anyone explain to me 'Basal Eurasians'?

"The reason it is thought to exist is because Neolithic European farmers as well as modern West Eurasians and North Africans are less closely related to East Asians etc than ancient European hunter-gatherers are"

Why would they speculate Middle Eastern HGs had admixture from this imaginary population instead of speculating European HGs had admixture from some asiatic population that made them more closely related to East Asians?
 
I think they would be able to spot such an admixture and haven't. Also, I believe there are a few other reasons to believe there was a Basal Eurasian populations group. For example, populations with a supposed Basal Eurasian admixture show a lower level of Neanderthal ancestry than other groups, indicating mixing with a group that separated from the out-of-Africa group before hybridizing with Neanderthals. I assume they have corrected for the possibility of an influx of genes from Africa ?

Anyway, I spotted this fascinating sentence in the paper: "Western PGNE populations, including Neolithic Anatolians, pre-pottery Neolithic farmers from the Levant (PPNB), Natufians, and Taforalt, can all be modeled as a mixture of Dzudzuana and additional ‘Deep’ ancestry that may represent an even earlier split than the Basal Eurasians."

Does anyone have any idea what this could refer to? Surely they would have said African if that was what they meant?
 
Many of the old theories that were floating around receive a lot of support in this paper.

07G2Wzf.png

qTyNet0


* North Africa as a source of massive populations movements, possible at several points during the Paleolithic & Mesolithic. These movements likely brought haplogroup E (back) to Eurasia.

* North Africa as a significant source of admixture in modern West Africans.

* ANE as a two-way mixture between a West Eurasian- and an East Eurasian source (here represented by Tianyuan). The East Eurasian population likely brought with it haplogroups R & Q from South-East Asia.

RqCZXlB

DXgB7Jg.png


* The new Caucasus genome is most related to Saudis, Palestinians & Lybians.

* As per the authors, Vilalbruna primarily is what "differentiates Europeans" from non-European populations.

* Villabruna most related to Basques out of all modern populations by a significant margin. Virtually every PCA showed this.

* AG3 as a source mostly for Europeans. Siberians, Caucasians and Iranians prefer deeper ANE-related admixture.
 
I know that by referring to Y-dna only, one tends to over-simplify things. But still... here's my (not adamantly sustained) scenario.

Perhaps "basal Eurasian" could be a population very similar, genetically, to the still-undifferentiated GIJK core before it split into subgroups. A group of "leftovers", somehow, that would have remained left behind and isolated for millenia in some corner of Anatolia, without too much genetic drift. GIJK came out of Africa via the Near East and stayed there a while. As fractions of it gradually spread away from the core, they grew genetically distinct. Very broadly: K went North, I went west, J went east, and G found refuge in the valleys of the Caucasus. But some of those who were in Anatolia remained autosomally homogeneous.

As for the "Deep" ancestry, it could be something like a previous Aurignacian-like population: y-dna C and mtdna M. They had come out of Africa long before, along the same route, and had met the Neanderthals. They didn't leave much of their y-dna behind. But some of them might have been assimilated by the next wave of newcomers, hence the autosomal remnants.

If such were the case, then Basal would show a lesser degree of Neanderthal admixture simply because the first wave of C people had already diluted the Neanderthal genes, and "Basal" got his Neanderthal by proxy, somehow, through "Deep".

I am looking forward to reading from Maciamo on this ground-breaking paper.
 
Last edited:
Can anyone explain to me 'Basal Eurasians'?

"The reason it is thought to exist is because Neolithic European farmers as well as modern West Eurasians and North Africans are less closely related to East Asians etc than ancient European hunter-gatherers are"

Why would they speculate Middle Eastern HGs had admixture from this imaginary population instead of speculating European HGs had admixture from some asiatic population that made them more closely related to East Asians?

Basal Eurasian reduces affinity to both Ust'Ishim and Tianyuan, so admixture between East and West Eurasians doesn't work as an explanation. Perhaps in the unlikely case that an ancient undifferentiated East Eurasian population still existed somewhere.
 
Basal Eurasian reduces affinity to both Ust'Ishim and Tianyuan, so admixture between East and West Eurasians doesn't work as an explanation.

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.
 
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.

But there seem to be no extant Eurasians that derive their ancestry from before the East-West split, which means it probably happened soon after OOA. Both Basal & Ancestral North African come from branches that predate this split.


Assuming the Europeans are pure while the middle Easterns are mixed looks like a political statement rather than anything scientific.

Are you joking?
 
But there seem to be no extant Eurasians that derive their ancestry from before the East-West split, which means it probably happened soon after OOA. Both Basal & Ancestral North African come from branches that predate this split.


What I'm saying is that the 'East-West split' is between East Asians who are the easternmost people and Middle Eastern HGs who are the westernmost people, with European HGs being a mixture of eastern and western peoples, which is what you clearly see in a global PCA:

YhjfcQ3.png


No need for a 'Basal Eurasian' population that doesn't exist to explain why Middle East HGs are the westernmost people if instead you just consider European HGs have some asiatic admixture.
 
What I'm saying is that the 'East-West split' is between East Asians who are the easternmost people and Middle Eastern HGs who are the westernmost people, with European HGs being a mixture of eastern and western peoples, which is what you clearly see in a global PCA:

YhjfcQ3.png


No need for a 'Basal Eurasian' population that doesn't exist to explain why Middle East HGs are the westernmost people if instead you just consider European HGs have some asiatic admixture.

If that were the case ancient Western Eurasian samples would have Basal Eurasian. With Vestonice, Goyet, Sungir etc. we already have plenty.
 
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?

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?
 
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
 
I think the authors ask the most important and intersting question at least as far as European population genetics are concerned:

However, it is unlikely that the Villabruna cluster sojourned in mainland Europe, as members of the cluster have been attested there only by ~14kya, marking an increased affinity of these European populations of the time to NearEastern ones . Was there migration at the time from mainland Europe to the Near East or vice versa, or, indeed from a geographically intermediate Ice Age refugium in southeast Europe, Anatolia, or the circum-Pontic (Black Sea) region that might explain the affinity of postglacialLevantine and Anatolian populations to those of Europe ? It is also unknown how the affinity between early populations in the eastern European-Caucasus-Iran zone first arose.

Where did the Villabruna cluster and by extension also its common West Eurasian ancestor come from? IJ*, the common ancestors of the haplogroups that should be associated with that expansions survives in Persians at about ~2%:

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0041252

In the supplements Lazaridis also confirms the presence of the Near Eastern 'stuff' in Eastern European and Scandinavian HGs that's been the subject of debate before:

It has been suggested that there is an Anatolia Neolithic-related affinity in hunter-gatherers from the Iron Gates. Our analysis confirms this by showing that this population has Dzudzuana-related ancestry as do many hunter-gatherer populations from southeastern Europe, eastern Europe and Scandinavia. These populations cannot be modeled as a simple mixture of Villabruna and AG3 but require extra Dzudzuana-related ancestry even in the conservative estimates, with a positive admixture proportion inferred for several more in the speculative ones.

Glad this one is finally settled :grin:
 
Here's another bombshell or two:
"This analysis180 shows that we cannot reject the hypothesis that Dzudzuana and the much later Neolithic181 Anatolians form a clade with respect to ESHG (P=0.286), consistent with the latter being a182 population largely descended from Dzudzuana-like pre-Neolithic populations whose183 geographical extent spanned both Anatolia and the Caucasus. Dzudzuana itself can be184 modeled as a 2-way mixture of Villabruna-related ancestry and a Basal Eurasian lineage.185 Western PGNE populations, including Neolithic Anatolians, pre-pottery Neolithic farmers186 from the Levant (PPNB), Natufians, and Taforalt, can all be modeled as a mixture of187 Dzudzuana and additional ‘Deep’ ancestry that may represent an even earlier split than the188 Basal Eurasians. Considering 2-way mixtures, we can model Karelia_HG as deriving189 34±2.8% of its ancestry from a Villabruna-related source, with the remainder mainly fromANE represented by the AfontovaGora3 (AG3) sample from Lake Baikal3190 ~17kya. Finally,191 we can model CHG and samples from Neolithic Iran (Iran_N) as deriving their ancestry192 largely (~58-64% using qpAdm and ~45-62% using qpGraph) from a Dzudzuana-like193 population, but with ancestry from both ‘Deep’ and ANE sources, thus proving that ANE194 ancestry had reached Western Eurasia long before the Bronze Age Eurasian steppe migrations that carried further westward into mainland Europe."

"In qpAdm modeling, a deeply divergent hunter-gatherer lineage that contributed in relatively197 unmixed form to the much later hunter-gatherers of the Villabruna cluster is specified as198 contributing to earlier hunter-gatherer groups (Gravettian Vestonice16: 35.7±11.3% and199 Magdalenian ElMiron: 60.6±11.3%) and to populations of the Caucasus (Dzudzuana:200 72.5±3.7%, virtually identical to that inferred using ADMIXTUREGRAPH). In Europe,201 descendants of this lineage admixed with pre-existing hunter-gatherers related to Sunghir3from Russia4 for the Gravettians and GoyetQ116-1 from Belgium3202 for the Magdalenians, while in the Near East it did so with Basal Eurasians. Later Europeans prior to the arrival of204 agriculture were the product of re-settlement of this lineage after ~15kya in mainland Europe,205 while in eastern Europe they admixed with Siberian hunter-gatherers forming the WHG-ANE206 cline of ancestry (Fig. 1c). In the Near East, the Dzudzuana-related population admixed with207 North African-related ancestry in the Levant and with Siberian hunter-gatherer and eastern208 non-African-related ancestry in Iran and the Caucasus. Thus, the highly differentiatedpopulations at the dawn of the Neolithic6209 were primarily descended from Villabruna Cluster210 and Dzudzuana-related ancestors, with varying degrees of additional input related to both211 North Africa and Ancient North/East Eurasia whose proximate sources may be clarified by212 future sampling of geographically and temporally intermediate populations."

"while in the Near East it did so with Basal Eurasians. Later Europeans prior to the arrival of204 agriculture were the product of re-settlement of this lineage after ~15kya in mainland Europe,205 while in eastern Europe they admixed with Siberian hunter-gatherers forming the WHG-ANE206 cline of ancestry (Fig. 1c). In the Near East, the Dzudzuana-related population admixed with207 North African-related ancestry in the Levant and with Siberian hunter-gatherer and eastern208 non-African-related ancestry in Iran and the Caucasus. Thus, the highly differentiatedpopulations at the dawn of the Neolithic6209 were primarily descended from Villabruna Cluster210 and Dzudzuana-related ancestors, with varying degrees of additional input related to both211 North Africa and Ancient North/East Eurasia whose proximate sources may be clarified by212 future sampling of geographically and temporally intermediate populations."
 
New PCA of modern populations:
eRpWqtR.png
[/IMG]
 
Basal Eurasian of various populations:
p9hcCK7.png
[/IMG]

As we've speculated, was it perhaps around Mesopotamia?
 
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...
OnnxWp5.png
[/IMG]

vsWdN1M.png
[/IMG]
 

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