Massive paper on Stone age Europe and Eurasia. New HG ancestry in Steppe herders

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stone age eurasia

STONE AGE EURASIA


https://www.biorxiv.org/content/10.1101/2022.05.04.490594v1

Allenthoft & Willerslev et. al. 2022, Biorxiv.

Abstract:

The transitions from foraging to farming and later to pastoralism in Stone Age Eurasia (c. 11-3 thousand years before present, BP) represent some of the most dramatic lifestyle changes in human evolution. We sequenced 317 genomes of primarily Mesolithic and Neolithic individuals from across Eurasia combined with radiocarbon dates, stable isotope data, and pollen records. Genome imputation and co-analysis with previously published shotgun sequencing data resulted in >1600 complete ancient genome sequences offering fine-grained resolution into the Stone Age populations. We observe that: 1) Hunter-gatherer groups were more genetically diverse than previously known, and deeply divergent between western and eastern Eurasia. 2) We identify hitherto genetically undescribed hunter-gatherers from the Middle Don region that contributed ancestry to the later Yamnaya steppe pastoralists; 3) The genetic impact of the Neolithic transition was highly distinct, east and west of a boundary zone extending from the Black Sea to the Baltic. Large-scale shifts in genetic ancestry occurred to the west of this "Great Divide", including an almost complete replacement of hunter-gatherers in Denmark, while no substantial ancestry shifts took place during the same period to the east. This difference is also reflected in genetic relatedness within the populations, decreasing substantially in the west but not in the east where it remained high until c. 4,000 BP; 4) The second major genetic transformation around 5,000 BP happened at a much faster pace with Steppe-related ancestry reaching most parts of Europe within 1,000-years. Local Neolithic farmers admixed with incoming pastoralists in eastern, western, and southern Europe whereas Scandinavia experienced another near-complete population replacement. Similar dramatic turnover-patterns are evident in western Siberia; 5) Extensive regional differences in the ancestry components involved in these early events remain visible to this day, even within countries. Neolithic farmer ancestry is highest in southern and eastern England while Steppe-related ancestry is highest in the Celtic populations of Scotland, Wales, and Cornwall (this research has been conducted using the UK Biobank resource); 6) Shifts in diet, lifestyle and environment introduced new selection pressures involving at least 21 genomic regions. Most such variants were not universally selected across populations but were only advantageous in particular ancestral backgrounds. Contrary to previous claims, we find that selection on the FADS regions, associated with fatty acid metabolism, began before the Neolithisation of Europe. Similarly, the lactase persistence allele started increasing in frequency before the expansion of Steppe-related groups into Europe and has continued to increase up to the present. Along the genetic cline separating Mesolithic hunter-gatherers from Neolithic farmers, we find significant correlations with trait associations related to skin disorders, diet and lifestyle and mental health status, suggesting marked phenotypic differences between these groups with very different lifestyles. This work provides new insights into major transformations in recent human evolution, elucidating the complex interplay between selection and admixture that shaped patterns of genetic variation in modern populations.


Our study comprises the largest genomic dataset on European hunter-gatherers to date, including
329 113 imputed hunter-gatherer genomes of which 79 were sequenced in this study. Among them, we
330 report a 0.83X genome of an Upper Palaeolithic (UP) skeleton from Kotias Klde Cave in Georgia,
331 Caucasus (NEO283), directly dated to 26,052 - 25,323 cal BP (95%)
. In the PCA of all non-African
332 individuals, it occupies a position distinct from other previously sequenced UP individuals, shifted
333 towards west Eurasians along PC1 (Supplementary Note 3d). Using admixture graph modelling, we
334 find that this Caucasus UP lineage derives from a mixture of predominantly West Eurasian UP
335 hunter-gatherer ancestry (76%) with ~24% contribution from a “basal Eurasian” ghost population,
first observed in West Asian Neolithic individuals29 336 (Extended Data Fig. 5A).
Models attempting to
337 reconstruct major post-LGM clusters such as European hunter-gatherers and Anatolian farmers
338 without contributions from this Caucasus UP lineage provided poor admixture graph fits or were
339 rejected in qpAdm analyses (Extended Data Fig. 5B,C). These results thus suggest a central role of
340 the descendants related to this Caucasus UP lineage in the formation of later West Eurasian
341 populations, consistent with recent genetic data from the nearby Dzudzuana Cave, also in
Georgia30 342
.
We replicate previous results of broadscale genetic structure correlated to geography in European hunter-gatherers after the LGM17 347 , while
348 also revealing novel insights into their fine-scale structure. Ancestry related to southern European
349 hunter-gatherers (source: Italy_15000BP_9000 BP) predominates in western Europe.
This includes
350 Denmark, where our 28 sequenced and imputed hunter-gatherer genomes derive almost exclusively
351 from this cluster, with remarkable homogeneity across a 5,000 year transect (Fig. 3A). In contrast,
352 hunter-gatherer individuals from the eastern and far northern reaches of Europe show the highest
353 proportions of Russian hunter-gatherer ancestry (source: RussiaNW_11000BP_8000BP; Fig. 2B,
354 D), with genetic continuity until ~5,000 BP in Russia.
Ancestry related to Mesolithic hunter355 gatherer populations from Ukraine (source: Ukraine_10000BP_4000BP) is carried in highest
356 proportions in hunter-gatherers from a geographic corridor extending from south-eastern Europe
357 towards the Baltic and southern Scandinavia.
Swedish Mesolithic individuals derive up to 60% of
358 their ancestry from that source (Fig. 2C). Our results thus indicate northwards migrations of at least
359 three distinct waves of hunter-gatherer ancestry into Scandinavia: a predominantly southern
360 European source into Denmark; a source related to Ukrainian and south-eastern European hunter361 gatherers into the Baltic and southern Sweden; and a northwest Russian source into the far north,
before venturing south along the Atlantic coast of Norway31 362 (Fig. 2).
These movements are likely to
represent post glacial expansions from refugia areas shared with many plant and animal species32,33 363 .



Interestingly, two herein reported ~7,300-year-old imputed
383 genomes from the Middle Don River region in the Pontic-Caspian steppe (Golubaya Krinitsa,
384 NEO113 & NEO212) derive ~20-30% of their ancestry from a source cluster of hunter-gatherers
385 from the Caucasus (Caucasus_13000BP_10000BP) (Fig. 3). Additional lower coverage (non386 imputed) genomes from the same site project in the same PCA space (Fig. 1D), shifted away from
387 the European hunter-gatherer cline towards Iran and the Caucasus.
Our results thus document
388 genetic contact between populations from the Caucasus and the Steppe region as early as 7,300
389 years ago...




From approximately 5,000 BP, an ancestry component appears on the eastern European plains in
425 Early Bronze Age Steppe pastoralists associated with the Yamnaya culture and it rapidly spreads
across Europe through the expansion of the Corded Ware complex (CWC) and related cultures20,21 426 .
427 We demonstrate that this “steppe” ancestry (Steppe_5000BP_4300BP) can be modelled as a
428 mixture of ~65% ancestry related to herein reported hunter-gatherer genomes from the Middle Don
429 River region (MiddleDon_7500BP) and ~35% ancestry related to hunter-gatherers from Caucasus
430 (Caucasus_13000BP_10000BP) (Extended Data Fig. 4).
Thus, Middle Don hunter-gatherers, who
431 already carry ancestry related to Caucasus hunter-gatherers (Fig. 2), serve as a hitherto unknown
432 proximal source
for the majority ancestry contribution into Yamnaya genomes. The individuals in
433 question derive from the burial ground Golubaya Krinitsa (Supplementary Note 3). Material culture
434 and burial practices at this site are similar to the Mariupol-type graves, which are widely found in
435 neighbouring regions of Ukraine, for instance along the Dnepr River. They belong to the group of
436 complex pottery-using hunter-gatherers mentioned above, but the genetic composition at Golubaya
437 Krinitsa is different from the remaining Ukrainian sites (Fig 2A, Extended Data Fig. 4).




Individuals associated with Neolithic
470 farming cultures from Denmark show some of the highest overall hunter-gatherer ancestry
471 proportions (up to ~25%), mostly derived from Western European-related hunter-gatherers
472 (EuropeW_13500BP_8000BP) supplemented with marginal contribution from local Danish groups
473 in some individuals (Extended Data Fig. 7D; Supplementary Note 3f). We estimated the timing of
the admixture using the linkage-disequilibrium-based method DATES48 474 at ~6,000 BP. Both lines of
475 evidence thus suggest that a significant part of the hunter-gatherer admixture observed in Danish
476 Neolithic individuals occurred already before the arrival of the incoming Neolithic people in the
477 region (Extended Data Fig. 7), and further imply Central Europe as a key region in the resurgence
478 of HG ancestry.



The second continental-wide and CWC-mediated transition from Neolithic farmer ancestry to
497 Steppe-related ancestry was found to differ markedly between geographic regions. The contribution
498 of local Neolithic farmer ancestry to the incoming groups was high in eastern, western and southern
Europe, reaching >50% on the Iberian Peninsula (“postNeol” set; Extended Data Fig. 4, 6B, C)34 499 .

500 Scandinavia, however, portrays a dramatically different picture, with a near-complete replacement
501 of the local Neolithic farmer population inferred across all sampled individuals (Extended Data Fig.
502 7B, C). Following the second transition, Neolithic Anatolian-related farmer ancestry remains in
503 Scandinavia, but the source is now different. It can be modelled as deriving almost exclusively from
504 a genetic cluster associated with the Late Neolithic Globular Amphora Culture (GAC)
505 (Poland_5000BP_4700BP; Extended Data Fig. 4).
Strikingly, after the Steppe-related ancestry was
506 first introduced into Europe (Steppe_5000BP_4300BP), it expanded together with GAC-related
507 ancestry across all sampled European regions (Extended Data Fig. 7I).
This suggests that the spread
508 of steppe-related ancestry throughout Europe was predominantly mediated through groups that were
509 already admixed with GAC-related farmer groups of the eastern European plains.




The Neolithic transition also
610 marks a considerable rise in frequency of major effect alleles associated with light hair
pigmentation79 611
, whereas polygenic score predictions for height are generally low throughout the
612 first millennium of the Neolithic (Funnel Beaker epoch), echoing previous findings based on a
smaller set of individuals45,80 613 .



. The most recent individual
618 in our Danish dataset with Mesolithic WHG ancestry is “Dragsholm Man” (NEO962), dated to
619 5,947-5,664 cal. BP (95%) and archaeologically assigned to the Neolithic Funnel Beaker farming
culture based on his grave goods81,82 620 . Our data confirms a typical Neolithic diet matching the
621 cultural affinity but contrasting his WHG ancestry. Thus, Dragsholm Man represents a local person
622 of Mesolithic ancestry who lived in the short Mesolithic-Neolithic transition period
and adopted a
623 Neolithic culture and diet.
 
Thanks for sharing.
Damn, this paper is huge and I don’t have any free time to read it.
 
Thanks.
I'm particulary curious about this.

2) We identify hitherto genetically undescribed hunter-gatherers from the Middle Don region that contributed ancestry to the later Yamnaya steppe pastoralists; their fine-scale structure. .
 
“Genome imputation and co-analysis with previously published shotgun sequencing data resulted in >1600 complete ancient genome sequences offering fine-grained resolution into the Stone Age populations „

The paper says it is based on imputation, so I will not take the results serious.
Imputation needs a base in modern samples, because there are not thousands of ancient samples available.

Even with modern people, imputation stays a kind of scam and cannot be used for specific SNPs that are disease related or associated with physical or metabolic traits. All traist will be created based on the associated population in the Imputer database and does not show individual differences and cannot simulate populations that where never sequenced before.
My experience with Imputation is very bad.

This is the downfall of ancient DNA research as I often was afraid of. Cheap cost, low quality DNA, big papers.
 
This paper is huge indeed, and more than 300 samples of ancient DNA bring us a lot of new information but at the same time there are some really ridiculous charts in this paper and some statements reek of eugenics. Genetic testing is a powerful tool, but many geneticists are still not up to it. I still have to read it carefully though.

1oRlaB9.png
 
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Concerning the steppe part of this paper:

Interestingly, two herein reported ~7,300-year-old imputed genomes from the Middle Don River region in the Pontic-Caspian steppe (Golubaya Krinitsa, NEO113 & NEO212) derive ~20-30% of their ancestry from a source cluster of hunter-gatherers from the Caucasus (Caucasus_13000BP_10000BP) (Fig. 3). Additional lower coverage (non imputed) genomes from the same site project in the same PCA space (Fig. 1D), shifted away from the European hunter-gatherer cline towards Iran and the Caucasus. Our results thus document genetic contact between populations from the Caucasus and the Steppe region as early as 7,300 years ago...

From approximately 5,000 BP, an ancestry component appears on the eastern European plains in Early Bronze Age Steppe pastoralists associated with the Yamnaya culture and it rapidly spreads across Europe through the expansion of the Corded Ware complex (CWC) and related cultures. We demonstrate that this “steppe” ancestry (Steppe_5000BP_4300BP) can be modelled as a mixture of ~65% ancestry related to herein reported hunter-gatherer genomes from the Middle Don River region (MiddleDon_7500BP) and ~35% ancestry related to hunter-gatherers from Caucasus (Caucasus_13000BP_10000BP) (Extended Data Fig. 4). Thus, Middle Don hunter-gatherers, who already carry ancestry related to Caucasus hunter-gatherers (Fig. 2), serve as a hitherto unknown proximal source for the majority ancestry contribution into Yamnaya genomes. The individuals in question derive from the burial ground Golubaya Krinitsa (Supplementary Note 3). Material culture and burial practices at this site are similar to the Mariupol-type graves, which are widely found in neighbouring regions of Ukraine, for instance along the Dnepr River. They belong to the group of complex pottery-using hunter-gatherers mentioned above, but the genetic composition at Golubaya Krinitsa is different from the remaining Ukrainian sites (Fig 2A, Extended Data Fig. 4).

In my opinion, the burial ground of Golubaya Krinitsa looks like the western-most spread of the EHG-CHG/Iran mating network in 5300BC (Neolithic), because neighbouring sites from Ukraine do have a different genetic composition, even though the material culture and burial practices are similar to the Mariupol-type graves.

Y-DNA from the Middle Don is R1a and I2a, just like Sredny Stog:
NEO113 Golubaya Krinitsa Russia CentralEasternEurope Russia_Neolithic_MiddleDon 50.073 39.878 thisStudy 7,423 7,172 7,298 direct XY R1a R1a 0.11 0.983 0 4.1.3.2.2 MiddleDon_7500BP Europe_15000BP_4000BP HG_EuropeE

NEO212 Golubaya Krinitsa Russia CentralEasternEurope Russia_Neolithic_MiddleDon 50.072 39.894 thisStudy 7,475 7,311 7,393 direct XY I2a I2a1b1a2 3.18 0.996 0 4.1.3.1.1.1 MiddleDon_7500BP Europe_15000BP_4000BP HG_EuropeE
 
Thus we reach the magic 50% Caucasus/Iran in the steppe people, and the presence of Basal Eurasian. Some will no doubt not be happy with that conclusion.

Likewise, they firmly place the LP gene uptick "before" the arrival of the steppe people, and the appearance of blonde hair to the Neolithic transition.

They also claim to be able to pinpoint the source of the farmer ancestry in steppe invaders in admixture with GAC, which always seemed likely.

That Willerslev is involved does give me pause.

I have to read the whole thing carefully.
 
Concerning the steppe part of this paper:.
In my opinion, the burial ground of Golubaya Krinitsa looks like the western-most spread of the EHG-CHG/Iran mating network in 5300BC (Neolithic), because neighbouring sites from Ukraine do have a different genetic composition, even though the material culture and burial practices are similar to the Mariupol-type graves.
Y-DNA from the Middle Don is R1a and I2a, just like Sredny Stog:
"And they also found one J1 here:
NEO163 Vasilyevskiy kordon 17 Russia CentralEasternEurope Russia_Neolithic 52.9 40.03 thisStudy 5,721 5,486 5,604 direct XY J1 J1 0.23 0.990 0 4.1.1.2.1.2 DonRiver_5800BP_5300BP Europe_15000BP_4000BP HG_EuropeE"

I think the R1a seems to be related with karelian R1a with mt DNA C and yDNA J. EHG were buried in the supine position, but SS in the supine and flexed leg position like yamna.

Recent studies of ancient mitochondrial DNA (mtDNA) lineages have revealed the presence of East Eurasian mtDNA haplogroups in the Central European Neolithic. Here we report the finding of East Eurasian lineages in ancient mtDNA from two Neolithic cemeteries of the North Pontic Region (NPR) in Ukraine. In our study, comprehensive haplotyping information was obtained for 7 out of 18 specimens. Although the majority of identified mtDNA haplogroups belonged to the traditional West Eurasian lineages of H and U, three specimens were determined to belong to the lineages of mtDNA haplogroup C. This find extends the presence of East Eurasian lineages in Neolithic Europe from the Carpathian Mountains to the northern shores of the Black Sea and provides the first genetic account of Neolithic mtDNA lineages from the NPR.

During the Neolithic, the North Pontic Region (NPR) was home to major prehistoric cultural conglomerates, among them—the Dnieper-Donets cultural complex (DD). The DD culture has been studied in approximately 200 sites in Ukraine and Byelorussia, including settlements and large collective cemeteries of the Mariupol-type (M-t).1 The main feature of M-t cemeteries is inhumation burial in the supine position. This burial rite differs from most local Mesolithic burial traditions and is characteristic of the ‘Euro-Siberian’ zone of extended burials, which are found from Lake Baikal and the forest and forest-steppe zones of the East European Plain to the northern part of Central Europe and Scandinavia.2, 3
The distinct burial tradition of Neolithic populations of the NPR as well as their anthropological characteristics suggests an influx of external population sources. We set out to quantify the extent of gene flow into the NPR during the Neolithic. Recent advances in mitochondrial DNA (mtDNA) analysis have revealed global patterns of neutral marker variation that appear to correlate with the geographic origin of the source population.4, 5 To elucidate the maternal genetic lineages of the population that constructed the M-t cemeteries, we undertook a genetic analysis of ancient mtDNA extracted from specimens from two Neolithic NPR cemeteries2


https://www.nature.com/articles/jhg...ted&code=5d5a23f8-4738-4427-8c60-6fe8245e2732
 
CHG admixture existed in Pontic Caspian region more than 5000 BC (Eneolithic). Don HG, a Ukraine_Meso and CHG mix, discovered on the Don River
 
CHG admixture existed in Pontic Caspian region more than 5000 BC (Eneolithic). Don HG, a Ukraine_Meso and CHG mix, discovered on the Don River

There is already a thread about this paper:
https://www.eupedia.com/forum/threads/42516-stone-age-eurasia?p=647097#post647097

But where do they model or say that it is a Ukraine_Meso mix ? Ukraine_Meso has way to much WHG:

Target: UKR_Meso
Distance: 4.3532% / 0.04353210
69.0RUS_Karelia_HG
31.0WHG

It's funny because when modeling with Middle Don, there is no WHG in Europeans. If Middle Don is really that WHG heavy, it is not a good proxy for steppe ancestry.
See my post here:https://www.eupedia.com/forum/threa...n-Steppe/page7?p=647104&viewfull=1#post647104
 
There is already a thread about this paper:
https://www.eupedia.com/forum/threads/42516-stone-age-eurasia?p=647097#post647097
But where do they model or say that it is a Ukraine_Meso mix ? Ukraine_Meso has way to much WHG:
Target: UKR_Meso
Distance: 4.3532% / 0.04353210
69.0RUS_Karelia_HG
31.0WHG
It's funny because when modeling with Middle Don, there is no WHG in Europeans. If Middle Don is really that WHG heavy, it is not a good proxy for steppe ancestry.
See my post here:https://www.eupedia.com/forum/threa...n-Steppe/page7?p=647104&viewfull=1#post647104
Don't know. Should have used a more EHG proxy. Still its Interesting to see how far Iranian descent groups like CHG, BMAC, Zagros Farmers, Eastern Iranian pastorialists etc. From Steppes of Russia that had great impact in Nothern Europe to East African pastorialists who carried lactose persistant genes that orignate in West Asia (tho their eurasian ancestry is mostly Levant Neolithic) to Bronze age Anatolians who carried Zagros ancestry and spread it across the balkans and Med. HotuIII cave people would be proud of their progeny as they had changed world history
 
That being said. I don't think Don HG played a major role in Steppe pastoralist formation. I still think Steppe Eneolithic was formed more to the east. Don HG just only shown how far CHG spread could have spread. But this paper seemed to have suggested that yamnaya is 2/3 Don HG
 
Yes, this paper suggests Yamnaya is 2/3 Middle Don HG but the same could roughly be said about Khvalynsk if someone would model them as ancestor to Yamnaya. The thing is we need additional CHG/Iran in Middle Don and Khvalysnk to reach the levels we see in Yamnaya. The Y-DNA also doesn't match.
 
Yes, this paper suggests Yamnaya is 2/3 Middle Don HG but the same could roughly be said about Khvalynsk if someone would model them as ancestor to Yamnaya. The thing is we need additional CHG/Iran in Middle Don and Khvalysnk to reach the levels we see in Yamnaya. The Y-DNA also doesn't match.
Also it does not fit with what we see in the archeological record. Its clear the steppe population had technological diffusion from the south that give it a technological lead over other groups. The spread of the pastoral economy and the usage of Arsenic bronzeware coupled with ceramic types and pattern usage and the presence of foreign items in archeological sites shows that steppe folks clearly had important interactions with southern groups
 
Yes, this paper suggests Yamnaya is 2/3 Middle Don HG but the same could roughly be said about Khvalynsk if someone would model them as ancestor to Yamnaya. The thing is we need additional CHG/Iran in Middle Don and Khvalysnk to reach the levels we see in Yamnaya. The Y-DNA also doesn't match.


The non caucasian part ( georgia Upper paleolithic and georgia mesolithic) of Middle Don HG in the paper in fig. 2 is clearly labeled as ukraine mesolithic. Middle Don HG were likely the easternmost tail of the ukranian HG that populated the north pontic steppe. Obviously since we must follow the Y line these ukranian HG provided the typical PIE Y dna like R1a and I2 which were present in ukraine since the mesolithic. The smydovo ( Bulgaria) sample that is R1b M269 dated at around 45000 BC shows that eastern ukraine harbored also the right type of R1b. The smydovo sample can be modeled IIRC as EEF/Middle Don mix.
So the long quest of the PIE origin is finally over. PIE were a mix of WHG/EHG that inhabited the north pontic region since the mesolithic. This is in full accordance with the linguistic criteria of PIE. Since PIE had agricoltural terminology and since the Dneper/ Donets foragers ( all WHG/EHG) were the only steppe populations that switched to agropastoralism around 4500/5000 BC ( time of PIE formation).
Game over.
 
Also it does not fit with what we see in the archeological record. Its clear the steppe population had technological diffusion from the south that give it a technological lead over other groups. The spread of the pastoral economy and the usage of Arsenic bronzeware coupled with ceramic types and pattern usage and the presence of foreign items in archeological sites shows that steppe folks clearly had important interactions with southern groups



Nope

from the Kotova paper

[h=2]The contacts of the Eastern European steppe people with the Balkan population during the transition period from Neolithic to Eneolithic[/h]

This article is devoted to cultural contacts of steppe population and Balkan people about 5300–4800 BC. Numerous imports (adornments from copper, cornelian, marine shells, pots, plates from the bone and nacre, pendants from the teeth of red deer), radical changes in the cultural traditions (new type ornamental compositions, flexed inhumations, stone in graves and above them, pits with alcove) and imitation of pottery have been fixed for the Late Neolithic in the Eastern European steppe. Acquaintance with first metal and strong western impact caused the formation of the new Sredniy Stog culture.
 
The non caucasian part ( georgia Upper paleolithic and georgia mesolithic) of Middle Don HG in the paper in fig. 2 is clearly labeled as ukraine mesolithic. Middle Don HG were likely the easternmost tail of the ukranian HG that populated the north pontic steppe. Obviously since we must follow the Y line these ukranian HG provided the typical PIE Y dna like R1a and I2 which were present in ukraine since the mesolithic. The smydovo ( Bulgaria) sample that is R1b M269 dated at around 45000 BC shows that eastern ukraine harbored also the right type of R1b. The smydovo sample can be modeled IIRC as EEF/Middle Don mix.
So the long quest of the PIE origin is finally over. PIE were a mix of WHG/EHG that inhabited the north pontic region since the mesolithic. This is in full accordance with the linguistic criteria of PIE. Since PIE had agricoltural terminology and since the Dneper/ Donets foragers ( all WHG/EHG) were the only steppe populations that switched to agropastoralism around 4500/5000 BC ( time of PIE formation).
Game over.

In short I have these points:
1. Middle Don needs 35% additional CHG/Iran it is alone not the proximal source for Yamnaya. Additional CHG/Iran has to come from sites more to the East and South.
2. There is barely any WHG in Yamnaya nor in Steppe Eneolithic.
3. Middle Don eats up all of the WHG in modern Europeans, there must be something very wrong with this proxy.
4. The Y-DNA doesn't match.

Do you have anything to say about these points ?
 
Nope

from the Kotova paper

[h=2]The contacts of the Eastern European steppe people with the Balkan population during the transition period from Neolithic to Eneolithic[/h]

This article is devoted to cultural contacts of steppe population and Balkan people about 5300–4800 BC. Numerous imports (adornments from copper, cornelian, marine shells, pots, plates from the bone and nacre, pendants from the teeth of red deer), radical changes in the cultural traditions (new type ornamental compositions, flexed inhumations, stone in graves and above them, pits with alcove) and imitation of pottery have been fixed for the Late Neolithic in the Eastern European steppe. Acquaintance with first metal and strong western impact caused the formation of the new Sredniy Stog culture.

The Cucuteni Tripolye culture did use much metallurgy though they had very sophesticated lithic culture. Steppe population obveriously did interacted with Neolithic SE European cultures looking at their 10% Anatolian farmers but balkan/Cuceteni cultures were not the only cultures they interacted with. Steppe bronzeware seem to have Caucasus roots who in turn got it from Transcaucasian/Zagrozian groups. Arsenic bronze making had it roots in West Asia.

"The earliest artifacts so far known coming from the Iranian plateau, in the 5th millennium BCE, and are smelted from native arsenical copper and copper-arsenides, such as algodonite and domeykite" Thornton, C. et al (2002). "On pins and needles: tracing the evolution of copper-based alloying at Tepe Yahya, Iran, via ICP-MS analysis of Common-place items". Journal of Archaeological Science. 29 (12): 1451?60.

Arsenic bronze tool making was found in the Cacasus Piedmount, with similar Iranian techniques. Later balkan bronzewares are different
 
Btw, Dnieper-Donets foragers were largely replaced by Sredny Stog according to Anthony et al. 2022 in the Eneolithic.
 

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