A genomic history of the North Pontic Region from the Neolithic to the Bronze Age

[RCO]

In the Supplementary Information they use the correct term of CHG-IRAN, unfortunately in the article the authors don't question or investigate how the Caucasus-Lower Volga (CLV) was originally formed by a movement or invasion by a CHG-IRAN population from the South and the Caspian Sea, the local EHG was native and originally formed before in the Volga and the steppe, afterwards the CHG-IRAN population/component gradually arrived (The Arrival) and invaded that region in good numbers to keep a perdurable proportion, the first beachhead of the CHG-IRAN conquest was the Caucasus-Lower Volga cline, where they created new admixed populations that bred early pioneers and vanguards from the Caucasus-Lower Volga (CLV) cline and their descendants moved westward. A secondary different Caucasus-Lower Volga group also moved westward later in a distinct but temporally overlapping wave and created other admixed group know as Sredny Stog (Serednii Stih). A third wave of expansion occurred when Yamna descendants of the Sredny Stog forming ca. 4000 BCE expanded during the Early Bronze Age (3300 BCE).

Bonus from the Suppl.

The J-Y6313-deived J-FT265222 lineage of Y haplogroup J1 identified in a genetically Usatove individual from the Revova kurgan (Burial 19) is present in modern populations of 30 Europe, as well as Saudi Arabia and Iraq. Another Usatove male from Mayaky carried the R1a lineage, has a widespread Eurasian distribution, but its initial diversification is thought to have started in Iran

[Mithra]

We'll see how many samples they have from the Lower Don and regardless, Sredny Stog was born there and not to the East. The true PIE stage is SSC.

I didn’t even mention Sredni Stog lol. Just accept that you were wrong the whole time with your Lower Don culture theory. It’s clear that Sredni Stog played a major role in PIE formation but the people that brought most of the uniparentals and autosomal in it’s formation are the Caucasus-Lower Volga people. Progress/Vonuchka+Ukraine_N+minor EEF=Sredni Stog.

I said they formed at the Lower Don, I had no explicit opinion about how the Caucasian admixture got there. What would prove me partly wrong is, if sites like R. yar would yield completely different people which had nothing to do with the ethnogenesis of PIE and Sredny Stog.
I highly doubt that's the case still and that Sredny Stog evolved from around those sites. Like you say, Sredny Stog had minor EEF, the question is also where they picked it up. If to the West, at the Lower Don, it would prove my point.
The Lower Don cultures had a more specific profile and started to use husandry and more advanced buildings and techniques. I think they still don't tested them, or did they?

Sorry, after reading the paper the second time I have to correct myself the authors says no EEF in Sredni Stog but also no EEF in Core Yamnaya but instead up to 21% Armenia_N. We will see how that plays out in upcoming papers but what is clear now is that the Caucasus_Lower Volga is were the PIE party is.

[pelop]

Based on the model presented in this paper and the other upcoming one [Lazaridis, I., Patterson, N., Anthony, D. & & others. The Genetic Origin of the IndoEuropeans. in Submission. (2024)], the key population in this whole complicated picture was the "BPgroup".




The pre-print says:

The Eneolithic 97 (apart from the SSAC) and BA individuals in Fig. 2a are mostly located towards the “farmer” end of the EFHG cline. Four NPR individuals form a cline stretching from the Core Yamna cluster towards steppe Maykop and traversing the CLV-Volga cline proximate to a key Eneolithic population represented by the Berezhnovka-2-Progress 2 individuals (BPgroup), a genetically homogeneous people between the northeast Caucasus and lower Volga that can be approximately modeled as a mixture of EHG, CHG, and Siberian/Central Asian Neolithic ancestries. Two of these (I20078 and I17974) are late Eneolithic (3300-3000 BCE) individuals from Moldova. The other two, I18740 from Hungary7 and I20072 from Moldova, dated to ca. 4300-4000 BCE, are archaeologically associated with the Volga-Caucasus – lower Dnipro pulse of the steppe people that left “ochre graves” across the NPR and adjacent Balkan-Carpathian area.

On their ADMIXTURE run, the "BPgroup" is modelled as ~50% CHG - 50% EHG:

[pelop]

If I'm reading this right, it would mean that the "BPgroup" profile existed contemporaneously in Moldova, Hungary, the lower Volga and the North Caucasus (Progress 2). This would certainly throw a wrench in the "Anatolian from the west or the east" debate

[elflock]

With a first glance it looks like one of the more important papers for Europe/Anatolia/Caucasus.

by computing the ratio of Y chromosome to sum of X and Y chromosome sequences which is expected to be very low for females and to have a very much higher value for males. We determined a consensus sequence for mitochondrial DNA using bcftools (https://github.com/samtools/bcftools) and SAMTools58 requiring a minimum of 2- fold coverage to call the nucleotide and a majority rule to determine its value. We used HaploGrep2 to determine the mitochondrial haplogroups based on this consensus sequence, leveraging the phylotree database (mtDNA tree build 17)

It seems there was no analysis of the Y-DNA results in the paper itself. I do not understand why.
I was not able to extract the Suppl. Table S1 completely as CSV, but from the 78 (90?) individuals there seem to be only 3 J results. I say only because there are also 3 Q

Show Content

Spoiler
№;Genetic ID;Specimen code;Site, Burial;14C uncalBP (Lab Code);BCE or Calibrated BCE, 2σ (95.4%);Genetic sex;MtDNA haplogroup;Y chromosome haplogroup
33;I7929;REV3.19;Revova, Kurgan 3, Burial 1913;4905±20 (PSUAMS-4763);3711-3639 calBCE;M;U4d3;J1 (J-FT265222)
19;I7923;RL2.05 (VRT-LR1);Verteba Cave, Site 26, Individual 1;4955±30 (PSUAMS-8692);3789-3649 calBCE;M;T2b+16362;J2a1
49;I17973;Br/K1/B21/S1;Bursuceni, Kurgan 1, Burial 21, Skeleton 123;4516±13 (weighted mean10 of 4530±20 (PSUAMS-8723), 4520±25 (PSUAMS-8310) and 4500±20 (PSUAMS-8722));3354-3103 calBCE;M;U1a1a;J2b2b2~ (J-Z42942)

Hopefully I7923 J2a1 can also be assigned to a more terminal SNP.

The J2a1 sample most likely belongs to Y7010+. I7929 from Revova is the third J1b-Y6313+ sample in Eneolithic Eastern Europe. The Eneolithic Bursuceni sample belongs to J2b2b2-Z42942 under which today there's quite some Azhkenazi Jewish, Italkhim and Judeo-North African clades i.e. founder effects that preserved this rare branch.

[alanarchae]

It’s very in line with what Mallory said in the late 1980s He said Stedny Stog was a key thing in the formation of archaic phase of PIE BUT he also noted the formation of Stedny Stog involved a pulse westwards from the Volga. THEN Stedny Stog elements ‘returned eastwards’ to the Volga where the eastern Stedny Stog were a major part of the formation of Yamnaya. Then of course Yamnaya spread west.

So east-west then west-east then east-west!

[old europe]

It’s very in line with what Mallor said in the late 1980s  He said Stedny  Stog was a key thing in the formation of archaic phase of PIE BUT he also noted the formation of Stedny Stog involved a pulse westwards from the Volga. THEN Stedny Stog elements ‘returned eastwards’ to the Volga where the eastern Stedny Stog were a major part of the formation of Yamnaya. Then of course Yamnaya spread west.

So east-west then west-east then east-west!

The problem lies in the source of the Ylines. If you remember it is the same problem for the relationship between EEF and R1b bell beaker. You have italic speakers with R1b in central Italy that are something like 80% local copper age ancestry but still their language stems from their steppe beaker component. If the volga-caucasus cluster is the source of PIE then it means the vector of PIE is only R1b and the R1a and I2 folks at the Don Dneper were IEzed by Progress people. Is this a realistic scenary?

But we already know we have a R1b Z103 full fledged Yamnaya line in dereivka totally deprived of steppe ancestry. It is sample I5884 ( in the figure)
But again Allentoft already settled the question last year.

Although the broader effects of the steppe migrations around 5,000 cal. bp are well known, the origin of this ancestry has remained a mystery. Here we show that the steppe ancestry composition (Steppe_5000BP_4300BP) can be modelled as a mixture of around 65% ancestry related to herein-reported HG genomes from the Middle Don River region (MiddleDon_7500BP) and around 35% ancestry related to HGs from Caucasus (Caucasus_13000BP_10000BP) (Extended Data Fig. 6 and Supplementary Data 9). Thus, Middle Don HGs, who already carried ancestry related to Caucasus HGs (Extended Data Fig. 4a), serve as a hitherto-unknown proximal source for the majority ancestry contribution into Yamnaya-related 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 HGs mentioned above, but the genetic composition at Golubaya Krinitsa is different from that in the remaining Ukrainian sites (Fig. 2a and Extended Data Fig. 5). A previous study30 suggested a model for the formation of Yamnaya ancestry that includes a ‘northern’ steppe source (EHG + CHG ancestry) and a ‘southern’ Caucasus Chalcolithic source (CHG ancestry), but did not identify the exact origin of these sources. The Middle Don genomes analysed here show the appropriate balance of EHG and CHG ancestry, suggesting that they are candidates for the missing northern proximate source for Yamnaya ancestry.

[rafc]

Wow, seems they now put the origin of Anatolian north of the Caucasus, that's quite a change.

"The Proto-Indo-Anatolian homeland was thus probably in the North Caucasus-Lower Volga area"

[old europe]

Wow, seems they now put the origin of Anatolian north of the Caucasus, that's quite a change.

"The Proto-Indo-Anatolian homeland was thus probably in the North Caucasus-Lower Volga area"

The putatively Sredni Stog area has the majority of its component from the Dneper Don foragers in at least 2 of its three clusters. And they were all R1a I2a and maybe even R1b. I wonder why are they so sure that the only vector of PIE is R1b V136

[alanarchae]

paper has nailed it. And kudos to Gimbutas and Mallory who had this worked out long ago without ancient DNA. His mentor Gimbutas died a few decades ago but im delighted Mallory is still alive and well to see this. He was actually digging at Navan Fort (Emain Macha) in Ireland only a couple of months ago so he’s in good nick for a guy aged 78!

[alanarchae]

Wow, seems they now put the origin of Anatolian north of the Caucasus, that's quite a change.

"The Proto-Indo-Anatolian homeland was thus probably in the North Caucasus-Lower Volga area"

even

That's likely true but there is a 1000-2000 year period between that moment and evidence or even inference of its presence where it survived - Anatolia..  The prop date of the proto language of the recorded Anatolian branched is 3000-2500BC r that is obvious not the same as the branching off even which was likely a bit earlier. The big question in my mind has always been this - how did Anatolian avoid the kind of contact that shifted all the other branches to later fully formed PIE by e3300BC if not a few cevturies earlier. It must have found an isolated location from the rest..  It had a long period that it could have been in an intermediate location. And those steppe groups couod really travel vast distances when you look at the waves

[alanarchae]

if really makes me wonder what became of the Usatovo population. A genetically distinctive c.50-50
blend of the steppe pastoralists and Trypole farmers. But also intersting because they are a relatively early group who you would think spoke a relatively early branching off dialect of IE (if they spoke the language of the steppe half of their ancestry -perhaps they didn’t) related to Strdny astigmatism derived Suvorovo-Nov groups and commencing c. 3900BC according to this recent paper https://www.zurnalai.vu.lt/archaeologia-...845/30685/

The combination of early date and Stedny Stog roots would seem to me to indicate they should have spoken something more like Anatolian if they retained the steppe language after their 50-50 mixing with farmers. The suggested date of the commencement of this culture c. 3800/3700BC or so predates the currently most accepted date for Afanasievo of c.3300BC by 4 or 5 centuries. So you’d expect a language more archaic than Tocharian and perhaps closer to an Anatolian type early branching. .

Their location seems to be where later the Yamnaya subgroup Budzak (hope I spelled that right) took over. So I suppose their demise has an explanation. Or did they move and survive for a time?

[Southpaw]

We have 1 potential E-V13 from Usatovo

I12704 Mau6 Mayaky, Kurgan 7,
Burial 211
5144±20 (weighted mean10 of
5530±32 (OxA-22959)
12,
5390±30 (BETA-441235)
5, and
5545±40 (PSUAMS-7793, this
report)
3620-3030 calBCEg M T2h2 E1b1b1a1

Among the specimens in our selection, a CTAC individual from Verteba Cave and a
proto-Usatove individual from Mayaky carried E1b1b1a1b* Y chromosomal lineages. The protoUsatove designation of the Mayaky individual is based on the 14C date that predates Usatove
even after adjusting for reservoir effect5 (Section 1.2.1). The E1b1b1a1b lineage is not
associated with the Balkan-Danubian route of farming expansion from Anatolia to central
Europe in the Neolithic137. On the other hand, the E1b1b1a1b~ expansion in the
Mediterranean, which is timed to the late Mesolithic in southeast Europe 137, raises a possibility
that it coincided with the spread of agriculture out of the Fertile Crescent into southern Europe
via the Mediterranean coast beginning ca. 9000 years ago 141. Such as, Y chromosomal lineage
diversity in the Epicardial culture of the Cardial Ware complex of the Neolithic Mediterranean
shows Near Eastern influence and Cardial/Epicardial mtDNA lineage frequencies and diversity
are comparable to those from Near Eastern Pre-Pottery Neolithic B sites142. A bearer of the
E1b1b1a1b1 haplogroup belonging to the Cardial Ware archaeological complex was reported
from the Croatian Zemunica Cave in western Balkans 8. Cardial Ware complex is considered to
have influenced the Late Neolithic-Eneolithic Hamangia culture of the west-northwest Pontic
143. Hamangia, in turn, is considered to have influenced the formation of Precucuteni-Trypillia A
144. The presence of the E1b1b1a1b1 lineage in Trypillia and a proto-Usaove individual
strengthens the link between Hamangia and CTAC as well as CTAC and Usatove and connects
the genetic ancestry of CTAC and Usatove with Cardial Ware.

[Southpaw]

Why did the early linguists suggest Germanic branched off from Usatovo? Any particular reason for that, or it was just a wild guess/guesstimate?

Because doesn't look like the case at all, unless more Usatovo samples are in line.

[Jaska]

Why did the early linguists suggest Germanic branched off from Usatovo? Any particular reason for that, or it was just a wild guess/guesstimate?

Because doesn't look like the case at all, unless more Usatovo samples are in line.

Who early linguists?