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

[Rozenfeld]

I think that this preprint deserves separate thread

https://www.biorxiv.org/content/10.1101/...89600v1?ct

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

Abstract

The north Black Sea (Pontic) Region was the nexus of the farmers of Old Europe and the foragers and pastoralists of the Eurasian steppe, and the source of waves of migrants that expanded deep into Europe. We report genome-wide data from 78 prehistoric North Pontic individuals to understand the genetic makeup of the people involved in these migrations and discover the reasons for their success. First, we show that native North Pontic foragers had ancestry not only from Balkan and Eastern hunter-gatherers but also from European farmers and, occasionally, Caucasus hunter-gatherers. More dramatic inflows ensued during the Eneolithic, when migrants from the Caucasus-Lower Volga area moved westward, bypassing the local foragers to mix with Trypillian farmers advancing eastward. People of the Usatove archaeological group in the Northwest Pontic were formed ca. 4500 BCE with an equal measure of ancestry from the two expanding groups. A different Caucasus-Lower Volga group, moving westward in a distinct but temporally overlapping wave, avoided the farmers altogether, and blended with the foragers instead to form the people of the Serednii Stih archaeological complex. A third wave of expansion occurred when Yamna descendants of the Serednii Stih forming ca. 4000 BCE expanded during the Early Bronze Age (3300 BCE). The temporal gap between Serednii Stih and the Yamna expansion is bridged by a genetically Yamna individual from Mykhailivka in Ukraine (3635-3383 BCE), a site of uninterrupted archaeological continuity across the Eneolithic-Bronze Age transition, and the likely epicenter of Yamna formation. Each of these three waves propagated distinctive ancestries while also incorporating outsiders during its advance, a flexible strategy forged in the North Pontic region that may explain its peoples' outsized success in spreading their genes and culture across Eurasia.

https://www.biorxiv.org/content/10.1101/...89600v1?ct


Most impoprtant: Sredni Stog is a mix of Ukraine neolithic ( Middle Don) and Progress like with the first component around 40% on average. Basically they are confirming even if they do not admit that the results from Allentoft

Important take for Corded Ware

An individual from Durankulak in Bulgaria is of particular interest as he possesses the “Corded  Ware”-related R-M417 Y-haplogroup and a similar mix of Core Yamna and Globular Amphora
ancestry as the Corded Ware (but with more ancestry from the Globular Amphora). This individual may stem from the admixture zone between the Core Yamna and the Globular
Amphora from which the characteristic 3:1 blend2,31 of the two components in the ancestry of the Corded Ware is derived

[rafc]

I'm honestly a bit surprised they say Multi Cordoned Ware (MCW) can only be modeled as Yamnaya + EEF + BHG, I thought it was more CW related because it's mostly R1a. Interesting.

[old europe]

Hre is the profile of the Durankulak R1a sample. It is overloaded of GAC dna


For this individual (I1456 / 3500-3000 BCE) from Durankulak only a single 2-way feasible model exists
that involves a fairly even mix of Core Yamna (~45%) and Globular Amphora (~55%) ancestries (Table
S 3). Models with Trypillian (p=1e-5) or YUN_CA (p=3e-13) alternative sources of European farmer
ancestry both fail.

[alanarchae]

pretty much what Davidski has been saying for a few years?

[Riverman]

It was always most likely that the Lower Don area and Sredny Stog was the ultimate PIE source, with Yamnaya being just an offshot.
Looks like we're getting there based on sampling as well, finally...

Can anyone check the autosomal profile and haplogroup of the Usatovo related E1b1b individual?

[old europe]

pretty much what Davidski has been saying for a few years?

more or less yes. The big picture is now clear.
The Dneper-Donets-Don foragers  made up of WHG/EHG were the Proto indoeuropeans. They gave to the Sredni Stog folks and then Yamnaya their paternal Y lines R1a and I2 ( R1b Z103 has already been found in Ukraine with only Ukraine Neo and EEF ancestry and we now know that Yamnaya is born in Ukraine)
The physical aspect also of the Yamnaya ( proto europoid) was given also by the Dneper Donets foragers.

[old europe]

IIRC the Smydovo R1b M 269 sample was something like that ( circa 4700 BC)

EEF 51%
WHG 19%
EHG 10%
CHG 20%

with such a profile it seems clear that it was from the rich HG of the Dneper cline who had also a good amount of caucasian dna

[Mithra]

It was always most likely that the Lower Don area and Sredny Stog was the ultimate PIE source, with Yamnaya being just an offshot.
Looks like we're getting there based on sampling as well, finally...

Can anyone check the autosomal profile and haplogroup of the Usatovo related E1b1b individual?

Lower Don is dead Riverman. The paper says that there was westward migration during the Eneolithic of Caucasus-Lower Volga people to the North Pontic.

[Riverman]

It was always most likely that the Lower Don area and Sredny Stog was the ultimate PIE source, with Yamnaya being just an offshot.
Looks like we're getting there based on sampling as well, finally...

Can anyone check the autosomal profile and haplogroup of the Usatovo related E1b1b individual?

Lower Don is dead Riverman. The paper says that there was westward migration during the Eneolithic of Caucasus-Lower Volga people to the North Pontic.

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.

[Mithra]

It was always most likely that the Lower Don area and Sredny Stog was the ultimate PIE source, with Yamnaya being just an offshot.
Looks like we're getting there based on sampling as well, finally...

Can anyone check the autosomal profile and haplogroup of the Usatovo related E1b1b individual?

Lower Don is dead Riverman. The paper says that there was westward migration during the Eneolithic of Caucasus-Lower Volga people to the North Pontic.

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.

[Andar]

Hre is the profile of the Durankulak R1a sample. It is overloaded of GAC dna


For this individual (I1456 / 3500-3000 BCE) from Durankulak only a single 2-way feasible model exists
that involves a fairly even mix of Core Yamna (~45%) and Globular Amphora (~55%) ancestries (Table
S 3). Models with Trypillian (p=1e-5) or YUN_CA (p=3e-13) alternative sources of European farmer
ancestry both fail.

Probably misdated and possible also the Usatovo R1a. When we get their BAMs and they also have something quite downstream like for example under Z93 would also strongly point to this

[ChrisR]

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.

[Capsian20]

It was always most likely that the Lower Don area and Sredny Stog was the ultimate PIE source, with Yamnaya being just an offshot.
Looks like we're getting there based on sampling as well, finally...

Can anyone check the autosomal profile and haplogroup of the Usatovo related E1b1b individual?

I did G25-K12b for sample I3151 according cordonnier K12b in theytree
this admixture of this sample
Target: I3151
Distance: 5.5048% / 0.05504786
50.0 TUR_Barcin_N
21.0 WHG
16.4 Yamnaya_RUS_Samara
6.6 IRN_Shahr_I_Sokhta_BA2_I8728
3.0 Gambian
2.0 MAR_Taforalt
1.0 Jarawa
I tihnk maybe for admixtrue SSA is comme via Taforalt ? ( im not sure if this K12b is accurate for samples ancient or no )
Anway this cordonnier sample

I3151,0.085258,0.132347,0.035311,0.037767,0.061860,-0.002906,0.003623,0.017645,0.042760,0.052724,-0.003706,0.008235,-0.015196,-0.006185,0.000865,-0.005638,0.000757,-0.000818,-0.001159,0.001218,0.002660,0.000127,-0.003362,-0.001041,0.001479

[Riverman]

Lower Don is dead Riverman. The paper says that there was westward migration during the Eneolithic of Caucasus-Lower Volga people to the North Pontic.

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?

[Riverman]

It was always most likely that the Lower Don area and Sredny Stog was the ultimate PIE source, with Yamnaya being just an offshot.
Looks like we're getting there based on sampling as well, finally...

Can anyone check the autosomal profile and haplogroup of the Usatovo related E1b1b individual?

I did G25-K12b for sample I3151 according cordonnier K12b in theytree
this admixture of this sample
Target: I3151
Distance: 5.5048% / 0.05504786
50.0 TUR_Barcin_N
21.0 WHG
16.4 Yamnaya_RUS_Samara
6.6 IRN_Shahr_I_Sokhta_BA2_I8728
3.0 Gambian
2.0 MAR_Taforalt
1.0 Jarawa
I tihnk maybe for admixtrue SSA is comme via Taforalt ? ( im not sure if this K12b is accurate for samples ancient or no )
Anway this cordonnier sample

I3151,0.085258,0.132347,0.035311,0.037767,0.061860,-0.002906,0.003623,0.017645,0.042760,0.052724,-0.003706,0.008235,-0.015196,-0.006185,0.000865,-0.005638,0.000757,-0.000818,-0.001159,0.001218,0.002660,0.000127,-0.003362,-0.001041,0.001479

Thank you. Seems that sample has rather bad coverage with lots of noise in the result.