‘Proto-Yamnaya’ Eneolithic individuals from Kuban steppe c. 3700 BC ? (guest post)

This is a guest post by an anonymous contributor. I don't necessarily agree with its findings, but I think it's a good way to get the ball rolling here again. Feel free to let me know what you think. Please note, however, that any comments that show mental instability will be blocked. No more crazy talk on this blog.

In order to understand who Yamnaya people were, one must first define ‘Yamnaya’. We will adopt a strictu sensu view (e.g. Anthony, Heyd) encompassing burials dating 3200-2600 BC, with a characteristic body position, mound construction, and copper artefacts. These complexes can be linked to a core group of people whose autosomal make-up is quite homogeneous throughout their wide geographic range. Moreover, almost all males belong to Y-haplogroup R1b-M269-Z2103. In this light, ‘core Yamnaya’ does not represent a ‘proto-Indo-European’ population, as commonly proclaimed, but a group which contributed to several post-PIE population-language complexes, such as Tocharian, Armenian and some Paleo-Balkan languages. However, historical linguistics is not the focus of this post.

Archeologists had linked Yamnaya to earlier complexes such as Khvalynsk, Repin and/or Mikhalivka. Given that cultural markers such as pottery and burial customs can be borrowed and copied, ancient DNA can offer a more objective assessment of population origins. However, the cacophony of clusters, clines and other statistical constructs in publications can be confusing. A more rationalized approach is required, and one way is to co-analyse phylogenetically linked individuals across space and time. Apart from a lower-quality individual from Smyadovo (Bulgaria c. 4300 BC), the earliest attestation of R1b-M269 is in two individuals from the Kuban steppe (Stavropol region) c. 3700 BC -NV3003 and KST001 (Ghaliachi et al 2024). However, Y-hg R1b-M269 is missing in currently sampled Kuban steppe and north Caucasian males from the preceding period (5000-4000 BC). Males of the ‘Kuban steppe 4500bc’ group (Progress, Vojnucka, Sengeleevskiy, etc) are instead derived for the phylogenetically divergent Y-hg Rb-V1636. Males from the Nalchik cemetery are also derived for Y-hg R1b-V1636, or related haplotypes, although they were buried in a ‘Caucasian Farmer’ pose and heavily infused with such ancestry, but probably also had a burial mound thrown above. We do not know when the R1b-V1636 clans entered the northern Caucasus region, or from where, but they appear to have been attracted by trade with North Caucasian Famer (~Eneolithic) groups- termed as ‘Meshoko-Zamok’, ‘Chokh’, etc, in literature. Curiously the Nalchik group has minimal Central Asian (“TTK-related”) ancestry, whilst the Kuban steppe group has high levels. This suggests that TTK-related ancestry arrived after R1b-V1636 dominant EHG clans entered the North Caucasus region, but other scenarios are possible. Lastly, two ‘Meshoko culture’ males from Unakozovskaya have been assigned to Y-hg J2a-L26.

A shake-up occurred in the north Caucasus after 4000 BC. As we know, this corresponds to the emergence of the Majkop phenomenon, catalysed by renewed migrations from the south. These were not ‘Uruk migrants’ as sometimes proposed - the Uruk phenomenon occurred several hundred years later and was a south Mesopotamian phenomenon. Instead, these newcomers emerge from southern Caucasus- north Mesopotamian ‘Late Chalcolithic’ groups. They brought with them multiple West Asian lineages, such as Y-hg T, L2, J2a-, J2b, G2. Over time they mixed with preceding north Caucasian Eneolithic groups, culminating in the Novosvobodnaja phenomenon.

The emergence of Majkop as a new socio-cultural complex broke down the previous system dominated by Y-hg R1b-V1636 clans. The Majkop sphere consisted of a ‘core’ of heterarchical chiefs buried in elaborate kurgans near the Mountains, and a dynamic northern ‘frontier’ in the steppe lands (as far as the lower Don) between 4000 and 3000 BC. At least 3 ‘‘Majkop periphery’ genetic groups can be defined; in fact all these groups can be termed ‘steppe Majkop’:

1- Group with western Siberian/ north central Asian ancestry (the ‘genetic steppe Majkop’ as defined in Wang et al, 2023)
2- The South Caucasian/north Iranian ‘Zolotarevka’ group
3- The R1b-M269 duo.

Regardless of their lineages and genomic affinities, these individuals were often buried in kurgans which over time formed groups. These were not continuations of pre-4000 BC kurgans, but the communities instead made a conscious choice to build new kurgans after 4000 BC, adding to the idea of discontinuity. But once built, these kurgan clusters continued to be developed for hundreds of years, into the Yamnaya period. This does imply ethnic homogeneity or continuity, just a ‘continuity of place’. Without a direct attestation of a phylogenetic ancestor, and guestimating from their (non-identical) genomic profile, we are left to speculate that Y-hg R1b-M269 individuals moved down from somewhere in the Volga-Don interfluve. Perhaps amongst groups utilizing Repin pottery, but if so, they did not continue its use in their new contexts. By 3000 BC, the Majkop system collapsed. Yamnaya groups and their ‘Catacomb’ descendants took control of the north Caucasus region, having benefitted from years of trade/ exchange and knowledge gathering. Whether Yamnaya actually descend from individuals like KST-1 or NV3003 remains to be seen, however these are the closest leads we have. Certainly, we can model Yamnaya as deriving from KST-1 (88%) + Dnieper_N (12%), but we should be cautious when using singular individuals as ‘sources’.

See also...

The PIE homeland controversy: December 2024 open thread

The story of the Khvalynsk people

I'm totally serious when I say that this video is more objective, informative and accurate than any peer-reviewed paper published to date when it comes to the genetic origins of the Khvalynsk people.

However, that's not to say it's perfect. I think it misses some important details. See here...

The Caucasus is a semipermeable barrier to gene flow

Dear David, Nick, Iosif...let's set the record straight

Understanding the Eneolithic steppe

Dear David, Nick, Iosif...let's set the record straight

Almost a decade ago scientists at the David Reich Lab extracted DNA from the remains of three men from the Khvalynsk II cemetery at the northern end of the Pontic-Caspian (PC) steppe.

These Eneolithic Eastern Europeans showed significant genetic heterogeneity, with highly variable levels of Eastern Hunter-Gatherer (EHG) and Near Eastern-related ancestry components.

As a result, the people at the David Reich Lab concluded that the Eneolithic populations of the PC steppe formed from a relatively recent admixture between local hunter-gatherers and Near Eastern migrants.

Unfortunately, this view has since become the consensus among scientists working with ancient DNA.

I say unfortunately because there's a more straightforward and indeed obvious explanation for the genetic heterogeneity among the samples from Khvalynsk II. It's also the only correct explanation, and it doesn't involve any recent gene flow from the Near East.

Here it is, in point form, as simply as I can put it:

- EHG is best represented by samples from Karelia and Lebyazhinka, which are modern-day Russian localities in the forest zone and on the border between the steppe and the forest-steppe, respectively

- Khvalynsk II is also located on the boundary between the steppe and the forest-steppe, and very far from the Near East

- so the genetic structure of the people buried at Khvalynsk II does represent an admixture event

- however, this admixture event simply involved an EHG population from the forest-steppe and a very distantly Near Eastern-related group native to the steppe (that is, two different Eastern European populations).

I've written this blog post because I think David Reich, Nick Patterson, Iosif Lazaridis and colleagues should finally admit that they didn't quite get this right. And it'd be nice if they could put out a paper sometime soon in which they set the record straight.

See also...

The PIE homeland controversy: August 2019 status report

Archeologist David Anthony has a new paper on the Indo-European homeland debate titled Archaeology, Genetics, and Language in the Steppes: A Comment on Bomhard. It's part of a series of articles dealing with Allan R. Bomhard's "Caucasian substrate hypothesis" in the latest edition of The Journal of Indo-European Studies. It's also available, without any restrictions, here.

Any thoughts? Feel free to share them in the comments below. Admittedly, I found this part somewhat puzzling (emphasis is mine):

It was the faint trace of WHG, perhaps 3% of whole Yamnaya genomes, that identified this admixture as coming from Europe, not the Caucasus, according to Wang et al. (2018). Colleagues in David Reich’s lab commented that this small fraction of WHG ancestry could have come from many different geographic places and populations.

I think that's highly optimistic. It really should be obvious by now thanks to archeological and ancient genomic data, including both uniparental and genome-wide variants, that the Yamnaya people were practically entirely derived from Eneolithic populations native to the Pontic-Caspian (PC) steppe. So, in all likelihood, this was also the source of their minor WHG ancestry.

Indeed, they clearly weren't some mishmash of geographically, culturally and genetically disparate groups that had just arrived in Eastern Europe, but the direct descendants of closely related and already significantly Yamnaya-like peoples associated with long-standing PC steppe archeological cultures such as Khvalynsk and Sredny Stog. I discussed this earlier this year, soon after the Wang et al. paper was published:

On Maykop ancestry in Yamnaya

I hope I'm wrong, but I get the feeling that the scientists at the Reich Lab are finding this difficult to accept, because it doesn't gel with their theory that archaic Proto-Indo-European (PIE) wasn't spoken on the PC steppe, but rather south of the Caucasus, and that late or rather nuclear PIE was introduced into the PC steppe by migrants from the Maykop culture who were somehow involved in the formation of the Yamnaya horizon.

Inexplicably, after citing Wang et al. on multiple occasions and arguing against any significant gene flow between Maykop and Yamnaya groups, Anthony fails to mention Steppe Maykop. But the Steppe Maykop people are an awesome argument against the idea that there was anything more than occasional mating between the Maykop and Yamnaya populations, because they were wedged between them, and yet clearly distinct from both, with a surprisingly high ratio of West Siberian forager-related ancestry (see here and here).

Despite all the talk lately about the potential cultural, linguistic and genetic ties between Maykop and Yamnaya, including claims that the latter possibly acquired its wagons from the former, my view is that the Steppe Maykop and Yamnaya wagon drivers may have competed with each other and eventually clashed in a big way. Indeed, take a look at what happens after Yamnaya burials rather suddenly replace those of Steppe Maykop just north of the Caucasus around 3,000 BCE.

Yamnaya_RUS_Caucasus
RUS_Progress_En_PG2001 0.808±0.058
RUS_Steppe_Maykop 0.000
UKR_Sredny_Stog_II_En_I6561 0.192±0.058
chisq 13.859
tail prob 0.383882
Full output

Yep, total population replacement with no significant gene flow between the two groups. Apparently, as far as I can tell, there's not even a hint that a few Steppe Maykop stragglers were incorporated into the ranks of the newcomers. Where did they go? Hard to say for now. Maybe they ran for the hills nearby?

Intriguingly, Anthony reveals a few details about new samples from three different Eneolithic steppe burial sites associated with the Khvalynsk culture:

The Reich lab now has whole-genome aDNA data from more than 30 individuals from three Eneolithic cemeteries in the Volga steppes between the cities of Saratov and Samara (Khlopkov Bugor, Khvalynsk, and Ekaterinovka), all dated around the middle of the fifth millennium BC.

...

Most of the males belonged to Y-chromosome haplogroup R1b1a, like almost all Yamnaya males, but Khvalynsk also had some minority Y-chromosome haplogroups (R1a, Q1a, J, I2a2) that do not appear or appear only rarely (I2a2) in Yamnaya graves.

As far as I can tell, he suggests that they'll be published in the forthcoming Narasimhan et al. paper. If so, it sounds like the paper will have many more ancient samples than its early preprint that was posted at bioRxiv last year.

For me the really fascinating thing in regards to these new samples is how scarce Y-haplogroup R1a appears to have been everywhere before the expansion by the putative Indo-European-speaking steppe ancestors of the Corded Ware culture (CWC) people. It's basically always outnumbered by other haplogroups wherever it's found prior to about 3,000 BCE, even on the PC steppe. But then, suddenly, its R1a-M417 subclade goes BOOM! And that's why I call it...

The beast among Y-haplogroups

At this stage, I'm not sure how to interpret the presence of Y-haplogroup J in the Khvalynsk population. It may or may not be important to the PIE homeland debate. Keep in mind that J is present in two foragers from Karelia and Popovo, northern Russia, dated to the Mesolithic period and with no obvious foreign ancestry. So it need not have arrived north of the Caspian as late as the Eneolithic with migrants rich in southern ancestry from the Caucasus or what is now Iran. In other words, for the time being, the steppe PIE homeland theory appears safe.

Update 20/12/2019: A note on Steppe Maykop

See also...

Is Yamnaya overrated?

The PIE homeland controversy: January 2019 status report

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...

On Maykop ancestry in Yamnaya

What Maykop ancestry in Yamnaya? There is none, or at least not enough worth discussing, except in one highly unusual female outlier from a burial in what is now eastern Ukraine. But apparently this is still up for debate? Well it shouldn't be.

To anyone with even a passing interest in the Yamnaya culture, it should be rather obvious that it formed during the tail end of the Eneolithic on the Pontic-Caspian steppe, as basically a direct offshoot of the earlier Repin culture, but perhaps also with significant influences from the earlier still Khvalynsk and Sredny Stog cultures. So why should its population history be much different from this?

It isn't, and this is fairly easy to demonstrate now despite the still rather poor sampling of Eneolithic remains from the Pontic-Caspian steppe.

Below is a series of qpAdm analyses in which I modeled several Yamnaya groups, as well as the closely related Afanasievo and Poltavka populations, exclusively and successfully as two- and three-way mixtures of a few Eneolithic singletons from various parts of the Pontic-Caspian steppe (obviously, I'd love to use homogeneous population sets instead, but, as per my point above, that's not possible yet). The models are sorted by their statistical fits, best to worst. Also note the large number and wide range of right pops or outgroups. I wanted to make sure that I wasn't missing anything.

Yamnaya_Samara
Dereivka_I_I4110 0.324±0.035
Progress_Eneolithic_PG2004 0.676±0.035
chisq 6.797
tail prob 0.976979
Full output

Afanasievo
Progress_Eneolithic_PG2004 0.638±0.038
Sredny_Stog_II_I6561 0.362±0.038
chisq 10.855
tail prob 0.818366
Full output

Yamnaya_Ukraine
Progress_Eneolithic_PG2001 0.655±0.073
Sredny_Stog_II_I6561 0.345±0.073
chisq 12.676
tail prob 0.696277
Full output

Poltavka
Dereivka_I_I4110 0.324±0.038
Progress_Eneolithic_PG2004 0.676±0.038
chisq 12.895
tail prob 0.680437
Full output

Yamnaya_Caucasus
Khvalynsk_Eneolithic_I0122 0.086±0.054
Sredny_Stog_II_I6561 0.221±0.070
Vonyuchka_Eneolithic_VJ1001 0.693±0.101
chisq 13.113
tail prob 0.593562
Full output

So, you might ask, is there any way to add Maykop to these models? Nope, it's pointless, because it doesn't improve the stats (for instance, see here, here and here). In other words, the situation is this: I already have awesome models, and I can't readily fit Maykop into my framework, so why do it? But if anyone out there wants to try, then by all means, and feel free to share the results with us in the comments.

Of course, the fact that most of these Yamnaya and Yamnaya-related populations are best modeled with somewhat different Eneolithic steppe singletons doesn't mean that they have radically different origins. In fact, they're all very closely related and they're basically like one Bronze Age steppe family. They just harbor somewhat different ratios of the same ancient ancestral components.

For the sake of being thorough, as per scientific literature, I pooled all of the above Afanasievo, Poltavka and Yamnaya samples into a Steppe_EMBA set and analyzed it with several genetically and geographically matching pairs of the Eneolithic singletons. This was one of the best fitting models, which I think is interesting, because the region roughly between the burial sites of these pairs of Eneolithic individuals was the home of the Repin culture.

Steppe_EMBA
North_Pontic_Eneolithic_I4110-I656 0.313±0.027
Progress_Eneolithic_PG2001-PG2004 0.687±0.027
chisq 15.378
tail prob 0.497157
Full output

Again, adding Maykop to this model makes no sense (see here, here and here). Clearly, I'd have to come up with a very different framework to successfully model Steppe_EMBA with a Maykop population. However, it's unlikely that such a model would make much sense in the context of various other types of genetic analyses and archeological data.

See also...

Yamnaya: home-grown

Big deal of 2018: Yamnaya not related to Maykop

Yamnaya isn't from Iran just like R1a isn't from India

Yamnaya: home-grown

I have some interesting news. It looks like Khvalynsk_Eneolithic I0434 can be used as essentially a perfect proxy for the Eneolithic steppe trio from Wang et al. 2018 when modeling the ancestry of the Yamnaya people of what is now the Samara region of Russia. Consider the qpAdm mixture models below, sorted by taildiff.

One of the best fitting models that also fairly closely matches archeological data, which suggest that Yamnaya was an amalgamation of the Khvalynsk, Repin and Sredny Stog cultures, is in bold. The worst fitting, and basically failed, models are listed below the dotted line. Note that almost all of these models feature reference populations from West and Central Asia.

Khvalynsk_I0434 + Iberia_ChL 0.681534184 > full output

Khvalynsk_I0434 + Globular_Amphora 0.525961242 > full output

Khvalynsk_I0434 + Iberia_Central_CA 0.515960444 > full output

Khvalynsk_I0434 + Sredny_Stog_I6561 0.485311962 > full output

Khvalynsk_I0434 + Varna 0.430411416 > full output

Khvalynsk_I0434 + Blatterhole_MN 0.328782809 > full output

Khvalynsk_I0434 + Baden_LCA 0.234307235 > full output

Khvalynsk_I0434 + Protoboleraz_LCA 0.231310724 > full output

Khvalynsk_I0434 + ALPc_MN 0.200002422 > full output

Khvalynsk_I0434 + Trypillia 0.193900977 > full output

Khvalynsk_I0434 + Balaton_Lasinja_CA 0.187031564 > full output

Khvalynsk_I0434 + Tiszapolgar_ECA 0.153940224 > full output

Khvalynsk_I0434 + Tisza_LN 0.145465993 > full output

Khvalynsk_I0434 + Balkans_ChL 0.111720163 > full output

...

Khvalynsk_I0434 + Armenia_EBA 0.0108890099 > full output

Khvalynsk_I0434 + Armenia_ChL 0.00882375703 > full output

Khvalynsk_I0434 + Levant_BA_North 0.0078751978 > full output

Khvalynsk_I0434 + Minoan_Lasithi 0.0675240088 > full output

Khvalynsk_I0434 + Peloponnese_N 0.046998906 > full output

Khvalynsk_I0434 + Hajji_Firuz_ChL 0.00269860335 > full output

Khvalynsk_I0434 + Shahr_I_Sokhta_BA1 0.00261908387 > full output

Khvalynsk_I0434 + Sarazm_Eneolithic 0.00120345503 > full output

Khvalynsk_I0434 + Seh_Gabi_ChL 0.00111898703 > full output

Khvalynsk_I0434 + Geoksiur_Eneolithic 0.000178295163 > full output

Khvalynsk_I0434 + Tepe_Hissar_ChL 0.000163698274 > full output

Khvalynsk_I0434 + Bustan_BA 0.000151088148 > full output

Why is this potentially important? Because unless Khvalynsk_Eneolithic I0434 was a recent migrant from the North Caucasus piedmont steppe, which is where the remains of the Eneolithic steppe trio were excavated, then Yamnaya's ethnogenesis might not have anything at all to do with Asia or even the Caucasus region. At least not within any reasonable time frame anyway. Here's a map showing the geographic locations of all of the populations relevant to the highlighted mixture model above.

I won't be fussed if it turns out that the majority of the ancestry of the Yamnaya, Corded Ware and other closely related ancient peoples was sourced from the Eneolithic populations of the North Caucasus piedmont steppe. But I think it's useful to make the point that there are still very few ancient samples available from the steppes between the Black and Caspian seas, so we don't yet have much of a clue how the groups living throughout this region during the Eneolithic and earlier fit into the grand scheme of things.

Update 24/12/2018: I decided to repeat the analysis, but this time with Caucasus Hunter-Gatherers (CHG) as one of the outgroups (or right pops). The reason I initially didn't include CHG in the outgroups was because I didn't want to discriminate, perhaps unfairly, against West and Central Asians with high levels of CHG-related ancestry, and in favor of Europeans with no or minimal CHG-related input. But in my opinion, the new results clearly make more sense, with Sredny Stog and Varna at the top of the list.

Khvalynsk_I0434 + Sredny_Stog_I6561 0.410719649 > full output

Khvalynsk_I0434 + Varna 0.394089365 > full output

Khvalynsk_I0434 + Iberia_ChL 0.16554258 > full output

Khvalynsk_I0434 + Globular_Amphora 0.128348823 > full output

Khvalynsk_I0434 + Iberia_Central_CA 0.126100242 > full output

Khvalynsk_I0434 + Trypillia 0.135306664 > full output

Khvalynsk_I0434 + Baden_LCA 0.0853031796 > full output

Khvalynsk_I0434 + Protoboleraz_LCA 0.0766892008 > full output

Khvalynsk_I0434 + Tisza_LN 0.0661622403 > full output

Khvalynsk_I0434 + Tiszapolgar_ECA 0.0626469042 > full output

Khvalynsk_I0434 + Balaton_Lasinja_CA 0.0536293042 > full output

Khvalynsk_I0434 + ALPc_MN 0.0505788809 > full output

...

Khvalynsk_I0434 + Minoan_Lasithi 0.0439451605 > full output

Khvalynsk_I0434 + Balkans_ChL 0.0436885241 > full output

Khvalynsk_I0434 + Blatterhole_MN 0.0329758292 > full output

Khvalynsk_I0434 + Peloponnese_N 0.0181930605 > full output

Khvalynsk_I0434 + Armenia_EBA 0.014715999 > full output

Khvalynsk_I0434 + Armenia_ChL 0.0060437014 > full output

Khvalynsk_I0434 + Levant_BA_North 0.00514574731 > full output

Khvalynsk_I0434 + Shahr_I_Sokhta_BA1 0.00350059625 > full output

Khvalynsk_I0434 + Hajji_Firuz_ChL 0.00228771991 > full output

Khvalynsk_I0434 + Seh_Gabi_ChL 0.00117061206 > full output

Khvalynsk_I0434 + Sarazm_Eneolithic 0.001118931 > full output

Khvalynsk_I0434 + Bustan_BA 0.00021203609 > full output

Khvalynsk_I0434 + Tepe_Hissar_ChL 0.000200643323 > full output

Khvalynsk_I0434 + Geoksiur_Eneolithic 0.000175941977 > full output

Update 17/02/2019: I basically managed to confirm my analysis with samples from the Wang et al. Caucasus paper. See here.

See also...

Big deal of 2018: Yamnaya not related to Maykop

"The Homeland: In the footprints of the early Indo-Europeans" time map

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...