‘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

Dear Iosif #2

In my last blog post I made a mistake in my interpretation of this quote from Lazaridis, Alpaslan-Roodenberg et al., because it confused the crap out of me:

However, the complete lack of association of R-haplogroup descendants and EHG ancestry in either Armenia or Iran is consistent with either a massive dilution of EHG ancestry in these populations resulting in the dissociation of Y-chromosome lineages from autosomal ancestry over time, or with a scenario in which R-M269 was not associated with substantial EHG ancestry to begin with.

I thought they meant that they couldn't find any Eastern European hunter-gatherer (EHG) ancestry in samples from Armenia or Iran bearing Y-chromosome R1b-M269.

Of course, they did find EHG ancestry in these individuals, it's just that they couldn't establish an association specifically between this type of ancestry and Y-haplogroup R1b.

That is, males with Y-haplogroup R1b in Armenia, Iran and everywhere else generally show about the same level of EHG ancestry as their ethnic kin with other Y-haplogroups.

But so what? Why mention this when discussing the origins of R1b-M269, when it has absolutely no value in this context?

Y-haplogroups aren't linked directly to autosomal DNA, and Lazaridis, Alpaslan-Roodenberg et al. are obviously aware of this (hence their point about the potential massive dilution of EHG ancestry).

In regards to the origins of R1b-M269, and the provenance of West Asian R1b-M269, the really powerful observation is that R1b-M269 shows up rather late and suddenly in the West Asian ancient DNA record along with EHG and steppe ancestry.

That, and the fact that Eastern Europe is an ancient R1b hotbed (while West Asia a desert), means there's virtually no chance that R1b-M269 is native to West Asia. In other words, there was no R1b-M269 in West Asia until the steppe people brought it there from north of the Caucasus.

See also...

Dear Iosif...

Dear Iosif #3

But Iosif, what about the Phrygians?

Dear Iosif, about that ~2%

Dear Iosif...Yamnaya

Dear Iosif...

Update 29/08/22: Dear Iosif #2

...


I'm skimming through the Lazaridis, Alpaslan-Roodenberg et al. paper that just came out at Science. And I feel like someone punched me in the face.

Nevertheless, I'll try to be diplomatic. Suffice to say, for now, that there's some rather strange stuff in this paper.

The main problem is that the authors are attempting to study fine scale ancestry with a somewhat rough distal model. As a result, they miss important details.

For instance, this quote is from the paper's supplementary PDF file, freely available here.

However, the complete lack of association of R-haplogroup descendants and EHG ancestry in either Armenia or Iran is consistent with either a massive dilution of EHG ancestry in these populations resulting in the dissociation of Y-chromosome lineages from autosomal ancestry over time, or with a scenario in which R-M269 was not associated with substantial EHG ancestry to begin with.

Obviously, EHG means Eastern European Hunter-Gatherer. But why focus on EHG? Surely, this makes little sense when looking at the genetic prehistory of West Asia, because no one ever argued that this region was settled by EHG populations. It was widely settled by Yamnaya-related groups, with already heavily diluted EHG ancestry, during the metal ages.

OK, so the authors are actually aware about the potential dilution of EHG ancestry, but they don't really do anything about it.

If we're looking at the origins of West Asian R1b-M269, and using its association with autosomal DNA components as a guide, then we should be focusing on Yamnaya-related ancestry.

For instance, here's a fine scale ancient ancestry model based on Principal Component Analysis (PCA) data. It shows the ancestry proportions of two relatively high coverage Iron Age males from two different sites in Iran from the Lazaridis, Alpaslan-Roodenberg et al. dataset. Both belong to R1b-M269 and both show significant Yamnaya-related ancestry.

Target: IRN_HajjiFiruz_IA:I2327_all
Distance: 2.2930% / 0.02292994
39.6 Kura-Araxes_ARM_Kaps
24.2 IRN_Ganj_Dareh_N
18.2 Levant_PPNB
12.4 Yamnaya_RUS_Samara
4.4 Anatolia_Tepecik_Ciftlik_N
1.2 Han

Target: IRN_Hasanlu_IA:I4232_all
Distance: 2.5179% / 0.02517895
26.0 IRN_Ganj_Dareh_N
25.6 Kura-Araxes_ARM_Kaps
24.4 Anatolia_Tepecik_Ciftlik_N
15.8 Yamnaya_RUS_Samara
7.6 Levant_PPNB
0.6 IRN_Shahr_I_Sokhta_BA2

As a control, here's an earlier, Chalcolithic sample bearing Y-haplogroup J2b from the same region. Not surprisingly, this individual totally lacks the Yamnaya-related signal.

Target: IRN_HajjiFiruz_ChL:I4241_all
Distance: 2.7938% / 0.02793782
32.6 Kura-Araxes_ARM_Kaps
25.6 IRN_Ganj_Dareh_N
23.6 Anatolia_Tepecik_Ciftlik_N
18.2 Levant_PPNB

Overall, these results make perfect sense. I could probably locate very minor signals of EHG ancestry in the Iron Age samples, but that would be more difficult and much less certain, so I won't bother.

Soon I'll be able to rerun these analyses with Bronze Age samples from Dagestan and surrounds. That should bump up the levels of Yamnaya-related ancestry and improve the statistical fits (wink, wink, nudge, nudge).

Disappointingly, Lazaridis, Alpaslan-Roodenberg et al. go so far as to suggest that R1b-M269 may have originated in West Asia.

However, considering the scores of ancient Eastern European populations rich in R1b-M269 and many near and far related subclades of R1b, this makes no sense whatsoever.

Indeed, contemplating nowadays that R1b-M269 might be native to West Asia, where R1b only starts showing up in the ancient DNA record during the Copper Age, is about as stupid as claiming that gravity doesn't exist.

Largely due to their distal model approach, Lazaridis, Alpaslan-Roodenberg et al. also argue that the Indo-Anatolian homeland was located in what is now Armenia and surrounds. I'm far from convinced that this solution will stand the test of time.

In terms of the more widely accepted theory that the Indo-Anatolian homeland was located on the Pontic-Caspian steppe in Eastern Europe, the most important samples in the paper are the three Bronze Age individuals from Yassitepe in western Anatolia. That's because they're from a region that is traditionally seen as the entry point of Indo-Anatolian speakers into Anatolia from the European steppe via the Balkans.

Interestingly, individual I5737, dated to 2035-1900 calBCE or the Middle Bronze Age, belongs to Y-chromosome haplogroup I2a-P78, which surely must be a signal of European ancestry. I see this as a significant result.

Here's how the trio from Yassitepe look in my fine scale ancient ancestry model. Minor Yamnaya-related ancestry does show up, although, admittedly, it might just be noise in individual I5735.

Target: TUR_Aegean_Izmir_Yassitepe_MBA:I5737
Distance: 2.7507% / 0.02750748
58.4 Anatolia_Barcin_N
20.4 Kura-Araxes_ARM_Kaps
9.2 Anatolia_Tepecik_Ciftlik_N
5.6 IRN_Ganj_Dareh_N
3.8 Yamnaya_RUS_Samara
2.6 Levant_PPNB

Target: TUR_Aegean_Izmir_Yassıtepe_EBA:I5733
Distance: 2.7969% / 0.02796887
52.0 Anatolia_Barcin_N
27.2 Kura-Araxes_ARM_Kaps
8.6 Levant_PPNB
6.2 Yamnaya_RUS_Samara
6.0 IRN_Ganj_Dareh_N

Target: TUR_Aegean_Izmir_Yassıtepe_EBA:I5735
Distance: 3.1270% / 0.03127009
36.0 Kura-Araxes_ARM_Kaps
32.4 Anatolia_Tepecik_Ciftlik_N
26.0 Anatolia_Barcin_N
2.8 IRN_Shahr_I_Sokhta_BA2
1.2 Yamnaya_RUS_Samara
1.0 Levant_PPNB
0.6 MAR_Taforalt

This isn't much, especially considering it's already late 2022, but it's better than nothing. Fortunately, more samples from Bronze Age western Anatolia are on the way (wink, wink, nudge, nudge).

However, I'm not done with the Lazaridis, Alpaslan-Roodenberg et al. dataset yet. I'm planning to spend much more time on this blog in the coming weeks and months and will be using their samples in a wide range of analyses.

Citation...

Iosif Lazaridis, Songül Alpaslan-Roodenberg et al., The genetic history of the Southern Arc:A bridge between West Asia and Europe, Science 377, eabm4247 (2022)

See also...

Dear Iosif #3

But Iosif, what about the Phrygians?

Dear Iosif, about that ~2%

Dear Iosif...Yamnaya

Crazy stuff

I'm hoping that 2022 is the year when this problem is finally straightened out. Over to you David Reich, Nick Patterson, Iosif Lazaridis, David Anthony, Wolfgang Haak, Johannes Krause and colleagues.

See also...

An early Iranian, obviously

The Hajji Firuz fiasco

A Mycenaean and an Iron Age Iranian walk into a bar...

Local origins of the earliest Tarim Basin mummies (Zhang et al. 2021)

Over at Nature at this LINK. It's nice to see yet another huge surprise courtesy of ancient DNA. Please note that most of the ancients from this paper are already in the Global25 datasheets. Here's the abstract:

The identity of the earliest inhabitants of Xinjiang, in the heart of Inner Asia, and the languages that they spoke have long been debated and remain contentious 1. Here we present genomic data from 5 individuals dating to around 3000–2800 bc from the Dzungarian Basin and 13 individuals dating to around 2100–1700 bc from the Tarim Basin, representing the earliest yet discovered human remains from North and South Xinjiang, respectively. We find that the Early Bronze Age Dzungarian individuals exhibit a predominantly Afanasievo ancestry with an additional local contribution, and the Early–Middle Bronze Age Tarim individuals contain only a local ancestry. The Tarim individuals from the site of Xiaohe further exhibit strong evidence of milk proteins in their dental calculus, indicating a reliance on dairy pastoralism at the site since its founding. Our results do not support previous hypotheses for the origin of the Tarim mummies, who were argued to be Proto-Tocharian-speaking pastoralists descended from the Afanasievo 1,2 or to have originated among the Bactria–Margiana Archaeological Complex 3 or Inner Asian Mountain Corridor cultures 4. Instead, although Tocharian may have been plausibly introduced to the Dzungarian Basin by Afanasievo migrants during the Early Bronze Age, we find that the earliest Tarim Basin cultures appear to have arisen from a genetically isolated local population that adopted neighbouring pastoralist and agriculturalist practices, which allowed them to settle and thrive along the shifting riverine oases of the Taklamakan Desert.

Zhang, F., Ning, C., Scott, A. et al. The genomic origins of the Bronze Age Tarim Basin mummies. Nature (2021). https://doi.org/10.1038/s41586-021-04052-7

See also...

How the Shirenzigou nomads became Proto-Tocharians

A comedy of errors

A couple of years ago, the authors of a paper about a group of Iron Age nomads from the site of Shirenzigou, in the eastern Tian Shan, made a mistake. They wrongly assigned two of these nomads to Y-haplogroup R1b-M269.

This faux pas made them believe that the Shirenzigou nomads were closely related to the M269-rich population associated with the Afanasievo culture.

Indeed, since the Afanasievo culture was often credited with the spread of Tocharian languages to the Tarim Basin, these authors, led by Chao Ning, also concluded that the Shirenzigou nomads were potentially the missing link between the Afanasievo culture and the Tocharians (see here).

Moreover, Ning et al. used formal statistics to argue that the Shirenzegou nomads harbored Afanasievo-related genome-wide ancestry, rather than Sintashta-related genome-wide ancestry, despite the fact that the latter ancestry was widespread in the Tian Shan and surrounds during the Bronze and Iron ages. Soon after, another group of authors, led by Chuan-Chao Wang, also went out of their way to link the Shirenzigou nomads to the Afanasievo people with genome-wide DNA using formal statistics (see here).

Interestingly, one of the Shirenzigou nomads belongs to Y-haplogroup R1a-Z93, which is an obvious Sintashta-related lineage. Both Ning et al. and Wang et al. missed this important fact.

They also missed the key fact that the R1b lineage found in the Shirenzigou nomads actually belongs to an Inner Asian subclade, which is only very distantly related to the originally Eastern European R1b-M269.

Now, formal stats are a very useful tool for studying genome-wide ancestry. But they're not infallible, and that's actually something of an understatement. Indeed, if you don't run sanity checks when using formal stats, you're likely to come to some unusual, even arse about face, conclusions. Uniparental markers, like Y-chromosome haplogroups, can provide a robust sanity check when running formal stats on genome-wide data.

One problem with formal stats is that Sintashta-related ancestry often looks very much like Afanasievo-related ancestry when it's mixed with indigenous Central Asian ancestry. Basically, the reason why this happens is that the Central Asian ancestry dampens the Early European Farmer (EEF) signal in the Sintashta-related ancestry.

This is an artifact that once caused scientists at Harvard to believe that Central Asian Scythians and present-day South Asians lacked Sintashta-related ancestry.

Unfortunately, since the publication of the Ning et al. paper, a consensus has emerged in academia that the Shirenzigou nomads are indeed the missing link between the Afanasievo culture and the Tocharians. But, let's be objective and honest here, it's a consensus based on nothing more than a comedy of errors.

On the other hand, me and most of the commentators at this blog have formed opinions about the Shirenzigou nomads that are totally at odds with the academic consensus, that:

- they're a complex mixture of Sintashta-related, indigenous Central Asian and Tibetan-related ancestries, with no clear, unambiguous signal of Afanasievo-related ancestry

- they weren't the speakers of Proto-Tocharian or even related in any specific way to the Tocharians

- they were probably the speakers of a now extinct Indo-Iranian language, and, at least based on geographic proximity, possibly related to the Yuezhi.

Feel free to make up your own mind. But for me, the question of how Tocharian languages ended up in the Tarim Basin remains wide open. I admit though, I'm currently quite partial to the idea floated here by commentator Copper Axe that the Chemurchek culture may have had something to do with it.

See also...

Don't believe everything you read in peer reviewed papers

On the exotic origins of the Hungarian Arpad Dynasty (Nagy et al. 2020)

Hungarians speak a Uralic and Finno-Ugric language. However, the founders of the Medieval Hungarian state, the Arpad Dynasty, probably had Irano-Turkic paternal origins. There's a very interesting new paper on this topic at the European Journal of Human Genetics (see here). From the paper, emphasis is mine:

The phylogenetic origins of the Hungarians who occupied the Carpathian basin has been much contested [40]. Based on linguistic arguments it was proposed that they represented a predominantly Finno-Ugric speaking population while the oral and written tradition of the Árpád dynasty suggests a relationship with the Huns. Based on the genetic analysis of two members of the Árpád Dynasty, it appears that they derived from a lineage (R-Z2125) that is currently predominantly present among ethnic groups (Pashtun, Tadjik, Turkmen, Uzbek, and Bashkir) speaking Iranian or Turkic languages. However, their closest kin, the Bashkirs live in close proximity with Finno-Ugric speaking populations with the N-B539 haplogroup. A recent study shows that this haplogroup is also found in modern Hungarians [41]. Intriguingly, the most recent separation of the N-B539 derived lineages found in Hungarians and Bashkirs is estimated to have occurred ~2000 years before present [42]. This would suggest that a group of people consisting of a Turkic (R-SUR51) component and a Finno-Ugric (N-B539) component left the Volga Ural region about 2000 years ago and started a migration that eventually culminated in settlement in the Carpathian Basin.

Citation...

Nagy, P.L., Olasz, J., Neparáczki, E. et al. Determination of the phylogenetic origins of the Árpád Dynasty based on Y chromosome sequencing of Béla the Third. Eur J Hum Genet (2020). https://doi.org/10.1038/s41431-020-0683-z

See also...

Hungarian Conquerors were rich in Y-haplogroup N

On the association between Uralic expansions and Y-haplogroup N

More on the association between Uralic expansions and Y-haplogroup N

Ancient DNA confirms the link between Y-haplogroup N and Uralic expansions

An early Mitanni?

I've updated my Global25 datasheets with most of the ancients from the new Skourtanioti et al. paper. Here's a Principal Component Analysis (PCA) based on the data. It was produced with the Vahaduo PCA tools freely available here and the text file here.

Note that one of the Bronze Age females from Alalakh, labeled ALA019, appears to have ancestry from Turan and the Eurasian steppe. She may well have been a Mitanni of Indo-Aryan origin.

Interestingly, a Copper Age male from Arslantepe, ART038, belongs to Y-haplogroup R1b1a2 aka R1b-V1636. This is an unusual find, because R1b hasn't yet been reported in any Copper Age or earlier samples from outside of Europe and the Eurasian steppe.

As far as I can tell, this individual doesn't harbor any genome-wide ancestry from north of the Caucasus. However, R1b-V1636 is a rare lineage that is first attested in Eneolithic samples from the North Caucasus Piedmont steppe, so ART038's Y-chromosome might be the first evidence of the presence of steppe ancestry in Copper Age Anatolia.

I've also added most of the ancients from the new Agranat-Tamir et al. paper to the Gobal25 datasheets. The PCA below is based on the text file available here.

The Megiddo samples include a trio of interesting outliers dated to 1600-1500 BCE with significant ancestry from the steppe. One of these individuals is a male, I2189, who belongs to Y-haplogroup R and probably R1a. So he might also be of Indo-Aryan origin.

Another Megiddo male, S10768, belongs to R1b-M269 and probably shows a few per cent of steppe ancestry. I've already discussed how R1b and steppe ancestry may have ended up in the Bronze Age Near East in a couple of my previous posts:

R1b-M269 in the Bronze Age Levant

How did steppe ancestry spread into the Biblical-era Levant?

R-V1636: Eneolithic steppe > Kura-Araxes?

A significant finding

At least five individuals from Neolithic burial sites in what is now Ukraine harbor ancestry that is normally associated with much later steppe populations. Labeled UKR_N_admixed in the plot below, these samples were part of the Mathieson et al. 2018 dataset and most were radiocarbon dated to well before 5,000 BCE. An interactive version of the plot is available here.

Their unusual ancestry probably explains why they form a cluster that appears to be pulling away from the ancient European hunter-gatherer cline towards the part of the plot home to RUS_Progress_En (from the Progress-2 Eneolithic burial site in the North Caucasus piedmont region). But, of course, there's more to this. For instance, consider the formal statistics-based qpAdm mixture models below:

UKR_N_admixed
RUS_Progress_En 0.083±0.021
UKR_N 0.917±0.021
chisq 7.461
tail prob 0.589238
Full output

UKR_N_admixed
RUS_Progress_En 0.172±0.021
SRB_Iron_Gates_HG 0.332±0.024
UKR_Meso 0.495±0.035
chisq 9.255
tail prob 0.321282
Full output

UKR_N_I1738
RUS_Progress_En 0.196±0.035
SRB_Iron_Gates_HG 0.414±0.039
UKR_Meso 0.390±0.056
chisq 7.913
tail prob 0.442006
Full output

Ergo, as much as a quarter of the genome of individual I1738, dated to 5473-5326 calBCE, might be derived from a population very similar to RUS_Progress_En. This is a big deal, because it's still widely believed that this type of ancestry didn't exist until the Eneolithic, and that it didn't spread significantly until the migrations of steppe pastoralists associated with the Early Bronze Age Yamnaya culture.

I'm confident, nay, certain, that my findings will be confirmed directly with more Neolithic samples from present-day Ukraine and surrounds.

See also...

Understanding the Eneolithic steppe

Ancient DNA vs Ex Oriente Lux

Mixed marriages on the early Eneolithic steppe

Understanding the Eneolithic steppe

Archeologist David Anthony has teamed up with Harvard's David Reich Lab to work on a paper about the Eneolithic period on the Pontic-Caspian steppe.

A couple of other labs are also preparing papers on similar topics, and they've already sequenced and analyzed many of their ancient samples (for instance, see here). However, I don't have a clue when these papers will be published. My guess is that we'll have to wait a year or so.

Needless to say, knowing what happened on the Pontic-Caspian (PC) steppe and surrounds during the Eneolithic is crucial to understanding the origins of the present-day European gene pool. It's also likely to be highly relevant to the debate about the location of the Proto-Indo-European (PIE) homeland.

In this blog post I'll explain what I've learned about the Eneolithic peoples of the PC steppe based on already published data.

If we ignore Steppe Maykop samples, the currently available Eneolithic individuals from the eastern part of the PC steppe form an essentially perfect cline in my Principal Component Analysis (PCA) of ancient West Eurasian genetic variation.

The cline runs from the Mesolithic hunter-fishers of the Eastern European forest zone to those of the Eneolithic sites of Progress 2 and Vonyuchka in the North Caucasus foothills. Let's call this the Khvalynsk cline, because three of the samples are from a burial site in the Volga River valley associated with the Khvalynsk culture. The relevant datasheet is available here.

The reason that these samples form the cline is because they carry different ratios of admixture related to Caucasus hunter-gatherers (CHG) from what is now Georgia. Moreover, the Khvalynsk individuals appear to be relatively recent mixtures between sources rich and poor in this type of ancestry.

I also marked a Maykop cline on the plot. This cline is made up of individuals associated with the Maykop and Steppe Maykop cultures from the Caucasus Mountains and nearby parts of the PC steppe, respectively. The Maykop culture is dated to the Early Bronze Age (EBA) period, but the PC steppe was still part of the Eneolithic world at the time.

The Maykop cline is more complicated than the Khvalynsk cline, because some of the Maykop individuals carry genetic components that the others lack. These genetic components are closely related to the aforementioned CHG, as well as Anatolian Neolithic farmers (ANF) and Western Siberian hunter-gatherers (WSHG).

Note that the two clines intersect, but this isn't because any of the Khvalynsk cline samples harbor Maykop-related ancestry. It's largely because the Steppe Maykop individuals carry high levels of Vonyuchka-related ancestry.

So unless we're dealing here with a remarkable string of coincidences, then the Vonyuchka hunter-fisher must be a decent proxy for the people who spread significant levels of CHG-related ancestry north of the Caucasus.

The important question, therefore, is where and when exactly did this population form? And it's a question that the authors of the aforementioned upcoming papers should be aiming to answer comprehensively.

In my view, it was the result of interactions between the hunter-fishers of the North Caucasus and the southernmost parts of the PC steppe during the Neolithic period, perhaps around 6,000 BCE, just before significant ANF-related ancestry spread across the Caucasus during the Eneolithic. That's because the Progress 2/Vonyuchka samples lack ANF-related ancestry, or at least an obvious signal of it, and are dated to ~4,200 BCE. And when I say Neolithic in this context, I don't mean the Near Eastern type of Neolithic with well developed farming, but rather the local type of Neolithic still based on hunting and fishing.

Now, obviously, the people of the Corded Ware and Yamnaya cultures were the children of the Eneolithic PC steppe. So you might be wondering how they fit into all of this. I still don't know, and apparently neither do the scientists at Harvard (see here). However, I'd say that the Maykop cline isn't relevant to this question. The Khvalynsk cline might be relevant, but even if it is, this doesn't necessarily mean that the Yamnaya people are by and large derived from the Khvalynsk people.

Here's the same PCA plot as above, but this time with early Corded Ware and Yamnaya samples also highlighted. Note that, apart from a few outliers, they form a rather tight cluster that is shifted slightly away from the Khvalynsk cline, but probably not in the direction of the Maykop cline.

A couple of the Yamnaya outliers are shifted towards the "eastern" end of the Khvalynsk cline, and thus near the Progress 2/Vonyuchka samples. This isn't surprising because these Yamnaya individuals are from burial sites close to the North Caucasus and probably harbor significant levels of local ancestry.

The most extreme Yamnaya outlier, from a site in what is now Ukraine, is clearly shifted towards the Maykop cline, and even towards the Caucasus Maykop cluster. However, this is a female with no grave goods and she may have been a foreign bride or captive, possibly from a late Maykop settlement. It's also possible that her 3095-2915 calBCE dating is wrong.

I'm pretty sure that when we find out why the Yamnaya cluster is so deliberately shifted away from the Khvalynsk cline, we'll also discover how the early Corded Ware and Yamnaya populations formed. For now, I strongly suspect that this has something to do with gene flow from the western edge of the PC steppe and the ethnogenesis of the Sredny Stog culture, which was located just west of the Khvalynsk culture.

By and large, the PC steppe is still seen by historical linguists and archeologists as the most sensible place to put the PIE homeland.

However, a theory that the PIE homeland was located somewhere south of the Caucasus, and that instead the PC steppe was the late or nuclear PIE dispersal point, has gained popularity in recent years, largely thanks to the apparent lack of PC steppe ancestry in a handful of samples from Hittite era Anatolia. In this scheme, the Maykop culture took PIE into Eastern Europe and the Yamnaya culture subsequently spread late/nuclear PIE from the PC steppe, while Proto-Anatolian, the ancestor of Hittite, was introduced into Anatolia from the east along with Maykop-related ancestry.

This is possible, in the sense that almost anything is possible, but it doesn't strike me as the most parsimonious interpretation of the facts.

Even before ancient DNA, it was known that the Maykop culture colonized parts of the PC steppe, at least for a short time, and probably had contacts with the Yamnaya people and/or their antecedents. But it was generally seen as the vector for Caucasian and other non-Indo-European influences in PIE.

Moreover, not only were the Maykop and Yamnaya populations of fundamentally different genetic origins, but apparently the Yamnaya people didn't absorb any perceptible Maykop ancestry as they expanded into the North Caucasus region at the tail end of the Maykop period.

That's really difficult to explain if we assume that these groups were close linguistic relatives, and much easier to reconcile with the assumption that they were derived from different worlds culturally and linguistically.

Another important question is what happened to the Steppe Maykop people, because right now it looks like they vanished almost without a trace, essentially as if they were pushed out or even erased by the Yamnaya expansion. If they were indeed pushed out or erased, then it's likely that their language was as well.

As for the lack of PC steppe ancestry in Hittite era Anatolians, I honestly can't see this is as a significant obstacle to a PIE homeland on the steppe, especially if we consider that the most widely accepted Indo-European phylogenies show the Anatolian family as the most basal node.

In the opinion of the vast majority of experts, it's the most basal node because the Proto-Anatolian speakers were the first to leave the PIE homeland. And if they were indeed the first to leave the homeland, then why should we expect their descendants to harbor significant ancestry from the homeland? In my view, such an assumption would contradict the most widely accepted Indo-European phylogenies.

See also...

The Caucasus is a semipermeable barrier to gene flow

Aesch25

During the early 3rd Millennium BC much of Central and Northern Europe was being infiltrated by pioneer herders, often young men, from the east associated with the Corded Ware culture (CWC).

In some important ways, this expansion may have been very similar to the European colonization of the more remote parts of the Americas during the 16th and 17th centuries.

For instance, the European newcomers weren't always able to dominate the indigenous peoples, and, sometimes, instead of trying to impose their culture on them, they accepted theirs.

I suspect that Aesch25, an ancient sample from the recent Furtwängler et al. paper on the social and genetic structure of the prehistoric populations of the Swiss Plateau, represents a similar case.

Aesch25 wasn't buried with grave goods so he wasn't given a cultural context in the said paper. However, dated to 2864-2501 calBC, he's the earliest individual in this part of Europe with the originally Eastern European Y-haplogroup R1b-M269 and a CWC-like genome-wide genetic structure.

Indeed, the other fourteen samples from the same burial site, dated to more or less the same period as Aesch25, are overwhelmingly of local Neolithic farmer origin.

In any case, irrespective of his cultural affiliation and life story, Aesch25 represents an important data point in the search for the homeland of the so called Bell Beakers who spread across much of Europe during the Copper Age. That's because most Bell Beaker males belong to R1b-M269 and are very similar to Aesch25 in terms of overall genetic structure, apart from an excess of Neolithic farmer ancestry.

My view is that the Bell Beakers were an offshoot of the Single Grave culture (SGC), the westernmost variant of CWC. Of course, the SGC was centered on what is now northwestern Germany and surrounds, and didn't reach into the Swiss Plateau. However, in all likelihood it was founded by men closely related to Aesch25.

Below is a Principal Component Analysis (PCA) based on Global25 data featuring Aesch25 and several other individuals from the Furtwängler et al. paper. To view an interactive version of the plot, copy paste the data from the text file here into the relevant field here, then press Add to PCA. Also, you should copy paste each population separately to make sure that they don't form one grouping in the PCA key.

Aesch25 can easily pass for a CWC individual from what is now Germany (DEU_CWC_LN). On the other hand, the CWC samples from the Swiss Plateau (CHE_CWC_LN) are clearly shifted "south" relative to the German CWC cluster, which suggests that they harbor more Neolithic farmer ancestry. Indeed, they all belong to Y-haplogroup I2, which is especially closely associated with Middle Neolithic European farmers.

MX265, from Singen in southwest Germany, is the only sample in the Furtwängler et al. dataset that belongs to Y-haplogroup R1a. This is a somewhat unexpected outcome, because R1a is, overall, the most common Y-haplogroup in CWC males (see here).

Another surprise is that this individual is dated to just 763-431 calBC, which is a period that overlaps with the Hallstatt and La Tene cultures in Central Europe. Considering that these cultures are often associated with early Celts, was this person perhaps the speaker of a long lost Celtic language?

See also...

Single Grave > Bell Beakers

Dutch Beakers: like no other Beakers

Hungarian Yamnaya > Bell Beakers?

Hungarian Yamnaya predictions

The Battle Axe people came from the steppe

Corded Ware cultural and genetic complexity (Linderholm et al. 2020)

Open access at Scientific Reports at this LINK. Although very useful and broadly accurate, I'm really not sure what to make of this paper yet, especially in regards to its more nuanced inferences. I'll need to look at the genotype data at some point. Worthy of note is that most of the Corded Ware males sampled by the authors belong to Y-haplogroup R1b-M269, rather than R1a-M417, which is the dominant Y-haplogroup in previously published Corded Ware samples. From the paper:

During the Final Eneolithic the Corded Ware Complex (CWC) emerges, chiefly identified by its specific burial rites. This complex spanned most of central Europe and exhibits demographic and cultural associations to the Yamnaya culture. To study the genetic structure and kin relations in CWC communities, we sequenced the genomes of 19 individuals located in the heartland of the CWC complex region, south-eastern Poland. Whole genome sequence and strontium isotope data allowed us to investigate genetic ancestry, admixture, kinship and mobility. The analysis showed a unique pattern, not detected in other parts of Poland; maternally the individuals are linked to earlier Neolithic lineages, whereas on the paternal side a Steppe ancestry is clearly visible. We identified three cases of kinship. Of these two were between individuals buried in double graves. Interestingly, we identified kinship between a local and a non-local individual thus discovering a novel, previously unknown burial custom.

...

The PCA revealed that despite geographical proximity there is a distinct genetic separation between CWC and BBC individuals from southern Poland. The genetic variation of CWC individuals from southern Poland overlaps with the majority of previously published CWC individuals from Germany while the eight published CWC individuals from the Polish lowland [10,11] more closely resemble BBC individuals (Fig. S21). This fact is not unexpected if we consider the CWC communities in Polish lowlands as representatives of north-western parts of the CWC world called as the Single-Grave culture (see supplementary information). The genetic variation of BBC individuals from south-eastern Poland overlaps with the broad variation of BBC individuals from Central Europe (Bohemia, Moravia, Germany, south-western Poland and Hungary) (Fig. S22) which corresponds well with archaeological data.

Linderholm, A., Kılınç, G.M., Szczepanek, A. et al. Corded Ware cultural complexity uncovered using genomic and isotopic analysis from south-eastern Poland. Sci Rep 10, 6885 (2020). https://doi.org/10.1038/s41598-020-63138-w

See also...

The Battle Axe people came from the steppe

Is Yamnaya overrated?

Single Grave > Bell Beakers

Ancient DNA vs Ex Oriente Lux

In recent years you may have read academic papers, books and press articles claiming that the Early Bronze Age Yamnaya culture of the Pontic-Caspian steppe was founded by migrants from the Caucasus, Mesopotamia or even Central Asia.

Of course, none of this is true.

The Yamnaya herders and closely related groups, such as the people associated with the Corded Ware culture, expanded from the steppe between the Black and Caspian seas, and, thanks to ancient DNA, it's now certain that they were overwhelmingly derived from a population that had existed in this region since at least the mid-5th millennium BCE (see here).

So rather than being culturally advanced colonists from some Near Eastern civilization, the ancestors of the Yamnaya herders were a relatively primitive local people who still largely relied on hunting and fishing for their subsistence. They also sometimes buried their dead with flint blades and adzes, but hardly ever with metal objects, despite living in the Eneolithic epoch or the Copper Age.

As far as I know, this group doesn't have a specific name. But in recent scientific literature it's referred to as Eneolithic steppe, so let's use that.

It's not yet clear how the Yamnaya people became pastoralists. Some scholars believe that they were basically an offshoot of the cattle herding Maykop culture of the North Caucasus. However, the obvious problem with this idea is that the Yamnaya and Maykop populations probably didn't share any recent ancestry. In fact, ancient DNA shows that the former wasn't derived from the latter in any important or even discernible way (see here).

On the other hand, Yamnaya samples do harbor a subtle signal of recent gene flow from the west that appears to be most closely associated with Middle to Late Neolithic European agropastoralists (see here). Therefore, it's possible that herding was adopted by the ancestors of the Yamnaya people as a result of their sporadic contacts with populations living on the western edge of the Pontic-Caspian steppe.

Eneolithic steppe is currently represented by just three samples in the ancient DNA record, and all of these individuals are from sites on the North Caucasus Piedmont steppe (two from Progress 2 and one from Vonyuchka 1).

As a result, it might be tempting to argue that cultural, if not genetic, impulses from the Caucasus did play an important role in the formation of the Yamnaya and related peoples. However, it's important to note that the North Caucasus Piedmont steppe was the southern periphery of Eneolithic steppe territory.

Below is a map of Eneolithic steppe burial sites featured in recent scientific literature. It's based on data from Gresky et al. 2016, a paper that focused on a specific and complex type of cranial surgery or trepanation often practiced by groups associated with this archeological culture (see here).

Incredibly, one of the skeletons from Vertoletnoe pole has been radiocarbon dated to the mid-6th millennium BCE. My suspicion, however, is that this result was blown out by the so called reservoir effect (see here). In any case, the academic consensus seems to be that the roots of Eneolithic steppe should be sought in the Lower Don region, rather than in the Caucasus foothills (see page 36 here).

Considering that nine Eneolithic steppe skulls from the Lower Don were analyzed by Gresky et al., I'd say it's only a matter of time before we see the publication of genome-wide data for at least of couple of these samples. Indeed, the paper's lead author is from the Deutsches Archäologisches Institut, which is currently involved in a major archaeogenetic project on the ancient Caucasus and surrounds. Unfortunately, the study is scheduled to be completed in about four years (see here).

But whatever happens, the story of Eneolithic steppe deserves to be investigated in as much detail as possible, because it obviously had a profound impact on Europe and its people.

In my estimation, at least a third of the ancestry of present-day Northern Europeans, all the way from Ireland to the Ural Mountains in Russia, is ultimately derived from Eneolithic steppe groups. It's also possible that R1a-M417 and R1b-L51, the two most frequent Y-chromosome haplogroups in European males today, derive from a couple of Eneolithic steppe founders. If so, that's a very impressive effort for such an obscure archeological culture from what is generally regarded as a peripheral part of Europe.

See also...

A note on Steppe Maykop

I'm reading a new book titled Dispersals and Diversification: Linguistic and Archaeological Perspectives on the Early Stages of Indo-European (see here). One of the chapters is authored by archeologist David Anthony, in which he makes the following claims:

A previously unknown genetic population actually was identified in Wang et al. (2019), but it was a peculiar relict-seeming group related to Paleo Siberians and American Indians (Kennewick) that had survived isolated somewhere in the Caspian steppes or perhaps in the North Caucasus Mountains. The Maykop people did admix with this previously isolated Siberian/Kennewick population in graves labeled "Steppe Maykop" in Wang et al. (2019).

But this just makes it clearer that a cultural choice motivated the Maykop people to exclude marriages with Yamnaya and pre-Yamnaya people specifically, even while exchanges of material goods, ideas, technologies continued. Neither the Maykop nor the North Caucasus/Siberian/Kennewick population can be the source of most of the CHG [Caucasus hunter-gatherer] ancestry in Yamnaya. In order to narrow down when and where CHG ancestry entered the steppes, we must widen our geographic frame beyond the Caucasus.

Unfortunately, this is way off the mark. Especially unsound is his inference that the CHG-related ancestry in the Yamnaya population may have come from beyond the Caucasus.

In fact, the chances that the Steppe Maykop people were derived from a relict Siberian/Kennewick-related group that survived into the Maykop era in the Caspian steppes or the North Caucasus are exactly zero.

The real story was surely more complicated. In my opinion, it initially involved the migration during the Eneolithic or earlier of a people rich in CHG ancestry from the southernmost steppes into the Volga Delta and surrounds, and then the back-migration during the Early Bronze Age (EBA) of their descendants with around 50% admixture from Central Asian foragers. If so, these foragers were very similar to indigenous West Siberians and also relatively closely related to Native Americans.

I don't know why such an exotic people migrated into the North Caucasus steppes to form the bulk of the Steppe Maykop population, but I'm certain they did, and one interesting possibility is that they were recruited by Maykop chiefs to create a buffer zone against hostile Yamnaya-related groups trying to push into the Caucasus, possibly from the lower Don region.

Of course, the same ancient northward migration of the CHG-rich population that may have eventually given rise to the Steppe Maykop people might also explain the deep origins of the Yamnaya people.

The key sample in all of this is VJ1001 from the Wang et al. paper. This female comes from an Eneolithic (4332-4238 calBCE) kurgan burial in the North Caucasus steppes. But despite her early date, she's genetically very similar to most Yamnaya individuals. And she's also a perfect proxy for half of the ancestry of three out of the six Steppe Maykop individuals. Here's a mixture model that I put together using the Broad MIT/Harvard software qpAdm:

RUS_Steppe_Maykop (3/6)
RUS_Eneolithic_steppe_VJ1001 0.452±0.023
RUS_Tyumen_HG 0.548±0.023
chisq 7.494
tail prob 0.874914
Full output

Indeed, these Steppe Maykop samples don't harbor any Maykop ancestry. They're simply a two-way mixture between a population closely resembling VJ1001 and another one similar to hunter-gatherers from Tyumen, West Siberia.

Importantly, a couple of Steppe Maykop-related populations were inadvertently discovered by Narasimhan et al. northeast of the Caspian Sea in what is now Kazakhstan. One of these groups is labeled Kumsay_EBA, after the location of its cemetery. It's roughly contemporaneous with Steppe Maykop and basically identical to the aforementioned Steppe Maykop trio.

KAZ_Kumsay_EBA
RUS_Eneolithic_steppe_VJ1001 0.440±0.022
RUS_Tyumen_HG 0.560±0.022
chisq 10.573
tail prob 0.646513
Full output

I suppose it's possible that Kumsay_EBA represents the migration of Steppe Maykop people into the Kazakh steppes. But even if this is true, then there had to have been an earlier migration of a group from the Kazakh steppes or West Siberia that mixed with the VJ1001-related natives of the North Caucasus steppes to give rise to Steppe Maykop.

I'm assuming that the Yamnaya-like VJ1001 and her people were the indigenous population of the North Caucasus steppes because there are no indications that they or their ancestors migrated there within any reasonable time frame from anywhere else, and certainly not from as far afield as, say, what is now Iran.

The other three Steppe Maykop individuals, who are genetic outliers in varying degrees from the main Steppe Makyop cluster, show variable levels of Maykop ancestry, with an average of about 50%. But they too harbor significant VJ1001-related ancestry. So despite the fact that there was some irregular mixing between the Maykop and Steppe Maykop peoples, this is not what created the typical Steppe Maykop genetic profile.

RUS_Steppe_Maykop_o
RUS_Eneolithic_steppe_VJ1001 0.234±0.074
RUS_Maykop_Novosvobodnaya 0.461±0.046
RUS_Tyumen_HG 0.305±0.033
chisq 7.378
tail prob 0.831667
Full output

And, of course, it should be obvious by now that the ancestry of the vast majority of Yamnaya individuals is better modeled without any input whatsoever from the Maykop or Steppe Maykop samples.

In fact, early indications are that the Yamnaya people flooded into Steppe Maykop territory from the north and completely replaced its population (see here). Despite this, in Dispersals and Diversification archeologist Kristian Kristiansen makes the following claim: "steppe Maykop expanded north, leading to the formation of the Yamnaya Culture and Proto-Indo-European". Not a chance in hell Professor.

See also...

A final note for the year

The PIE homeland controversy: August 2019 status report

Some myths die hard

An exceptional burial indeed, but not that of an Indo-European

Is Yamnaya overrated?

Four years after the publication of the seminal ancient DNA paper Massive migration from the steppe is a source for Indo-European languages in Europe by Haak et al., we're still waiting for some of its loose ends to be finally tied up with new samples. In particular...

- if the men of the Corded Ware culture (CWC) were, by and large, derived from the population of the Yamnaya culture, then where are the Yamnaya samples with R1a-M417, the main CWC Y-haplogroup?

- if the men of the Bell Beaker culture (BBC) were also, by and large, derived from the population of the Yamnaya culture, then where are the Yamnaya samples with R1b-P312, the main BBC Y-haplogroup?

- and, most crucially, if R1b-L51, which includes R1b-P312, and is nowadays by far the most important Y-haplogroup in Western Europe, arrived there from the Pontic-Caspian steppe, then why hasn't it yet appeared in any of the ancient DNA from this part of Eastern Europe or surrounds, except of course in samples that are too young to be relevant?

I'm certainly not suggesting that, in hindsight, the said paper now looks fundamentally flawed. In fact, I'd say that it has aged remarkably well, especially considering how fast things are moving in the field of ancient genomics.

But those loose ends really need tying up, one way or another. It's now time.

So someone out there, please, let us know finally if you have the relevant Yamnaya samples. And if you don't, that's OK too, just tell us what you do have. Indeed, it'd be nice know a few basic details about the thousands of samples that have been successfully sequenced in various labs and are waiting to be published. A lot of people would appreciate it.

See also...

Corded Ware as an offshoot of Hungarian Yamnaya (Anthony 2017)

Hungarian Yamnaya > Bell Beakers?

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

Commoner or elite?

I recently started looking at the correlations between Y-chromosome haplogroups and social standing in ancient Europe, and was surprised by what I learned about the five currently sampled prehistoric Scandinavians belonging to Y-haplogroup R1b. I certainly wasn't expecting to uncover these stories about a mass human sacrifice, a bog body, and an Arctic circle warrior:

- The earliest Scandinavian in the ancient DNA record belonging to R1b comes from a grave site in what is now northern Norway (VK531, Margaryan et al. 2019). This individual has a genome-wide profile similar to that of local Mesolithic hunter-gatherers, but is dated to just ~2,400 BCE. During this time, Scandinavia was dominated by a "new" population associated with the Battle-Axe culture (BAC), with high levels of ancestry from the steppes of Eastern Europe. Since VK531 wasn't buried with any BAC grave goods, and indeed with no grave goods at all, it's possible that he may have been from a remnant forager population that was displaced and ultimately forced into extinction.

- R1b-U106 is today by far the most common R1b subclade in Scandinavia, but it's not yet clear how it managed to attain this status. Was it perhaps through elite dominance? The earliest ancient individual belonging to R1b-U106 is dated to 2275-2032 calBCE and comes from a Late Neolithic, likely post-BAC burial ground in what is now Sweden (RISE98, Lilla Beddinge, grave 49, southern skeleton, Allentoft et al. 2015). However, RISE98 wasn't buried in any way that would suggest he was an individual of high social standing. In fact, he was found in a mass grave, along with two other adults and two infants, possibly representing a human sacrifice. The only artefact in the grave was a bone needle. More details are available here.

- During the Nordic Bronze Age it became customary for Scandinavian elites to be laid to rest in richly furnished barrows, while commoners were buried in flat graves with few or no offerings. Human remains recovered from a "commoner" flat grave cemetery dated to the Early Bronze Age near the present-day city of Aalborg, northern Denmark, included the skeleton of a male belonging to Y-haplogroup R1b-M269 (RISE47, grave 3, skeleton 8, Allentoft et al. 2015). Keep in mind, however, that this might have been another case of an ancient Scandinavian R1b-U106 if not for missing data. A flint dagger was found alongside one of the skeletons in this cemetery, but RISE47 wasn't accompanied by any grave goods (see here).

- One of the most amazing archeological discoveries made in Scandinavia is the Trundholm Sun Chariot. Found in a peat bog on the island of Zealand, Denmark, in 1902, it's thought to be an Indo-European religious artefact dating back to the Nordic Bronze Age; a representation of a horse pulling the sun and perhaps also the moon in a spoked wheel chariot. Another important discovery in a peat bog near Trundholm dating to the Nordic Bronze Age was the body of a man belonging to R1b-M269 (RISE276, Trundholm mose II, bog find 1940, Allentoft et al. 2015). However, chances are slim that RISE276 was a charioteer or, say, a spiritual guru who accidentally drowned in the bog. Most Danish bog bodies are thought to have belonged to sacrificial victims or executed criminals.

- Interestingly, the earliest likely Scandinavian warrior belonging to R1b, and also R1b-U106, is from an early Iron Age burial in present-day northwestern Norway (VK418, Margaryan et al. 2019). This site isn't quite as far north as the grave of the above mentioned VK531, but it's still well within the Arctic circle. Apparently, VK418 was buried with some impressive weapons, potentially of "eastern origin", including a shield, spearheads and a sword. Who knows, he may even have been an elite warrior for his time and place?

The other two main Scandinavian Y-haplogroups, I1a and R1a, haven't yet been found in prehistoric Nordic remains from such, shall we say, depressing burials. That's not to say, of course, that they won't be sooner or later. RISE175, from Allentoft et al. 2015, is currently the only individual who fits the bill as a representative of the Nordic Bronze Age elite. He was buried in a barrow grave in what is now southwest Sweden and probably belongs to Y-haplogroup I1a. That's not much to go on, but perhaps it's a sign of things to come?

See also...

Isotopes vs ancient DNA in prehistoric Scandinavia

Who were the people of the Nordic Bronze Age?

They came, they saw, and they mixed

Isotopes vs ancient DNA in prehistoric Scandinavia

Four of the samples from the recent Frei et al. paper on human mobility in prehistoric southern Scandinavia are in my Global25 datasheets. Their genomes were published along with Allentoft et al. back in 2015. So I thought it might be interesting to check whether their strontium isotope ratios correlated with their genomic profiles.

In the Principal Component Analysis (PCA) below, RISE61 is a subtle outlier along the horizontal axis compared to the other three Nordic ancients, as well as a Danish individual representative of the present-day Danish gene pool. Also note that RISE61 shows the most unusual strontium isotope ratio (0.712588). The PCA was run with an online tool freely available here.

To help drive the point home, here's a figure from Frei et al., edited by me to show the positions of RISE47, RISE61 and RISE71. If RISE276 was also in this graph, he'd be sitting well under the "local" baseline, in roughly the same spot along the vertical axis as RISE47.

Interestingly, RISE61 belongs to Y-chromosome haplogroup R1a-M417, while RISE47 and RISE276, who appear to have been locals, both belong to R1b-M269. My guess is that RISE61 was a recent migrant from a more northerly part of Scandinavia dominated by the Battle-Axe culture (BAC). The BAC population was probably rich in R1a-M417 because it moved into Scandinavia from the Pontic-Caspian steppe via the East Baltic. This is what Frei et al. say about RISE61 and his burial site:

The double passage grave of Kyndeløse (Fig 1, S1 File) located on the island of Zealand yielded 70 individuals as well as a large number of grave goods, including flint artefacts, ceramics, and tooth and amber beads. We conducted strontium isotope analyses of seven individuals from Kyndeløse encompassing a period of c. 1000 years, indicating the prolonged use of this passage grave. The oldest of the seven individuals is a female (RISE 65) from whom we measured a “local” strontium isotope signature ( 87 Sr/ 86 Sr = 0.7099). Similar values were measured in five other individuals, including adult males and females. Only a single individual from Kyndeløse, an adult male (RISE 61) yielded a somewhat different strontium isotope signature of 87 Sr/ 86 Sr = 0.7126 which seems to indicate a non-local provenance. The skull of this male individual revealed healed porosities in the eye orbits, cribra orbitalia, a condition which is possibly linked to a vitamin deficiency during childhood, such as iron deficiency.

By the way, RISE47 was buried in a flat grave, which suggests that he was a commoner. RISE276 was found in a peat bog in Trundholm, where the famous Trundholm sun chariot was discovered (see here). He may have been a human sacrifice.

Citation...

Frei KM, Bergerbrant S, Sjögren K-G, Jørkov ML, Lynnerup N, Harvig L, et al. (2019) Mapping human mobility during the third and second millennia BC in present-day Denmark. PLoS ONE 14(8): e0219850. https://doi.org/10.1371/journal.pone.0219850

See also...

Commoner or elite?

Who were the people of the Nordic Bronze Age?

They came, they saw, and they mixed

A surprising twist to the Shirenzigou nomads story

Remember those potentially Afanasievo-derived and Tocharian-related Shirenzigou nomads from the Ning et al. paper? Well, in my opinion, they're probably neither. The genotypes and other data for these Iron Age individuals from the eastern Tian Shan are available here.

Below are a few successful and not so successful qpAdm mixture models for them. Note that I tried to use a wide range of relevant "right pops", but also retain a lot of markers, specifically to be able to discriminate between different types of steppe and steppe-derived sources of gene flow (refer to the full output). Admittedly, the Shirenzigou nomads can be modeled with Afanasievo-related ancestry, but...

CHN_Shirenzigou_IA
KAZ_Botai 0.161±0.023
KAZ_Wusun 0.490±0.023
NPL_Mebrak_2125BP 0.349±0.019
chisq 5.793
tail prob 0.926172
Full output

CHN_Shirenzigou_IA
KAZ_Botai 0.143±0.022
NPL_Mebrak_2125BP 0.295±0.019
Saka_Tian_Shan 0.562±0.024
chisq 6.796
tail prob 0.870794
Full output

CHN_Shirenzigou_IA
KAZ_Botai 0.185±0.023
NPL_Mebrak_2125BP 0.428±0.021
RUS_Sintashta_MLBA 0.270±0.026
TJK_Sarazm_En 0.117±0.027
chisq 11.351
tail prob 0.414345
Full output

CHN_Shirenzigou_IA
KAZ_Botai 0.032±0.027
KAZ_Zevakinskiy_LBA 0.567±0.025
NPL_Mebrak_2125BP 0.401±0.019
chisq 15.157
tail prob 0.232961
Full output

CHN_Shirenzigou_IA
NPL_Mebrak_2125BP 0.452±0.031
RUS_Afanasievo 0.435±0.025
RUS_Okunevo_BA 0.114±0.049
chisq 19.808
tail prob 0.0708003
Full output

CHN_Shirenzigou_IA
NPL_Mebrak_2125BP 0.409±0.031
RUS_Okunevo_BA 0.173±0.050
Yamnaya_RUS_Caucasus 0.418±0.026
chisq 20.453
tail prob 0.0589872
Full output

CHN_Shirenzigou_IA
NPL_Mebrak_2125BP 0.464±0.033
RUS_Okunevo_BA 0.104±0.053
Yamnaya_RUS_Samara 0.432±0.027
chisq 27.189
tail prob 0.0072566
Full output

Both the Wusun and Saka are generally accepted to have been the speakers of Indo-Iranian languages. So it's possible that the Shirenzigou nomads were Indo-Iranian speakers too, or at least derived from such peoples.

Surprisingly, NPL_Mebrak_2125BP was the key to obtaining the best statistical fits. This is a trio of samples, roughly contemporaneous with the Shirenzigou nomads, from a burial site high up in the Himalayas in what is now Nepal (see here).

To be honest, I'm not quite sure why the Himalayan ancients work so well in my models. Perhaps they're just a really good proxy for an Iron Age population from the northern edge of the Tibetan Plateau?

By the way, most of the Shirenzigou nomads made it into the latest Global25 datasheets (see here). They can be analyzed in a variety of ways described in this blog post: Getting the most out of the Global25. Below is a screen cap of me comparing the effectiveness of Afanasievo, Sintashta and Wusun samples as proxies for the steppe ancestry in the Shirenzigou nomads with an online tool freely available here. As expected, the algorithm picks Sintashta ahead of Afanasievo, and the Wusun ahead of both.

See also...

They mixed up Huns with Tocharians

Some myths die hard

The mystery of the Sintashta people

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...

They mixed up Huns with Tocharians

I don't yet have the genomes from the recent Ning et al. paper on the Iron Age nomads from the Shirenzigou site in the eastern Tian Shan. But I do have most of the previously published data featured in the paper, including the Damgaard et al. 2018 Hun and Saka samples from the western Tian Shan.

After reading the Ning et al. paper between the lines and running a few analyses of my own, it's clear to me that most of the supposedly Tocharian-related Shirenzigou individuals actually share a very close relationship with the Tian Shan Huns, and indeed may have been their ancestors.

For instance, Ning et al. found that a large part of the ancestry of the Shirenzigou ancients could be modeled with the Tian Shan Huns, which was an anachronistic approach because the former are older than the latter. They also found that Ulchi-related ancestry was a key part of the genetic structure of eight out of the ten Shirenzigou individuals, and this likewise appears to be an important part of the genetic structure of the Tian Shan Huns.

Note the strong statistical fits in the Global25/nMonte and qpAdm mixture models below, respectively, which characterize these Huns as a two-way mixture between the Ulchi and the earlier Tian Shan Saka. And keep in mind that the Saka also harbor significant Ulchi-related ancestry.

Hun_Tian_Shan
Saka_Tian_Shan,92
Ulchi,8
distance%=1.2553

Hun_Tian_Shan
Saka_Tian_Shan 0.928±0.009
Ulchi 0.072±0.009
chisq 4.409
tail prob 0.992464
Full output

Moreover, the Shirenzigou males belong to Y-haplogroups Q1a and R1b (two instances of each), and they share the latter with one of the Tian Shan Huns. Judging by the data from the relevant BAM files, it's also possible that the Shirenzigou males share a very rare subclade of R1b with the Hun, defined by the PH155 mutation (see here). The Y-haplogroup assignments for the other Tian Shan Huns end at R and R1, but that's almost certainly due to missing data.

On the other hand, two Tian Shan Sakas belong to Y-haplogroup R1a but none to R1b, which fits with the pattern from currently available ancient DNA that R1a was more common than R1b in Saka-related groups, such as the Scythians and Sarmatians (see here).

This is all very interesting, because the Huns replaced the Saka in the western Tian Shan, and, considering their R1b and excess Ulchi-related ancestry, very likely moved into the region from the direction of Shirenzigou. Indeed, in my opinion a strong argument can now be made that the Iron Age population from the Shirenzigou region took part in the formation of the Hunnic confederacy.

So where does that leave the theory presented by Ning et al. that the Shirenzigou ancients may have been closely related, and perhaps even ancestral, to the Tocharians, simply because they packed a lot of Yamnaya-related and possibly proto-Tocharian Afanasievo ancestry, and were living close to the Tarim Basin, where Tocharian languages were subsequently first attested?

I'm not sure, but I now find it difficult to reconcile this theory with the fact that they were closely related, and probably ancestral, to the Tian Shan Huns. As far as I'm aware, Huns cannot be linked to Tocharians in any meaningful way.

Of course it's possible that different Afanasievo-derived groups were living in the Tarim Basin and surrounds, and, as some merged with new populations pushing into the region from the east and adopted non-Indo-European languages, others retained their Tocharian speech and eventually split into communities speaking Tocharian A, B and apparently also C (see here).

But this has to be demonstrated directly with ancient DNA from archeological sites where Tocharian languages were attested. Till then, I'll keep thinking that Ning et al. wrote a paper about Tocharians that really should've been a paper about Huns.

Here's a famous wall painting of Tocharian princes from the cave of the sixteen sword-bearers in the Tarim Basin, dated to 432–538 AD. They don't look like guys with a lot of Ulchi-related admixture to me, but I might be wrong. Feel free to let me know what you think in the comments below.

Update 08/17/2019: The Shirenzigou nomads are now in my dataset. Below are a few successful and not so successful qpAdm mixture models for them. Note that I tried to use a wide range of relevant "right pops", but also retain a lot of markers, specifically to be able to discriminate between different types of steppe and steppe-derived sources of gene flow (refer to the full output). Admittedly, the Shirenzigou nomads can be modeled with Afanasievo-related ancestry, but...

CHN_Shirenzigou_IA
KAZ_Botai 0.161±0.023
KAZ_Wusun 0.490±0.023
NPL_Mebrak_2125BP 0.349±0.019
chisq 5.793
tail prob 0.926172
Full output

CHN_Shirenzigou_IA
KAZ_Botai 0.143±0.022
NPL_Mebrak_2125BP 0.295±0.019
Saka_Tian_Shan 0.562±0.024
chisq 6.796
tail prob 0.870794
Full output

CHN_Shirenzigou_IA
KAZ_Botai 0.185±0.023
NPL_Mebrak_2125BP 0.428±0.021
RUS_Sintashta_MLBA 0.270±0.026
TJK_Sarazm_En 0.117±0.027
chisq 11.351
tail prob 0.414345
Full output

CHN_Shirenzigou_IA
KAZ_Botai 0.032±0.027
KAZ_Zevakinskiy_LBA 0.567±0.025
NPL_Mebrak_2125BP 0.401±0.019
chisq 15.157
tail prob 0.232961
Full output

CHN_Shirenzigou_IA
NPL_Mebrak_2125BP 0.452±0.031
RUS_Afanasievo 0.435±0.025
RUS_Okunevo_BA 0.114±0.049
chisq 19.808
tail prob 0.0708003
Full output

CHN_Shirenzigou_IA
NPL_Mebrak_2125BP 0.409±0.031
RUS_Okunevo_BA 0.173±0.050
Yamnaya_RUS_Caucasus 0.418±0.026
chisq 20.453
tail prob 0.0589872
Full output

CHN_Shirenzigou_IA
NPL_Mebrak_2125BP 0.464±0.033
RUS_Okunevo_BA 0.104±0.053
Yamnaya_RUS_Samara 0.432±0.027
chisq 27.189
tail prob 0.0072566
Full output

Both the Wusun and Saka are generally accepted to have been the speakers of Indo-Iranian languages. So it's possible that the Shirenzigou nomads were Indo-Iranian speakers too, or at least derived from such peoples.

Surprisingly, NPL_Mebrak_2125BP was the key to obtaining the best statistical fits. This is a trio of samples, roughly contemporaneous with the Shirenzigou nomads, from a burial site high up in the Himalayas in what is now Nepal (see here).

To be honest, I'm not quite sure why the Himalayan ancients work so well in my models. Perhaps they're just a really good proxy for an Iron Age population from the northern part of the Tibetan Plateau? By the way, most of the Shirenzigou nomads made it into the latest Global25 datasheets (see here).

See also...

Almost everything you ever wanted to know about the Xiaohe-Gumugou cemeteries

The mystery of the Sintashta people

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