R-V1636: Eneolithic steppe > Kura-Araxes?

Ancient samples from the Wang et al. preprint on the genetic prehistory of the Greater Caucasus are now available as BAM files at the European Nucleotide Archive (see here). I've requested the genotype data from the authors and I'm eagerly awaiting their response.

But various online genetic genealogy communities are already studying in detail the Y-chromosome data from the BAM files. One interesting outcome is that both of the Eneolithic steppe males, PG2001 and PG2004, apparently belong to Y-haplogroup R-V1636 (see here). This extremely rare subclade of R1b has apparently also been found in an ancient individual from what is now Armenia associated with the Kura-Araxes culture: Armenia_EBA I1635.

Importantly, the Eneolithic steppe males are dated to 4336-4047 calBCE, and don't show any recent genome-wide ancestry from south of the Caucasus, while the Kura-Araxes individual is dated to just 2619-2465 calBCE.

It'll be interesting to see whether Armenia_EBA I163 shows any genome-wide admixture from north of the Caucasus when I can test this with these new Wang et al. Eneolithic samples from the southernmost steppes. But in any case, if the R-V1636 link between the Eneolithic steppe and Kura-Araxes is real, then this is more evidence of migrations from the steppe across the Greater Caucasus into the Near East during the Eneolithic and/or Bronze Age.

Such population movements could potentially explain the appearance of Hittite and other closely related Indo-European languages in Anatolia during the Bronze Age.

See also...

Steppe ancestry in Chalcolithic Transcaucasia (aka Armenia_ChL explained)

Likely Yamnaya incursion(s) into Northwestern Iran

A potentially violent end to the Kura-Araxes Culture (Alizadeh et al. 2018)

The Hajji Firuz fiasco

The specter of Hajji_Firuz_ChL I2327 still haunts us. Judging by some recent comments that I've seen here and elsewhere, it seems that a good number of confused souls haven't yet given up hope that this ancient sample represents a Near Eastern population ancestral to the Yamnaya people of Early Bronze Age Eastern Europe. But the chances of this are slim to none, because...

- Hajji_Firuz_ChL I2327 is the only (supposedly) pre-Yamnaya individual to date in the now ample West Asian ancient DNA record who belongs to Y-haplogroup R1b-Z2103, R1b-M269, or even R1b, which has got to tell you something about the reliability of his early dating

- overall the genome-wide structure of Hajji_Firuz_ChL I2327 most certainly doesn't fit the profile of the Near Eastern-related half of the Yamnaya genotype

- in fact, practically every analysis that I've run with Hajji_Firuz_ChL I2327 suggests that he harbors Yamnaya or Yamnaya-related genome-wide ancestry, which makes sense considering his Yamnaya-specific Y-haplogroup, don't you think?

Heck, even if Hajji_Firuz_ChL I2327 is more or less accurately dated, and really was alive during the Chalcolithic period, then considering the points I've made above, the only honest explanation for his presence that early in what is now Iran is that there was a migration of a Yamnaya-like people from the steppes across the Caucasus during the Chalcolithic.

I already wrote a post on this topic back in April, and a lengthy discussion ensued, with most of the commentators agreeing with my stance. But my efforts haven't had much of an impact outside of this blog. It's possible that my post was too confusing, so I went back today and rewrote it, also adding new stats and mixture models to help me drive home my point. Here's the link...

Likely Yamnaya incursion(s) into Northwestern Iran

Of course, no matter how strong my arguments are, many people will choose to disagree with me nevertheless and believe what they want to believe, because this is such an emotional issue for them. I don't want to get into the details about that here, but suffice to say that it's imperative for many people, particularly those of Near Eastern and Southern European backgrounds, that the origin of Yamnaya is somehow, by hook or by crook, put south of the Caucasus. I'm not kidding. It's a pointless cause though, especially now considering all of the new ancient DNA data from Eastern Europe that make this scenario about as likely as Out-of-India (see here).

See also...

Yamnaya: home-grown

Big deal of 2018: Yamnaya not related to Maykop

Ahead of the pack

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

Italians are interesting people (Raveane et al. 2018 preprint)

Over at bioRxiv at this LINK. As far as I can see from skimming through the preprint, it's a thorough effort with conclusions that make good sense. But, needless to say, it'll be very useful to plug the dataset from this study into the Global25 to see what these new Italian samples are really made of. Here's the abstract, emphasis is mine.

European populations display low genetic diversity as the result of long term blending of the small number of ancient founding ancestries. However it is still unclear how the combination of ancient ancestries related to early European foragers, Neolithic farmers and Bronze Age nomadic pastoralists can fully explain genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the overall continental diversity, but to date have been systematically understudied. Here we characterised the ancestry profiles of modern-day Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe and the rest of the world. Italian genomes captured several ancient signatures, including a non-steppe related substantial ancestry contribution ultimately from the Caucasus. Differences in ancestry composition as the result of migration and admixture generated in Italy the largest degree of population structure detected so far in the continent and shaped the amount of Neanderthal DNA present in modern-day populations.

Raveane et al., Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe, Posted December 13, 2018, bioRxiv, doi: https://doi.org/10.1101/494898

See also...

Greeks in a Longobard cemetery

Migration of the Bell Beakers—but not from Iberia (Olalde et al. 2018)

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

How did Y-haplogroup N1c get to Bolshoy Oleni Ostrov?

Y-haplogroup N1c probably entered Europe from Siberia during the Bronze Age or the Eneolithic period. It first appears in the European ancient DNA record in two samples from a burial site at Bolshoy Oleni Ostrov, in the Kola Peninsula, dated to 1523±87 calBCE (see here). These individuals also harbor significant Siberian genome-wide ancestry, but it's possible that this is in large part a coincidence, and that N1c spread into the Kola Peninsula from the south in a population of overwhelmingly European ancestry.

Crazy, huh? Not really. Consider the qpAdm mixture models below for BOO002 and BOO004, the two males from the Bolshoy Oleni Ostrov site belonging to N1c, and BOO006, a female and the most Siberian-admixed individual from the same site. Although BOO002 and BOO004 show a lot of Nganasan-related and thus Siberian ancestry, they also require significant input from a source closely related to Baltic_BA, a fully European Bronze Age population from the East Baltic region. On the other hand, BOO006 doesn't need Baltic_BA for a successful model.

BOO002_&_BOO004
Baltic_BA 0.124±0.029
EHG 0.406±0.032
Nganasan 0.469±0.017
chisq 10.847
tail prob 0.286316
Full output

BOO006
Baltic_BA 0.065±0.043
EHG 0.265±0.084
Nganasan 0.517±0.033
West_Siberia_N 0.152±0.074
chisq 8.847
tail prob 0.355397
Full output

BOO006
EHG 0.367±0.049
Nganasan 0.544±0.031
West_Siberia_N 0.089±0.063
chisq 9.878
tail prob 0.360451
Full output

Keep in mind that N1c is very common in the East Baltic today in populations with minimal Siberian genome-wide ancestry. Indeed, Latvians and Lithuanians can often be modeled with no Siberian input. Thus, it's likely that by the time N1c arrived in the East Baltic, probably during the Late Bronze Age or Early Iron Age, it did so with populations with heavily diluted Siberian genome-wide ancestry. Such groups may also have taken N1c north of the Baltic and into the Kola Peninsula.

See also...

On the trail of the Proto-Uralic speakers (work in progress)

Europe's ancient proto-cities may have been ravaged by the plague

The Cucuteni-Trypillia culture of the Eneolithic Balkans and Eastern Europe is best known for its mega-settlements or proto-cities, each one featuring hundreds of homes, temples and other structures, and likely to have been inhabited by as many as 20,000 people. But from around 3,400 BC these mega-settlements were no longer being built, and a few hundred years later the Cucuteni-Trypillia culture vanished.

Two main explanations have been given for its rather swift demise: violent invasions by steppe pastoralists from the east and/or a massive out-migration by its people as a result of environmental impacts from rapid climate change (see here). However, these theories have failed to gain wide acceptance due to a lack of hard evidence in their support.

Now, another potential explanation is being offered, and it is supported by hard evidence. According to Rascovan et al., the plague may have been a key factor in the decline of not only the Cucuteni-Trypillia culture, but much of Neolithic Europe (see here). From the paper, emphasis is mine...

Between 5,000 and 6,000 years ago, many Neolithic societies declined throughout western Eurasia due to a combination of factors that are still largely debated. Here, we report the discovery and genome reconstruction of Yersinia pestis, the etiological agent of plague, in Neolithic farmers in Sweden, pre-dating and basal to all modern and ancient known strains of this pathogen. We investigated the history of this strain by combining phylogenetic and molecular clock analyses of the bacterial genome, detailed archaeological information, and genomic analyses from infected individuals and hundreds of ancient human samples across Eurasia. These analyses revealed that multiple and independent lineages of Y. pestis branched and expanded across Eurasia during the Neolithic decline, spreading most likely through early trade networks rather than massive human migrations. Our results are consistent with the existence of a prehistoric plague pandemic that likely contributed to the decay of Neolithic populations in Europe.

...

In this work, we report the discovery of plague infecting Neolithic farmers in Scandinavia, which not only pre-dates all known cases of plague, but is also basal to all known modern and ancient strains of Y. pestis. We identified a remarkable overlap between the estimated radiation times of early lineages of Y. pestis, toward Europe and the Eurasian Steppe, and the collapse of Trypillia mega-settlements in the Balkans/Eastern Europe.

Citation...

Rascovan et al., Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline, Cell (2019), https://doi.org/10.1016/j.cell.2018.11.005

See also...

Migration of the Bell Beakers—but not from Iberia (Olalde et al. 2018)

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

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

On the trail of the Proto-Uralic speakers (work in progress)

Historical linguists have long posited that Fennoscandia was a busy contact zone between early Germanic and Uralic languages. The first ancient DNA samples from what is now Finland have corroborated their inferences, by showing that during the Iron Age the western part of the country was inhabited by a genetically heterogeneous population closely related to both the Uralic-speaking Saami and Germanic-speaking southern Scandinavians.

The samples were sequenced and analyzed by two different teams of researches, and their findings published recently in Lamnidis et al. and Sikora et al. (see here and here, respectively).

This is how most of these ancients, whose remains were excavated from the Levanluhta burial site dated to 300–800 CE, behave in a Principal Component Analysis (PCA) based on my Global25 data. Levanluhta_IA are the Saami-related samples, while Levanluhta_IA_o is an Scandinavian-like outlier. Baltic_IA is an Iron Age individual from what is now Lithuania from the recent Damgaard et al. paper (see here). Note the accuracy of the Global25 data in pinpointing their genetic affinities and also the trajectory of the Levanluhta_IA cluster, which seems to be "pulling" towards Levanluhta_IA_o.

The Saami and Levanluhta_IA are clear outliers from the main Northern European cluster. There are two reasons for this: excess East Asian/Siberian-related ancestry and Saami-specific genetic drift. However, this eastern admixture and genetic drift are shared in varying degrees by other North European populations, especially those that also speak Uralic languages, and this is why they appear to be "pulling" towards the Saami/Levanluhta_IA clusters in my PCA. Thus, what this suggests is that the expansion of Uralic languages across Northeastern Europe was intimately linked with the spread of Siberian-related ancestry into the region.

This idea has been around for a long time and is now becoming even more widely accepted (see here). However, Lamnidis et al. also featured samples from a likely pre-Uralic (1523±87 calBCE) burial site at Bolshoy Oleni Ostrov in the Kola Peninsula, present-day northern Russia, and, perhaps surprisingly, found that they showed even more Siberian-related ancestry than Levanluhta_IA. So what's going on?

I'm confident that this discrepancy can be explained by multiple waves of migrations from the east into Northeastern Europe, possibly before, during and after the time of the people buried at Bolshoy Oleni Ostrov, by pre-Uralic, para-Uralic and/or Proto-Uralic-speaking populations.

Consider the following qpAdm output, in which Levanluhta_IA is just barely modeled successfully as a two-way mixture between Levanluhta_IA_o and Bolshoy_Oleni_Ostrov. The statistical fit improves significantly with the addition of Glazkovo_EBA as a third mixture source. This is an ancient population from near Lake Baikal dated to 4597-3726 BC from the aforementioned Damgaard et al. paper.

Levanluhta_IA
Bolshoy_Oleni_Ostrov 0.468±0.036
Levanluhta_IA_o 0.532±0.036
chisq 19.129
tail prob 0.0854706
Full output

Levanluhta_IA
Bolshoy_Oleni_Ostrov 0.241±0.092
Glazkovo_EBA 0.162±0.059
Levanluhta_IA_o 0.597±0.046
chisq 7.756
tail prob 0.734966
Full output

For the sake of being complete, I also tested whether Levanluhta_IA_o could be substituted by other similar ancient samples from the neighborhood, including those associated with the Battle-Axe and Corded Ware cultures. There's not much to report; qpAdm returned poor statistical fits and/or implausible ancestry proportions (for the full output from my runs, see here). Baltic_IA did produce a statistically sound model, but with excess Glazkovo_EBA-related ancestry. I also had to drop Bolshoy_Oleni_Ostrov from the analysis to make things work, which suggests to me that the result shouldn't be taken too literally.

Levanluhta_IA
Baltic_IA 0.677±0.034
Glazkovo_EBA 0.323±0.034
chisq 8.547
tail prob 0.741095
Full output

So as far as I can see, the western ancestry in Levanluhta_IA is likely to be mostly of Germanic origin, and thus Indo-European, meaning that it's logical to look east, perhaps far to the east, for the source of its Uralic ancestry. This might seem like a complicated and uncertain task, considering that Levanluhta_IA could well be at least a thousand years younger than the first entry of Uralic speakers into Fennoscandia. However, take a look what happens when I substitute Glazkovo_EBA with a variety of Uralic-speaking populations from around the Ural Mountains, which is where the Proto-Uralic homeland is generally considered to have been located.

Levanluhta_IA
Bolshoy_Oleni_Ostrov 0.210±0.091
Khanty 0.283±0.090
Levanluhta_IA_o 0.507±0.035
chisq 7.007
tail prob 0.798532
Full output

Levanluhta_IA
Bolshoy_Oleni_Ostrov 0.193±0.098
Levanluhta_IA_o 0.495±0.035
Mansi 0.312±0.100
chisq 7.884
tail prob 0.7237
Full output

Levanluhta_IA
Bolshoy_Oleni_Ostrov 0.300±0.065
Levanluhta_IA_o 0.337±0.072
Mari 0.363±0.121
chisq 8.393
tail prob 0.677705
Full output

Levanluhta_IA
Bolshoy_Oleni_Ostrov 0.238±0.084
Levanluhta_IA_o 0.553±0.036
Nenets 0.209±0.067
chisq 7.210
tail prob 0.78181
Full output

Levanluhta_IA
Bolshoy_Oleni_Ostrov 0.302±0.069
Levanluhta_IA_o 0.324±0.081
Udmurt 0.373±0.135
chisq 9.195
tail prob 0.60393
Full output

All of these models look great, and easily rival the best model with Glazkovo_EBA. Moreover, they make good sense in terms of linguistics. The only problem is that they're anachronistic, because the Uralic-speaking reference populations are younger than Levanluhta_IA. So I can't be certain that they reflect reality without corroboration from ancient DNA. It might turn out, for instance, that a Glazkovo_EBA-like population was already present somewhere deep in Europe before or during the time of Bolshoy_Oleni_Ostrov, while no such population existed around the Ural Mountains until the time of Levanluhta_IA.

By the way, it might be important to note that the present-day Finnish samples in my dataset can't be modeled as a mixture between Levanluhta_IA and Levanluhta_IA_o. But they can be modeled as a mixture between Baltic_IA and Levanluhta_IA. I don't know which part of Finland they're from exactly; probably all over the place, so it'd be useful to test regional Finnish populations to see how they behave in such models. Of course, Finns aren't Saamic speakers, they're Finnic speakers, and they're probably the result of a more recent Uralic expansion into Fennoscandia than the one that gave rise to the Saami.

Finnish
Baltic_IA 0.671±0.076
Levanluhta_IA 0.329±0.076
chisq 14.114
tail prob 0.293508
Full output

Damgaard et al. didn't report the Y-haplogroup for Baltic_IA, but the word round the campfire is that this individual belonged to N1c, which is today the most common Y-haplogroup among Uralic speakers. Obviously, we need a lot more ancient DNA to sort all of this out, but things are already looking pretty much as expected. Stay tuned for new posts in this series following the publication of more ancient DNA relevant to this fascinating topic.

See also...

How did Y-haplogroup N1c get to Bolshoy Oleni Ostrov?

The Uralic cline in the Global25

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

How should we interpret the movements of people throughout Bronze Age Europe?

Below are a couple of interesting talk abstracts from the upcoming Genes, Isotopes and Artefacts conference in Vienna (see here). The first one looks like the abstract from a rewritten version of the Wang et al. preprint on the genetic prehistory of the Greater Caucasus. But I could be wrong. In any case, check out the links at the bottom of the post to see what I've said about this manuscript. Admittedly I've said a lot, maybe too much. Feel free to speculate to your heart's content in the comments about what these abstracts "really" mean, but try to keep it real. Emphasis is mine:

At the interface of culture and biology – First results from a paleogenetic transect through Bronze Age populations of the Caucasus

Svend Hansen, Sabine Reinhold, Wolfgang Haak, Chuan-Chao Wang

The Caucasus is one of the most important geographical joints in Western Eurasia. Linking Europe, Western Asia and the Eurasian steppe zone, this region today is one of the genetically and linguistically most diverse spots of Eurasia. It is easy to imagine that repeated population influx and drain, but similarly compartmentalisation in the remote mountain valley is behind this modern situation. Eneolithic and Bronze Age populations play an important role in this scenario, as they represent the first epochs of formations, which can be regarded either as associated ‘cultures’ and/or coherent biological populations. A first study on the paleogenetic background of 50 individuals from the 5th to the 2nd millennium BC, which represent all cultural formations of Bronze Age Caucasia, give a first insight into highly complex scenarios of interaction. The paleogenetic perspective could proof the presence of populations with different genetic-make ups and different biological vectors of formation among these individuals. Affiliation by material cultural and other archaeological attributes, however, revealed epochs of interaction, where cultural and biological borders were crossed, and those, where no population exchange seemed to have happened among the neighbouring inhabitants of one area. This region thus allows to study in detail the mixing and interdigitation of people, their materiality and cultural systems and challenge many of the too simple models developed for another interface of the Eurasian steppe zone those directed towards Europe.

...

Steppe and Iranian ancestry among Bronze Age Central and Western Mediterranean populations

Ron Pinhasi, Daniel Fernandes, David Reich

Steppe-related ancestry is known to have reached central Europe ca. 3000 BCE, while Iran-related ancestry reached Greece by 1500 BCE. However, the time course and extent of their spread into the central/western Mediterranean remains a mystery. We analysed 48 Neolithic and Bronze Age individuals from Sicily, Sardinia and the Balearic Islands aiming to investigate when and how continental European and Aegean influences affected these insular populations. Results show that the first Balearic settlers had substantial Steppe-related ancestry which was subsequently diluted by increasing proportions of farmer-related ancestry. In Sardinia, we identified the appearance of Iran-related ancestry from the Aegean as early as the Middle Bronze Age, with no genetic influences seen from populations carrying Steppe-related ancestry despite cultural or commercial exchanges with Bell Beaker populations. In Sicily, during the Early Bronze Age, and possibly earlier, we found evidence for admixture with groups carrying both these ancestries. These results suggest that Steppe-related migrants had a crucial role in the settlement of the Balearic Islands and their ancestry reached as far south as Sicily, and that the population movements that brought Iran-related ancestry to the Aegean also impacted the Western Mediterranean around the same time the first civilizations started to develop.

See also...

Yamnaya: home-grown

Big deal of 2018: Yamnaya not related to Maykop

Steppe Maykop: a buffer zone?

Ahead of the pack

Genetic borders are usually linguistic borders too

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

On the genetic prehistory of the Greater Caucasus (Wang et al. 2018 preprint)

The Uralic cline in the Global25

The Uralic cline is a concept that was discussed in some detail in the recent Lamnidis et al. palaeogenomics paper on the origin and spread of Siberian ancestry in Europe (see here). It pertains to the most northerly genetic cline that links the populations of West and East Eurasia, and is largely made up of Uralic-speaking peoples rich in Y-haplogroup N1c.

This is what the Uralic cline looks like when inferred from my Global25 Principal Component Analysis (PCA) data. Note that the plot features most of the Lamnidis et al. ancient samples, and they're all more or less sitting along my version of the said cline. The relevant datasheet is available here.

Admittedly though, as pointed out by Lamnidis et al., the Bolshoy samples probably aren't those of Uralic speakers because they're dated to 1523±87 calBCE, which predates most linguistic estimates of the spread of known Uralic languages into the Kola Peninsula. So the important question is why do they cluster along the Uralic cline and 2/2 of the male samples belong to N1c?

The most logical explanation, I'd say, is that the Uralic cline actually represents an older, pre-Uralic contact zone between the east and west. Nevertheless, I think it's likely that the Proto-Uralic language formed somewhere in this ancient contact zone, and the early Uralic-speaking peoples used it to their advantage to spread rapidly both east and west, especially during the Late Bronze/Early Iron Age, when they, and their N1c, finally reached the East Baltic region (see here).

See also...

Corded Ware people =/= Proto-Uralics (Tambets et al. 2018)

How did Y-haplogroup N1c get to Bolshoy Oleni Ostrov?

The mystery of the Sintashta people

Steppe ancestry in Chalcolithic Transcaucasia (aka Armenia_ChL explained)

In 2016 Lazaridis et al. published a paper featuring five ancient samples from the famous Areni-1 cave complex, in what is now Armenia, dated to the Chalcolithic (see here). This is how they described the ancestry of these ancients, which they labeled Armenia_ChL, in the supplementary PDF to their paper (page 94):

We do not have a pre-Chalcolithic sample from Armenia. We first model it [Armenia_ChL] as a 2-way mixture of any of WHG, EHG, CHG, Iran_N, Levant_N, Anatolia_N (Table S7.18), but we find no pair of these populations that could be ancestral to Armenia_ChL. We next model it as a 3-way mixture (Table S7.19), and determine that Armenia_ChL can be modeled as 18.3±1.5 EHG, 29.2±2.4% Iran_N, and 52.5±2.2% Anatolia_N. In the absence of a pre-Chalcolithic sample, we cannot be certain whether the Neolithic population of Armenia (which borders Anatolia from the east) was similar to that of Northwestern Anatolia and experienced gene flow from the east and north, or the reverse.

Since then, a lot of opinions have been posted in the comments at this blog and elsewhere about the possible origin and significance of Armenia_ChL. It seems to me that many people see Armenia_ChL as more or less an example of the indigenous Neolithic and Chalcolithic peoples of the South Caucasus. But some have argued that Armenia_ChL was in large part of Central Asian origin and concocted various mixture models to try and back up this rather strange claim.

To me, it was always obvious that Armenia_ChL harbored very recent admixture from the Pontic-Caspian steppe, because I couldn't reconcile its relatively high level of Eastern European Hunter-Gatherer (EHG) ancestry with a deep origin south of the Greater Caucasus range.

Moreover, in any decent Principal Component Analysis (PCA), like the one below, Armenia_ChL appears to form two subtle sub-clusters, with three of its individuals "pulling" more strongly towards Eastern Europe. This suggests that the EHG admixture in Armenia_ChL was present at variable levels and thus likely to be recent, because it didn't yet have time to diffuse evenly throughout the population.

Also, two out of the three Armenia_ChL individuals who are "pulling" north belong to steppe-specific mitochondrial (mtDNA) haplogroups. Armenia_ChL I1634 belongs to mtDNA haplogroup H2a1, which is seen in ancient samples from the Pontic-Caspian steppe associated with the Khvalynsk, Sredny Stog and Catacomb cultures, while Armenia_ChL I1409 belongs to mtDNA haplogroup U4a, which is found in numerous ancient samples, especially foragers, from the Pontic-Caspian steppe and other parts of Eastern Europe (see here). Coincidence? Surely not.

The idea that Armenia_ChL represents a long-standing indigenous Transcaucasian population also took a major hit recently with the release of the Wang et al. manuscript on the genetic prehistory of the Greater Caucasus. The preprint included samples from the Eneolithic Caucasus dated to earlier than Armenia_ChL (4594-4404 calBCE vs 4330-3985 calBCE) which looked typically Caucasian and lacked any discernible signals of ancestry from the steppe. Below is a PCA from Wang et al. featuring both the Eneolithic Caucasus and Armenia_ChL samples.

Unfortunately, modeling the recent ancestry of Armenia_ChL is still difficult, because the genotype data from Wang et al. haven't yet been released, so currently there is still no pre-Armenia_ChL sample available from the Caucasus for me to work with.

The earliest post-Armenia_ChL sample is Armenia_EBA I1658, dated to around a thousand years too late (3347-3092 calBCE). However, this individual is associated with the Kura-Araxes culture, which is generally seen as a direct successor to the native Neolithic cultures of Transcaucasia, and appears to be practically indistinguishable from the Eneolithic Caucasus trio in the Wang et al. PCA. Thus, pending the release of a pre-Armenia_ChL sample I might be able to use Armenia_EBA I1658 as an effective proxy for such a population.

Below are a couple of successful two-way qpAdm mixture models for Armenia_ChL and Armenia_ChL I1634, featuring Armenia_EBA I1658 and Sredny_Stog I6561 (the output for Armenia_ChL I1409 looked wobbly, probably due to a lack of markers). The reason I decided on Sredny_Stog from the North Pontic steppe as the surrogate for the steppe ancestry is because of the position of Armenia_ChL in the Wang et al. PCA relative to Eneolithic Caucasus, which suggests gene flow into the former from a more westerly steppe source than, say, Khvalynsk from the Samara region. Using these reference samples, the inferred ratio of steppe admixture in Armenia_ChL is around 15%, which I think makes sense, more or less, considering its position in both of the PCA above.

Armenia_ChL
Armenia_EBA_I1658 0.862±0.050
Sredny_Stog_I6561 0.138±0.050
chisq 17.038
tail prob 0.148174
Full output

Armenia_ChL_I1634
Armenia_EBA_I1658 0.836±0.065
Sredny_Stog_I6561 0.164±0.065
chisq 13.813
tail prob 0.312808
Full output

The presence of a significant, unambiguous signal of steppe ancestry in a group from a rich archeological site in Chalcolithic Transcaucasia might be very important in the context of the Proto-Indo-European (PIE) homeland debate. That's because it suggests that there was a movement of peoples potentially speaking dialects of PIE from the Eneolithic Pontic-Caspian steppe, the main candidate for the PIE homeland based on historical linguistics data, into cultural hubs south of the Caucasus, which may have acted as early dispersal points for Indo-European languages into other parts of the Near East, such as Anatolia. Admittedly, though, I'm still a fan of the Balkan route for the introduction of Hittite and other Anatolian languages into Anatolia, despite recent claims in scientific literature that this scenario wasn't corroborated by ancient DNA (see here).

Citation...

Lazaridis et al., Genomic insights into the origin of farming in the ancient Near East, Nature volume 536, pages 419–424 (25 August 2016), DOI: https://doi.org/10.1038/nature19310

See also...

Yamnaya: home-grown

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...