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)

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...