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Sunday, January 23, 2022


I'm seeing increasing numbers of Bronze and Iron Age samples from Central Europe and surrounds with this peculiar set of traits:

- shared genetic drift with present-day Balto-Slavic speakers to the exclusion of most other Europeans

- and yet, an unusually low level of Yamnaya-related steppe ancestry

- so much so, in fact, that they're often outside the range of modern European genetic variation.

As far as I can tell, currently the best examples of this unusual population are HUN_Mako_EBA_o:I1502 (Mathieson et al. Nature 2015) and HUN_EIA_Prescythian_Mezocsat_o1:I18241 (Patterson et al. Nature 2021). Both are from the Carpathian Basin in what is now Hungary.

I ran a series of qpAdm mixture models to try and learn more about their origins. The most robust outcomes, out of about 50 different attempts, are these:

right pops:

Baltic_LTU_Narva 0.149 ∓0.028
POL_Globular_Amphora 0.613 ∓0.028
Yamnaya_RUS_Samara 0.238 ∓0.029
chisq 10.836
tail prob 0.370463
Full output

Baltic_LTU_Narva 0.186 ∓0.028
POL_Globular_Amphora 0.592 ∓0.027
Yamnaya_RUS_Samara 0.222 ∓0.029
chisq 12.492
tail prob 0.253499
Full output

Combining the two genomes produces a very similar result:

Baltic_LTU_Narva 0.160 ∓0.023
POL_Globular_Amphora 0.612 ∓0.023
Yamnaya_RUS_Samara 0.227 ∓0.023
chisq 14.653
tail prob 0.14524
Full output

Importantly, when I move RUS_Karelia_HG from the right pops to the left pops, to test whether HUN_EBA-EIA_o really has steppe ancestry, as opposed to closely related hunter-gatherer ancestry, I still get a very similar outcome:

Baltic_LTU_Narva 0.158 ∓0.027
POL_Globular_Amphora 0.605 ∓0.033
RUS_Karelia_HG 0.014 ∓0.038
Yamnaya_RUS_Samara 0.223 ∓0.053
chisq 10.461
tail prob 0.234171
Full output

So these largely Globular Amphora-related individuals do harbor as much as a quarter of steppe ancestry, which is to be expected considering the massive genetic turn-over that most of Europe experienced just before their time as a result of population expansions from the Pontic-Caspian steppe.

Nevertheless, this is ~20% less steppe ancestry than in the present-day populations of the region, and it clearly shows in any decent Principal Component Analysis (PCA) of West Eurasia. For instance:
At the same time, the relatively close genetic relationship between these ancients and present-day Balto-Slavic speaking populations shows up in fine-scale intra-European PCA.

The origins and implications of this population are still a mystery to me. I don't think it's native to the Carpathian Basin. Indeed, my qpAdm models suggest that it may have moved into this region from somewhere to the northeast, because its ancestry is best modeled with ancient groups from present-day Lithuania, Poland and Russia.

I'm adamant that these people weren't Balto-Slavic speakers, and certainly not proto-Slavs. Rather, I suspect that much like the Welzin warriors of Bronze Age North-Central Europe, they were closely related to a contemporaneous group that eventually gave rise to proto-Slavs. At best, they may have somehow contributed to the ethnogenesis of Balto-Slavs.

By the way, using the Global25 to model their ancestry is highly problematic, because of the strong Balto-Slavic genetic drift that affects some of the dimensions. So be careful when you try it, or better yet, don't try it at all, and stick to formal stats in this particular instance.

See also...

Tollense Valley Bronze Age warriors were very close relatives of modern-day Slavs

Friday, January 21, 2022

Yamnaya is from Europe, but it's really from Asia

I was about to post a comment under a new preprint at bioRxiv, but the comment section isn't there anymore. Hopefully, this is just a temporary glitch.

The preprint in question is titled Reconstructing the spatiotemporal patterns of admixture during the European Holocene using a novel genomic dating method [LINK]. It's co-authored by Harvard/Broad MIT scientist Nick Patterson who occasionally comments at this blog.

My impression is that the authors see the people associated with the Yamnaya culture as Asians who simply used "far" Eastern Europe as a springboard to expand into other parts of Europe.

If so, they're dead wrong.

There are at least three arguments why the Yamnaya population should be seen as quintessentially European:

- its home was initially and overwhelmingly the Pontic-Caspian steppe, which is entirely located within the present-day borders of Europe

- Yamnaya genomes are clearly different from those of older populations native to nearby parts of Asia, and, in fact, these differences show a very strong correlation with the present-day borders between Europe and Asia

- the Yamnaya people weren't a new population in Europe by any stretch, but must have been overwhelmingly derived from the very similar Eneolithic peoples of the Pontic-Caspian steppe and/or the nearby forest steppe, both of which are located in Eastern Europe.

And yet, this is what the preprint claims:

The beginning of the Bronze Age was a period of major cultural and demographic change in Eurasia, accompanied by the spread of Yamnaya Steppe Pastoralist-related ancestry from Pontic-Caspian steppes into Europe and South Asia (16).

In fact, what really happened at this time was that Yamnaya steppe pastoralist-related ancestry spread from Eastern Europe to other parts of Europe, as well as to Central and West Asia.

The preprint does eventually explain that present-day South Asians derive their Yamnaya-related ancestry from a later eastward expansion of the European Corded Ware culture (CWC), but it completely ignores the fact that the Afanasievo culture was the result of the initial eastward expansion from Europe to Asia. That is, the ancestors of the Afanasievo people were recent migrants from the Pontic-Caspian steppe to Central Asia and Siberia.

There's also this:

Over the following millennium, the Yamnaya-derived groups of the Corded Ware Complex (CWC) and Bell Beaker complex (BBC) cultures brought Steppe pastoralist-related ancestry to Europe.

Seriously? Both the CWC and BBC, just like the Yamnaya culture, were from Europe. In fact, as per above, the descendants of the CWC expanded into Asia.

And this:

The second major migration occurred when populations associated with the Yamnaya culture in the Pontic-Caspian steppe expanded to central and western Europe from far eastern Europe.

The authors basically admit here that Yamnaya came from Eastern Europe, but they call it "far" Eastern Europe. Perhaps they know something I don't, but as things stand, there's no evidence that Yamnaya came from "far" Eastern Europe. In fact, the emerging consensus based on ancient DNA, including pre-publication data, is that Yamnaya may have originated in what is now Ukraine. In my opinion, Ukraine isn't located in "far" Eastern Europe, but more or less in the middle of it.

Inexplicably, this is what they say about the genetic origins of the Yamnaya and Afanasievo peoples:

These groups were likely the result of a genetic admixture between the descendants of EHG-related groups and CHG-related groups associated with the first farmers from Iran (8, 22, 36).


Thus, we combined all early Steppe pastoralist individuals in one group to obtain a more precise estimate for the genetic formation of proto-Yamnaya of ~4,400 to 4,000 BCE (Figure 2). These dates are noteworthy as they pre-date the archeological evidence by more than a millennium (37) and have important implications for understanding the origin of proto-Pontic Caspian cultures and their spread to Europe and South Asia.

Not really.

Like I said, the Yamnaya population was overwhelmingly derived from the Eneolithic peoples of the Eastern European steppe and/or forest steppe. And these Yamnaya-like Eneolithic peoples were spread out across a vast area of Eastern Europe by at least ~4,500 BCE. Some of their genomes have been available for several years, and many more are on the way.

It is possible that the Yamnaya and Afanasievo genotype formed in 4,400-4,000 BCE, but if so, then this was due to mixing between the Eneolithic steppe peoples and nearby European farmers. That's because the difference between the Yamnaya and Eneolithic steppe genotypes is minor (~15%) European farmer admixture in the former.

The really interesting puzzle is exactly where and when the peculiar Eneolithic steppe genotype came into being. Any ideas Dr Patterson?

See also...

Matters of geography

Understanding the Eneolithic steppe

Tuesday, January 18, 2022

Mistaken identity?

Ancient Bohemian I20509 is dated to 400-200 BCE, or the La Tene period, in Patterson et al. 2021 (see here). However, he belongs to Y-chromosome N-L550 and is most similar to northern Swedes in my Global25 analysis. So I reckon he's a Swedish soldier who may have died during the Thirty Years' War. In any case, he seems to be a lot younger than the La Tene period, so, for now, I've labeled him CZE_IA_La_Tene_oFennoscandian in the Global25 datasheets (see here).

See also...

They came, they saw, and they mixed

Tuesday, January 11, 2022

Population genetics is a state of mind

Years of blogging about population genetics has seriously eroded my faith in the peer review process.

During the past decade I've witnessed an inordinate amount of crap published in basically all of the major science journals. Often the work is misguided in some way, sometimes even quite strange, and occasionally outright wrong.

Back in 2014, a team of scientists from the UK published a paper in Science emphatically titled A Genetic Atlas of Human Admixture History. These people were Garrett Hellenthal, George B. J. Busby, Gavin Band, James F. Wilson, Cristian Capelli, Daniel Falush, and Simon Myers. See here.

The thing that really sticks out for me in this paper is Figure 3, which shows the present-day Polish population as largely a mixture between Northern European- and Turkish-related ancestries. Incredibly, the Turkish-related ratio appears to be about 25% and dated to 438 CE.

This is not just inexplicable, but utterly wrong. It's a result that is impossible to reproduce with any standard population genetics methods.

In fact, in terms of deep ancient ancestry, present-day Poles are very similar to present-day Scandinavians, and even to Viking Age, Iron Age and Bronze Age Scandinavians. This is easy to demonstrate, for instance, with f4-statistics, in part based on samples from the Hellenthal et al. paper.

Chimp Yamnaya_Samara Swedish_modern Polish_modern -0.000311 -1.574
Chimp Yamnaya_Samara Ollsjo_Bronze_Age Polish_modern -0.000044 -0.152
Chimp Yamnaya_Samara Sealand_Iron_Age Polish_modern -0.000072 -0.293
Chimp Yamnaya_Samara Sealand_Viking_Age Polish_modern 0.000078 0.525
Chimp Yamnaya_Samara Gotland_Viking_Age Polish_modern -0.000141 -1.322

Chimp Barcin_N Swedish_modern Polish_modern -0.000318 -1.662
Chimp Barcin_N Ollsjo_Bronze_Age Polish_modern 0.000216 0.798
Chimp Barcin_N Sealand_Iron_Age Polish_modern -0.000023 -0.104
Chimp Barcin_N Sealand_Viking_Age Polish_modern -0.000186 -1.310
Chimp Barcin_N Gotland_Viking_Age Polish_modern 0.000083 0.788

Chimp Karelia_HG Swedish_modern Polish_modern -0.000134 -0.540
Chimp Karelia_HG Ollsjo_Bronze_Age Polish_modern 0.000056 0.162
Chimp Karelia_HG Sealand_Iron_Age Polish_modern 0.000047 0.153
Chimp Karelia_HG Sealand_Viking_Age Polish_modern 0.000424 2.241
Chimp Karelia_HG Gotland_Viking_Age Polish_modern 0.000134 0.959

Simply put, if Poles have ~25% ancestry from a Turkish-related source, then so do Swedes, Norwegians and basically all other Northern Europeans going back hundreds and even thousands of years. This is obviously not the case, and it's also not what Hellenthal et al. claimed anyway.

A year later, a team of scientists that again included Garrett Hellenthal, George B. J. Busby, James F. Wilson, Cristian Capelli and Simon Myers, published another, similar paper in Current Biology. And guess what? This paper also claimed that present-day Poles had Turkish-related ancestry, but this time dating to a somewhat later period. See Busby et al. 2015 Figure 4.C here.

I've got most of the samples from that paper, so I can analyze them myself, and I think I know what the problem is. Basically, the Turks are mixed. So what appears to have happened is that Busby et al. got things backwards.

Below are three plots from a Principal Component Analysis (PCA) largely based on data from Busby et al., featuring samples from England, Germany, Norway, Poland and Turkey. The first plot is based on dimensions 1 and 2, the second plot on dimensions 1 and 3, and the third plot on dimensions 1 and 4. The relevant data file is available here.

Note that the Europeans are more or less symmetrically related to the Turks, which means none of these European populations has significantly more Turkish-related ancestry than the others. Indeed, it's the Turks who show more variation in the first (horizontal) dimension, suggesting that they might have variable levels of European ancestry.

I chose the aforementioned papers to make my point here because they made quite an impression on me. In other words, they really pissed me off.

For the sake of completeness, I'm now going to try and get in touch with the authors and ask them how on earth they managed to make these Poles Turkish-related, and also why they never corrected their mistake.

See also...

Don't believe everything you read in peer reviewed papers