Alexey Nikitin: Interpreting the genetic ancestry of the first kurgan builders

Click on the image below to view the talk. Thoughts?

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Dear David, Nick, Iosif...let me tell you about Yamnaya

Dear Harald...

I've started analyzing the Identity-by-Descent (IBD) data from the recent Ringbauer et al. preprint (see here). Unfortunately, it'll take me a few weeks to do this properly, so I won't be able to write anything detailed on the topic for a while.

Meantime, this is the comment that I left for the authors at bioRxiv (at this time it's still being approved, but it should appear there within a day or so, possibly along with a reply from the authors):

Hello authors,

Thanks for the interesting preprint and data. However, I'd like to see you address a couple of technical issues and perhaps one theoretical issue in the final manuscript:

- the output you posted shows some unusual results, which are potentially false positives that appear to be concentrated among the shotgun and noUDG samples. I'm guessing that this is due to the same types of ancient DNA damage creating IBD-like patterns in these samples. If so, isn't there a risk that many or even most of the individuals in your analysis are affected by this problem to some degree, which might be skewing your estimates of genealogical relatedness between them?

- many individuals from groups that have experienced founder effects, such as Ashkenazi Jews, appear to be close genetic cousins, even though they're not genealogical cousins. Basically, the reason for this is reduced haplotype diversity in such populations. Have you considered the possibility that at least some of the close relationships that you're seeing between individuals and populations might be exaggerated by founder effects?

- thanks to ancient DNA we've learned that the Yamnaya phenomenon isn't just an archeological horizon, but also a closely related and genetically very similar group of people. Indeed, in my mind, ancient DNA has helped to redefine the Yamnaya concept, with Y-chromosome haplogroup R1b-Z2103 now being one of the key traits of the Yamnaya identity. So considering that the Corded Ware people are not rich in R1b-Z2103, and even the earliest Corded Ware individuals are somewhat different from the Yamnaya people in terms of genome-wide genetic structure, it doesn't seem right to keep claiming that the Corded Ware population is derived from Yamnaya. I can't see anything in your IBD data that would preclude the idea that the Corded Ware and Yamnaya peoples were different populations derived from the same as yet unsampled pre-Yamnaya/post-Sredny steppe group.

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On the origin of the Corded Ware people

Dear David, Nick, Iosif...let me tell you about Yamnaya

Lazaridis, Alpaslan-Roodenberg et al. recently claimed that the Yamnaya people of the Pontic-Caspian (PC) steppe carried "substantial" ancestry from what is now Armenia or surrounds.

However, this claim is essentially false.

Only one individual associated with the Yamnaya culture shows an unambiguous signal of such ancestry. This is a female usually labeled Ukraine_Yamnaya_Ozera_o:I1917. The "o" suffix indicates that she is an outlier from the main Yamnaya genetic cluster.

Unlike I1917, typical Yamnaya individuals carry a few per cent of ancient European farmer admixture. This ancestry is only very distantly Armenian-related via Neolithic Anatolia (see here).

It's difficult for me to understand how Lazaridis, Alpaslan-Roodenberg et al. missed this. I suspect that they relied too heavily on formal statistics and overinterpreted their results.

Formal statistics are a very useful tool in ancient DNA work. Unfortunately, they're also a relatively blunt tool that often has problems distinguishing between similar sources of gene flow.

There are arguably better methods for studying fine scale ancestry, such as Principal Component Analysis (PCA).

Below is a somewhat special PCA featuring a wide range of ancient populations that plausibly might be relevant to the genetic origins of the Yamnaya people. Unlike most PCA with ancient samples, this PCA doesn't rely on any sort of projection, so that all of the actors are interacting with each other and directly affecting the outcome.

Here's another version of the same plot with a less complicated labeling system. Note that I designed this PCA specifically to differentiate between European populations and those from the Armenian highlands, the Iranian plateau and surrounds.

And here's a close up of the part of the plot that shows the Yamnaya cluster. This cluster is made up of samples associated with the Afanasievo, Catacomb, Poltavka and Yamnaya cultures. All of the individuals in this part of the plot are closely related, which is why they're so tightly packed together. The differentiation between them is caused by admixture from different groups mostly from outside of the PC steppe.

The Yamnaya cluster can be broadly characterized as a population that formed along the genetic continuum between the Eneolithic groups of the Progress region and Neolithic foragers from the Dnieper River valley (Progress_Eneolithic and Ukraine_N, respectively). However, this cluster also shows a slight western shift that is increasingly more pronounced in the Corded Ware samples. This shift is due to the aforementioned admixture from early European farmers.

Indeed, the plot reveals two parallel clines extending west from the Progress samples. One of the clines is made up of the Yamnaya cluster and the Corded Ware samples, and pulls towards the ancient European farmers. The other cline includes Ukraine_Yamnaya_Ozera_o:I1917 and pulls towards samples from the Armenian highlands and surrounds.

Being aware of these two clines and knowing how they came about is important to understanding the genetic prehistory of the PC steppe and indeed of much of Eurasia.

At some point, probably during the late Eneolithic, a Progress-related group experienced gene flow from the west and became the Yamnaya and Corded Ware populations. Sporadically, admixture from the Armenian highlands and the Iranian plateau also entered the PC steppe, giving rise to people like the Steppe Maykop outliers and Ukraine_Yamnaya_Ozera_o:I1917.

Unfortunately, this sort of PCA doesn't offer output suitable for mixture modeling, basically because the recent genetic drift shared by many of the samples creates significant noise.

However, to check that my inferences based on the plot are correct I can create composites with specific ancestry proportions to see how they behave. In the plot below Mix1 is 80% Progress_Eneolithic and 20% Iran_Hajji_Firuz_N, Mix2 is 80% Progress_Eneolithic and 20% Armenia_EBA_Kura_Araxes, while Mix3 is 80% Progress_Eneolithic, 15% Ukraine_N and 5% Hungary_MN_Vinca (Middle Neolithic farmers from the Carpathian Basin).

Obviously, we can't get Yamnaya by mixing Progress_Eneolithic with any ancients from the Armenian highlands or the Iranian plateau. On the other hand, Mix3 works quite well, at least in the first two dimensions. In some of the other dimensions genetic drift specific to Ukraine_N pulls it away from the Yamnaya cluster, but this is to be expected.

By the way, the plots were created with the excellent Vahaduo Custom PCA tool freely available here. It's well worth trying the interactive 3D option using my PCA data. The relevant datasheet is available here.

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

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

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

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

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

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

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

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

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

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

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

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

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

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Trying to catch up

For starters, I need population labels for many of these G25 coords:

Koptekin et al. 2022

Peltola et al. 2022

Skourtanioti et al. 2023

Varela et al. 2023

Wang et al. 2023

Yu et al. 2023

I'll be running more samples later this week, and I'll need help in organizing them for the G25 datasheets. See comments below for more details.