On the origin of steppe ancestry in Beaker people (work in progress)

One of the major themes in the recent Bell Beaker Behemoth (ie. Olalde et al. 2018) is the presence of Yamnaya- or steppe-related ancestry in most of the Beaker individuals. Up to a whopping 75% in one guy from what is now Hungary. However, as far as I can see, the authors don’t go into any specifics about the origin of this admixture. This is about as close as they come. Emphasis is mine:

However, migration had a key role in the further dissemination of the Beaker complex. We document this phenomenon most clearly in Britain, where the spread of the Beaker complex introduced high levels of steppe-related ancestry and was associated with the replacement of approximately 90% of Britain’s gene pool within a few hundred years, continuing the east-to-west expansion that had brought steppe-related ancestry into central and northern Europe over the previous centuries.
During the third millennium bc, two new archaeological pottery styles expanded across Europe and replaced many of the more localized styles that had preceded them [1]. The expansion of the ‘Corded Ware complex’ in north-central and northeastern Europe was associated with people who derived most of their ancestry from populations related to Early Bronze Age Yamnaya pastoralists from the Eurasian steppe [2–4] (henceforth referred to as ‘steppe’).

To be honest, I’m not quite sure what they’re saying there. Is it that the steppe ancestry in the Beakers comes from Corded Ware people, one way or another, or that it derives from a later, closely related but separate, population wave from the steppe? Or are they leaving the question wide open for now?
If they are leaving it open, then I’m not surprised. That’s because the only way to solve this mystery is to genotype at least a few hundred Eneolithic and Bronze Age skeletons from the Pontic-Caspian steppe in order to pinpoint the shared steppe homeland, or separate steppe homelands, of the Corded Ware and Beaker peoples. No doubt this will happen eventually, but it might take a few years for us to see the results. In the meantime, we can mess around with the data already available to see what it might reveal in regards to this topic.
Of course, I’m well aware that the Y-haplogroup most closely associated with the Corded Ware expansion is R1a, and in particular its R1a-M417 subclade, and that Beaker males with steppe ancestry almost exclusively belong to Y-haplogroup R1b, especially its R1b-P312 subclade. But this means very little for now, because considering the patchy sampling of ancient remains from Eneolithic/Bronze Age Europe, it’s still possible that, for instance, these Beakers descend from an as yet unsampled subset of the Corded Ware population rich in R1b.
So for now, as we wait for more ancient data, the pertinent question is: are there any genome-wide genetic signals specific to Corded Ware people that are missing in the Beaker people, and vice versa?
One possible way to catch something like this might be to focus on differences in hunter-gatherer (HG) ancestry. That’s because European hunter-gatherers are known to have had low effective populations and, as a result, a lot population-specific genetic drift. I can try to test this idea using the Global25/nMonte method (see here and here) and the following plausible, at least according to me, reference groups and individuals.

Barcin_N (Neolithic farmers from western Anatolia)
Blatterhole_HG (HG-like Middle Neolithic sample from Germany)
Koros_HG (HG-like Early Neolithic sample from Hungary)
Narva_Lithuania (late HGs from the southern Baltic)
Ukraine_Mesolithic (HGs from the North Pontic steppe)
Yamnaya_Samara (Bronze Age herders from the eastern end of the Pontic-Caspian steppe)

First up, the Corded Ware Culture (CWC) people, grouped into five sub-populations, based on geography and chronology:

[1] distance%=2.7491
CWC_Baltic_early
Yamnaya_Samara,81.6
Ukraine_Mesolithic,11.6
Barcin_N,6.8
[1] distance%=2.815
CWC_Baltic
Yamnaya_Samara,43.2
Barcin_N,23.6
Ukraine_Mesolithic,21
Narva_Lithuania,12.2
[1] distance%=1.9983
CWC_Czech
Yamnaya_Samara,61.2
Barcin_N,21.2
Ukraine_Mesolithic,11
Blatterhole_HG,6.6
[1] distance%=2.9738
CWC_Germany
Yamnaya_Samara,64.8
Barcin_N,19.6
Blatterhole_HG,11.8
Narva_Lithuania,2
Ukraine_Mesolithic,1.8
[1] distance%=3.2783
CWC_Sweden
Yamnaya_Samara,60.8
Barcin_N,26.2
Blatterhole_HG,10
Narva_Lithuania,3

I’m pretty happy with these results. They make a lot of sense considering everything that we’ve seen about these samples to date. For instance, CWC_Baltic_early looks like it might have arrived in the Baltic region straight from the North Pontic steppe, which agrees with scientific literature and my earlier analyses (for instance, see here). Note also the exceptionally high Baltic HG signal in CWC_Baltic, which is missing in CWC_Baltic_early, no doubt caused by increasing gene flow from the indigenous Baltic population into the Corded Ware people. Now the Beakers:

[1] distance%=3.0892
Beaker_Britain
Yamnaya_Samara,52.8
Barcin_N,26.8
Blatterhole_HG,17.6
Ukraine_Mesolithic,2.8
[1] distance%=2.3366
Beaker_Central_Europe
Yamnaya_Samara,43.4
Barcin_N,37.2
Blatterhole_HG,16
Ukraine_Mesolithic,3.4
[1] distance%=3.0011
Beaker_The_Netherlands
Yamnaya_Samara,55.4
Barcin_N,24.6
Blatterhole_HG,16.4
Ukraine_Mesolithic,3.6

Again, these clearly are very solid outcomes. But what do they tell us about the relationship between these Beakers and the Corded Ware people? To be honest, I’m not sure. The Narva_Lithuania signal is missing, which might be important, but then again, it’s also missing in CWC_Czech. And now onto the Hungarian Beakers, grouped into three categories:

[1] distance%=1.9191
Beaker_Hungary
Barcin_N,49
Yamnaya_Samara,31.8
Narva_Lithuania,11.4
Blatterhole_HG,6
Ukraine_Mesolithic,1.8
[1] distance%=4.9659
Beaker_Hungary_no_steppe
Barcin_N,76.2
Blatterhole_HG,23.8
[1] distance%=2.4992
Beaker_Hungary_outlier
Yamnaya_Samara,76
Barcin_N,19
Koros_HG,4.4
Blatterhole_HG,0.6

Check out the imposing level of Narva_Lithuania ancestry in Beaker_Hungary. Admittedly, I wasn’t expecting this. Is there a chance that it’s real? I honestly don’t know, but we’ve certainly seen similar signals from Northeastern Europe in later Bronze Age samples from Hungary. On the other hand, Beaker_Hungary_outlier is the guy estimated by Olalde et al. to be as much as 75% steppe-derived. Here he gets a very similar figure of 76% of Yamnaya-like ancestry. Very nice! Finally, here are the Southern European Beakers:

[1] distance%=3.818
Beaker_Iberia
Barcin_N,52.4
Blatterhole_HG,27.6
Yamnaya_Samara,20
[1] distance%=5.4342
Beaker_Iberia_no_steppe
Barcin_N,69
Blatterhole_HG,31
[1] distance%=2.992
Beaker_Northern_Italy
Barcin_N,61.4
Yamnaya_Samara,25
Blatterhole_HG,13.6
[1] distance%=4.8488
Beaker_Northern_Italy_no_steppe
Barcin_N,82.4
Blatterhole_HG,17.6
[1] distance%=4.7903
Beaker_Sicily_no_steppe
Barcin_N,54
Anatolia_ChL,40.2
Blatterhole_HG,5.8
[1] distance%=3.7945
Beaker_Southern_France
Barcin_N,48.4
Yamnaya_Samara,27.8
Blatterhole_HG,20.4
Ukraine_Mesolithic,3.4

It might be worth noting the lack of Narva_Lithuania and almost complete lack of Ukraine_Mesolithic ancestry proportions in these models. If this is not an artifact of the method, and please note that it very well might be, then it perhaps suggests that the steppe ancestors of the Beakers were basically like Samara Yamnaya, and that the northern and eastern Beakers picked up their Narva_Lithuania and/or Ukraine_Mesolithic-related ancestry by mixing with the descendants of the Corded Ware people.
Or not? At the very least, am I on the right track? How can I improve this analysis? Feel free to let me know in the comments.
Also, I should mention that I had to add a sample from Chalcolithic Anatolia (Anatolia_ChL) to the model for Beaker_Sicily_no_steppe to obtain more plausible ancestry proportions and a better statistical fit. It’s intriguing that this type of ancestry is present in this southern Beaker, and missing in all the rest, but we’ve discussed this issue at length already in an earlier thread (see here).
On a related note, Danish linguist Guus Kroonen has a new article with his interpretations of the main findings by Olalde et al., freely available at his Academia.edu page at the link below.
Comments to Olalde et al. 2018 on the Bell Beaker phenomenon
It’s interesting, I think, that he sees two distinct, and indeed “potentially competing”, Indo-European migrations from the steppe, represented by the R1a-rich Corded Ware people and the R1b-P312-rich Beakers.

The identification of two different Y-chromosomal haplogroups deriving from the Steppe/Caucasus area is relevant for the prehistoric formation of the European linguistic landscape. What it implies is that Europe may have been confronted with originally separated networks of different, potentially competing, steppe-derived groups. It is through these cultural networks that Indo-European dialects may have diffused, probably existing alongside now extinct, non-Indo-European languages (cf. Iversen & Kroonen 2017).

See also…
Late PIE ground zero now obvious; location of PIE homeland still uncertain, but…

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