It's usually not a good idea to try and force people who've been dead for thousands of years into analyses based on modern genetic variation. However, that's what I've done here by running 20 of what I consider the most interesting samples from the freshly published Haak et al. 2015 paper with the Eurogenes K15 and 4A Oracle.
My experience is that the K15 is an excellent tool for exploring ancient genomes, and I think it's done a great job here. Below are a few of my observations based on the output:
- the best two-way mixture model for the Yamnaya genomes, from the Samara region near the Russo-Kazakh border, is Samara_HG/Tabassaran, rather than Karelia_HG/Armenian as per Haak et al. (see discussion below)
- far Eastern Europeans like Volga Tatars and Finns are the most similar modern populations to these Yamnaya samples, which makes good sense considering uniparental marker data and geography (for instance, see this map posted by Richard recently in the comments)
- the unusually high Amerindian and South Asian ancestry proportions among the Yamnaya genomes are very likely the result of their extreme levels of Ancient North Eurasian (ANE) ancestry, estimated by me with the West Eurasia K8 to be around 35%
- the German Bell Beaker sample appears to be a complex mixture of populations from several different parts of Europe, including the Yamnaya horizon, so based on this data it's impossible to pinpoint the main geographic source of the Bell Beaker population expansion, if indeed there was such a source
- three out of the four German Corded Ware genomes are obviously of mixed origin, presumably between Corded Ware migrants from Eastern Europe and earlier middle Neolithic inhabitants of North-Central Europe, but still largely of Yamnaya or very similar ancestry
- Eastern European foragers Karelia_HG and Samara_HG don't show any hints of Near Eastern admixture
I'll post the K8 ancestry proportions for the same 20 ancient genomes in a couple of days. A lot of people will probably be surprised by the results of the Yamnaya samples. Not only do they show unusually high levels of ANE, but also only around 25% of Near Eastern or Early Neolithic Farmer (ENF) ancestry.
Admittedly, these results are somewhat at odds with the findings of Haak et al., who were able to fit the Yamnaya as 50/50 Karelia_HG/present-day Armenian or Iraqi Jewish. Well, this might be a statistically valid fit, but I'm simply not seeing any obvious connection between Armenians or Iraqi Jews and the Yamnaya samples.
As per above, a more sensible solution appears to be Samara_HG/Tabassaran, but based on the K8 output I'd say an even better solution would be to model the Yamnaya as a three-way mixture between Eastern European foragers, early Neolithic farmers straight from the Near East, and perhaps some sort of Central Asian population very similar to the main ANE-proxy MA-1 or Mal'ta boy. But more on that later.
Update 04/03/2015: I've also now analyzed most of the early and middle Neolithic samples from Haak et al. (see here). The results clearly suggest that a profound genetic shift took place in Germany from the middle to the late Neolithic.
Haak et al., Massive migration from the steppe was a source for Indo-European languages in Europe, Nature, Advance online publication, doi:10.1038/nature14317
Fitting the Yamnaya with qpAdm