Villabruna cluster =/= Near Eastern migrants

I've been running a lot of Treemix analyses with the samples from the recent Qiaomei Fu et al. paper. And the impression I'm getting is that the authors missed the elephant in the room; the one with R1b painted on its big butt.

Now, it's true that Treemix output can't be used as unambiguous evidence in support of complex models. That's because in the absence of key samples the algorithm can get exceedingly creative in modeling the available data, sometimes to such extremes that the results might seem absurd.

However, when something keeps showing up again and again, even when using somewhat different samples and marker sets, and makes sense in the context of haploid and archaeological data, then at the very least it deserves serious consideration.

Here's a nice Treemix series that more or less captures the meat and potatoes of my many Treemix experiments with the Qiaomei Fu et al. dataset. For the archaeological contexts and other details about these ancient samples see here.

Below is my interpretation of the results:

- Villabruna is a sister clade of the earlier European Vestonice clade, but with significant input from an AfontovaGora3-related North Eurasian population, perhaps one that was living north of the Black Sea after the Kostenki people went the way of the dodo

- Hence, the R1b lineage carried by Villabruna I9030, the individual in this Treemix series, probably comes from the Eurasian steppe

- Kotias, a Caucasus Hunter-Gatherer, is in large part derived from the same North Eurasian population, hence the close relationship between Villabruna and Caucasus Hunter-Gatherers

- Villabruna and/or closely related foragers contributed significant ancestry to Neolithic Anatolians, and thus, indirectly, possibly to all extant Near Eastern and even many African populations

- Kotias is also closely related to Neolithic Anatolians, but probably mostly via a more basal population, perhaps the so called Basal Eurasians, native to the Near East prior to the Villabruna and/or related gene flow across the Near East and parts of Africa

- Present-day East Asians might be ancient hybrids with admixture from the same or very similar North Eurasian population, although as per the above mentioned quirks of Treemix, it's possible that the North Eurasians that contributed ancestry to Villabruna, Caucasus foragers and Eurasian steppe populations were in fact partly East Asian

So basically what I'm seeing are back migrations from Europe and the Eurasian steppe or Siberia to the Near East soon after the Ice Age. Yes, from Europe, although I admit that things can get fuzzy here.

That's because at the time much of the Aegean Sea was dry land, and thus there was no geographic barrier between the European Balkans and Asian Anatolia. The two regions, which might seem very distinct to us today, were basically one. So when I say Europe, I actually mean the ancient landmass now divided between the Balkans and Anatolia.

Or not? Are there any D-stats that we can run to either confirm or debunk my Treemix-based hypothesis? Feel free to post your proposals in the comments and I'll try and run them as soon as possible.

Update 07/05/2016: The plot thickens somewhat. I added MA1 to the line up, and now Villabruna shows minor Kotias-related ancestry. In other words, probably something from the Caucasus. The full series is available in a zip file here.

However, although interesting, this result doesn't change much. In fact, it adds more weight to the argument that Villabruna inherited his Y-chromosome from steppe foragers. That's because if this migration edge was a reflection of gene flow from Anatolia to Europe, I'd expect it to run from the Anatolia Neolithic branch, rather than the Kotias branch.

See also...

Following the mammoth herds?