Who's your (proto) daddy Western Europeans?

Considering the increasingly large numbers of paleogenomic samples being released online nowadays, it's no longer practical for me to try to highlight most archaeological cultures and even genetic clusters in my Principal Component Analyses (PCA) of the ancient world. Thus, from now on, I'll be focusing attention in such PCA on the main population shifts that have led to the formation of the modern-day West Eurasian gene pool and genetic substructures, like on the PCA plot below, which includes the new Lipson et al. 2017 data (available at the Reich Lab here).

The relevant PCA datasheet can be gotten here. By grouping several hundred ancient samples into just nine clusters, I'm attempting to highlight four key processes and resulting genetic shifts in Europe, the Near East and Central Asia:

- European forger populations mixing with genetically much more southern early farmers of Near Eastern origin, mostly during the Neolithic, bringing about the total disintegration of the Europe to Siberia Hunter-Gatherer cline

- "Old Europeans" being overrun and largely absorbed by Y-haplogroup R1-rich Kurgan pastoralists from the Pontic-Caspian steppe during the Eneolithic and Bronze Age, leading to the formation of at least one major new cline from the Bronze Age steppe into post-Kurgan expansion Europe

- the ancient Near East "imploding" or becoming significantly more compact in terms of genetic structure, likely due to a variety of major population expansions from the chalcolithic onwards from the eastern and western parts of the Fertile Crescent, as well as probably the Caucasus and Europe (note how the post-Neolithic western Asian cluster stretches out towards Europe)

- fully nomadic and very wide ranging pastoral and warrior cultures dominating the entire Eurasian steppe during the Iron Age, leading to the emergence of progressively more East Asian-admixed populations from west to east across the Eurasian steppe

An interesting outcome of the denser sampling from space and time in West Eurasia is that Y-haplogroup R1b, once so elusive in the ancient DNA record, is now popping up all over the place. The new Lipson et al. dataset, for instance, includes two R1b "Old Europeans" from Blatterhole in Germany dated to the Middle Neolithic. Below is the same PCA as above except with all of the ancients belonging to R1b marked with an X. The two Blatterhole samples are sitting in the largely empty space between the European/Siberian Hunter-Gatherer cline and most of the "Old Europe" cluster. The relevant PCA datasheet is available here.

So it may seem that we're back to square one in the long running effort to pinpoint the origin of Y-haplogroup R1b-L51, which encompasses almost 100% of modern-day Western European R1b lineages, and thus probably ranks as Europe's most common Y-haplogroup. But at this stage I'd say no, because R1b-L51 is a subclade of R1b-M269, of which the oldest sample comes from the Bronze Age steppe. In fact, as can be seen in the above PCA, this sample is sitting in exactly the right spot to be one of those pastoralists who overran "Old Europe", or at least a very close relative thereof.

Or am I wrong? Feel free to let me know in the comments.

I didn't bother creating a similar plot of ancient samples belonging to Y-haplogroup R1a, because, unlike R1b, this marker is still non-existent in samples from outside of Eastern Europe and Siberia dating to before the late Neolithic. And I doubt that this is simply due to a lack of the right ancient material. Moreover, the recent discovery of Y-haplogroup R1a-M417, which encompasses almost 100% of all modern-day R1a lineages on the planet, in a North Pontic steppe sample belonging to the Eneolithic Sredny Stog culture means that it's game over for the naysayers as far as the steppe origin of most modern-day R1a lineages is concerned (see here and here).

In other words, if you're still hoping to see R1a, and especially R1a-M417, pop up in non-steppe derived ancient individuals in, say, such far away places as South Asia, then you'll probably be waiting forever.

For the linguistic implications of all of this, see...

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...

Update 15/11/2017: After a couple of days of messing around with the Lipson et al. dataset, I'm certain that Late Copper Age sample Protoboleraz_LCA I2788 shows significant steppe-related admixture. This is the only sample from Lipson et al. with such an obvious signal of steppe-related input that had enough data to be analyzed individually by me with PCA and D-stats.

For the time being, amongst the best proxies for this signal appear to be Yamnaya_Samara and Samara_Eneolithic. But it's likely that the real source of the admixture is yet to enter the ancient DNA record, or at least my dataset. When it does, it'll probably be an Eneolithic pastoralist population from the North Pontic steppe.

Yamnaya_Samara also gives the best statistical fit as the single source population in qpAdm (see here). It's an important result, because it suggests that steppe peoples very similar to Yamnaya were already expanding on and out of the steppe as far back as ~3500 BCE, and perhaps a few hundred years earlier.

See also...

Migration of the Bell Beakers—but not from Iberia (Olalde et al. 2018)