Genetic and archaeological continuity from Khvalynsk to Yamnaya

Over a year ago, using the D-stats/nMonte method of mixture modeling (see here), I noticed that Yamnaya did not appear to be simply a two-way mixture between Eastern European and Caucasus Hunter-Gatherers (EHG and CHG, respectively), but the result of a much more complex process:

Using the most plausible reference samples currently available - almost all of them older than Yamnaya, and thus unlikely to skew the results with Yamnaya admixture - reveals the following models for the two Yamnaya sets from Kalmykia and Samara, respectively.

Yamnaya_Kalmykia
Khvalynsk 57.7
Kotias 28.3
Hungary_EN 12.9
Ulchi 1.1
AfontovaGora3 0
Anatolia_Neolithic 0
Karelia_HG 0
Loschbour 0
MA1 0
Motala_HG 0

distance%=1.9125 / distance=0.019125

Yamnaya_Samara
Khvalynsk 56.75
Kotias 26.4
Hungary_EN 10.85
Karelia_HG 4.4
Loschbour 1.6
AfontovaGora3 0
Anatolia_Neolithic 0
MA1 0
Motala_HG 0
Ulchi 0

distance%=2.1354 / distance=0.021354

Very interesting but hardly surprising. Essentially what we're seeing there is potentially very strong genetic continuity from the Eneolithic to the Early Bronze Age on the Pontic-Caspian Steppe. In other words, from Khvalynsk to Yamnaya.

However, at some point between the Eneolithic and the Early Bronze Age, the steppes saw a major influx of extra CHG, represented by the ~27% of Kotias-related admixture. Considering the relevant uniparental data, with lots of Y-HG R1b and no Y-HG J among Yamnaya males, I'd say this CHG came with women.

Also, the relatively high admixture related to early Hungarian Plain farmers (Hungary EN) is a fairly curious detail that has not been reported before. If real, it probably represents gene flow from the Neolithic and/or Chalcolithic Balkans to the Pontic-Caspian Steppe. Again, in all likelihood it mostly came with women, perhaps from Tripolye-Cucuteni and/or Varna communities.

The reason I mention this now is because I can reproduce basically the same model using the updated qpAdm methodology described recently in Lazaridis et al. 2017, which relies on a relatively large number (≥16) of ancient genomes/populations as outgroups (see here), and, in my experience, causes many formerly successful models to fail miserably (the taildiff dives from >0.05 to <0.05). Note that in my dataset Khvalynsk is now labeled Samara_Eneolithic, Kotias as CHG, and Hungary_EN as Hungary_N.

Yamnaya_Kalmykia
CHG 0.334±0.044
Hungary_N 0.115±0.031
Samara_Eneolithic 0.550±0.032
taildiff: 0.419775785
chisq: 13.368
Full output

Yamnaya_Samara
CHG 0.267±0.040
Hungary_N 0.130±0.027
Samara_Eneolithic 0.603±0.030
taildiff: 0.300777879
chisq: 15.106
Full output

Here's a formerly successful model in which Steppe_EMBA (a grouping which includes Afanasievo, Poltavka, Russia_EBA and Yamnaya) is posited as a mixture between EHG and Chalcolithic farmers from the Zagros Mountains in what is now Iran. It clearly fails when I use CHG as one of the outgroups.

Steppe_EMBA
EHG 0.544±0.020
Iran_ChL 0.456±0.020
taildiff: 0.00279643007
chisq: 31.553
Full output

vs.

Steppe_EMBA
CHG 0.310±0.034
Hungary_N 0.121±0.023
Samara_Eneolithic 0.568±0.025
taildiff: 0.50194795
chisq: 12.316
Full output

Now, tight statistical fits are great, but they don't always reflect reality, especially when fine scale genetic structure is being tested. So does my model have any support from archeology? In other words, does archaeological data show continuity between Khvalynsk and Yamnaya (Pit-Grave culture)? According to Morgunova and Turetskij 2016 it does. Emphasis is mine:

Abstract: The aim of the paper is to provide the research results concerning the Pit-Grave culture sites of the south Ural region, which is a part of the Volga-Ural interfluve. The Pit-Grave culture developed mostly out of the Khvalynsk Eneolithic culture at the turn of the 5th–4th millennium cal BC. People of the Sredny Stog and forest-steppe Eneolithic cultures from the Middle Volga region also influenced the Pit-Grave culture. The paper considers the radiocarbon data (more than 120 dates), specifies the periodization of the Pit-Grave culture of the Volga-Ural interfluve, singles out the three stages of its development. The chronology of the culture is determined 3900–2300 cal BC. The authors provide new information about the Pit-Grave economy. Paleopedology, palynology, anthropology, metallography, ceramic technical, and technological analyses were used together with archaeological methods to make a more detailed description of the culture.

...

A number of steppe Eneolithic features remained at the Repin stage. The cultural continuity between the Pit-Grave, Khvalynsk, and Sredny Stog Eneolithic cultures was proved by the following features: skeletons in crouched supine position with bent legs to the left or to the right, heads at the eastern sector of burials, ochre coverage with high or low density, multiple burials, egg-shaped ceramics with neck and crushed shell impurity. Technical and technological analysis of pottery was another evidence demonstrating the pottery continuity between the Khvalynsk and Repin traditions (Vasilyeva 2002; Salugina 2005). Big soil burial grounds were substituted by individual burials under the barrow. The spread of local production copper articles was a distinctive feature of the Pit-Grave culture. This was the phenomenon, which archaeologists consider to be the beginning of the Early Bronze Age in steppe of Eastern Europe.

Morgunova N. and Turetskij M., Archaeological and natural scientific studies of Pit-Grave culture barrows in the Volga-Ural interfluve, Estonian Journal of Archaeology, Vol. 20, Issue 2, doi: 10.3176/arch.2016.2.02

See also...

Another look at the genetic structure of Yamnaya