Yamnaya = Khvalynsk + extra CHG + maybe something else

Thanks to recently published ancient DNA it's now generally accepted that the Yamnaya pastoralists of the Pontic-Caspian Steppe were basically a mixture of Eastern European Hunter-Gatherers (EHG) and Caucasus Hunter-Gatherers (CHG).

However, I thought it might be useful to dig a little deeper with the D-stats/nMonte method to see what else crops up. I put together a special datasheet for the job, with Yamnaya Samara featured both in the rows and columns. It's available for download here. The nMonte R script can be gotten here.

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.

But, to make sure the results weren't erroneous - perhaps skewed by the worryingly high affinity between the two CHG genomes, Kotias and Satsurblia, both pseudo-diploid sequences - I reran the tests using a different version of the same datasheet (available here). In this version, Kotias and Satsurblia are part of a single Caucasus HG sample included in the rows.

Yamnaya_Kalmykia
Khvalynsk 53.95
Caucasus_HG 38.45
Hungary_EN 4.7
Motala_HG 2.9
AfontovaGora3 0
Anatolia_Neolithic 0
Karelia_HG 0
Loschbour 0
MA1 0
Ulchi 0

distance%=1.7492 / distance=0.017492

Yamnaya_Samara
Khvalynsk 56.7
Caucasus_HG 33.55
Hungary_EN 4.25
Loschbour 2.95
Motala_HG 2.55
AfontovaGora3 0
Anatolia_Neolithic 0
Karelia_HG 0
MA1 0
Ulchi 0

distance%=2.0964 / distance=0.020964

Yup, the Hungary EN contributions take a dive. But they're still above noise level (>2%), so they might well represent a real signal that entered the Yamnaya horizon or late Khvalynsk from the west. Can't wait to see how Yamnaya genomes from north of the Black Sea come out.

Update 20/08/2017: It appears that I was onto something. See here.

See also...

Modeling Steppe_EMBA

Yamnaya =/= Eastern Hunter-Gatherers + Iran Chalcolithic

Another look at the genetic structure of Yamnaya