Piedmont Ancestry in Chalcolithic West Asia (It’s not just Armenia)

Thanks to Skourtanioti et al , 2020, We now have samples that can help to fill in the picture of how populations in West Asia formed. Some of the most important, in my opinion, are the Halaf-era samples from Tell Kurdu and the Shulaveri-Shomu individuals from Azerbaijan. These were a couple of the important groups yet to be seen.

One of the interesting individuals is ART038, a Chalcolithic individual from Arslantepe. The interesting part of this individual is that they are R1b-V1636. While the paper does not delve into this individual much or look at complex models, I wanted to double check on this myself.

First things was to make sure that it was Halaf (Tell Kurdu) and not another group like Buyukkaya_EC that delivered the Anatolian ancestry. Several different looks at this in qpAdm confirmed for me that the Chalcolithic of Eastern Anatolia and the Caucasus required excess Levant PPN ancestry found in the Tell Kurdu individuals.

To flesh out any Piedmont ancestry and the different streams such as CHG and Iranian, I used the Late Neolithic individual from Ganj Dareh in the left pops (pleft) and Meshoko, with Ganj Dareh in the right pops, or outgroups (pright). The populations in the pright are Chimp, Ust_Ishim, Kostenki14, Brazil_LapaDoSanto_9600BP, Yana, WHG, EHG, Tianyuan, Mongolia_N_North, Taiwan_Hanben, West_Siberia_N, Levant_N, Ganj_Dareh_N, IBM, Barcin_N and Meshoko. This group allowed for the best resulting outputs.

Not only did I look to see if EHG or Piedmont ancestry is in these Chalcolithic samples, but even in the Late Neolithic Shulaveri-Shomu. Interestingly enough, they can be modeled with minor ancestry from a group like the Piedmont Eneolithic.

Shulaveri-Shomu

left pops:

Shulaveri_Shomu

TellKurdu_EC

CHG

Iran_LN

Piedmont_Eneolithic

numsnps used: 286501

best coefficients: 0.617 0.143 0.152 0.087

std. errors: 0.026 0.077 0.047 0.032

fixed pat wt dof chisq tail prob

0000 0 12 6.866 0.866351 0.617 0.143 0.152 0.087

While not completely necessary, Shulaveri Shomu can be modeled as deriving ~9% of their ancestry from the Piedmont.

Armenia Chalcolithic

left pops:

Armenia_ChL

TellKurdu_EC

CHG

Piedmont_Eneolithic

numsnps used: 471814

best coefficients: 0.483 0.226 0.291

std. errors: 0.016 0.029 0.023

fixed pat wt dof chisq tail prob

000 0 13 20.801 0.0769555 0.483 0.226 0.291

Armenia is a bit of an enigma here. It does stand out from the Shulaveri Shomu and Hajji Firuz individuals in that they lack any Iran_LN ancestry. The ancestry there is never larger than the standard error, which was around 6%. It seems that we may not have a great representative for Shulaveri Shomu in Armenia. I also looked to see if adding an Iranian Plateau or Central Asian group would help, but they were small contributions and never above the standard error. So, those models were left out.

Arslantepe Late Chalcolithic

Here, I will include two models. The first, is a minimal failure that does not include Steppe input.

left pops:

Arslantepe_LC

TellKurdu_EC

CHG

Iran_LN

numsnps used: 300549

best coefficients: 0.693 0.220 0.086

std. errors: 0.015 0.038 0.031

fixed pat wt dof chisq tail prob

000 0 13 25.383 0.0205459 0.693 0.220 0.086

This second model includes the Piedmont in the pleft, and is a success. Which may be more parsimonious beings that there is a legitimate steppe lineage there. While R1b-V1636 is certainly old enough to be part of the northern ancestry of CHG and there since the beginning, it is more in-line with data to withhold that assumption for the moment.

left pops:

Arslantepe_LC

TellKurdu_EC

CHG

Iran_LN

Piedmont_Eneolithic

numsnps used: 296251

best coefficients: 0.704 0.082 0.125 0.088

std. errors: 0.015 0.048 0.030 0.021

fixed pat wt dof chisq tail prob

0000 0 12 8.727 0.726049 0.704 0.082 0.125 0.088

Sources

Skourtanioti et al (2020) Genomic History of Neolithic to Bronze Age Anatolia, Northern Levant, and Southern Caucasus. https://www.sciencedirect.com/science/article/abs/pii/S0092867420305092

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