Outgroups AG3-MA1 Chukchi Dusun Igorot Iran_Neolithic Karitiana Kosipe Kostenki14 Lebbo Levant_Neolithic Mbuti Satsurblia Ust_Ishim Villabruna Samara_Eneolithic:I0122 Anatolia_Chalcolithic 0.070±0.059 Caucasus_HG 0.136±0.050 Eastern_HG 0.794±0.037 chisq 7.964 tail_prob 0.716545 Samara_Eneolithic:I0433 Anatolia_Chalcolithic 0.046±0.065 Caucasus_HG 0.155±0.058 Eastern_HG 0.799±0.038 chisq 7.970 tail_prob 0.715965 Samara_Eneolithic:I0434 Anatolia_Chalcolithic 0.195±0.200 Caucasus_HG 0.238±0.192 Eastern_HG 0.567±0.076 chisq 10.965 tail_prob 0.446237 ... Samara_Eneolithic_merge Anatolia_Chalcolithic 0.082±0.048 Caucasus_HG 0.135±0.042 Eastern_HG 0.783±0.030 chisq 5.610 tail_prob 0.898074 Samara_Eneolithic_merge Caucasus_HG 0.065±0.047 Eastern_HG 0.804±0.025 Iran_Chalcolithic 0.132±0.051 chisq 6.909 tail_prob 0.806405 Samara_Eneolithic_merge Caucasus_HG 0.147±0.033 Eastern_HG 0.797±0.027 Lengyel_LN 0.057±0.036 chisq 7.040 tail_prob 0.795835 Samara_Eneolithic_merge Caucasus_HG 0.105±0.055 Eastern_HG 0.809±0.028 Iran_Late_Neolithic 0.086±0.051 chisq 8.304 tail_prob 0.685822 Samara_Eneolithic_merge Armenia_Chalcolithic 0.130±0.056 Caucasus_HG 0.088±0.043 Eastern_HG 0.782±0.030 chisq 9.121 tail_prob 0.610719 ... Yamnaya_Samara:I0429 (3339-2917 calBCE) Anatolia_Chalcolithic 0.190±0.063 Caucasus_HG 0.277±0.056 Eastern_HG 0.533±0.034 chisq 11.732 tail_prob 0.38412I tried a number of different combinations of reference samples, and the three I settled for produced the best fits and lowest standard errors overall. That doesn't mean they literally show what happened; they're just the best we've got for the time being. The results are very interesting, and perhaps unexpected, with Samara Eneolithic I0434 packing the highest ratio of Anatolia- and Caucasus-related ancestry, and, as per above, almost looking like he could be an early Yamnaya sample. I say perhaps unexpected because this individual belongs to Y-haplogroup Q1a and mitochondrial haplogroup U4a2, so his uniparental markers don't suggest any strong southern affinities. But the result, even though only based on 13527 SNPs, looks robust enough, and it basically matches the Principal Component Analysis (PCA) that I featured in my original post.
Keep in mind that 10434 is the individual that appears to have been whacked over the head a few times and simply thrown into a ditch. Perhaps this suggests that the genetic shift in the Samara region from the Eneolithic to the Bronze Age, which saw the dilution of Eastern Hunter-Gatherer (EHG) ancestry by Anatolian- and Caucasus-related gene flows, was not always a peaceful and migrant-friendly process.