All four of the Estonian CWC individuals could be assigned to the R1a-Z645 sub-clade of hg R1a-M417 which together with N is one of the most common Y chromosome haplogroups in present-day Estonians (33%)  . Importantly, this R1a lineage is only distantly related to the R1a5 lineage we found in the CCC sample. The finding of high frequency of R1a-M417 in Estonian CWC samples is consistent with the observations made for other Corded Ware sites that, along with Late Bronze Age remains associated with Sintashta Culture, also show high frequency of hg R1a-M417 [2,25]. ... The coalescent time for the R1a-Z645 clade, estimated from modern data at 5,400 yr BP (95% CI 4,950–6,000) 43 , predates the time when the CWC individuals carrying the R1a-Z645 lineages lived in Estonia (4,000–4,800 yr BP). The fact that all four of the CWC male individuals from two distinct sites in Estonia belonged to this recently expanded R1a branch, different from the one carried by CCC, suggests that admixture between CWC farmers and CCC hunter-gatherers may have been limited at least in the male lineages during the early stages of farming in Estonia.Now, can anyone explain to me how the authors came to this conclusion? Was it based on their ADMIXTURE output?
Furthermore, the presence of a genetic component associated with Caucasus hunter-gatherers and later with people representing the Yamnaya Culture in Eastern hunter-gatherers and Estonian CCC individuals means that the expansion of the CWC cannot be seen as the sole means for the spread of this genetic component, at least in Eastern Europe.If it is indeed based on ADMIXTURE, then they really need to back it up with some robust formal stats and qpAdm, because ADMIXTURE is not a formal mixture test. Moreover, they used the projection (P) option in their ADMIXTURE analysis. I'm not a huge fan of this option when running fine scale intra-continental analyses, because I find that it usually results in severe projection bias. In other words, the test samples are treated differently from the reference samples, and essentially show results that they shouldn't. Speaking of projection bias, I'm quite certain that their Principal Component Analysis (PCA) suffers from it. The ancient samples look like they're being pulled into the middle of the plot, so much so that one of the foragers basically clusters with modern-day Lithuanians, while the CWC individuals appear too western. They need to fix this. Extensive farming in Estonia started through a sex-biased migration from the Steppe, bioRxiv, March 2, 2017, doi: https://doi.org/10.1101/112714