A new version of the Lazaridis et al. ancient genomes preprint has just appeared at arXiv (see here). It includes several new Principal Component Analyses (PCA), TreeMix graphs, a ChromoPainter/fineSTRUCTURE co-ancestry matrix, and an updated ADMIXTURE analysis. The revised text underlines the relatively close genetic relationship between indigenous European hunter-gatherers and present-day Eastern Europeans:
The co-ancestry matrix (Fig. S19.3) confirms the ability of this method to meaningfully cluster individuals. We highlight two clusters: Stuttgart joins all Sardinian individuals in cluster A and Loschbour joins a cluster B that encompasses all Belarusian, Ukrainian, Mordovian, Russian, Estonian, Finnish, and Lithuanian individuals. These results confirm Sardinia as a refuge area where ancestry related to Early European Farmers has been best preserved, and also the greater persistence of WHG-related ancestry in present-day Eastern European populations. The latter finding suggests that West European Hunter-Gatherers (so-named because of the prevalence of Loschbour and La Braña) or populations related to them have contributed to the ancestry of present-day Eastern European groups. Additional research is needed to determine the distribution of WHG-related populations in ancient Europe.
Fig. S10.5 suggests that the main axis of differentiation in Europe when the subcontinent is considered as a whole may tend to Northeastern Europe rather than SSE/NNW (8). This is consistent with our analysis of ancestry proportions in European populations (Fig. 2B, Extended Data Table 3) which indicate a cline of reduced EEF (and increasing WHG) ancestry along that direction.
Iosif Lazaridis, Nick Patterson, Alissa Mittnik, et al., Ancient human genomes suggest three ancestral populations for present-day Europeans, arXiv, April 2, 2014, arXiv:1312.6639v2