The Luxembourg sample is similar to the Iberian La Brana samples and the Swedish Mesolithic samples are similar to Swedish Neolithic hunter-gatherers. The LBK farmer is similar to Oetzi and a Swedish TRB farmer and to Sardinians. The authors also study the recently published Mal'ta Upper Paleolithic sample from Lake Baikal and find that it is part of an "Ancient North Eurasian" population that also admixed into West Eurasians on top of the Neolithic/Mesolithic mix.
The authors' proposed model and admixture estimates:
It seems that the estimates go all the way to "almost pure" Early European farmer ancestry but "West European Hunter-Gatherer" and "Ancient North Eurasian" ancestry isn't found unmixed in any modern populations. The model seems to agree with Raghavan et al. that Karitiana are "Mal'ta"-admixed but also finds the most basal Eurasian ancestry in the European Neolithic farmer. The authors write:
The successful model (Fig. 2A) also suggests 44 ± 10% “Basal Eurasian” admixture into the ancestors of Stuttgart: gene flow into their Near Eastern ancestors from a lineage that diverged prior to the separation of the ancestors of Loschbour and Onge. Such a scenario, while never suggested previously, is plausible given the early presence of modern humans in the Levant25, African-related tools made by modern humans in Arabia26, 27, and the geographic opportunity for continuous gene flow between the Near East and Africa28
An interesting finding is that the Luxembourg hunter-gatherer probably had blue eyes (like a Mesolithic La Brana Iberian, a paper on which seems to be in the works) but darker skin than the LBK farmer who had brown eyes but lighter skin. Raghavan et al. did not find light pigmentation in Mal'ta (but that was a very old sample), so with the exception of light eyes that seem established for Western European hunter-gatherers (and may have been "darker" in European steppe populations, but "lighter" in Bronze Age South Siberians?), the origin of depigmentation of many recent Europeans remains a mystery. Ancient DNA continues to surprise at every turn.
UPDATE (4/4/2014): a new version of the preprint.
bioRxiv doi: 10.1101/001552
Ancient human genomes suggest three ancestral populations for present-day Europeans
Iosif Lazaridis et al.
Analysis of ancient DNA can reveal historical events that are difficult to discern through study of present-day individuals. To investigate European population history around the time of the agricultural transition, we sequenced complete genomes from a ~7,500 year old early farmer from the Linearbandkeramik (LBK) culture from Stuttgart in Germany and an ~8,000 year old hunter-gatherer from the Loschbour rock shelter in Luxembourg. We also generated data from seven ~8,000 year old hunter-gatherers from Motala in Sweden. We compared these genomes and published ancient DNA to new data from 2,196 samples from 185 diverse populations to show that at least three ancestral groups contributed to present-day Europeans. The first are Ancient North Eurasians (ANE), who are more closely related to Upper Paleolithic Siberians than to any present-day population. The second are West European Hunter-Gatherers (WHG), related to the Loschbour individual, who contributed to all Europeans but not to Near Easterners. The third are Early European Farmers (EEF), related to the Stuttgart individual, who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model the deep relationships of these populations and show that about ~44% of the ancestry of EEF derived from a basal Eurasian lineage that split prior to the separation of other non-Africans.