The Swedish hunter-gatherers appear to be similar to those of Lazaridis et al. (2013) in that their ancestry is a mixture of both European hunter-gatherers like LaBrana1 and ~15% of something related to MA1, which seems quite close to the 19% of ANE ancestry for the older Motala hunter-gatherer also from Sweden. The finding of Y-haplogroup I2a1 also parallels the Motala hunter-gatherers, so everything seems quite consistent with the Mesolithic Swedes being genetically very close to the Pitted Ware Neolithic ones. However, there is one difference in that the new hunter-gatherers were ancestral for SLC24A5 while the Motala one was derived (this is the "skin lightening" allele that was curiously missing in both Iberia and Luxembourg hunter-gatherers).
The authors also find that the Iceman and Gökhem2 are a mixture of Basal Eurasians and something related to hunter-gatherers. A interesting new detail is that the Swedish farmer had more of the hunter-gatherer ancestry than the Iceman (the estimated difference in their non-Basal Eurasian ancestry is 77.2-56=21.2%) which seems reasonably close to the 16% difference in the related "Atlantic_Baltic" ancestry for the previous lower-quality Gok4 farmer and the Iceman I estimated in 2012.
The Scandinavian Neolithic hunter-gatherer group had significantly lower conditional nucleotide diversity (0.181±0.0015) compared to the Scandinavian Neolithic farmer group (0.201±0.0038, Figs 3A and S9). While the specific properties of ancient DNA may still affect comparisons with sequence data from modern-day individuals, the conditional nucleotide diversity in the hunter-gatherers was also lower than in any modern-day European and a Chinese population (22) analyzed using the same approach as for the ancient groups.It is not easy to estimate nucleotide diversity with low coverage data (because you can't tell whether a sample is heterozygous in some position if you only have a handful of reads covering it), but the authors cleverly use the fact that they have multiple individuals from the hunter-gatherer population to estimate this. The low diversity in hunter-gatherers also parallels the finding of low genetic diversity in the Luxembourgeois Mesolithic hunter-gatherer, so it does seem that hunter-gatherers in Europe were a very low diversity population, which seems reasonable for people engaging in foraging (which does not allow for growth to large population numbers) and having ancestors who endured the Ice Age in Europe.
The last few months have been extremely generous in new ancient DNA studies and I hope that more stuff is coming this year as in 2013.
UPDATE: Also important (from the Independent):
“We see clear evidence that people from hunter-gatherer groups were incorporated into farming groups as they expanded across Europe. This might be clues towards something that happens also when agriculture spread to other parts of the world,” Dr Skoglund said.
Science DOI: 10.1126/science.1253448
Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers
Pontus Skoglund, Helena Malmström et al.
Prehistoric population structure associated with the transition to an agricultural lifestyle in Europe remains contentious. Population-genomic data from eleven Scandinavian Stone-Age human remains suggest that hunter-gatherers had lower genetic diversity than farmers. Despite their close geographical proximity, the genetic differentiation between the two Stone-Age groups was greater than that observed among extant European populations. Additionally, the Scandinavian Neolithic farmers exhibited a greater degree of hunter-gatherer-related admixture than that of the Tyrolean Iceman, who also originated from a farming context. In contrast, Scandinavian hunter-gatherers displayed no significant evidence of introgression from farmers. Our findings suggest that Stone-Age foraging groups were historically in low numbers, likely due to oscillating living conditions or restricted carrying-capacity, and that they were partially incorporated into expanding farming groups.