A paper in Current Biology reports on the partial genome sequences of two 7,000-year-old Mesolithic skeletons from a cave in northwestern Spain. It shows that these hunter-gatherer samples fall outside the range of contemporary European genetic variation, but are much more similar to present-day Northern Europeans than Iberians.
They also seem to be closely related to prehistoric hunter-gatherers from as far away as the Baltic region, because like them they belong to mtDNA haplogroup U. That's basically the angle that Science Now has taken in covering the story:
Although the first farmers spread quickly across Europe, trading and exchanging culture across thousands of kilometres, many researchers had assumed that Mesolithic nomadic hunter-gatherers lived in small, isolated bands with little contact over long distances. But the genetic picture, Lalueza-Fox says, suggests "highly mobile" groups that kept in touch and interbred continent-wide.
These are interesting outcomes, because modern-day Northern Europeans, all the way from the Atlantic to the Volga, commonly share a very robust "ancestral" cluster when analyzed with the ADMIXTURE program. This cluster usually peaks in Lithuanians and other Baltic groups, and is difficult to break down (see here). Also, it correlates very well with clusters that peak in Swedish hunter-gatherers analyzed recently by Skoglund et al. (see here). As a result, I have no doubt now that this modern ADMIXTURE cluster is largely of Mesolithic hunter-gatherer origin, and its widespread range in Europe today is at least partly due to the fact that hunter-gatherers from across Europe were very similar genetically.
Unfortunately, the Iberian hunter-gatherers weren't compared to modern-day Lithuanians. Instead, the authors used the samples from the 1000 Genomes Project as references. However, it seems they oversampled the Finns when running their intra-European PCA. This showed clearly that these Finns were different from other Europeans, largely due to fairly recent founder effect and genetic drift, but provided very little information about the hunter-gatherers (marked "Brana" below).
The global PCA was more informative, because it wasn't skewed by the Finns, who were still there, but didn't have enough influence to dominate things at global level. Remarkably, this analysis showed that the prehistoric Iberians were shifted towards both East Asia and Sub-Saharan Africa relative to modern-day Europeans.
However, I suspect that if many more Mesolithic samples were present on that plot, things would look somewhat different. It’s difficult to say how different though. We’ll have to wait and see when more ancient samples come in.
The genetic background of the European Mesolithic and the extent of population replacement during the Neolithic [1,2,3,4,5,6,7,8,9,10] is poorly understood, both due to the scarcity of human remains from that period [11,12,13,14,15,16,17,18] and the inherent methodological difficulties of ancient DNA research. However, advances in sequencing technologies are both increasing data yields and providing supporting evidence for data authenticity, such as nucleotide misincorporation patterns [19,20,21,22]. We use these methods to characterize both the mitochondrial DNA genome and generate shotgun genomic data from two exceptionally well-preserved 7,000-year-old Mesolithic individuals from La Braña-Arintero site in León (Northwestern Spain) . The mitochondria of both individuals are assigned to U5b2c1, a haplotype common among the small number of other previously studied Mesolithic individuals from Northern and Central Europe. This suggests a remarkable genetic uniformity and little phylogeographic structure over a large geographic area of the pre-Neolithic populations. Using Approximate Bayesian Computation, a model of genetic continuity from Mesolithic to Neolithic populations is poorly supported. Furthermore, analyses of 1.34% and 0.53% of their nuclear genomes, containing about 50,000 and 20,000 ancestry informative SNPs, respectively, show that these two Mesolithic individuals are not related to current populations from either the Iberian Peninsula or Southern Europe.
Sánchez-Quinto et al., Genomic Affinities of Two 7,000-Year-Old Iberian Hunter-Gatherers, Current Biology, 28 June 2012 doi: 10.1016/j.cub.2012.06.005