I believe the remains analyzed by Lazardis et al from Motala, Sweden are part of the set discussed in prior archaeological papers such as the one to which I allude further on in this post. (If that isn't the case, then the following comments would not be apropos.)
This group of remains dates to 6.000 B.C. which is very "recent" as far as human history in Europe is concerned, and while it tested positive for SLC24A5, which has reached virtual fixation in Europe with a few minor exceptions (unlike Loschbour and La Brana, which Nobody 1 pointed out) it did not test positive for SLC45A2, which has a north/south cline in Europe, and which in some areas only reaches around 80% levels. The effect of SLC45A2 in explaining differences in pigmentation between African Americans and European Americans has been shown in numerous studies. In Europe, the presence of one ancestral allele on this snp has been tied to the "olive toned" skin phenotype.
Specifically with regard to the Motala samples, I'm not sure that the scientists are sure if the remains are those of people native to that specific area.
See the following media report on one of the latest papers on the remains,
http://www.history.com/news/human-skulls-mounted-on-stakes-found-at-stone-age-burial-site:
"The stakes could have been used for secondary burial rites, in which individuals’ bones were removed from their graves and reinterred after their bodies decomposed, Hallgren said. At least one other Mesolithic site in Sweden bears traces of this tradition."
"Another hypothesis about this macabre practice holds that the skulls belonged to enemies killed in combat, not departed loved ones whose mourners gave them two funerals. Perhaps, Hallgren said, victorious Stone Age warriors mounted the heads of their foes on stakes and carried them home from battle as war trophies. The researchers believe laboratory analysis of the remains might support or rule out this scenario. “Sulphur and strontium isotopes in the bones will give information on whether the skulls represent locals or come from a distant place, and DNA analysis will hopefully elucidate if the interred individuals are related or unrelated strangers,” said Hallgren. “These data will give clues to if the depositions represent secondary burial rituals or trophies of defeated enemies.”
This is the actual academic study. The authors mention that further analysis would be done to see if the samples belonged to people raised in the area, but I haven't been able to find any subsequent studies by the authors. Perhaps if someone has access to Swedish Archaeology Journals they might be able to find something.
http://www.academia.edu/3122672/Mesolithic_skull_depositions_at_Kanaljorden_Motala_Sweden
Personally, it has always seemed to me that mtDNA U2e, for example, was perhaps a more recent addition to the genetic landscape in northeastern Europe and northern Eurasia in general that might have come by way of the Caucasus in the very late Mesolithic. If these people in Motala, for example, originally came from a tribe that traded with groups in the Caucasus, the light skin allele might have entered the areas north of the Caucasus through intermarriage or the taking of captives etc. by tribes that had such contact with the greater Caucasus area. This is pure speculation, of course.
Just as a reminder, numerous studies of pigmentation genes done by looking at the actual runs of alleles finds that SLC24A5 at any rate is relatively recent (from 9-12,000 years ago to 25,000 years ago depending on the mutation rate used) and can be traced to an area somewhere between the Middle East and India.
See Canfield et al...
http://www.g3journal.org/content/3/11/2059.full
The distributions of C11 and its parental haplotypes make it most likely that these two last steps [leading to SLC24A5] occurred between the Middle East and the Indian subcontinent, with the
A111T mutation occurring after the split between the ancestors of Europeans and East Asians.
Of course, the factors affecting the much more recent selective sweep in Europe are an entirely separate issue. I haven't yet seen anything better in terms of a hypothesis than the one which posits a correlation between the new Neolithic diet and levels of UV radiation, but time will tell.
For those who are fascinated by this topic, I think any more clarity is going to depend on getting more ancient DNA samples.
What
I find fascinating is the continued resistance to the idea that ancient Europeans, specifically ancient western Europeans, a la Loschbour and La Brana, might not have had fair skin. All I can tell you, with absolute 100% certainty, is that if a sample was analyzed by the NYPD or the FBI and produced pigmentation alleles like those of Loschbour and La Brana, the authorities would be looking for an African American with blue eyes.