Wasting my time refuting such a study should be unnecessary. Briefly, though, the Barbujani/Chikhi/Dupanloup method generally entails taking a sample of Basques and a sample of Near Easterners and using these as "parental populations" for calculating "Paleolithic" and "Neolithic" "admixture" in various European populations.
Any "admixture" estimate can make only as much sense as the choice of "parental populations". Given our knowledge of genetic variation in Europe, it is nonsensical to use Basques as stand-ins for Paleolithic Europeans in this sort of calculation. This is particularly obvious when we look at the uniparentally inherited loci, which feature prominently in this and other Barbujani/Chikhi papers. Basque men overwhelmingly belong to Y haplogroup R1b--but the phylogeographic evidence says R1b represents far from the totality of Paleolithic European Y chromosomes (which also include, most prominently, hgs R1a1 and I). Barbujani and Chikhi are aware of this evidence, but keep pushing their own bizarre estimates and insisting it is better to ignore phylogeography.
The Basque mtDNA pool seems to be highly fragmented (Alfonso-Sánchez 2008). It's unclear how representative the mtDNA haplogroup profile of a given sample of Basque mtDNA is for Basques in general, much less for all "Paleolithic Europeans".
In truth, the Basque are "little more of a Mesolithic relict than any other European population" (Richards 2003).
In the 2004 paper, Dupanloup et al. stretch a little and throw in a second European parental population for some of their calculations. Their choice: "North-Eastern Europe". Yep. Another set of genetic outliers, from the opposite corner of Europe, who we know from phylogeography are dissimilar from most other Europeans. Makes complete sense. Unsurprisingly, they find:
In general, the estimated contributions from North-Eastern Europe are higher than the African contributions, but they still represent a small component of genetic diversity, accounting for between 10.5% (molecular estimates) and 17.4% (frequency estimates) of the total. Variation among regions is high, and most groups show little or no North-Eastern Europe admixture. The exceptions are Finland and Eastern Europe, where roughly 95% and 50% of the gene pools, respectively, seem to come from North-Eastern European ancestors.
The lesson they take from this?
The main components in the European genomes appear to derive from ancestors whose features were similar to those of modern Basques and Near Easterners, with average values greater than 35% for both these parental populations, regardless of whether or not molecular information is taken into account. The lowest degree of both Basque and Near Eastern admixture is found in Finland, whereas the highest values are, respectively, 70% in Spain and more than 60% in the Balkans.
The authors then switch back to their favored two parental population (Basque / Near Eastern) model.
The Near Eastern contribution is generally high, with a mean of 49.4% across Europe (range: 20.8% in England, 79.0% in the Balkans) when considering molecular information and 54.5% (22.1% in England, 95.6% in Finland) when considering only the frequency of haplotypes. However, there is reason to mistrust the estimates obtained for Finland. Indeed, more than 90% of the alleles observed there seem to have come from North-Eastern Europe (table 3), so its population can by no means be regarded as a hybrid between Basques and Near Easterners (table 4).
You don't say? But the >50% Neolithic Near Eastern estimate for Scandinavia, on the other hand, makes perfect sense.
The authors have discovered that, stunningly, Spaniards tend to be similar to Basques, Finns tend to be similar to North-Eastern Europeans, and those from the Balkans tend to be similar to Near Easterners. Choose a parental population from Central or Northern Europe, and you will find, amazingly, that Central Europeans are most similar to Central Europeans and Northern Europeans are most similar to Northern Europeans. Apart from demonstrating the obvious, the calculations in this paper are meaningless.
Alfonso-Sánchez et al. 2008. Mitochondrial DNA haplogroup diversity in Basques: A reassessment based on HVI and HVII polymorphisms. Am J Hum Biol. Mar-Apr;20(2):154-64.
Dupanloup et al.. 2004. Estimating the impact of prehistoric admixture on the genome of Europeans. Mol Biol Evol. Jul;21(7):1361-72. Epub 2004 Mar 24.
Richards, Martin. 2003 The Neolithic invasion of. Europe. Annual Review of Anthropology. 32, 135-62.