These are very blunt tools looking at total affinity to very ancient population groups.Going by IBD analysis there are differences within Europe in terms of substructure..
Ralph and Coop et al
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001555
"One of the striking patterns we see is the relatively high level of sharing of IBD between pairs of individuals
across eastern Europe, as high or higher than that observed within other, much smaller populations. This is consistent with these individuals having a comparatively large proportion of ancestry drawn from a relatively small population that expanded over a large geographic area. The “smooth” estimates of
Figure 4 (and more generally
Figures 5 and
S17) suggest that this increase in ancestry stems from around 1,000–2,000 ya, since during this time pairs of eastern individuals are expected to share a substantial number of common ancestors, while this is only true of pairs of noneastern individuals if they are from the same population. The eastern populations with high rates of IBD are highly coincident with the modern distribution of Slavic languages, so it is natural to speculate that much of the higher rates were due to this expansion."
"On the other hand, we find that
France and the
Italian and
Iberian peninsulas have the lowest rates of genetic common ancestry in the last 1,500 years (other than Turkey and Cyprus), and are the regions of continental Europe thought to have been least affected by the Slavic and Hunnic migrations. These regions were, however, moved into by Germanic tribes (e.g., the Goths, Ostrogoths, and Vandals), which suggests that perhaps the Germanic migrations/invasions of these regions entailed a smaller degree of population replacement than the Slavic and/or Hunnic, or perhaps that the Germanic groups were less genealogically cohesive. This is consistent with the argument that the Slavs moved into relatively depopulated areas, while Gothic “migrations” may have been takeovers by small groups of extant populations
[54],
[55].
In addition to the very few genetic common ancestors that Italians share both with each other and with other Europeans, we have seen significant modern substructure within Italy (i.e.,
Figure 2) that predates most of this common ancestry, and estimate that most of the common ancestry shared between Italy and other populations is older than about 2,300 years (
Figure S16). Also recall that most populations show no substructure with regards to the number of blocks shared with Italians, implying that the common ancestors other populations share with Italy predate divisions within these other populations. This suggests significant old substructure and large population sizes within Italy, strong enough that different groups within Italy share as little recent common ancestry as other distinct, modern-day countries, substructure that was not homogenized during the migration period. These patterns could also reflect in part geographic isolation within Italy as well as a long history of settlement of Italy from diverse sources.
In contrast to Italy, the rate of sharing of IBD within the Iberian peninsula is similar to that within other populations in Europe. There is furthermore much less evidence of substructure within our Iberian samples than within the Italians, as shown in
Figure S2. This suggests that the reduced rate of shared ancestry is due to geographic isolation (by distance and/or the Pyrenees) rather than long-term stable substructure within the peninsula."
Unfortunately, they didn't go into great detail about the Germans. As to them, I think I would tend to agree with Fire Haired's speculations. Also, this doesn't specifically address how much substructure there is in France compared to Germany or compared to Spain. The amount of substructure in Italy is of another order. They go into detail about it in the paper.
