The American Journal of Human Genetics has an article up examining population substructure within Europe (or, more precisely, the varation of genes), Measuring European Population Stratification with Microarray Genotype Data. From the discussion:
PC1 [the largest principle component of variance] largely separates northern from southeastern individuals…and is consistent with the clines observed in classic gene-frequency…Y-chromosome…mtDNA…and whole-genome…studies of European diversity. PC2 [the second largest principle component of variance] reflects mainly east-west geographic separation and, particularly, identifies the two Iberian populations (Spanish and Basques) in our analysis as distinct…Furthermore, PC3 and PC4 emphasize the separation of the Basques and Finns, respectively, from other Europeans…The Basques are known to have unusual allele frequencies for several marker systems…and speak a unique non-Indo-European language. In line with their non-Indo-European Uralic language and previous study of their Y-chromosomesthe Finns show evidence of an increased affinity to the Central Asian populations when placed in an intercontinental context (fig. 1A and 1B)…STRUCTURE analysis of the European populations is highly consistent with PCoA; for example, when the number of populations (K) is 3, the major divisions correspond to the northern, southeastern, and Iberian populations (fig. 4B). In cases of higher K values, first the Finns (K = 4) and then the Basques (K = 5) emerge as distinctive….
The southeast-north cline that they speak of is straight out of L.L.Cavalli-Sforza’s History and Geography of Human Genes. Cavalli-Sforza argued in that book that this reflected the “demic diffusion” of agriculture and was a residue from a genetic wave of advance generated by population expansion initiated in the region of the Levant-Anatolia. By its nature a wave of advance is exhibits a weaker genetic signal in relation to the source because of dilution via intermarriage, so it is no surprise that the British, for example, are predominantly descended from the Paleolithic hunter-gatherers of northern Europe. The detection of east-west gradients, as well as the diversity of the Iberian sample, also points to the demographic expansions out of the Ice Age refugia when the glaciers retreated and northern Europe was repopulated. Note that the sample sizes for some of the local populations were very small. From the paper, “western Irish (n = 6), eastern English (n = 8), French (n = 1), German (n = 8), Valencian Spanish (n = 20), Basque Spanish (n = 8), Italian (n = 9), Polish (n = 8), Greek (n = 8), Finnish (n = 7), Armenian (n = 8), and Ashkenazi Jewish (n = 5)….”This is the most informative figure.