Recent papers using genome-wide SNP data have indicated higher levels of haplotype diversity in Southern vs. Northern Europe. The authors have typically attributed this finding to south to north migrations within Europe. While such migrations no doubt must have occurred (at some remote date), it seems strange to me to ignore the subsequent extra-European gene flow into Southern Europe which also undoubtedly occurred. An ASHG 2008 abstract, after repeating the intra-European migration theory, includes some additional observations:
Interestingly, we find that within Europe there is a south-to-north gradient with decreasing levels of haplotype diversity moving north, consistent with south to north migrations. We also find that the southwestern European sample has higher haplotype diversity than the southeastern European sample. Additionally, a higher proportion of haplotypes are shared between the southwestern European sample and the Yoruba sample than between southeastern European sample and the Yoruba sample. These two patterns are consistent with recent admixture across the Mediterranean from Northern Africa.Increased genetic affinity between SW Euros and Yorubans is consistent with mtDNA data indicating sub-Saharan admixture in Iberia (Spain and particularly Portugal) at levels higher than typically observed elsewhere in Europe. My guess is a similar analysis would show an increased similarity between SE Euros and NE Africans -- as well as between SE Euros and Middle Easterners, obviously.
(Inference of human demographic parameters using haplotype patterns from genome-wide SNP data.)