For years now I've been waiting for a comprehensive paper on the genetic relationship between modern Polish and German populations. Such a study would require a large number of samples from all over Poland and Germany, and it would have to take into account Y-chromosome haplogroups (Y-DNA), mitochondrial DNA (mtDNA), and high density genome-wide markers. In particular, it should look at Identity-by-Descent (IBD) sharing between many different Polish and German populations, including those from pre-WWII eastern Germany.
But I have a feeling that this sort of thing won't come from Poland. When it does come, it'll probably be a by-product of a large-scale study on European genetic substructures from another country. Meantime, it seems, we'll be treated to piecemeal efforts from Polish scientists focusing on limited markers. Here's the latest one, which samples various West Slavic cultural isolates from Poland and Germany, and doesn’t go beyond Y-DNA. Interestingly, it seems as if the Lusatian Sorbs from Eastern Germany are more Slavic paternally than Slavs to the east (see PCA plots below). But that's probably just an effect of founder effect, drift, and cultural isolation, which has skewed their Y-DNA haplogroup frequencies over time.
Homogeneous Proto-Slavic genetic substrate and/or extensive mixing after World War II were suggested to explain homogeneity of contemporary Polish paternal lineages. Alternatively, Polish local populations might have displayed pre-war genetic heterogeneity owing to genetic drift and/or gene flow with neighbouring populations. Although sharp genetic discontinuity along the political border between Poland and Germany indisputably results from war-mediated resettlements and homogenisation, it remained unknown whether Y-chromosomal diversity in ethnically/linguistically defined populations was clinal or discontinuous before the war. In order to answer these questions and elucidate early Slavic migrations, 1156 individuals from several Slavic and German populations were analysed, including Polish pre-war regional populations and an autochthonous Slavic population from Germany. Y chromosomes were assigned to 39 haplogroups and genotyped for 19 STRs. Genetic distances revealed similar degree of differentiation of Slavic-speaking pre-war populations from German populations irrespective of duration and intensity of contacts with German speakers. Admixture estimates showed minor Slavic paternal ancestry (~20%) in modern eastern Germans and hardly detectable German paternal ancestry in Slavs neighbouring German populations for centuries. BATWING analysis of isolated Slavic populations revealed that their divergence was preceded by rapid demographic growth, undermining theory that Slavic expansion was primarily linguistic rather than population spread. Polish pre-war regional populations showed within-group heterogeneity and lower STR variation within R-M17 subclades compared with modern populations, which might have been homogenised by war resettlements. Our results suggest that genetic studies on early human history in the Vistula and Oder basins should rely on reconstructed pre-war rather than modern populations.
Below are the Y-chromosome haplogroup frequencies from the study: Ka = Kaszubs, Ko = Kociewie, Ku = Kurpie, Lu = Lusatia, Sl = Slovakia, Me = Mecklenburg, Ba = Bavaria. The authors studied potential German paternal admixture in the Lusatian Sorbs and Kaszubs by comparing them to the Kociewie on the one hand, who were used as a proxy for (pure?) West Slavs, and Bavarians on the other hand, who were supposed to represent the Germans who might have mixed with the Kaszubs and Sorbs.
I'd say that using the Kociewie as a reference group in this case might not have been a wise move, considering the fairly high frequency of R-U106 in that sample (as per the table above), which surely must be one of the highest in East Central Europe. R-U106 actually shows maximum frequencies in Northwestern Europe and is usually considered a Germanic marker. However, if Rebala et al. are indeed correct and Kaszubs carry very little paternal German ancestry, then there has to be some other way to explain their relatively high frequency of I-M253. Again, this marker is most commonly seen today in Northwestern Europe, especially in Scandinavia. If anyone runs an analysis of the Kaszub I-M253 haplotypes from this study (available here), please let me know what you find. See also... Y-DNA vs. genome-wide ancestry in Poles, Germans and Scandinavians Rebala et al., Contemporary paternal genetic landscape of Polish and German populations: from early medieval Slavic expansion to post-World War II resettlements, European Journal of Human Genetics advance online publication 12 September 2012; doi: 10.1038/ejhg.2012.190