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Saturday, May 9, 2009

Northwestern (or rather Eastern) Poles compared to other Europeans across more than 260K SNPs

The 45 Poles sampled in this PLoS ONE paper come from West Pomerania. This means they're mostly the descendants of migrants from what was eastern Poland before World War II, and what is now Lithuania and Belarus. So we might expect many of them to carry Baltic and East Slavic admixture. But even if that's the case, they generally don't differ from the Warsaw and Lodz cohorts I blogged about earlier, and cluster just east of North-Central Europe. Here's the Multidimensional Scaling (MDS) plot from the study, which is almost identical to the Principal Component Analysis (PCA) also shown in the paper.

In terms of fixation index (Fst) genetic distance scores, the West Pomeranians are closest to Czechs, Russians, Hungarians, North Germans, Estonians, Austrians and Lithuanians (all 0.001), and most distant from the Kussamo Finns (0.012) and Southern Italians (0.010). Their relatively inflated Fst with Sweden (0.002) is somewhat surprising, considering geography. It's about the same as between the aforementioned Warsaw and Lodz cohorts and Sweden, so perhaps the Baltic Sea has hindered more recent contacts between Poland and Scandinavia? This appears to be confirmed when Nelis et al. run a barrier analysis using the pairwise Fst data (see here). However, we're yet to see a Polish sample featured in these sorts of studies with pre-WWII origins from near the Baltic shore. Their results might be somewhat different in this context, due to more frequent contacts with countries to the northwest of Poland compared to other Poles.

The inflation factor lambda results are in line with the Fst distances, at least for the Polish sample. Here, the Poles appear most similar to Czechs (1.09), Hungarians (1.14), Estonians (1.17), North Germans (1.18), Russians (1.18) and Austrians (1.19). They're again most distant from the Kussamo Finns (2.49) and Southern Italians (1.99).

It's also interesting to note that the West Pomeranians show the highest Linkage Disequilibrium (LD) pattern after the Kuusamo Finns, who are known to be an extreme genetic isolate. This might suggest a lack of outbreeding in recent times, but the authors aren't exactly sure:

Surprisingly, the Polish cohort showed a similar LD pattern as the Kuusamo population, which is probably reflecting the homogeneity of the Polish population. Here the similarity could be attributed to the founder effect or admixture as the Polish sample comes from West Pomerania, a region that was repopulated after the Second World War, after the expulsion of the German population, with other people from (Eastern Poland) and also some Ukrainians. Small sample size (n = 45) does not provide a sufficient explanation for this finding because the Hungarian and Bulgarian samples were also similar in size (Table 1), but gave LD patterns distinct from the Polish and Kuusamo samples (Figure 1).

Nelis M, Esko T, M├Ągi R, Zimprich F, Zimprich A, et al. (2009) Genetic Structure of Europeans: A View from the North–East. PLoS ONE 4(5): e5472. doi:10.1371/journal.pone.0005472

See also...

More on genetic substructure within Europe, this time focusing on the Northeast