The Finnish Experiment

Baltic Finns show about 5-6% per cent more North and/or East Eurasian influence than Central Europeans. This affects their results on inter-continental analyses, like PCA-MDS, where they overlap with North Russians, with whom they're not particularly close genetically, apart from the fact that they share about the same level of the aforementioned eastern affinity. Does it also affect their results in intra-European tests? In other words, would Finns turn into Scandinavians or maybe Balts if their North/East Eurasian segments were removed? Let's check that.

Below are two MDS plots of five test Finns (FI1, FI2, FI5, FI6 and FI7). The first plot was produced using a random batch of 166K SNPs from the filtered 238K SNP set that I use in most analyses. The second one was done with 166K SNPs not contained within segments identified by me as North Eurasian, East Eurasian or Amerindian in the five test samples. Removing the putative eastern segments does have an affect on the results, with the Finns clearly shifting from the North Russian cluster towards the other Europeans with 5-8% less North/East Eurasian affinity (BY = Belarus, HU = Hungary, LT = Lithuania, NO = Norway, SE = Sweden). However, in all other aspects the two plots are very similar.






So it's safe to say the prep work was relatively successful. The targeted segments made up 3% to 5% of the total genomes in the test samples, and usually showed highest affinity to North Eurasian references like the Nganassan and Dolgan. In the near future, I plan to reconstruct some significant tracts made up of such eastern segments, sourced from various European and West Asian groups, to analyze more precisely their origins. If possible, it'd be really interesting to reconstruct entire genomes and run them on MDS plots.

Anyway, let's now have a look what sort of effect the two different sets of SNPs have on the behavior of the test samples on intra-European plots. The first pair of plots includes the test Finns, reference Finns with low level North/East Eurasian influence to begin with, as well as various groups that might have had an impact on the modern Finnish gene pool (Scandinavians, Balts, Russians and Germans).

- Random 166K SNPs

- Selected 166K SNPs

I can't see much of a change, except that the second plot looks more choppy, which is understandable, considering that the sampling of markers is less even. And now, here's another pair of plots, this time including a large set of Finns, from all over the country.

- Random 166K SNPs

- Selected 166K SNPs

Again, not a huge change. The test Finns don't shift their positions in the same meaningful way as on the inter-continental plots. Indeed, it's the same story on other plots, with different combinations of reference sets, which I won't bother posting here. It seems as if Finns are not significantly affected by their relatively increased North/East Eurasian affinity when placed on intra-European plots. Rather, their behavior on such plots, which often looks like fairly strong isolation compared to other Europeans, is affected by something else. That something else, I suspect, are fairly unique allele frequencies due to...isolation in the north followed by genetic drift.

The other interesting thing that came out of this exercise was a plot that, in my opinion, basically looks like a map of some of the major population movements and admixture events around the Baltic. Enjoy...