sunnuntai 18. tammikuuta 2015

Fst-distances in Europe, Finnish Rolloff-analyses

Many studies report European Fst-distances, but usually give us results only of few  populations.  I am now going to fix this shortage.  You’re welcome to use these results in your analyses and comparisons.  I did this work to correct some erroneous results seen earlier in Finnish numbers due to a bad sample qualification.  

Two Finnish groups are defined as follows: using European PCA and Finnish samples from the 1000 genomes project  I first removed obvious outliers, then picked 20 most eastern and most western samples compared to PCA dimensions 1 and 2.  So the eastern group is built from the most eastern 25% of the 1000g Finnish sample set and the western one from the most western 25%. 

Despite of using extremities in Finland the genetic distance (Fst) between Finnish groups is only 0.002, similar to the distance between Estonians and Belarussians, which also corresponds to the result between Finnish old and new settlements in the study “The Genome-wide Patterns of Variation Expose Significant Substructure in a Founder Population” ( Jakkula et al.)   Often heard claim that the distance between Finnish groups is extremely big seems to be false and obtained only by using certain minor Finnish settlements.

 Distances between West Finns and other populations are a bit smaller than in Jakkula et al. (CEU:0.006/0.004, Sweden 0.004/0.003), but regarding East Finns there is no difference.  Comparing results of Finnish groups to other results we see more differences in west than in east.   However, it sounds almost ridiculous to mention that all Finns are genetically closer Sicilians than Finno-Ugric Mari-people who live in Russia, alongside the Volga river (Finnish Fst-distances respectively 0.017/0.013 for Sicilians and 0.021/0.020 for Maris).

The data is gathered from publicly available sources released by universities and international projects.  Each country’s data consists of 10-20 samples, each sample holds around 300000 SNPs, without LD-pruning.  If you want the data I can send it to you.

Fst-distances are determined using Eigensoft’s Smartpca, Rolloff analyses using Eigensofts’s Rolloff.

Genetic distances (Fst/Std.error): Click here to see the table and click here to dowload xls-data.

 I am also returning back to Rolloff-analyses.  Rolloff is a useful tool when used together with another analyses and information about genetic distances.  Admixture datings together with genetic distance makes it possible to try to evaluate results with known history.  Unfortunately it is also possible to run Rolloff-analyses for two arbitrary populations with large genetic distance and with very small real admixture, and make wrong conclusions.   In that case there is no guarantee that results are sensible.  I try now to move forward in order to take into account genetic distances, admixture datings and connect results with the generally known and researched history. 

Rolloff-results (generations/std.error):

Swedish admixture in West Finland:   126.632   26.533 (close to the I1-Bothnian clade age)
Swedish admixture in East Finland:    58.173   10.535 (close to the Tavastian or Viking migration to the east)
Western Finnish admixture in East Finland:  50.154   18.967 (close to the Tavastian migration to Karelia)
Eastern Finnish admixture in West Finland:    96.104   12.999 (close to the common Baltic-Finnic root?)
West-Russian admixture in East Finland:     52.609   15.212 (close to the foundation of Novgorod)

 Click here to download related graphics.

One of the most impressive Rolloff results I have seen so far shows West Russian admixture in Eastern Finland.   In Western Finland West Russian admixture is much older and negligible.  West Russia consists of  Orjol, Kursk, Smolensk and Voron Russians, ethnic names are got from the data (Estonian BC).  As far as I can understand the graphic, it tells about a short genetic pulse among East Finns.


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