Wednesday, October 21, 2015

Dedicated admixture analyses for Scandinavians and Finns

It has gone a while since the last admixture analysis because I saw them unreliable.   In priciple you can make very bad admixture abalyses, and probably do if you have not any method to confirm the coverage of allele frequencies regarding used k-populations.  But today it is possible to check the coverage using qpAdm. It is easy to see that most admixture analyses I have done before have been very bad.  Checking things using qpAdm revealst tha we can't do one analysis for all people on the earth, not even for one continent.

My first experiment is now downloadable here and consists of two local analyses, one for Finns, one for Scandinavians.   Both analyses are taylored giving best possible allele frequency match checked by qpAdm before running allele distribution files.  However, admixture analyses in general have two big disadvantages:

-  admixture analyses can't reach deep prehistory.  If you want to test for example Bronze Age migrations you have to use other tools, like qpDstat and qpAdm. 

- admixture analyses (like Structure and Admixture)  try to model linkages between individuals, but fail to detect right gene flows.  For that reason admixture analyses can at best give only estimates and the quality depends strongly on the data preparation.  I have tried to minimize this gene flow error, but results are still biased in some extent and in gereral the resolution is too low and actual differeces between k-group results are higher than given by these analyses.  My analysis gives maximum difference of 15% in Ladogan admixture in Southern and Central Finland and the right maximum is around 25% estimated using regional Fst-values and qpAdm. 

Some notes

- Ladogan means eastern Finnic people nearby Ladoga lake.

- North-Baltic means Latvians and applicable Estonians.

- Fennoscandinavian means old common genetic background for Finns and Scandinavians.  It mainly refers to Scandinavian migrations, but I prefer to call it Fennoscandinavian to avoid confusion between prehistoric and historic migrations.

- West-Europe means mainly western Germanic affinity (Northwest Europe).

- it is useless to use analysis not dedicated to your ethnicity (Finns/Swedes), because using wrong test files leads to obvious coverage mismatch of allele distributions.  The same mismatch happens less or more in all analyses of this same type.

Diydodecad files for both tests are downloadable here.

In running analyses use parameters “scan.par" and "fin.par".   More detailed instructions about Diydodecad and installation can be found here and original Diydodecad files are downloadable here.  My download package however includes all necessary to run tests.


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