I had earlier problems discriminating norwegians and swedes using the MDS plots and the ADMIXTURE program. This is have been problem that needed to be solved. I have for that reason (and some other reasons) learned a new genetic software called LAMP 2.5.
This program have been specially designed to seperate individuals from closely related populations and it is able to specify what segment of the chromosome came from which population. The end result is quite similar to what is offered by 23andme's Ancestry Painting but instead of showing the dull labels "European", "African" and "East-Asian" you instead will see "Norwegian", "Swede", "Finn/Suomi" and "Saami" labels on your chromosome.

In this test run I have limited the analysis to the X-chromosome but the analysis shouldnt be problem to escalate to the rest of the chromosome and to include more distant surrounding populations to investigate the relationship to continental Europe. The program may also be useful to detect specific segments for mixed dispora populations.

The X-chromosome is a sex chromosome. It never pass two male generations. If you are a male you get your X-chromosome from your mother. If your female you get your fathers X-chromosome and one of the two of your mothers X-chromosome. If you are a male and have a Swedish mother and a Finnic father you would in a autosomal DNA analysis look like a 50/50 Swede/Finn but your X-chromosome you would appear as 100% Swedish because as a male you get your X-chromosome only from your mother.

Whats do the analysis show?

1 The program is suprisingly good to label the main ancestry for each participants:
a) All Norwegian participants where placed in correct category including two persons with large Saami and some Finnic mixture.
b) Most Swedes participants where placed in correct category but 5 Swedes appeared to look more genetically similar to Norwegians than Swedes. This was also the case for a Swedish Finn (even a Estonian) who appeared to look more similar to Norwegians than to Swedes. Also worth to note that these Norwegian looking Swedes had some Finnic and even Saami admixture other Swedes didnt have. It may suggest that these participants have ancestry from the northern parts of Sweden.
c) The Finns also have a good fit but there are some exceptions like the Swedish Finn mentioned above. This Finnic "outlieers" appears to come from border sones with other populations.
d) The Saami appears to cluster nicely togheter. There appears to be some variation for one individual when assuming less time since the admixture event begun. There doesnt seem to have been more geneflow from scandinavians than finns or viceversa to the Saami.

The most intriging question that arise from the above analysis are why do some swedes appears as more Norwegian than Swedish togheter with some Finnic and even Saami admixture in other words political borders do not seem to match the genetical borders completly. The traces of Finnic and Saami from this individuals suggest it is a northern phenomena in Sweden maybe from earlier migrations but it doesnt explain why a Swedish Finn and even a Estonian get so huge "Norwegian" percentages.

Whats next?

* More LAMP analyses trying to track origins to continental Europe
* IBD analysis using newest technology. This will involve phasing of the genome for all participants. All will get their phased haplotypes for their chromosomes if they want.
* ADMIXTURE analysis
* MDS plots