I already made a Finestructure analysis before my previous Admixture based work, but didn't publish it because it gave so little additional information. I used same data than with Admixture. The workflow:
1 extracting chrpmosomes 1 and 6
2 running haplotypes (HAPI-UR ten times and making consensus)
3 running Chromopainter in linked mode, without defining donor haplotypes
4 running Finestructure with parameters burning 200000 and runtine 2000000
As a result we see a very obvious grouping, each ethnic group are grouped together. Some cautions have to be made about Chromopainter-Finestrucure combination
- first at all, Finestructure doesn't really use dedicated haplotypes, but the number of shared haplotypes and haplotype lengths between individuals. So there is no guarantee that in a triple sample case (individuals a, b and c) all three share common haplotypes, even when the result of Finestructure shows up haplotype sharing for all three samples. This can lead to a pseudo-ancestry between individuals and also to a wrong tree grouping.
- using donor haplotypes can be methodically unreliable. We can assign donor haplotypes for people living in Americas, but it is not equally reliable for people living in the old world. It is a chicken egg question. If we really know donors before testing we know the result before we have the result. I have seen methods creating donor types (selections of prepared haplotypes), but I can't see how it could really work reliably. Note also that speaking about donor populations (I have seen it) makes this even a more problematic question; to know donor populations we already know the population grouping before the analysis and bind donor populations to something that exists today, but did not necessarily exist thousands years ago.
While checking the data I see there a questionable sample qroup: Swedes. They look more eastern than can be healthily suggested.
In general, looking at any results the first question is "does the result look obvious?". If we have two different results based on any kind supervised method (like using donor haplogroups/populations) it is only common sense to see the more obvious result being the better one. Here we have a philosophic question: what "the obvious" means for you and for me. It makes sense, but an idea as "too obvious" lead us to tin foil hat theories. Perfection is suspicious. We don't want it, although also it is in practice possible. Another, much more sensible question in regards to donor haplotypes would be if we could assign donor haplotypes of Bronze Age Europeans based on ancient samples. It would make sense.
Dowload Finestructure picture here.