[adegenet-forum] Different population clusters with DAPC and STRUCTURE

[Simon Dures]

Dear Dr Jombart and others,

I am using DAPC, STRUCTURE and TESS to look at genetic structure across my population (lions), using 20 microsat markers.
The STRUCTURE and TESS results suggest k=2 but with substructuring of k=4. These results make very good ecological sense and have significant Fst.
When I run find.clusters the suggestion is for either 3 or 4 clusters. DAPC using k=4 gives a very nice output that also makes ecological sense, however the cluster membership is very different to those identified by STRUCTURE analysis.
DAPC appears to pick up more detail about the substructure in one instance, however it completely removes one cluster identified by STRUCTURE.
Running many different combinations of my data in structure with different settings never removes this additional group, and likewise in DAPC it never appears.
Do you have any suggestions as to what may be causing this and how I can resolve the conflicting results?
My thought are it may be either because DAPC is not based on genetic models and so is missing some details, or that DAPC is reducing some of the data too much, however I am not knowledgeable enough to really have a strong ideas about the theory involved.

I hope you are able to suggest some possibilities.
Many thanks for any help that you can provide

Kind regards
Simon



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