[adegenet-forum] DAPC on clonal plants

[Rebecca Citroen]

Hi there.
 
We are trying to gain an understanding of population structure in a rare, clonal, sterile, triploid plant using microsatellite data.  Analyses assuming Hardy-Weinberg equilibrium and no linkage-disequilibrium are obviously not appropriate for this data and we are hoping that DAPC can help.  Having performed the DAPC, it seems to run really nicely, showing sensible clustering and even identifying two plants from one site we believe originated from a different group/site.  Our concern is whether or not the results we are seeing are due to genuine structuring or are a reflection of our clonal data.
 
We have genotypes for 131 individuals using 6 microsatellite markers.  Being triploid, many genotypes are incomplete.  We have therefore transformed the data into a binary data set, containining presence / absence data for the 131 individuals for 41 alleles.  Within these 131 individuals, however, there are in fact only 21 different genotypes.  The rest are simply clones of these 21.  The number of clones (duplicates) of each genotype range from 1 to 16.
 
What we are after is a little guidance as to the appropriateness of our data for a DAPC.  Is DAPC sensible / okay to use even though we only have 21 genotypes?  Will the uneven duplication of these 21 genotypes across the 131 individuals bias the results giving a reflection of the sampling rather than population structure?  Are there any other assumptions or biases we need to consider when examining the results?
 
We'd be very grateful for any thoughts anyone has on this issue.  Thanks so much!
 
Warm regards,
Rebecca.

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