[adegenet-forum] DAPC on clonal plants

[Rebecca Citroen]

Fantastic!
Thanks muchly.
 
Warm regards,
Rebecca.

>>> "Jombart, Thibaut" <t.jombart at imperial.ac.uk> 10/06/2011 3:08 AM >>>
Dear Rebecca, 

there is no restriction concerning DAPC as to the ploidy of the data. The method also incorporates no-uniform weights for the groups, so that under-represented groups should not be overlooked by the analysis. So uneven number of duplicates should not be a massive problem. Note that this would be a problem in PCA. However, the fact that you actually have 21 unique genotypes necessarily limits the number of genetic clusters that can be (decently) represented in your data; I would not trust results with more than a few groups (say 5, but that's entirely ad hoc).

Otherwise, I can't see any problem a priori with this analysis. And if it makes biological sense, that's surely a good sign...

All the best

Thibaut


From: adegenet-forum-bounces at r-forge.wu-wien.ac.at [adegenet-forum-bounces at r-forge.wu-wien.ac.at] on behalf of Rebecca Citroen [Rebecca.Citroen at rbg.vic.gov.au]
Sent: 09 June 2011 06:22
To: adegenet-forum at r-forge.wu-wien.ac.at
Subject: [adegenet-forum] DAPC on clonal plants

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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