[adegenet-forum] DAPC: shall I keep or exclude repeated genotypes ?

[Adrien Rieux]

Hi there,

I’ve got a question regarding the assessment of genetic structure from 
microsatellite data using the DAPC method. My dataset contains around 
30% of repeated genotypes. I observe different and contrasted results 
(BIC as a function of the number of clusters) when I keep or exclude 
repeated genotypes (find.clusters function). Has someone ever 
experienced this situation and how would you explain it ? I would have 
predicted that finding the optimal number of clusters should not be 
influenced by repeated genotypes as the DAPC is only based on the 
variation between genotypes. Is there a general recommendation whether 
keeping or excluding repeated genotypes when performing DAPC ?


Cheers,

Adrien


-- 

Adrien RIEUX
CIRAD - Dpt BIOS - UMR PVBMT
Tel: 0262499219

https://adrienrieux.wordpress.com/home/

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