[adegenet-forum] Spca and inbreeding

[anne DaSilva]

Dear all,
I have a question that concerns me a little bit. I realised a sPCA considering 20 breeds. The Spca showed a global spatial structure (genetic cline) and 3 breeds appeared "particular" (local structure). These 3 breeds are characterized by the lowest Allelic richness, and one of them showed the greatest inbreeding coefficient. So I am very embarrassed.... is this a spurious clustering (as Spca would be skewed by the poorest genetic diversity of these breeds....), or can I really conclude that these breeds are isolated and so genetically original (as a result  genetic diversity is lower for these breeds). which came first the chicken or the egg?....does anyone has an idea on how consolidate my results (or must I live with this ambiquity?)
Thanks a lot,
kind regards,
Anne
 		 	   		  
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