[adegenet-forum] Spca and inbreeding

Jombart, Thibaut t.jombart at imperial.ac.uk
Thu Oct 29 18:51:50 CET 2015

Hi Anne,

local structures do not correspond to 'isolation'. They merely indicate that some individuals look genetically different from their neighbours (more so than would be expected at random), which is compatible with what you describe about your populations.


From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of anne DaSilva [anne_dasilva at hotmail.com]
Sent: 28 October 2015 10:28
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] Spca and inbreeding

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,
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