[adegenet-forum] sPCA in populations presenting a strong genetic structure

[Jombart, Thibaut]

Hello, 

it depends on what your biological question is. If you want to study spatial genetic structures per variety, then separate analyses make sense. From what you describe, if you performed an analysis on the entire dataset, you'd be left with some trivial local structures due to the different varieties.

Cheers
Thibaut
________________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of vanesse labeyrie [vanesse.labeyrie at gmail.com]
Sent: 29 January 2014 09:59
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] sPCA in populations presenting a strong genetic       structure

Hello,
I have some questions concerning sPCA in a particular case:
I'm working on a crop population (sorghum) which is mainly inbreeding. My population of study presents a very strong genetic structure, with four main genetic clusters, and STRUCTURE results suggest there are little gene flows among clusters.

In a farm (same spatial location) I sampled individuals belonging to different varieties, and they belong to different genetic clusters.
I am wondering whether sPCA is adapted to this kind of situation, or if it would be better to perform a sPCA among individuals within each main genetic cluster separately.
Many thanks for your advice.

Vanesse