Factorial Correspondence Analysis: Axes choice

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Hello,
I am using a Factorial Correspondence Analysis to study genetic structure of some animal populations. I am using the Genetix software (_at_ http://www.univ-montp2.fr/~genetix/). In the 2D FCA when I chose axes 1 and 2 or 1 and 3 the individuals clouds are quite linear because they were stretched by some particular allele associated with few individuals ! whereas when I use axes 1 and 4 I obtain the general trend for most of the studied individuals. Therefore I chose to adopt axes 1 & 4 for the 2D FCA! My problem is that I am writing a paper and a reviewer asked me to explain my choice more precisely and to show that this was the case for other studies or can be done?
Any help?
Thanks