I can only find haplotype examples. I am confused as to why degrees of freedom is double the number of individuals in the AMOVAs I have run with GenAlEx. Is it because the two alleles for each locus are considered separately in the distance matrix? A reference on microsatellite AMOVA is appreciated.
Arlequin software (http://cmpg.unibe.ch/software/arlequin35/) along its manual might answer your question.
Best wishes
Hi Suzanne
It is true Arlequin has a very complete manual. However, AMOVA might be calculated differently with different programs, Therefore I suggest you follow the advice given in GenAlEx (page 7 of GenAlEx guidel)
"The calculations performed by GenAlEx are detailed in a separate Appendix 1: Methods and statistics in GenAlEx 6.5, by Rod Peakall and Peter Smouse. For further information on the calculations, users are advised to consult this appendix, together with the references provided therein"
Hope this helps.
Pablo
Hi Suzanne
I advise you used Arlequin sotftware, Mr Raed keep you a good informations.
Before asking this question, I read the manual and tutorials for GenAlEx, but could not find the referenced Appendix 1 because it was not attached to the manual. I was able to finally find the Appendix 1 within a zip file on this page (http://biology-assets.anu.edu.au/GenAlEx/Download.html) under "previous versions".
Now I have the answer to my question about the degrees of freedom:
"This Codom-Allelic option generates a 2N x 2N genetic distance matrix, representing the pairwise distances between all alleles. The first allele of individual 1 is presented, followed by the second allele of individual 1, then the first allele of individual 2, and so on. The distance between alleles is either 0 (alleles are identical) or 1 (alleles are different)."
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