Dear Priscila,

You can use SPAGeDi (Spatial Pattern Analysis of Genetic Diversity) which is a computer package primarily designed to characterize the spatial genetic structure of mapped individuals and/or mapped populations using genotype data of any ploidy level.

Good luck!

Dear Priscila:

As far as you have coded your molecular phenotypes as binary states (that is not taking into account allele dosage) you can use ARLEQUIN to perform several analyses and POPULATIONS to compute distances between individuals and/or populations. However, if you are sure you are dealing with an allopolyploid species I would recommend to try to code the individual genotypes taking into account the allele dosages from the amplification peak areas so that you can perform more refined analyses based on genotypic data.

Hope this helps your request.

Best regards

José Gabriel

Dear Priscilla,

without any doubt I would suggest R package POLYSAT: Molecular Ecology Resources 05/2011; 11(3):562-566.

Thank you all for your answers. I am actually trying Polysat, and it goes great! I want to try more features of it, but it seems promising.

All the best,

Priscila

I have gone further with these analyses. Although the species is known and cited as an allopolyploid, it seems to have partial or total polysomic inheritance, because there are homozygous individuals at most of loci, there is not fixed heterozigosity and when I tried the function allele.correlations in Polysat, for most of the loci there was not segregation of the two alleles into 2 groups.

So now I am treating the data as it is autopolyploid, but it seemed too risky to genotype based on allele dosage, as lot of my profiles were difficult to read, and I have a high number of alleles for a few loci.

Have someone tried to analyse data with genotypic ambiguity before? I am running analysis on polysat, Spagedi and Structure and results are coherent. 

Shoul I continue with genotypic ambiguity on the data, or stay with the phenotypes as binary states?

Thanks everyone for your help. Polyploid species are such a challenge when you do not expect it.