[adegenet-forum] Structure-like membership plot

[Cheng-Hua Huang]

Dear adegent users and Thibaut,

I would like to ask questions about using DAPC. I have used import2genind
and df2genind for importing Structure, Genepop, and Fstat files of the same
data set to find clusters and to plot Struture-like membership information.
Since I was working on a haploid, asexual fungus collected from three
regions, I coded data sets as a pseudo-diploid for Genepop and Fstat files
but used the original haploid data set for the Structure format. Even though
I got K=3 for biological interpretation based on BIC, the membership plot
derived from the Structure input file was different from those obtained from
the other two file formats. The result using the Structure input format
showed many admixture individuals, but the other two input files did not
exhibit any admixture individuals (all with membership probability = 1). The
latter makes sense to me because the fungus is asexual and genotype flow
plays a main role in shaping population structure. Moreover, recombination
is not possible for this fungus. Thus, admixture individuals may not occur.
What caused this difference between these input files? How do I interpret
these results? Thank you for your help.

Regards,

Arhua

 

 

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