[adegenet-forum] Analysing mixed ploidy datasets

[JEREMY SAMUEL BENWELL-CLARKE]

Hi everyone,

I'm trying to analyse a mixed ploidy dataset. The majority of my samples are diploid but there are a few triploids too. To make ploidy even in my raw data matrix I added zeros to all my diploid samples, which makes them triploids. I then use the read.genalex function from the poppr package to read in my data setting ploidy=3. However, I don't want '0' to be recognised as an extra allele and I want the true diploid samples to be separate from the true triploid samples. Therefore, I use the recode_polyploids function from poppr and set newploidy=T. Here is my code:

genclone<-read.genalex("C:/Users/...", ploidy = 3)
genclone<-recode_polyploids(genclone, newploidy = T)


I'm wondering if this the right way (statistically speaking) to analyse mixed ploidy datasets in R? Will my estimates of genetic diversity and structure be accurate?
I know there is the POLYSAT package, which seems to have been developed specifically for dealing with mixed ploidy datasets, however, I would rather stick to using adagenet and poppr, as I'm familiar with the functions and the structure of genind and genclone objects.

Any help would be much appreciated!

Cheers,

Jeremy
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