Recommendations and warning
Most population genetic analyses rely on accurate estimates of real populational genotype frequencies, including here ClonEstiMatePoly method. The number of different possible genotypes at one locus increases with the ploidy and the number of alleles (Reichel et al. 2015). We thus draw users’ attention on the fact that sample sizes should naturally be larger in polyploid organisms to accurately estimate their genotype frequencies, despite the fact that genotyping more alleles per individual may help assessing allele frequencies.
Missing values and null alleles compromise comparisons between individuals, lineages and populations, and are susceptible to create biases and misinterpretations. Suspected null allele can be coded as unknow allele with their own specific letters or positive integers, and should be clearly reported before interpretations. Indeed, no “correction” or “assumptions” can enhance a blurred and incomplete genotyping signals without deep consequences on the computed indices and then their interpretations, whatever the ‘correction’. We thus recommend users to rather remove genetic markers and individuals with missing values and uncertain genotypes.