Conclusion
GenAPoPop provide a user-friendly, multi-operating systems,
efficient mass processing way to analyse autopolyploid (including
diploid) genotypings with a special focus on interpreting the genetic
diversity and its structure within and between populations in regards
with their reproductive modes. It especially allows computing genotypic
indices to analyse clonal heterogeneity and clonal evenness for
polyploids due to repeated multilocus genotypes (MLGs) in samples. It
includes an extension of the robust and efficient ClonEstiMate
Bayesian method to quantitatively infer joint rates of clonality,
selfing and allogamy using populations genotyped at two-time steps. It
facilitates the interpretation of genetic diversity in partially clonal,
partially selfing autopolyploid populations with no or very-limited
double reduction. It has no vocation to include or encompass all methods
and population genetic indices that can be computed when analysing
autopolyploid genotypings. This is why it allows exporting datasets in
format that can be uploaded in other software like Spagedi
(Hardy & Vekemans 2002), Genodive (Meirmans 2020) and
Polygene (Huang et al. 2020). We thus warmly recommend
users to use GenAPoPop in complement to other dedicated
analyses that can be found in these other softwares, depending on the
tackled questions. GenAPoPop also answers the need of a
population genetic analysing software for autopolyploid dataset with
confident allele dosage that will come growing with the new
genotyping-by-sequencing methods with individually tagged sample and
locus. It finally answers the need of a user-friendly software for
practical course that doesn’t need teaching command-lines or scripting
languages as a prior to introduce students to population genetics for
polyploid species and to the genetic consequences of reproductive modes
on the genetic diversity and structure of populations.