Abstract
Autopolyploidy is quite common in most clades of eukaryotes. The
emergence of sequence-based genotyping methods with individual and
marker tags enables now confident allele dosage, overcoming the main
obstacle to the democratization of the population genetic approaches
when studying ecology and evolution of autopolyploid populations and
species. Reproductive modes, including clonality, selfing and allogamy,
have deep consequences on the ecology and evolution of population and
species. Analysing genetic diversity and its dynamics over generations
is one efficient way to infer the relative importance of clonality,
selfing and allogamy in populations.
GenAPoPop is a user-friendly solution to compute the specific
corpus of population genetic indices, including indices about genotypic
diversity, needed to analyse partially clonal, selfed and allogamous
polysomic populations genotyped with confident allele dosage. It also
easily provides the posterior probabilities of quantitative reproductive
modes in autopolyploid populations genotyped at two-time steps and a
graphical representation of the minimum spanning trees of the genetic
distances between polyploid individuals, facilitating the interpretation
of the genetic coancestry between individuals in hierarchically
structured populations.
GenAPoPop complements the previously existing solutions,
including SPAGEDI and POLYGENE, to use genotypings to study the ecology
and evolution of autopolyploid populations. It was specially developed
with a simple graphical interface and workflow, and comes with a
simulator to facilitate practical course and teaching of population
genetics for autopolyploid populations.