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GenAPoPop 1.0: a user-friendly software to analyse genetic diversity and structure in partially clonal and selfed polyploid organisms
  • +1
  • Solenn Stoeckel,
  • Ronan Becheler,
  • Ekaterina Bocharova,
  • Dominique Barloy
Solenn Stoeckel
INRA

Corresponding Author:[email protected]

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Ronan Becheler
INRAE
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Ekaterina Bocharova
Russian Academy of Sciences
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Dominique Barloy
AGROCAMPUS OUEST
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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.
21 Jul 2023Submitted to Molecular Ecology Resources
22 Jul 2023Submission Checks Completed
22 Jul 2023Assigned to Editor
22 Jul 2023Review(s) Completed, Editorial Evaluation Pending
27 Jul 2023Reviewer(s) Assigned
31 Aug 2023Editorial Decision: Revise Minor
29 Sep 20231st Revision Received
06 Oct 2023Submission Checks Completed
06 Oct 2023Assigned to Editor
06 Oct 2023Review(s) Completed, Editorial Evaluation Pending
16 Oct 2023Editorial Decision: Accept