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Communication Dans Un Congrès Année : 2021

GenAPoPop1.0: Computing population genetic indices and inferring reproductive modes from genotype diversity in polyploid populations

Résumé

Understanding the ecological and evolutionary impacts of autopolyploidy, especially on reproductive modes, implies to be able to easily compute population genetic indices and to quantitatively infer the respective rates of clonality, selfing and outcrossing producing current descendants. We developed a user-friendly software to analyze genotypes of spatio-temporally-sampled individuals, with a special focus on analyzing and interpreting reproductive modes in polyploid populations. This software, part of the project ANR Clonix2D, named GenAPoPop (for Genetic Analyses of Polyploid Populations), was written using Qt, python and fortran, works on Gnu/Linux, MacOS and Windows, and run locally with no internet connection. It allows computing major population genetic indices for polyploids (F-statistics, linkage disequilibrium, probability of identity, spatial and temporal Fst, genotypic and genetic diversities, etc.) only using a graphical interface. It also includes a new method to obtain posterior probabilities of reproductive modes in polyploid populations using temporal genotypings. It aims to ease and broaden the computation of genetic indices in research projects and facilitate polyploid population studies in population genetic courses and student trainings. We will present the software interface, and provide some results obtained on tetraploid sea anemones and one decaploid invasive plant species.
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hal-04459074 , version 1 (15-02-2024)

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Paternité - Pas d'utilisation commerciale - Pas de modification

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  • HAL Id : hal-04459074 , version 1

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Solenn Stoeckel, Ekaterina Bocharova, Dominique D. Barloy. GenAPoPop1.0: Computing population genetic indices and inferring reproductive modes from genotype diversity in polyploid populations. Polyploidy and Biodiversity, The International Research Network (IRN) Polyploidy and Biodiversity; The French « Plant Genome Dynamics » network (DYNAGEV), Oct 2021, Rennes (Campus de Beaulieu), France. ⟨hal-04459074⟩
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