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Polyploidy, resulting from whole genome duplication, is a widespread phenomenon throughout Eukaryotic kingdoms. It is estimated that 15% of speciation events in plants is due to polyploidization and 16% of plant species encompass ploidy variation. In spite of the evolutionary and economic significance of polyploidy, there is a limited set of tools that would allow routine population genetic and genomic analysis of polyploid systems, in particular for the inference of population diversity and differentiation from large genome-wide data
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