Tracing evolutionary history and admixture in mixed-ploidy systems

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 sets (Dufresne et al., 2014; Meirmans, 2020). Such a shortage is striking especially when compared to the rapid development of such tools in diploid systems over the last decade. Consequently, population genomic research in polyploids is still lagging behind diploids, especially in autopolyploids, for example, polyploids with multiple (>2) similar genome copies. In this issue of Molecular Ecology Resources, Shastry et al. (2021) develops the first software specifically designed to infer population structure and ancestry in large genome-wide mixed-ploidy data sets, opening novel opportunities for polyploid population genomic analysis.