Whole-genome duplication (WGD), a widespread macromutation across eukaryotes, is predicted to affect the tempo and modes of evolutionary processes. By theory, the additional set(s) of chromosomes present in polyploid organisms may reduce the efficiency of selection while, simultaneously, increasing heterozygosity and buffering deleterious mutations. Despite the theoretical significance of WGD, empirical genomic evidence from natural polyploid populations is scarce and direct comparisons of selection footprints between autopolyploids and closely related diploids remains completely unexplored. We therefore combined locally sampled soil data with resequenced genomes of 76 populations of diploid-autotetraploid Arabidopsis arenosa and tested whether the genomic signatures of adaptation to distinct siliceous and calcareous soils differ between the ploidies. Leveraging multiple independent transitions between these soil types in each ploidy, we identified a set of genes associated with ion transport and homeostasis that were repeatedly selected for across the species' range. Notably, polyploid populations have consistently retained greater variation at candidate loci compared with diploids, reflecting lower fixation rates. In tetraploids, positive selection predominantly acts on such a large pool of standing genetic variation, rather than targeting de novo mutations. Finally, selection in tetraploids targets genes that are more central within the protein-protein interaction network, potentially impacting a greater number of downstream fitness-related traits. In conclusion, both ploidies thrive across a broad gradient of substrate conditions, but WGD fundamentally alters the ploidies adaptive strategies: tetraploids leverage their greater genetic variation and redundancy to compensate for the predicted constraints on the efficacy of positive selection.

Czech Academy of Sciences Institute of Botany Průhonice Czech Republic

Department of Botany Faculty of Science Charles University Prague Czech Republic

Institute of Integrative Biology ETH Zurich Zurich Switzerland

Institute of Parasitology Biology Centre Czech Academy of Sciences České Budějovice Czech Republic

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