Ploidy-variable species allow direct inference of the effects of chromosome copy number on fundamental evolutionary processes. While an abundance of theoretical work suggests polyploidy should leave distinct population genomic signatures, empirical data remains sparse. We sequenced ~300 individuals from 39 populations of Arabidopsis arenosa, a naturally diploid-autotetraploid species. We find that the impacts of polyploidy on population genomic processes are subtle yet pervasive, such as reduced efficiency of purifying selection, differences in linked selection and rampant gene flow from diploids. Initial masking of deleterious mutations, faster rates of nucleotide substitution and interploidy introgression likely conspire to shape the evolutionary potential of polyploids.

Center for Communicable Disease Dynamics Department of Epidemiology Harvard T H Chan School of Public Health Boston MA USA

Department of Botany Faculty of Science Charles University Prague Czech Republic

Department of Botany University of Innsbruck Innsbruck Austria

Department of Cell and Developmental Biology John Innes Centre Norwich Research Park Norwich UK

Department of Ecology Environment and Plant Sciences Science for Life Laboratory Stockholm University Stockholm Sweden

Department of Organismic and Evolutionary Biology Harvard University Cambridge MA USA

Institute of Botany The Czech Academy of Sciences Průhonice Czech Republic

Plant Science and Biodiversity Centre Slovak Academy of Sciences Bratislava Slovak Republic

School of Life Sciences and Future Food Beacon University of Nottingham Nottingham UK

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