Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa

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 exhibit a number of distinct population genomic signatures, empirical data remains sparse, leaving predictions largely untested. We sequenced ~300 individuals from 15 diploid and 24 autotetaploid populations of Arabidopsis arenosa, a naturally ploidy-variable species. We find that the impacts of polyploidy on population genomic processes are subtle yet pervasive, including reduced efficiency on both linked and purifying selection as well as rampant gene flow from related diploids. Initial masking of deleterious mutations, faster effective rates of nucleotide substitution, and interploidy introgression, likely all conspire to shape the evolutionary potential of polyploids.