Data from: Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica

Genome duplication is widespread in wild and crop plants but little is known about genome-wide selection in polyploids due to the complexity of duplicated genomes. In polyploids, the patterns of purifying selection and adaptive substitutions are affected by masking owing to duplicated genes or ‘homeologs’ as well as by effective population size. We resequenced 25 accessions of the allotetraploid Arabidopsis kamchatica, which is derived from the diploid species A. halleri and A. lyrata. A reduction in purifying selection compared with the parental species was observed. Interestingly, proportions of adaptive non-synonymous substitutions were significantly positive in contrast to most plant species. A recurrent pattern observed in both frequency and divergence-diversity neutrality tests was that the genome-wide distributions of both subgenomes were similar, but the correlation between homeologous pairs was low. This may increase the opportunity of different evolutionary trajectories such as in the HMA4 gene involved in heavy metal hyperaccumulation.