Higher Rates of Protein Evolution in the Self-Fertilizing Plant Arabidopsis thaliana than in the Out-Crossers Arabidopsis lyrata and Arabidopsis halleri

The common transition from out-crossing to self-fertilization in plants decreases effective population size. This is expected to result in a reduced efficacy of natural selection and in increased rates of protein evolution in selfing plants compared with their outcrossing congeners. Prior analyses, based on a very limited number of genes, detected no differences between the rates of protein evolution in the selfing Arabidopsis thaliana compared with the out-crosser Arabidopsis lyrata. Here, we reevaluate this trend using the complete genomes of A. thaliana, A. lyrata, Arabidopsis halleri, and the outgroups Capsella rubella and Thellungiella parvula. Our analyses indicate slightly but measurably higher nonsynonymous divergences (d(N)), synonymous divergences (d(S)) and d(N)/d(S) ratios in A. thaliana compared with the other Arabidopsis species, indicating that purifying selection is indeed less efficacious in A. thaliana.