Quantification of selective constraint in the polyploid genomes of Arabidopsis thaliana and Brassica rapa

Polyploidy is an important mechanism in plant evolution. We are interested in studying how selective pressures change after a lineage experiences whole genome duplication (WGD) or triplication (WGT). Alpha duplication is the most recent WGD event in Arabidopsis. Then a WGT event occurred in genus Brassica when they diverged from Arabidopsis thaliana. We examined selection at both the population and the species level, by calculating the ratio of non-synonymous to synonymous polymorphisms (pN/pS) and computing Ka/Ks between species. In both lineages of Arabidopsis and Brassica, pN/pS values are larger than Ka/Ks, in accord with the expectation that most populations include individuals possessing mildly deleterious mutations that will eventually be removed by purifying selection. Naïve models of evolution after gene duplication would suggest that duplicates should experience some period of relaxed purifying selection as a result of the genetic redundancy. However, we found that alpha duplicates are actually under stronger constraint compared to other genes. Similarly, triplicated Brassica rapa genes have smaller pN/pS and Ka/Ks when compared to single copy genes. This indicates that the special classes of genes surviving after polyploidy are still under relatively strong selective pressure. Next, we mapped pN/pS and Ka/Ks onto the Arabidopsis thaliana metabolic network and looked for correlations between selection and network statistics. We found pN/pS and Ka/Ks are more variable for nodes with lower degree, while nodes with higher degree are more likely to have smaller pN/pS and Ka/Ks. These results suggest that more “important” nodes in network are generally more constrained selectively.