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). The alpha duplication is the most recent WGD event in Arabidopsis thaliana. A subsequent WGT event occurred in the genus Brassica when it diverged from Arabidopsis. We examined selection at both the population and the species level, by calculating the ratio of nonsynonymous to synonymous polymorphisms (pN/pS) within species and computing K_a/K_s, ratio of nonsynonymous to synonymous substitutions, between species. In both the Arabidopsis and Brassica lineages, pN/pS values are larger than K_a/K_s, 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 after WGD 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 K_a/K_s values than do single copy genes. This observation indicates that the special classes of genes surviving after polyploidy are still under relatively strong selective pressure. Next, we mapped pN/pS and K_a/K_s onto the Arabidopsis metabolic network and looked for correlations between selection and various network statistics. We found that pN/pS and K_a/K_s are more variable for nodes with lower degree, while high degree nodes are associated with smaller selection statistics. These results suggest that more “important” nodes in network are generally more constrained selectively.