Whole genome duplication (WGD), the doubling of the nuclear DNA of a species, contributes to biological innovation by creating genetic redundancy. One mode of WGD is allopolyploidization, wherein each genome from two ancestral species becomes a 'subgenom' of a polyploid descendant species. The evolutionary trajectory of a duplicated gene that arises from WGD is influenced both by natural selection, creating new or partitioning functions, and by gene silencing (pseudogenization). Here, we explored how these two phenomena varied over time and within allopolyploid genomes in several allotetraploid clawed frog species (Xenopus). Our analysis demonstrates that, across these polyploid genomes, purifying selection was greatly relaxed compared to a diploid outgroup, was asymmetric between each subgenome, and that coding regions are shorter in the subgenome with more relaxed purifying selection. As well, we found that the rate of gene loss was higher in the subgenome under weaker purifying selection and has remained relatively consistent over time after WGD. Our findings provide perspective from vertebrates on the evolutionary forces that likely shape allopolyploid genomes on other branches of the tree of life.