INCREASES in cellular DNA content have been important in the evolution of eukaryotes1–3. One mechanism for increasing DNA content is polyploidisation, which has been observed in a wide variety of organisms4–8, and which is believed to have preceded the evolution of the early vertebrates9. It has been suggested that, following gene duplication, many of the redundant copies would be silenced early in evolution by mutation10,11. Those duplicate genes remaining expressed are then available to diverge in structure and acquire new functions9. We present evidence of extensive gene silencing in the 50-Myr history of a family of tetraploid fishes. Furthermore, those species regarded by systematists as advanced (that is, morphologically divergent from the ancestral form) may have lost the expression of more duplicate genes than primitive species (that is, those with a morphology similar to the ancestral form).