LAUSR

Significance Most fish species live in shallow waters despite >90% of habitable ocean occurring in the deep sea. We show that present-day diversity patterns are the outcome of alternating phases over 200 million y that differentially favored shallow water or deep-sea fishes. The remarkable richness of shallow fishes is explained by rapid speciation during a time of extreme warm temperatures and continental flooding. Deep-sea colonization and speciation peaked twice throughout Earth’s history during colder periods, suggesting “windows of opportunity” for deep-sea fishes. Lineages with traits beneficial for food-limited environments (large jaws) and efficient swimming (tapered tails) were more likely to colonize the deep sea, indicating these are preadaptations to deep-sea life. Marine biodiversity today retains signatures of ancient evolutionary events.