The deep sea contains a surprising diversity of life, including iconic fish groups such as anglerfishes and lanternfishes. Still, > 65% of marine teleost fish species are restricted to the photic zone < 200 m, which comprises less than 10% of the ocean’s total volume. From a macroevolutionary perspective, this paradox may be explained by three hypotheses: 1) shallow-water lineages have had more time to diversify than deep-sea lineages, 2) shallow-water lineages have faster rates of speciation than deep-sea lineages, or 3) shallow-to-deep sea transition rates limit deep-sea richness. Here we use phylogenetic comparative methods to test among these three non-mutually exclusive hypotheses. While we found support for all hypotheses, the disparity in species richness is better described as the uneven outcome of alternating phases that favored shallow or deep diversification over the past 200 million y. Shallow marine teleosts became incredibly diverse 100 million years ago during a period of warm temperatures and high sea level, suggesting the importance of reefs and epicontinental settings. Conversely, deep-sea colonization and speciation were favored during brief episodes when cooling temperatures increased the efficiency of the ocean’s carbon pump. Finally, time-variable ecological filters limited shallow-to-deep colonization for much of teleost history, which helped maintain higher shallow richness. A pelagic lifestyle and large jaws were associated with early deep-sea colonists, while a demersal lifestyle and a tapered body plan were typical of later colonists. Therefore, we also suggest that some hallmark characteristics of deep-sea fishes evolved prior to colonizing the deep sea.

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