Phylogenomics establishes an Early Miocene reconstruction of reef vertebrate diversity.

Oceans blanket more than two-thirds of Earth's surface, yet marine biodiversity is disproportionately concentrated in coral reefs. Investigating the origins of this exceptional diversity is crucial for predicting how reefs will respond to anthropogenic disturbances. Here, we use a genome-scale dataset to reconstruct the evolutionary history of the wrasses and parrotfishes (), which rank among the most species-rich and ecologically diverse lineages of reef fishes. We show that major labrid clades experienced pulses of evolutionary innovation and accelerated diversification during the Miocene approximately 20 to 15 million years ago that the origin of no single phenotypic trait can explain. These results draw parallels to the evolutionary histories of many clades after mass extinctions and corroborate recent fossil evidence for an Early Miocene extinction event in oceanic vertebrates and changes in coral reef faunal composition. Our data provide genomic evidence for a major Early Miocene reassembly of reef faunas.