Cenozoic evolutionary history obscures the Mesozoic origins of acanthopterygian fishes

Sister lineage comparisons provide a valuable tool for understanding evolutionary origins of species-rich clades. Percomorpha, comprising over 18,900 species, represents one of the most species-rich vertebrate clades. However, the phylogenetic resolution of its sister lineage remains unclear, obscuring whether contrasts in histories of diversification provide insights into the factors that gave rise to this clade’s diversity. Using 887 ultraconserved element loci and Sanger-sequenced nuclear genes, we resolve the phylogenetic relationships of the three closest relatives of Percomorpha-the roughies, flashlightfishes, porcupinefishes, and fangtooths (Trachichthyiformes), the squirrelfishes and soldierfishes (Holocentridae), and the whalefishes, bigscales, and alfonsinos (Berycoidei)-and the placement of percomorphs among them. Contrary to expectations from the fossil record, we demonstrate that living lineages of Berycoidei, Holocentridae, and Trachichthyiformes all diversified after the Cretaceous-Paleogene mass extinction. Our findings show that multiple clades in Trachichthyiformes and Berycoidei independently colonized deep ocean habitats during the climatically unstable Eocene and Oligocene and shallow-water reefs during the extensive hotspot migration and faunal turnover of the Early Miocene. Due to their complex evolutionary history, the closest relatives of Percomorpha are not ideal for understanding the origins of this exceptionally species-rich clade.