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.