Genome-wide phylogenetic study of Percomorpha providing robust support for previous molecular classification

Percomorpha is the major branch of Actinopteri, comprising most of the acanthopterygian fishes. The relationships among different Percomorpha groups remain uncertain because of high species diversity, thereby creating challenges for phylogenetic studies on teleosts. The phylogenetic problems of Percomorpha have not been solved using mitochondrial genes and a few nuclear genes. In this study, genomes from 34 representative species from the 7 major taxa of Percomorpha were selected to solve this problem. In all, 29 592 conserved amino acid sites from 206 single-copy orthologous genes were chosen for the reconstruction of phylogenetic trees. The results showed that Gobiaria, whose position is different from that in previous studies, was the earliest branching lineage. The phylogenetic groups in this study were consistent with previous results using mitochondrial DNA and nuclear genes. Thus, this study provides a new perspective and directions for further research on the Percomorpha branch and other higher-order meta-taxonomic relationships of fish. The genome data obtained may be essential for future investigations of phylogeny and molecular evolution.