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

Abstract

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, 29592 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.

Comparative genomics of tarakihi (Nemadactylus macropterus) and five New Zealand fish species: assembly contiguity affects the identification of genic features but not transposable elements

“…Overall the phylogenetic tree (Figure 6) was consistent with recently reported molecular phylogenies of Percomorpha (Betancur-R et al, 2017; Sanciangco et al, 2016; Shou & Han, 2021). All nodes were strongly supported (posterior probability = 100%) and orders were retrieved as expected.…”

“…The Latridae family (which include tarakihi, king tarakihi, and blue moki), representing the order Centrarchiformes, was placed as a sister clade of “true” Perciformes (stickleback), which is consistent with Betancur-R et al (2017). There was one difference with the phylogenies from Betancur-R et al (2017), Sanciangco et al (2016) and Shou & Han (2021): the positions of the Pelagiaria (Scombriformes: Barracouta and Kahawai) and the Ovalentaria clades (which include Cyprinodontiformes, Beloniformes, and Cichliformes) are swapped. In Eupercaria, the Tetraodontiformes (pufferfishes) were placed as a sister clade of Labriformes (wrasses: butterfish) in our phylogeny, which is consistent with Shou & Han (2021) but not with Betancur-R et al (2017) and Sanciangco et al (2016).…”

“…There was one difference with the phylogenies from Betancur-R et al (2017), Sanciangco et al (2016) and Shou & Han (2021): the positions of the Pelagiaria (Scombriformes: Barracouta and Kahawai) and the Ovalentaria clades (which include Cyprinodontiformes, Beloniformes, and Cichliformes) are swapped. In Eupercaria, the Tetraodontiformes (pufferfishes) were placed as a sister clade of Labriformes (wrasses: butterfish) in our phylogeny, which is consistent with Shou & Han (2021) but not with Betancur-R et al (2017) and Sanciangco et al (2016). These studies placed pufferfishes as a sister clade of Perciformes + Centrarchiformes instead.…”

A genomic investigation of the marine teleost tarakihi (Nemadactylus macropterus) provides insights into its genome evolution and population structure

“…Overall the phylogenetic tree (Figure 4.6) was consistent with recently reported molecular phylogenies of Percomorpha (Betancur-R et al, 2017;Sanciangco et al, 2016;Shou & Han, 2021). All nodes were strongly supported (posterior probability = 100%) and orders were retrieved as expected.…”

“…There was one difference with the phylogenies fromBetancur-R et al (2017),Sanciangco et al (2016) andShou & Han (2021): the positions of the Pelagiaria (Scombriformes: Barracouta and Kahawai) and the Ovalentaria clades (which include Cyprinodontiformes, Beloniformes, and Cichliformes) are swapped. In Eupercaria, the Tetraodontiformes (pufferfishes) were placed as a sister clade of Labriformes (wrasses: butterfish) in our phylogeny, which is consistent withShou & Han (2021) but not withBetancur-R et al (2017) andSanciangco et al (2016).…”