Addressing the complex phylogenetic relationship of the Gempylidae fishes using mitogenome data

Abstract

The Gempylidae (snake mackerels) family, belonging to the order Perciformes, consists of about 24 species described in 16 genera primarily distributed in tropical, subtropical, and temperate seas worldwide. Despite substantial research on this family utilizing morphological and molecular approaches, taxonomy categorization in this group has remained puzzling for decades prompting the need for further investigation into the underlying evolutionary history among the gempylids using molecular tools. In this study, we assembled eight complete novel mitochondrial genomes for five Gempylidae species (Neoepinnula minetomai, Neoepinnula orientalis, Rexea antefurcata, Rexea prometheoides, and Thyrsites atun) using Ion Torrent sequencing to supplement publicly available mitogenome data for gempylids. Using Bayesian inference and maximum-likelihood tree search methods, we investigated the evolutionary relationships of 17 Gempylidae species using mitogenome data. In addition, we estimated divergence times for extant gempylids. We identified two major clades that formed approximately 48.05 (35.89-52.04) million years ago: Gempylidae 1 (Thyrsites atun, Promethichthys prometheus, Nealotus tripes, Diplospinus multistriatus, Paradiplospinus antarcticus, Rexea antefurcata, Rexea nakamurai, Rexea prometheoides, Rexea solandri, Thyrsitoides marleyi, Gempylus serpens, and Nesiarchus nasutus) and Gempylidae 2 (Lepidocybium flavobrunneum, Ruvettus pretiosus, Neoepinnula minetomai, Neoepinnula orientalis, and Epinnula magistralis). The present study demonstrated the superior performance of complete mitogenome data compared with individual genes in phylogenetic reconstruction. By including T. atun individuals from different regions, we demonstrated the potential for the application of mitogenomes in species phylogeography.

Comparative Mitogenome Characterization of Cryptic Asian Seabass (Lates calcarifer) in Captivity within Peninsular Malaysia

“…RSCU was defined as the observed frequency of codons to the expected frequency ratio where all the synonymous codons for the same amino acids were used equally. Like other fish mitogenome (Neoepinnula minetomai and Thyrsites atun) [39], the RSCU for the present study also shows preference towards A and C-ending compared to G and Tending codon. The frequency of codon used was like other degenerate codons when the RSCU value=1 and codon was often used when RSCU value > 1.…”

Comprehensive Analysis of Phylogenetic Relationship and Optimal Codons in Mitochondrial Genomes of the Genus Pseudogastromyzon

“…It is now widely recognized that the two genes can be used as specific molecular markers to evaluate the genetic diversity and phylogenetic relationships of various organisms. There were many reports in this field, such as ectoparasites [47], alga [48,49], mitten crab [50], fish [51,52], etc. Here, we compared and analyzed the rrnS and rrnL genes within the 11 Pseudogastromyzon mitogenomes.…”