Comparative Analysis of the Systematics and Evolution of the Pampus Genus of Fish (Perciformes: Stromateidae) Based on Osteology, Population Genetics and Complete Mitogenomes

Pampus is a widespread species of fish in the western Pacific and Indian Oceans that has significant commercial worth. Its evolutionary history and phylogenetics are still poorly understood, and details on its intraspecific taxonomy are debatable, despite some morphological and molecular research. Here, we analyzed this species using skeletal structure data as well as nuclear (S7 gene) and mitochondrial genetic information (COI, D-loop and mitogenomes). We found that the genetic distance between P. argenteus and P. echinogaster was much smaller than that between other Pampus species, and both maximum likelihood and Bayesian phylogenetic trees yielded almost identical tree topologies. An additional and adjacent M repeat was found in the downstream region of the IQM gene cluster of P. argenteus and P. echinogaster, and the trnL2 gene of P. minor was translocated. The genus Pampus experienced early rapid radiation during the Palaeocene with major lineages diversifying within a relatively narrow timescale. Additionally, three different methods were conducted to distinguish the genus Pampus species, proving that P. argenteus and P. echinogaster are the same species, and P. liuorum is speculated to be a valid species. Overall, our study provides new insights not only into the evolutionary history of Pampus but its intraspecific taxonomy as well.

Molecular systematics of Pampus (Perciformes: Stromateidae) based on thousands of nuclear loci using target-gene enrichment

Pomfret fishes of the genus Pampus are commercially important in the Indo-Pacific region, yet the phylogenetic relationships and taxonomy of Pampus remain contentious. Here, we sampled 151 specimens, representing all known species of the genus, as well as two outgroup species (two families). We collected sequences from 17,292 single-copy nuclear coding loci using target-gene enrichment and Illumina sequencing for a subset samples of P. echinogaster, P. argenteus, P. cinereus, P. liuorum, P. chinensis, P. minor, and P. punctatissimus, which were carefully examined according to their species descriptions. Concatenated gene tree and species tree analyses resulted in identical and highly supported phylogenies, in which P. argenteus was sister to P. minor in one clade and P. cinereus sister to P. chinensis and P. punctatissimus in the other clade. Phylogenetic reconstruction using sequences of cytochrome c oxidase subunit I (COI) collected by us and those retrieved from NCBI suggests extensive misidentification of Pampus species in the NCBI database. We also measured morphological characters of each species as well as observed their osteological structure using micro-CT. Both molecular and morphological results suggest that P. echinogaster is a synonym of P. argenteus, and P. liuorum is a synonym of P. cinereus. Pampus cinereus from China, Bangladesh and an uncertain origin were grouped into three clades according to their sampling localities, but we could not find decisive morphological characters to describe the "cryptic species" of P. cinereus. Finally, based on the results of the molecular analyses and morphological reexamination, we created an identification key for the genus of Pampus.