The Phylogenetic Relationships of the Family Sciaenidae Based on Genome-Wide Data Analysis

SIMPLE SUMMARY: Phylogenomics is an effective method to resolve phylogenetic problems. Herein, the phylogenetic relationships among 12 Sciaenidae species were reconstructed using genome-wide data. Two major phylogenetic groups were distinguished in our study, namely, the Western Atlantic species group, which contained four species, and the Eastern Atlantic, Indian Ocean, and West Pacific species group, which contained eight species. The Western Atlantic species were indicted as the more ancient group in the studied species. Meanwhile, the Eastern Atlantic, Indian Ocean, and West Pacific species were the younger group. However, a close phylogenetic relationship between the Collichthys and Larmichthys genera was not supported. ABSTRACT: Uncertainty and controversy exist in the phylogenetic status of the Sciaenidae family because of the limited genetic data availability. In this study, a data set of 69,098 bp, covering 309 shared orthologous genes, was extracted from 18 genomes and 5 transcriptomes of 12 species belonging to the Sciaenidae family and used for phylogenetic analysis. The maximum likelihood (ML) and Bayesian approach (BA) methods were used to reconstruct the phylogenetic trees. The resolved ML and BA trees showed similar topology, thus revealing two major evolutionary lineages within the Sciaenidae family, namely, Western Atlantic (WA) and Eastern Atlantic–Indo–West Pacific (EIP). The WA group included four species belonging to four genera: Cynoscion nebulosus, Equetus punctatus, Sciaenops ocellatus, and Micropogonias undulatus. Meanwhile, the EIP group formed one monophyletic clade, harboring eight species (Argyrosomus regius, A. japonicus, Pennahia anea, Nibea albiflora, Miichthys miiuy, Collichthys lucidus, Larimichthys polyactis, and L. crocea) from six genera. Our results indicated that the Western Atlantic (WA) group was more ancient in the studied species, while the Eastern Atlantic–Indo–West Pacific (EIP) group was a younger group. Within the studied species, the genera Collichthys and Larmichthys were the youngest lineages, and we do not suggest that Collichthys and Larmichthys should be considered as one genus. However, the origin of the Sciaenidae family and problems concerning the basal genus were not resolved because of the lack of genomes. Therefore, further sampling and sequencing efforts are needed.