Application of Combined Analyses of Stable Isotopes and Stomach Contents for Understanding Ontogenetic Niche Shifts in Silver Croaker (Pennahia argentata)

Stable isotope analysis (SIA) and stomach content analysis (SCA) were conducted to understand ontogenetic niche shifts in silver croaker Pennahia argentata inhabiting the southern coastal waters of the Korean peninsula. Sampled P. argentata were classified into three groups based on their total length (TL; 60-80 mm TL, 80-120 mm TL, and 120-210 mm TL). Carbon isotope (δ¹³C) ratios were distinguishable, whereas nitrogen isotope (δ¹⁵N) ratios were not significantly different among size classes, and Standard Ellipse Area (SEA), estimated by δ¹³C and δ¹⁵N, was expanded with increasing TL from 0.2 ‰² (60-80 mm TL) to 2.0 ‰² (120-210 mm TL). SCA results showed variable contribution of dietary items to each size class. In particular, higher dietary contribution of Polychaeta to P. argentata of 80-120 mm TL than 120-210 mm TL mirrored variation in δ¹³C values of P. argentata in those size classes. Based on the combined analyses involving SIA and SCA, we concluded that P. argentata underwent ontogenetic niche shifts, particularly dietary shifts, with growth stages. Ontogenetic niche shifting is a representative survival strategy in fish, and, therefore, represents essential information for managing fisheries. The present study demonstrated applicability of combined SIA and SCA analyses, not only for dietary resource tracing, but also for ecological niche studies.

Characterization of the Complete Mitochondrial Genome Sequences of Three Croakers (Perciformes, Sciaenidae) and Novel Insights into the Phylogenetics

The three croakers (Nibea coibor, Protonibea diacanthus and Argyrosomus amoyensis, Perciformes, Sciaenidae) are important commercial species inhabiting the Eastern Indian Ocean and Western Pacific. Molecular data employed in previous research on phylogenetic reconstruction have not been adequate and complete, and systematic and comprehensive phylogenetic relationships for these fish are unresolved. We sequenced the complete mitochondrial genomes of the three croakers using next-generation sequencing for the first time. We analyzed the composition and phylogenies between 19 species in the family Sciaenidae using the mitochondrial protein coding sequences of 204 species in the Series Eupercaria. We present the characterization of the complete mitochondrial genome sequences of the three croakers. Gene arrangement and distribution of the three croakers are canonically identical and consistent with other vertebrates. We found that the family Sciaenidae is an independent branch that is isolated from the order Perciformes and does not belong to any extant classification. Therefore, this family is expected to belong to a new classification at the order level and needs further analysis. The evolution of Sciaenidae has lagged far behind the Perciformes differentiation. This study presents a novel insight into the phylogenetics of the family Sciaenidae from the order Perciformes and facilitates additional studies on the evolution and phylogeny of Series Eupercaria.

The complete mitochondrial genome sequence of Hemibagrus sp. (Siluriformes: Bagridae)

At present, the phylogenetic and taxonomic positions of Bagridae and Siluriformes have long been unclear. In this paper, we sequenced and annotated the complete mitogenome of Hemibagrus sp. The total length was 16,529 bp, and was typically consist of 37 genes, including 13 protein-coding genes, 2 rRNAs, 22 tRNA, a light-strand replication origin (OL) and a single large control region (CR). Except for eight tRNA and ND6 genes, all other mitochondrial genes were encoded on the heavy strand (H-strand). The gene content, organization and arrangement were identical to that of a typical bony fish. The overall base composition was 26.5%, 26.8%, 31.7% and 15.0% for T, C, A and G, respectively, with a slight bias on AT content (58.2%). This information could not only contribute to provide useful molecular data for the species identification, but also to further taxonomic and phylogenetic studies of Hemibagrus and Bagridae.

The complete mitochondrial genome sequence of Eleutheronema tetradactylum (Mugiliformes: Polynemidae) and phylogenetic studies of Mugiliformes

To date, there has been much disagreement concerning the taxonomic status of Eleutheronema. In this study, the complete mitogenome sequence of Eleutheronema tetradactylum was determined and a Maximum Likelihood (ML) tree was constructed based on concatenated nucleotide sequences of 12 mitochondrial protein-coding genes. The complete mitogenome sequence is 16 490 bp in length, containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a putative control region (CR), and a light-strand replication origin (O_L). The overall base composition is 27.1% A, 26.0% T, 29.9% C, and 17.0% G, with a slight AT bias (53.1%), similar to most teleostean fishes. All protein-coding genes share the start codon ATG, except for COI, which begins with GTG. Most of them have TAA or TAG as the stop codon, while COII uses AGA, ND4 uses AGG and Cytb uses an incomplete stop codon T--. These results are expected to provide useful molecular data for phylogenetic studies of Polynemidae and Perciformes.

The complete mitochondrial genome sequence of Hemibagrus sp. (Siluriformes: Bagridae), molecular data for species identification

In this study, we determined and described the complete mitogenome sequence of Hemibagrus sp. for the first time, which is 16,513 bp in length, and contains 37 genes, including 13 protein-coding genes, 2 rRNAs, 22 tRNAs, 1 origin of replication on the light-strand (OL) and a putative control region. The overall base composition was 31.1% A, 26.9% T, 26.9% C, 15.1% G, with a slight AT bias (58.0%). All protein-coding genes shared the start codon ATG, except for COI, which began with GTG. The tRNA-Ser(UGC) couldn't be folded into the typical cloverleaf secondary structure because its dihydrouridine arm is replaced by a simple loop. These results are expected to provide useful molecular data for species identification and further phylogenetic studies of Bagridae and Siluriformes.

A surprising arrangement pattern and phylogenetic consideration: the complete mitochondrial genome of Belanger's croaker Johnius belangerii (Percoidei: Sciaenidae)

The complete mitochondrial genome of Johnius belangerii has been determined for the first time in this article. It was 19,154 base pairs in length, and is composed of 37 genes (13 protein-coding genes, 22 tRNA genes and 2 ribosomal RNA genes). Totally, 5 notable non-coding regions were observed, and a non-coding of 1091 bp was identified as control region based on its location and AT richness. An 800 bp tandem repeat sequence was identified in the fifth non-coding region. We investigated the mitochondrial gene arrangement pattern and found that that the tRNA(Val), 12SrRNA, 16SrRNA and tRNA(Phe) genes of J. belangerii mitogenome were orderly placed at the beginning of heavy strand. This order is different from other croakers. Combine with the phylogenetic reconstruction and genes arrangement pattern of J. belangerii mitochondrial genome, we consider J. belangerii is the most ancient genus within family Sciaenidae.