Sha Li’s research while affiliated with China Three Gorges University and other places

The genus Scomberomorus is economically important; however, the taxonomic status and phylogenetic relationships in this genus are not clearly resolved, making it difficult to effectively protect and exploit fish resources. To clarify the taxonomic status of Scomberomorus species, mitochondrial cytochrome c oxidase I (COI) gene sequences of 150 samples were analyzed. The average genetic distance among 14 species was approximately 11 times greater than the distances within species, in accordance with the ‘10× rule’ of species identification. Five of the 14 species did not form monophyletic clades based on a Bayesian inference gene tree. The application of four DNA-based species delimitation methods (automatic barcode gap discovery, barcode index numbers, Poisson tree process, and the K/θ method) yielded several key results. (1) Cryptic species were detected within Scomberomorus commerson . (2) A Scomberomorus queenslandicus sample from Australia was misidentified as S. commerson in the Barcode of Life Data System (BOLD). (3) Specimens originally identified as Scomberomorus guttatus was differentiated into four OTUs or species, two in the Yellow, South China, and Java seas, and two in geographically distant areas, one each in the Arabian Sea and the Bay of Bengal. (4) Six specimens from South Africa originally identified as S. plurilineatus most likely do not belong to the species. (5) Specimens identified as S. maculatus and S. regalis were conspecific; however, introgression cannot be ruled out. Our findings revealed cryptic diversity and difficulties in morphological identification of species in the genus Scomberomorus . This study provides scientifically based support for the conservation of germplasm resources of the genus Scomberomorus .

The Northwest Pacific marginal waters comprising the South China Sea, East China Sea, Yellow Sea, and the Sea of Japan have unique geomorphic features. The Japanese flounder Paralichthys olivaceus, which is endemic to the Northwest Pacific, has high nutritional, economic, and ecological value. To allow the examination of the demographic history and population structure of the most common P. olivaceus species range over the five marginal seas (East China Sea, Yellow Sea, Bohai Sea, Northwest Pacific Ocean, and the Sea of Japan), the mitochondrial DNA control region of 91 individuals from six populations in China was sequenced. These sequences were combined with 233 sequences from four populations distributed in the Northwestern Pacific Ocean for analysis. Higher levels of nucleotide diversity (0.032 ± 0.016) and haplotype diversity (0.996 ± 0.001) were observed. The peripheral Fuqing population in the East China Sea had the relatively lowest genetic diversity and highest differentiation. Furthermore, when the results of the isolation by distance test, spatial analysis of molecular variation and geographic barrier analysis are also considered, there is a clear need to prioritize resource conservation and enhancement measures in this area. The phylogenetic trees, structure assignment test, and haplotypes network revealed no significant differences in the genealogical structure among ten populations. Mismatch distribution analysis, Bayesian skyline plots, and neutrality tests suggested that P. olivaceus experienced population expansion during the Pleistocene. Ocean currents and climate change play important roles in shaping the geographical distribution and genetic population structure of P. olivaceus.

Despite the apparent absence of physical barriers in the ocean to prevent dispersal, recent studies have highlighted the importance of biological, geographical, physical, and historical barriers in the genetic structuring of marine species populations. This representation is essential for the sustainable exploitation of natural marine resources and for the setup of efficient protected area networks for the conservation of marine species. In this study, we used extensive sampling of Sebastiscus marmoratus, a commercially important inshore rockfish with high site fidelity, to characterize their population genetic structure along the China–Japan coast and to determine the effect of past geological and current biological–physical barriers on the current genetic footprint. A 461-bp fragment of the mtDNA hypervariable portion control region was sequenced for 675 individuals from 15 geographical locations. A total of 292 haplotypes were identified. The population of S. marmoratus showed high haplotype and nucleotide diversity. Pairwise fixation index (F ST) and analysis of molecular variance (AMOVA) revealed significant genetic differentiation among populations. The Bayesian skyline plots and neutrality statistics showed a sudden expansion of the S. marmoratus population around the Pleistocene. The Beibu Gulf group had the lowest mean number of pairwise differences, the lowest significant genetic differentiation, and the lowest haplotype and nucleotide diversity, and should be prioritized for protection in the future. Ocean currents, seascape discontinuity, geographical distance, and ecological characteristics may play an important role in shaping the contemporary phylogeographical patterns and population structures of S. marmoratus.

Comparative analysis of the mitogenomes of two Corydoras (Siluriformes, Loricarioidei) with nine known Corydoras, and a phylogenetic analysis of Loricarioidei. ZooKeys Abstract Corydoras is a speciose catfish genus from South America with widely investigated phylogenetic and evolutionary relationships. The complete mitogenomes of C. aeneus and C. paleatus were sequenced, assembled , and annotated using next-generation sequencing. The genome arrangements, gene contents, genome structures, base compositions, evolutionary features, codon usage, and tRNA structures of the two mi-togenomes were compared and analyzed with nine published mitogenomes of Corydoras. Phylogenetic analysis was performed using concatenated nucleotide sequences with 13 protein-coding genes and two rRNAs with 44 mitogenomes of Siluriformes. These results provide information on the mitogenomes of eleven Corydoras species and evolutionary relationships within the suborder Loricarioidei, which may be applicable for further phylogenetic and taxonomic studies on Siluriformes and Loricarioidei.