Variation in global distribution, population structures, and demographic history for four Trichiurus cutlassfishes

Genetic pattern and demographic history of cutlassfish (Trichiurus nanhaiensis) in South China Sea by the influence of Pleistocene climatic oscillations

Trichiurus nanhaiensis is one of the most important commercial fish species in the South China Sea. This study aimed to investigate the level of genetic variation and population genetic structure of T. nanhaiensis in the South China Sea for the first time, using 281 individuals collected from seven locations along the coast of mainland China, Taiwan, and Hainan Island. A high level of haplotype diversity and low nucleotide diversity were detected in the mitochondrial DNA cyt b gene and nuDNA RYR 3 gene. The overall expected heterozygosity (He = 0.693) among the seven populations ranged from 0.681 to 0.706 in microsatellite DNA data, which revealed high levels of genetic diversity. Significant genetic differentiation was found in Taidong populations in Taiwan, revealing the prevention of gene flow caused by the Kuroshio Current. Two major lineages based on the cyt b gene suggested that the Taiwan Strait acted as a geographic barrier for T. nanhaiensis during the glacier periods in the late Pleistocene. The Bayesian skyline plot also revealed that population demographic expansion of T. nanhaiensis was estimated to have occurred in 0.1 Mya. Our results indicated that all populations of T. nanhaiensis had experienced a recent genetic bottleneck following recent expansion based on ABC analysis.

High migratory propensity constitutes a single stock of an exploited cutlassfish species in the Northwest Pacific: A microsatellite approach

Cutlassfishes, also known as hairtails, include multiple predatory fishes of the family Trichiuridae. They constitute a top marine fish commodity globally, yet the knowledge about their composition and intraspecific genetic structures is still limited. Trichiurus japonicus accounts for a major amount in the northwest Pacific fishery. Previous studies based on mitochondrial DNA markers reported incongruences in its population structure, hence prompting the need for high-resolution markers and avoiding possible shortcomings in its management. Here we genotyped ten novel de novo-assembled transcriptome-derived microsatellite markers on a total of 150 samples across five major fishing grounds (encompassing latitudes 22–39°N). These markers presented a high number of alleles and heterozygosity compared to other marine fishes, corresponding to the large effective population size of ~20,000 per location and cohort differentiation. Population structuring analyses suggested T. japonicus to be a homogenous well-mixed population. This configuration is likely attributed to the majority of its effective population migrates across locations, and the absence of oceanographic barriers at the continental shelves. Qingdao with reportedly high ocean productivity could be a genetic pseudosink based on the high heterozygosity and migratory preference. Moreover, the results of sign tests suggest that T. japonicus experienced a recent bottleneck likely concurrent with historical glaciation events. Further, we demonstrated satisfactory cross-amplifications of our markers on several congeners, indicating a great promise to use these markers to study the population genetics of trichiurids. Together, our findings will serve as an essential groundwork for enhancing resource conservation and management of cutlassfishes.

Complete mitogenomes of four Trichiurus species: A taxonomic review of the T.lepturus species complex

Four Trichiurus species, T.japonicus, T.lepturus, T.nanhaiensis, and T.brevis, from the coasts of the China Seas, have been identified and their entire mitochondrial genomes (mitogenomes) have been sequenced by next-generation sequencing technology. A comparative analysis of five mitogenomes was conducted, including the mitogenome of T.gangeticus. The mitogenomes contained 16.568-16.840 bp and encoded 36 typical mitochondrial genes (13 protein-coding, 2 ribosomal RNA-coding, and 21 transfer RNA-coding genes) and two typical noncoding control regions. Although tRNAPro is absent from Trichiurus mitogenomes, when compared with the 22 tRNAs reported in other vertebrates, the gene arrangements in the mitogenomes of the studied species are consistent with those in most teleost mitogenomes. The full-length sequences and protein-coding genes (PCGs) in the mitogenomes of the five species had obvious AT biases and negative GC skew values. Our study indicate that the specimens in the Indian Ocean are neither T.lepturus nor T.nanhaiensis but they are T.gangeticus; the Trichiurus species composition in the Indian Ocean is totally different from that in Pacific and Atlantic oceans; there are at least two Trichiurus species in Indian Ocean; and the worldwide systematics and diversity of the genus Trichiurus need to be reviewed.