Xiaojie Dai

Impacts of spatial scales of fisheries and environmental data on catch per unit effort standardisation

Spatial scale is an important factor that needs to be considered in data collection and analysis in ecological studies. Studies focusing on the quantitative evaluation of impacts of spatial scales are, however, limited in fisheries. Using the Chinese squid-jigging fishery in the north-western Pacific Ocean as an example, we evaluated impacts of spatial scale used in grouping fisheries and environmental data on the standardisation of fisheries catch per unit effort (CPUE). We developed 18 scenarios of different spatial scales with a combination of three latitudinal levels (0.5°, 1° and 2°) and six longitudinal levels (0.5°, 1°, 2°, 3°, 4° and 5°) to aggregate the data. We then applied generalised additive models to analyse the 18 scenarios of data for the CPUE standardisation, and quantified differences among the scenarios. This study shows that longitudinal and latitudinal spatial scale and size of the spatial area for data aggregation can greatly influence the standardisation of CPUE. We recommend that similar studies be undertaken whenever possible to evaluate the roles of spatial scales and to identify the optimal spatial scale for data aggregations in the standardisation of CPUE and fisheries stock assessment.

Erratum to: Genetic Population Structure of Thunnus albacares in the Central Pacific Ocean Based on mtDNA COI Gene Sequences

Thunnus albacares is an important fishery species throughout the world. Polymorphisms of sequence variations in mtDNA COI genes were assessed to explore the genetic differentiations among 11 populations of T. albacares sampled from the central Pacific Ocean. Sixty-one mtDNA haplotypes and 38 variable sites were detected. Analysis of mtDNA COI sequences revealed that tuna from the 11 localities were characterized by moderately high haplotype diversity (h = 0.650 ± 0.040), while sequence divergence between haplotypes was relatively low (π = 0.00364 ± 0.00044). Analyses of molecular variance and FST analysis supported that significant genetic differentiations existed between some of the sampled populations. Tests of neutral evolution and mismatch distribution analysis suggested that T. albacares might have experienced a population expansion, which possibly occurred within the last 0.82 million years. Our study unraveled the genetic structure of the extant population of T. albacares and addressed the related fishery management issues including fishery stock identification and management.

Biological observations on the crocodile shark Pseudocarcharias kamoharai.

Sex ratios and gravid characteristics were analysed for the crocodile shark Pseudocarcharias kamoharai from the tropical eastern Pacific Ocean. Gravid females ranged from 80 to 102 cm fork length (L(F) ). The mode litter size was four (two embryos per uterus), mean embryo length was linearly correlated with maternal length (r = 0·465, n = 32); there was no significant difference in L(F) between female and male embryos.

Genetic differentiation in blue shark, Prionace glauca, from the central Pacific Ocean, as inferred by mitochondrial cytochrome b region.

Abstract Six hundred and ninety-seven base pairs of cytochrome b gene of mtDNA was sequenced and analyzed for 78 blue shark Prionace glauca individuals from three sampled locations in the central Pacific Ocean (CPO). In total, three polymorphic sites were detected which defined four haplotypes. The haplotype diversity (h) ranged from 0.517 to 0.768, and nucleotide diversity (π) was between 0.0007 and 0.0011. Analysis of molecular variance indicated a non-significant differentiation among subpopulations. Furthermore, pairwise FST score analysis revealed a non-significant differentiation among three sampled regions. Generally, low genetic differences were found between different geographic locations in the CPO. This study suggests a single panmictic population of P. glauca in the CPO.

Trophic ecology of sharks in the mid-east Pacific ocean inferred from stable isotopes

As apex predators, sharks are of ecological and conservation importance in marine ecosystems. In this study, trophic positions of sharks were estimated using stable isotope ratios of carbon and nitrogen for five representative species caught by the Chinese longline fleet in the mid-east Pacific, i.e., the blue shark (Prionace glauca), the bigeye thresher shark (Alopias superciliosus), the silky shark (Carcharhinus falciformis), the scalloped hammerhead (Sphyrna lewini), and the oceanic whitetip shark (Carcharhinus longimanus). Of these species, oceanic whitetip shark has the lowest trophic level and mean δ15N value (3.9 and 14.93‰ ± 0.84‰), whereas bigeye thresher shark has the highest level/values (4.5 and 17.02‰ ± 1.21‰, respectively). The bigeye thresher shark has significantly higher δ15N value than other shark species, indicating its higher trophic position. The blue shark and oceanic whitetip shark has significantly higher δ13C values than bigeye thresher shark, silky shark and scalloped hammerhead, possibly due to different diets and/or living habitats. The stable isotope data and stomach content data are highly consistent, suggesting that stable isotope analysis supplements traditional feeding ecology study of sharks, and thus contributes to understanding their trophic linkage.

Complete mitochondrial genome of the Taractes rubescens (Perciformes: Bramidae)

Abstract Taractes rubescens is a high vulnerable species which widely distributes in tropical and subtropical water in Pacific and Atlantic Ocean. The complete mitogenome sequence of T. rubescens was determined in this study. The complete mitogenome of T. rubescensis 16 720 bp in length, which contains 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs and a control region (D-loop). Furthermore, base composition of A, C, G and T is estimated to be 27.6%, 30.9%, 15.8% and 25.7%, respectively. The complete mtDNA sequence of T. rubescens provides a useful data for studying on the molecular systematic, stock assessment and conservation genetics.

Complete mitochondrial genome of Hemiculter bleekeri bleekeri

Abstract Hemiculter bleekeri bleekeri is a typical freshwater species that are mainly distributed in the river basins in China. The biological information of this species is very limited. In this study, we determined the complete mitogenome sequence of H. bleekeri bleekeri. The complete mitogenome of H. bleekeri bleekeri is 16 6173 bp in length, which contains 22 transfer RNAs, 2 ribosomal RNAs, 13 protein-coding genes and 2 non-coding region, a rep region (33 bp) and a control region (D-loop). This work provides new information which is helpful for comprehending the molecular systematic, taxonomic status and evolutionary biology of this species.

Characterization of the complete mitochondrial genome of Sickle pomfret Taractichthys steindachneri (Perciformes: Bramidae).

Abstract The complete mitogenome sequence of Taractichthys steindachneri was sequenced and analyzed in this study. The complete mitogenome of T. steindachneri is 16 723 bp in length, which contains 22 transfer RNAs, 2 ribosomal RNAs, 13 protein-coding genes and 2 non-coding region, a rep region and a control region (D-loop). This study will be useful for studying on the molecular systematic, taxonomic status and conservation genetics.

Complete mitochondrial genome of Toxabramis swinhonis (Cypriniformes, Cyprinidae)

Abstract Toxabramis swinhonis is a one of the main bycatch species in China’s freshwater fishery and an important food resource for the larger fishes in the main rivers and lakes in China. For better understanding the biology of this species, the complete mitochondrial genome of Toxabramis swinhonis was determined and analyzed in this study. The complete mitogenome of T. swinhonis is 16 622 bp in length, which contains 22 transfer RNAs, 2 ribosomal RNAs, 13 protein-coding genes and 2 non-coding regions: origin of light-strand replication (OL) and control region (D-loop). The determination of T. swinhonis mitogenome would play an important role in genetic diversity and evolution for Cyprinidae.

Phylogeny analysis of complete mitochondrial DNA sequences for pelagic fishes from tuna fishery

Abstract Pelagic fishes captured in the international tuna fisheries have attracted increasing attention in recent years because of declines in their populations. In this study, 58 complete mitochondrial genomes of pelagic species from the classes Teleostean and Chondrichthyans were analyzed. The length of the 58 mtDNA sequences ranged from 15,598 to 18,880 bp, and all of which contained 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. Our results suggested that mitochondrial genomes could be a powerful marker for resolving the phylogeny of pelagic fishes. Phylogenetic relationships based on the complete mitochondrial among 58 species indicated that Teleostean and Chondrichthyans are well separated. However, the control region length of Mobula japonicais was much larger than the other species in this study. Additionally, the Prionace glauca was divided into the clade in the genus Carcharhinus which provided a prospective taxonomic status of P.glauca.