Significant genetic differentiation between the Yellow Sea and East China Sea populations of cocktail shrimp Trachypenaeus curvirostris revealed by the mitochondrial DNA COI gene

Multiple genetic sources facilitate the northward range expansion of an intertidal oyster along China's coast

Coastal artificial structures on the former mudflats provide available habitats for the rocky intertidal species which can establish new populations in these emerging habitats over their former distribution range limits. As a former southern species, the oyster Crassostrea sikamea has become a pioneer and rapidly invaded the artificial shorelines in northern China. We used a seascape genomics approach to investigate the population structure and genetic sources of C. sikamea on the coastal artificial structures, which is crucial for understanding the genetic mechanisms driving species distribution range expansion and invasion pathway of intertidal species. Five C. sikamea populations, including two artificial substrate populations (WGZ and ZAP), one oyster reef population (LS), and two natural rocky shore populations (ZS and XM), were measured using single nucleotide polymorphism (SNPs) obtained from double digest restriction-site associated DNA sequencing (ddRAD-Seq). Redundancy analyses (RDA) were implemented for investigating the relationship between local temperature variables and the temperature adaptability of C. sikamea. Genetic diversity, direction and strength of gene flow, and population structure all revealed that the LS and ZS populations were the genetic sources for the oyster populations on the emerging northern coastal artificial structures. Results of RDA showed that there were different adaptive potentials for northern and southern populations to local temperature variables and the oyster reef population which frequently suffers from heat stress owned high heat adaptability. The ZS population as a genetic source nearby the Yangtze River estuary provided mass larvae for the northern populations, and the other genetic source, the heat-tolerant LS population, in the oyster reef played an important role in the post-settlement success by providing preadapted genotypes. These results highlight the importance of multiple sources with divergent adaptative capabilities for biological invasion, and also emphasize the importance of the oyster reef in coastal biodiversity and conservation.

Improving the size selectivity and exploitation pattern of cocktail shrimp (Trachypenaeus curvirostris) in shrimp trawl fishery of the South China Sea

In order to improve the size selectivity and exploitation pattern for cocktail shrimp (Trachypenaeus curvirostris) in shrimp trawl fishery of the South China Sea (SCS), selective properties of four codends were tested and compared. These experimental codends involved two mesh sizes, 30 and 35 mm, and two mesh shapes, diamond-mesh (T0) and diamond-mesh turned by 90 degree (T90), respectively. Our results demonstrated that increasing the mesh sizes in T0 codends or/and applying T90 codends would improve the selective properties for cocktail shrimp in the SCS. By comparing selectivity parameters, delta selectivity and exploitation pattern indicators, the T90 codend with 35-mm mesh size (T90_35) presented the best selective properties for cocktail shrimp in the studied areas. It will be a potential choice to substitute the currently legal codend in fisheries management to mitigate the bycatch of undersized cocktail shrimp in shrimp trawl fisheries of the SCS.

Comparative investigation of various modification methods on Trachypenaeus Curvirostris surimi gel: Gelling properties, rheological behaviors and structure characteristics

The aim of this study was to compare the investigations of various contents of egg white protein (2.0%-8.0%, EWP), microbial transglutaminase (0.1%-0.4%, MTGase), and konjac glucomannan (0.5%-2.0%, KGM) on the gelling properties and rheological behavior of Trachypenaeus Curvirostris shrimp surimi gel (SSG), and assessed the modification mechanisms through the analysis of structure characteristics. The findings suggested that all modified SSG samples (expect SSG-KGM2.0% ) had the higher gelling properties and the denser network structure than those of unmodified SSG. Meanwhile, EWP could give SSG a better appearance than MTGase and KGM. Rheological results showed that SSG-EWP6% and SSG-KGM1.0% had the highest G' and G″, demonstrating that the formation of higher levels of elasticity and hardness. All modifications could increase gelation rates of SSG along with the reduction of G″ during the degeneration of protein. According to the FTIR results, three modification methods changed SSG protein conformation with the increasing α-helix and β-sheet contents and the decreasing of random coil content. LF-NMR results indicated that more free water could be transformed into immobilized water in the modified SSG gels, which contributed to improve the gelling properties. Furthermore, molecular forces showed that EWP and KGM could further increase the hydrogen bonds and hydrophobic interaction in SSG gels, while MTGase could induce the formation of more disulfide bonds. Thus, compared with another two modifications, EWP modified SSG gels showed the highest gelling properties.

Genetic Variations and Expansion of the Blue Swimmer Crab (Portunus pelagicus) in Southeast Asia

Blue swimmer crabs (Portunus pelagicus) primarily inhabit the coastal regions of Southeast Asia. This study aimed to examine their population genetic structure, phylogeography, and historical demography by applying partial sequences to the control region in the mitochondrial DNA. The analysis focused on 6 populations comprising 166 individual samples collected from Taiwan (Kezailiao Kaohsiung (KK) and Penghu (PH)), mainland China (Xiamen (XM) and Hong Kong (HK)), Vietnam (Hanoi (VN)), and Singapore (SGP). The estimated nucleotide diversity (π) for all of the samples was 0.062, with values ranging between 0.018 (PH) and 0.045 (HK). Our study collected 116 haplotypes and classified them into lineages A and B. The XM, HK, VN, and SGP populations made up lineage A, and the PH and KK populations comprised lineage B. For each lineage, the results highlighted indications of demographic expansion. Lineage A can be traced back to the second-to-last interglacial period, while lineage B possibly originated in the last glacial period. There were significant differences in the FST values among the six populations, except for the pairs HK–XM and PH–KK. In conclusion, the phylogeography and genetic structure of P. pelagicus in Southeast Asia were potentially affected by the Pleistocene glacial cycles and human introduction. These findings further highlight the possible dispersal routes of P. pelagicus throughout Southeast Asia.

Identification of putative key genes for thermal adaptation in the Japanese mantis shrimp (Oratosquilla oratoria) through population genomic analysis

Little is known about the mechanisms underlying the relationship between genetic variation and the adaptation of Oratosquilla oratoria populations to different habitat temperature. Here, the genome-wide genetic information of three O. oratoria populations were obtained by IIB restriction site-associated DNA (2b-RAD) sequencing and 2403 single-nucleotide polymorphisms (SNPs) were identified. Based on the 2403 SNPs, we found a remarkable genetic differentiation between the Yellow Sea and the East China Sea groups of O. oratoria. Furthermore, 63 SNPs are thought to be associated with different sea temperatures. Based on the 63 SNPs, it is hypothesised that the long-term temperature differences may contribute to the variation of genes associated with multiple biological functions, such as material metabolism, cytoskeleton, cellular processes, inflammatory response and hormonal regulation. This study provides new information for elucidating the molecular mechanisms underlying the relationship between genetic variation and the adaptation of Oratosquilla oratoria populations to different temperature.

Nuclear microsatellites reveal population genetic structuring and fine-scale pattern of hybridization in the Japanese mantis shrimp Oratosquilla oratoria

The interplay between historical and contemporary processes can produce complex patterns of genetic differentiation in the marine realm. Recent mitochondrial and nuclear sequence analyses revealed cryptic speciation in the Japanese mantis shrimp Oratosquilla oratoria. Herein, we applied nuclear microsatellite markers to examine patterns and causes of genetic differentiation in this morphotaxon. Population structure analyses revealed two genetically divergent and geographically structured clades in O. oratoria, one dominating the temperate zone of the Northwestern (NW) Pacific and the other occurring in the subtropical and tropical waters where are influenced by the Kuroshio Current. Two sympatric zones, one around the Changjiang Estuary in China coast and the other in the northern Japan Sea, were demonstrated to be hybrid zones where introgressive hybridization occurred asymmetrically. The interaction between historical climate shifts and contemporary factors (e.g., freshwater discharge, temperature gradient and isolation by distance) may contribute to the present-day genetic architecture in the Japanese mantis shrimp. Range shift induced by climate changes and oceanographic factors may promote hybridization and gene flow between the O. oratoria complex. Our results provide insights into the interacting mechanisms that give rise to diversification and speciation of coastal species in the NW Pacific.

The complete mitochondrial genome of Trachypenaeus curvirostris (Stimpson, 1860)

Trachypenaeus curvirostris is a common and important shrimp species in the shallow waters of Indo-West Pacific. In this study, the mitochondrial genome of T. curvirostris was determined for the first time using next-generation sequencing; the overall base components of mitogenome consisting of 15968 bp was 35.16% (5614 bp) for A, 33.51% (5351 bp) for T, 11.54% (1842 bp) for G, 19.80% (3161 bp) for C, and its GC content was 31.34%. The mitochondrial circular genome was composed of 13 protein-coding genes, 22 transfer RNAs, 1 D-loop and 2 ribosomal RNAs. Polygenetic analysis showed that the T. curvirostris was more closed to Parapenaeopsis hardwickii.

DNA barcoding of Cloridopsis immaculata: genetic distance and phylogeny of stomatopods

The changes of coastal topography might have genetically altered the extant species diversity in Chilika Lake. The genetic assessment of stomatopods has never been attempted from this ecosystem. The study generate the first genetic information (mtCOI) of Cloridopsis immaculata. DNA sequences of C. immaculata shows 12.9% genetic divergence with Harpiosquilla harpax and clade as sister species in NJ tree. Alima, Harpiosquilla, and Oratosquilla shows high congeneric/conspecific genetic divergence (20.9%, 15.7%, and 7.2%) and cladded separately in the phylogeny; correlate to their diverse populations. We recommend more extensive survey of stomatopods and generation of molecular data to resolve the taxonomic uncertainty.

Genetic structure analysis of mantis shrimp Oratosquilla oratoria based on mitochondrial DNA control region sequence

The genetic relationships of mantis shrimp Oratosquilla oratoria between the coastal waters of China and Japan were not well studied. To reveal the genetic differentiation and genetic structure among populations, we collected populations of mantis shrimp O. oratoria from the coastal waters of China and Japan to analyze the mtDNA control region variation. A total of 309 individuals of O. oratoria were collected from 13 localities (11 from China and 2 from Japan) and a segment of mitochondrial DNA control region was sequenced. Three hundred nine haplotypes were defined, yielding a very high haplotype diversity and nucleotide diversity. Two lineages of O. oratoria were revealed and displayed strong differences in the geographical distribution. In the coastal waters of China, the geographic distribution of the two lineages was completely separated by the Yangtze River estuary; however, the lineages showed geographic sympatry in two populations from Japan. Based on the lineage distribution, three groups were defined. There was no significant genetic differentiation among the populations within the three groups, indicating high gene flow within each group. Significant and negative values for Tajima D and Fu's Fs tests, and mismatch distributions for two lineages indicated population expansion. The present result confirmed that the freshwater outflow from the Yangtze River formed a physical barrier and affected gene exchange. The different distribution patterns of the two lineages in coastal waters of China and Japan indicated that the larvae of O. oratoria were transferred from China to the coastal waters of Japan with a one-way gene flow.

Cryptic diversity in the Japanese mantis shrimp Oratosquilla oratoria (Crustacea: Squillidae): Allopatric diversification, secondary contact and hybridization

Mounting evidence of cryptic species in the marine realm emphasizes the necessity to thoroughly revise our current perceptions of marine biodiversity and species distributions. Here, we used mitochondrial cytochrome oxidase subunit I (mtDNA COI) and nuclear ribosomal internal transcribed spacer (nrDNA ITS) to investigate cryptic diversity and potential hybridization in the Japanese mantis shrimp Oratosquilla oratoria in the Northwestern (NW) Pacific. Both mitochondrial and nuclear gene genealogies revealed two cryptic species in this morphotaxon, which was further confirmed by extensive population-level analyses. One cryptic species is restricted to cold waters with a distribution range corresponding to temperate affinities, while the other dwelled warm waters influenced by the Kuroshio Current. Their divergence was postulated to be attributable to the vicariant event which resulted from the isolation of the Sea of Japan during the middle Pliocene (c. 3.85 Mya, 95% HPD 2.23–6.07 Mya). Allopatric speciation was maintained by limited genetic exchange due to their habitat preferences. Furthermore, the observation of recombinant nrDNA ITS sequence and intra-individual ITS polymorphism suggested recent hybridization event of the two cryptic species occurred in sympatric areas. Our study also illustrated that the Changjiang River outflow might act as an oceanic barrier to gene flow and promoted allopatric diversification in O. oratoria species complex.

Genetic structure and historical demography of the blue swimming crab (Portunus pelagicus) from southeastern sea of China based on mitochondrial COI gene

In this study, the population genetic structure and historical demography of the blue swimming crab, Portunus pelagicus, from southeastern sea of China were investigated using cytochrome c oxidase subunit I (COI) gene of mitochondrion. A total of 889 bp segment of COI gene was sequenced, which showed a high haplotype diversity (0.6833-0.8142) and low nucleotide diversity (0.0021-0.0034). Among 30 haplotypes defined in this study, one (H1) was the most dominant (47.7%) and shared by each locality, while the majority (23) were rare and only existed in one individual. The AMOVA analysis revealed a limited population genetic structure, which suggested a high level of gene flow along the distribution areas of China. This conclusion was supported by the pairwise F_ST comparison values. The topology of the neighbour-joining tree constructed using 30 haplotypes from four localities presented two distinct clades (clade A and clade B). Meanwhile, three sequences of P. pelagicus downloaded from NCBI database showed a high-level divergence with the individuals collected in our study, which might form a new cryptical species. The individuals of clade B were cryptically embedded in the whole population, with a low frequency (7.7-24.2%), while clade A accounted for 75.8-92.3%. Neutrality tests and mismatch analyses suggested a late Pleistocene population expansion for both clade A (47,000-66,000 years ago) and clade B (74,000-100,000 years ago). This study should provide insight into phylogeny, population genetic structure, conservation genetics, and sustainable management of P. pelagicus.