Abstract:DNA barcoding systems are efficient tools to standardize the management and sharing of barcode data. On the basis of collecting the voucher specimens and corresponding DNA barcodes of important Chinese fishery species, the project team unified and standardized species and barcode information, established the relationships among species, voucher specimens, and DNA barcodes, and constructed the Chinese Fishery DNA Barcoding System (www.fishery-barcode.cn). This system comprises species, voucher specimen, and sequence databases. It includes the voucher specimen and corresponding DNA barcodes of 6020 fishery species. The platform offers convenient and fast web searches and provides a tool to identify unknown fishery species. This study constructed a DNA barcoding system aimed at Chinese fishery species for the first time, and achieved data sharing and collaboration, and will provide a useful resource for species classification, germplasm resource utilization, protection of endangered species, and aquatic product species identification.

Abstract:This review introduces the environmental DNA (eDNA) method which is a newly developed technique to monitor biodiversity. eDNA are free DNA molecules contained in the shedding of skin, feces, saliva, gametes, and secretions. Recently, eDNA has become a global research hotspot owing to its sensitivity, accuracy, and easy implementation. Above all, eDNA can monitor biodiversity and biomass in real-time. Owing to the highly complicated characteristics of aquatic ecology, eDNA methods play a considerable role on this area. This review summarized the eDNA application and methods in aquatic ecosystems, outlined some aspects requiring improvement, and suggested future developments and innovations for research. eDNA methods were mainly applied in three research areas, namely biodiversity analysis, biomass evaluation, and invasive and endangered species monitoring. Currently, eDNA used for biodiversity research has mostly relied on meta-barcoding technology. Examples of different meta-barcoding applications, such as microscopic eukaryotes and aquatic animals have been summarized, and further research directions suggested. Regarding biomass evaluation, most eDNA achievements and limitations in this area have been summarized. Invasive and endangered species monitoring is possibly the most successful eDNA application, and many examples have been summarized to provide a comparative basis for relative researchers. The superiority and limitation of eDNA methods have been summarized based on published articles and the results from our laboratory. Finally, prospective eDNA applications have been listed to specify direction for further studies.

Abstract:The main purpose of this study was to analyze and identify the species of fish eggs from the Jiangmen marine environment in summer, based on DNA barcoding technology. In the present study, we acquired a total of 217 effective mitochondrial COI sequences from fish eggs, and the success rate of sequencing was up to 68.5%. After the alignment of the BOLD database, we found that besides 2 species, a total of 5 orders, 14 families, 19 genera, and 20 species were identified. Statistical analyses showed that the interspecific genetic distances were 0~0.006, and mean interspecific genetic distance was 0.002, whereas the intraspecific genetic distances were 0.149~0.325, and mean intraspecific genetic distance was 0.255, which was 128-fold higher than the former. Among the fish eggs, the most abundant order was Perciformes (51.8%), followed by Clupeiformes (24.8%); the most abundant species was Megalaspis cordyla, , and . In this investigation, the most abundant fish eggs were found in eastern Chuanshan Archipelago, both in numbers and species. The Chuanshan Archipelago is also known as the main spawning site of . However, nearly no fish eggs were found in the Huangmao Bay area or western Zhenhai Bay, possibly owing to environmental disruption and a decrease of effective parent number, triggered by environmental variation and contamination from land-sourced pollutants. In general, we revealed the distribution pattern of fish eggs from the Jiangmen marine environment in summer, which provided a theoretical basis for developing effective protective measures for spawning sites. Meanwhile, the results also showed that DNA barcoding technology could be effective and broadly applied to identify the species of fish eggs in the marine habitats of our country.

Abstract:The Southern Ocean accounts for 10% of the world's oceans, but has a relatively low species richness. Some areas have been subject to commercial fishing, and the species compositions and population structures have been underestimated. As a promising tool, DNA barcoding has advanced to aid species identification and discovery. Even for experts, despite extensive taxonomic studies, the identification of fishes can be problematic for many reasons. In the present study, 43 Antarctic fish species were identified and analyzed using DNA barcoding, and the data obtained was examined. We collected and morphologically identified specimens from the Southern Ocean during 2013 and 2016. In total, 97 individuals from 43 species pertaining to 22 genera of Notothenioidei and Channichthyidae were barcoded using the COI gene, sequenced, and compared with that of other species recorded in GenBank and the Barcode of Life Data System (BOLD). Our results indicated that the mean T, G, A, and C contents were 31.9%, 18.3%, 22.2%, and 27.6%, the GC content of codon position 1 averaged 51.3%, that of position 3 averaged 44.0%, and that of position 2 averaged 42.0%. Therefore, the COI sequences of Antarctic fishes were obviously base biased. The average value of transition/transversion ratios was 2.79. Using the Kimera-2-parameter model, the mean genetic distance among pairwise species (0.157) was calculated as 79 times higher than that within species (0.002). From the phylogenetic tree, 41 species, except , were clustered, which suggested that COI barcoding could effectively be used to identify the remaining 41 species. But, COI barcoding provided limited phylogenetic resolution of , since they shared COI haplotypes. The similarity in results indicated that we should develop multigene barcode technology to overcome the deficiency of the single COI gene sequence. For the two species, , that were difficult to distinguish using DNA barcoding, we need more samples to analyze their phylogenetic relationships, including morphological, cytological, and molecular evolution. Although this study compared the results with that of other studies, we found that different methods and sampling could lead to different results. To determine more comprehensive phylogenetic relationships of fishes, we need to analyze a variety of methods together to form more consistent results. During the course of the study, we found that for some sister species or recently differentiated subspecies, COI barcoding mostly can not be separated, and mitochondrial and nuclear genes should be analyzed together.

Abstract:Groupers (family Epinephelidae) are an important group of marine fishes, which inhabit coral reefs and rocky coastlines of the tropics and subtropics. They are top predators and keystone species, which are central to ecosystem stability and resilience, as well as major sources of food, economic income, recreation for fishermen, and display animals. However, many species are threatened by overfishing, habitat degradation and pollution, and hybridization with commercial stock escapees. Such threats to their longer term existence emphasize the need for well-developed management and protection plans that include best practices for their farming. To address these needs, we provided a comprehensive review of the literature on grouper biology, ecology, fishery resources, and farming. Specifically, we synthesized global research on grouper morphology, behavior, ecology, evolution, and biogeography with more applied knowledge on their artificial breeding, aquaculture, fishery management and public protection, and conservation status. In particular, we used our synthesis of grouper genetics to conclude that hybridization with commercial escapees remains a major, but largely overlooked threat to the long-term integrity of many natural groups. Thus, we suggested greater oversight on artificial hybrid breeding programs. Such focus should be a primary component of any future plans to ensure the sustainability of the Chinese fishery and farming industries for groupers.

Abstract:In May 2015, a fish species and fishery resources survey was carried out in the middle reaches of the Yarlung Zangbo River in Tibet, and one species suspected to be the natural hybrid of was found in the waters of Sangri and Langxian. Morphological analyses showed that the morphological characteristics of the head, including snout, mouth, jaw, and beard length, were in the middle form and distinct from . The head shape of the individuals in the population was stable and consistent, all with typical intermediate characteristics, and there was no significant difference between individuals. Barcode analysis based on the mitochondrial CO I gene showed that 4 of the 15 samples from the hybrid population were homologous with , and the genetic relationship was close to each other. This suggested that individuals with the genotype of were both present in the suspected hybrid population. In the present study, the results showed that could hybridize in natural waters to produce offspring. However, the hybrids produced by as the maternal parent were dominant in the population, and it was considered that specific environmental factors in the waters of Sangri could enhance spontaneous inter-species hybridization between .

Abstract:Catfish, important economic fishes, account for about one-third of the freshwater fishes globally, and are widely distributed with abundant species and population structures in China. Owing to limited bones in the muscle and good taste, catfishes are widely consumed and occupy an important position in the aquatic products market. In this study, using the COI (cytochrome oxidase subunit I) gene fragment as a molecular marker, phylogenetic analyses were carried out on some catfish species. A total of 134 sequences of 13 species of catfishes were amplified using universal primers, and the results were compared with 51 other sequences belonging to 15 species of catfishes obtained from GenBank. The results showed that Pelteobagrus fulvidraco included five insert-deletion sites. The average base A+T (55.5%) was significantly higher than that of G+C (44.5%). The average genetic distance of 28 pairwise and 23 within species were determined as 0.195 and 0.006, respectively using Kimura's 2-parameter (MEGA6.0). The phylogenetic tree analysis showed that a neighbor-joining tree was more suitable than the maximum likelihood tree for the genetic analysis of the catfish species. According to neighbor-joining tree for all 185 sequences of catfishes, the consistency with traditional taxonomy on family levels and below was higher (82.9%) than that of order levels (71%). Samples of each species formed highly supported monophyletic groups. The neighbor-joining tree showed that species of come from the same branch, and the . The results of this study showed that the COI gene could be used as a molecular assistive tool for the identification of catfish species, and could also be applied to molecular phylogenetic relationships. The results effectively expanded the species classification information of catfishes, and provided necessary evidence for traditional taxonomy.

Abstract:The Bagridae catfishes, belonging to the order Siluriformes and class Osteichthyes, are widely distributed in freshwater areas in Asia, such as China, Japan, Korean peninsula, and Vietnam. In China, Bagridae catfishes include more than 30 species across 4 genera. In recent years, due to environmental deterioration and human disturbance, populations of the native Bagridae had sharply decreased and some of them were difficult to collect. However, the classification of some Bagridae catfishes is ambiguous due to the difference of individuals, genders, or habitat. A species identification technique for various fishes based on DNA barcoding has been rapidly developed and widely employed. For many fishes, DNA barcoding requires additional validation before use. Herein, we have developed and evaluated DNA barcoding based on COI gene sequences for identifying Bagridae species. Altogether, 11 Bagridae catfish species were collected and sequenced with the standard DNA barcoding protocols, then combined with 8 available species acquired from the GenBank. A total of 60 sequences from 19 species pertaining to 4 genera were analyzed. DnaSP 5 and MEGA7.0 were employed to calculate the base composition, sequence characterization, and genetic distance, and construct the neighbor-joining phylogenetic tree. The mrbayes software was used to construct the Bayesian tree. The result showed that the mean base contents were:24.82% A, 30.44% T, 27.10% C, and 17.64% T. AT contents (55.26) were higher and the base composition was biased as others teleost fishes were also commonly observed. The nucleotide sequences included 226 variant sites, 195 parsimony informative sites, and 31 singleton sites. The average transition/transversion ratio was 3.35. Genetic distances within species, genus, and families were 0.0041, 0.1136, and 0.1268, respectively. The ratio of genetic distances between interspecies and intraspecies was 27.7, which indicated a notable genetic difference of the COI gene sequence. The efficiency of DNA barcoding based on the COI gene was reaffirmed from its successful identification of all 19 Bagridae catfishes in this study. This classification result is consistent with their morphologies. However, only catfishes can be clustered into a single phylogenetic tree branch. Other Bagridae species were intertwined, and their phylogenetic status needs further research combined with data from more samples. The results revealed that the COI gene was suitable as a DNA barcoding parameter for identifying species; it provided a useful reference for the phylogenetic relationships of Bagridae.

Abstract:The silver carp (), one of the four major Chinese carps, is widely distributed in the Yangtze, Pearl, and Heilongjiang River Basins of China. The wild silver carp populations in the Yangtze River, with an excellent production performance, is an important germplasm resource for artificial farming and breeding. Because of overfishing, habitat fragmentation, and water pollution, the natural carp populations have been continuously declining in recent years. The basic genetic background analysis of the silver carp would be theoretically and practically important for the conservation of germplasm resources and genetic improvement. In this study, mitochondrial cytochrome C oxidase subunit I gene (COI) was sequenced to determine the genetic diversity and variation of six geographical silver carp populations:Yibin, Zhongxian, Wanzhou, Shishou, Jianli, and Xiangjiang. The amplified fragment was 648 bp in length, and a total of 26 haplotypes were defined among 123 sequences of COI from the six silver carp populations. The haplotype and nucleotide diversity index of the six populations ranged from 0.0476 to 0.0945, and from 0.00196 to 0.00982, respectively. The six groups exhibited a high genetic diversity, of which the Wanzhou population showed the highest haplotype and nucleotide diversities; the lowest haplotype and nucleotide diversities were observed in the Zhongxian and Shishou populations, respectively. The molecular variance (AMOVA) analysis showed that the variation within populations (accounting for 88.72%) was the main source of variation, and only 11.28% of the variation was found among the groups. The haplotype network was radial, centering on the main haplotype. The neighbor-joining phylogenetic tree of haplotypes based on genetic distances were inconsistent with their geographical distances. According to the differentiation index (, there were high differences between the Yinbin, Wanzhou, and 3 populations from the middle reach ( < 0.05); meanwhile, the Jianli population showed a significant differentiation from the Shishou and Xiangjiang populations ( < 0.01). The results revealed that the upper-and middle-reach populations should have originated from different populations in the Yangtze River. This study could provide useful basic data for the scientific protection, and reasonable and sustainable utilization of this germplasm resource in the Yangtze River Basin.

Abstract:Snakeheads are of important cultural value as ornamental fishes in China. In this study, the mitochondrial COI (cytochrome oxidase subunit I) gene fragments 576 bp long were used to analyze the phylogenetic and diversity of snakeheads in and out of China, to probe the probability of the COI gene to be used as a barcoding sequence for species identification. Including 149 specimens of different geographic populations of native to China, and 122 sequences of other species downloaded from GenBank, a total of 271 snakehead individuals of 25 species, were analyzed. Of all the sequences, no insertion-deletion sites existed. The average content of A+T (51.4%) was higher than that of G+C (48.6%). The average intraspecies genetic distance was 0.028, but reached 0.137 in , which was higher than some interspecies distances. The interspecies distances ranged from 0.030 to 0.302, with an average of 0.217. The largest distance exists between , exceeding some distances to outgroup. Phylogenetic trees based on the neighbor-joining and maximum likelihood method were constructed. Most individuals from the same species formed a monophyly, and high bootstrap values were obtained for them, but this was not the case for several other species. However, the relationships of species have low bootstrap values, indicating improper phylogenetic analysis of the COI gene for snakeheads. Furtherly, a compound were formed according to the phylogenetic trees. The results of this research indicate that the COI gene is proper for the species identification of native species of snakeheads in China, but more information regarding imported ornamental snakeheads is needed.

Abstract:Kaluga () is the native sturgeon in the Amur river. Similar to other sturgeons, their populations have sharply decreased in recent decades; they have been identified as one of the most endangered species in the world. Unlike the rapid decline of wild populations, sturgeon farming has rapidly increased in China Mainland. The intra-specific hybridization of the female Kaluga and male Amur sturgeon () is widely performed, constituting a large part of sturgeon production in China. In this study, we use the Cyt gene and D-loop region of mitochondrial DNA to assess the genetic diversity of three Kaluga populations, including the wild population from the Amur river, and two populations cultured in national sturgeon breeding farms located in China:one from Fangshan, in Beijing city and the other from Quzhou, in the Zhejiang province. All of the tested individuals were of identical the Cyt haplotype, whereas 9 haplotypes were found in the D-loop region. There was no diversity detected at the nucleotide level on the Cyt d) reached 0.593, but nucleotide diversity () was only 0.00213. There were 6 D-loop haplotypes detected in 8 individuals from the wild population and 5 haplotypes detected in 58 individuals from the cultured populations. The results suggested the wild Kaluga population might have experienced a serious genetic bottleneck. Meanwhile, in the process of artificial propagation of Kaluga, only a few individuals might have been involved in reproduction each time in both the cultured populations. Phylogenetic tree analysis based on partial sequences of the Cyt genes supported the previous results from other researchers. The phylogenetic relationship between and other Pacific sturgeon species was close, but that between was not. Our result implied that the prevalence of the traditional genus was not supported by molecular genetic data.

Abstract:To further clarify the taxonomic status of species in the Suifen River in China, COI gene sequences of 53 samples including , their suspected hybrids in Suifen River, and , which was collected from Japan, were compared and analyzed. Eight haplotypes were obtained with an effective sequence length of 637 bp. Haplotype analysis showed that had three haplotypes, whereas collected from Japan had an independent haplotype. Although the suspected hybrids shared two haplotypes with their parents, 80% individuals shared the same main haplotype with . Phylogenetic analysis using the neighbor-joining method based on the K2P model showed that in the southern region of Russia (i.e., Primorsky krai), T. hakonensis in the northern region of Russia (i.e. Sakhalin Island and Khabarovski krai), and clustered singly. Therefore, anadromous spawning populations of species from the Japan Sea to the Suifen River actually are the southern forms of , respectively. The average genetic distance between the southern and northern forms of was 0.023, conforming to the basis of segregation of COI between groups (>0.02). We support the classification of the southern and northern forms of into two effective species or subspecies. Based on the results of the COI analysis, we speculate that hybrids of were probably produced in nature or by artificial propagation, and therefore, suggestions were proposed on how to protect and utilize the fish germplasm resources rationally.

Abstract:The germplasm and genetic diversity of three species introduced in the Sayram Lake of the Xinjiang Province, Baikal omul () and broad whitefish (), were characterized using DNA barcoding of the CO I gene. A total of 15 haplotypes were found in the three species of interest, of which five haplotypes were identified for the Baikal omul, seven for broad whitefish, and five for peled; the latter two shared two common haplotypes, indicative of gene introgression from , based on the haplotype analysis. Construction of a phylogenetic tree using the neighbor-joining method showed that 15 haplotypes were divided into three different branches, and each branch was respectively clustered with the published sequences, which indicated that the species introduced to the Sayram Lake had still been maintaining good provenance characteristics; , which had the largest genetic distance (0.027) to its close species , had clustered independently. Genetic diversity of the three species is moderate, and C. peled because of the possibility of hybridization between . We recommend that the fishery production department in the Sayram Lake continue planning the breeding, fishing, and other production activities scientifically, and importing advanced germplasm identification technology to avoid germplasm contamination caused by artificial hybridization. Meanwhile, it is necessary to improve and maintain the genetic diversity of the species, thus, ensuring the sustainable development of fishery in the lake.

Abstract:Genetic data have aided fishery conservation research and management by facilitating the detection of genetically distinct populations, the measurement of genetic connectivity, and the identification of the risks associated with demographic change and inbreeding. is an important economic marine fish species in China and inhabits in the Bohai Sea, Yellow Sea, East China Sea and South China Sea. has become an important fishing target in the East China Sea since 1974. Its annual catches were once second only to has declined sharply since 1990 due to overfishing and ocean environmental change. To provide better protection and effective recovery for this species, it is urgent to evaluate its population structure and genetic diversity. However, population surveys of in China's coastal waters were rare. No population structure research based on molecular makers was available. In this study, we amplified the partial mitochondrial Cyt gene sequences of 176 individuals from six populations (Dalian, Qinhuangdao, Penglai, Rizhao, Zhoushan, and Shantou). The results showed that 32 polymorphic nucleotide sites and 30 haplotypes were detected among all the Cyt sequences. The haplotype diversity ranged from 0.883 to 0.953, and the nucleotide diversity was 0.0032-0.0039. This genetic diversity pattern was probably caused by a recent demographic expansion in the Pleistocene, a rapid population growth after 1970, and the adaptable biological characteristics of . Although the haplotype diversity was high, the genetic diversity is still vulnerable to overfishing. AMOVA analysis showed that the genetic differentiation of mainly occurred within the population variation. The genetic differentiations among populations were weak and no groups were identified. The high gene exchange among populations is probably caused by the seasonal migration behaviors of the adults and the long-distance transportation of juveniles by the Kuroshio (Black) Current. Demographic history analysis showed that the six populations experienced rapid population growth 0.17-0.42 Mya. This time point was within the middle Pleistocene. During this period, sea levels changed dramatically due to unstable temperatures. We speculate that the sea level changes during the middle Pleistocene might have had significant influence on the population expansion of . To our knowledge, this is the first population genetics research on in China's coastal waters based on molecular markers. This study could deepen our understanding of how to optimize the utilization of the natural resources of .

Abstract:The swamp eel () belongs to the family Synbranchidae, order Synbrachiformes. It is widely distributed in shallow lakes, rice fields, and swamps areas, especially in the Yangtze River region in China. It is one of the most important economic freshwater fishes because of its high meat quality, delicious taste, and medicinal value. Recently, it has been widely cultured in some regions, such as Hubei, Jiangxi, Anhui, and Hunan provinces. The production of in China in 2016 was 386,137,000 kg. However, most fries are sourced from fishing natural populations owing to a scarcity in fingerling resources from artificial reproduction. Therefore, with the challenges of overfishing and environmental deterioration, natural resources are sharply decreasing. It is vital to analyze the genetic background to conserve and utilize this fish effectively. The genetic diversity of six populations with 187 individuals from Hubei, Jiangxi, Anhui, Hunan, Chongqing, and Shandong was investigated based on the mitochondrial cytochrome oxidase I (COI) gene sequence. The results showed that the nucleotide composition of 646 bp in length was similar in the six populations. The average content of T, C, A, and G was 27.7%, 30.7%, 24.5%, and 17.1%, respectively. There were 61 mutation sites containing 16 singleton mutation and 45 parsimony informative sites. A total of 38 haplotypes were defined in all populations, and overall haplotype diversity () were 0.886 and 0.01094, respectively. In the six populations, the genetic diversity of Hubei and Shandong populations were the highest ( > 0.8), Hunan and Jiangxi populations were relatively high ( > 0.5), and Anhui and Chongqing populations were the lowest ( < 0.5). There was obvious genetic differentiation among six populations and gene flow was limited. An AMOVA analysis indicated that the source of variation within the populations was higher than between the populations. The major genetic variation was derived from variation within populations. A neighbor-joining phylogenetic tree showed that the genetic distance between the Hunan and other five populations was distant. The Chongqing population could originate from one single ancestor and a few populations. To date, the genetic diversity of natural populations is abundant. Furthermore, the genetic diversity did not sharply decrease, owing to the impact of the transaction and culture of M. albus to the environment and its breeding potential make this species a potentially excellent germplasm resource.

Abstract:DNA barcodes can be used to identify existing biological groups and unknown biomaterials through shorter DNA sequences using polymerase chain reaction (PCR). The mitochondrial cytochrome coxidase I (COI) gene is one of the commonly used DNA barcoding genes. In the present study, to analyze the effectiveness of the COI gene for DNA barcoding in mollusk evolution, 353 sequences of 60 species belonging to 13 orders and 33 families were obtained by PCR amplification for clustering analysis. A neighbor-joining (NJ) phylogenetic tree was constructed by Mega, and the genetic evolution of seven species from different populations was also analyzed. The results showed that the universal primers of the COI gene were highly versatile for most shellfish. Although the amplification efficiency of primers in Pterioida was only 10%, it reached 82.7% for the individuals. Except for the evolutionary status of eight species, such as , the clustering relationships of other species were similar to results obtained using traditional methods. Based on the clustering analysis of 7 species from 26 geographical groups, it was found that the COI gene generally clustered the different geographical groups of the same species first, and some individuals in the population or group had clustering disorder. In conclusion, the COI gene could be applied to the identification and phylogenetic studies of shellfish species to a certain extent, which would enhance the role of the COI gene in practical applications of species identification, and provide reference data for the construction of shellfish DNA barcoding databases.

Abstract:Commonly known as mantis shrimps, stomatopods are commercially valuable and taxonomically diverse. In spite of high species diversity, stomatopod species exhibit subtle morphological differences, which make species identification a difficult task based on taxonomic keys alone. DNA barcoding has been proposed as a promising tool for species identification and discovery in a wide range of animal taxa. In this study, the performance of DNA barcoding in delineating stomatopod species in the China seas was assessed. The nucleotide sequences of mitochondrial cytochrome oxidase subunit-I (COI) gene were obtained from 204 individuals of 38 stomatopod species in 24 genera in a wide phylogenetic range. These 204 sequences were compared with the other 42 homologous sequences from 14 species of Stomatopoda retrieved from GenBank. Sequence comparisons revealed 223 polymorphic sites, 217 of which were parsimony informative, and no InDels were found. The COI sequences showed a strong AT bias (63.5%) in nucleotide composition. As expected, the mean Kimuara-2-parameter (K2P) genetic divergence increased with an increase in the taxonomic rank. The pairwise genetic divergences among conspecific individuals ranged from 0% to 3.91%, with a mean of 0.76%. The mean K2P pairwise divergence between individuals of congeneric species was 12.91%, ranging from 6.55% to 18.99%. The mean K2P pairwise divergence between individuals of different genera that belong to the same family was 16.89% (range 9.16%-23.32%), and mean K2P pairwise divergence between individuals of different stomatopod families was 21.31% (range 16.52%-26.6%). Thus, an obvious "barcoding gap" was found between intraspecific and interspecific divergences of COI sequences within Stomatopoda. The neighbor-joining phylogenetic tree reconstructed by COI sequences recovered most species as monophyletic with high bootstrap support, except for the species represented by a single individual. In addition, two reciprocally monophyletic, highly supported lineages together with large inter-lineage relative to intra-lineage divergences recovered from COI data concur in suggesting the existence of two possible cryptic species in (De Haan, 1844). These results demonstrate the effectiveness of mitochondrial COI-based DNA barcoding for species identification and cryptic discovery in stomatopods.

Abstract:In order to study the phylogenetic relationship of Euphausiacea, 50 Euphausiacea species were selected and used for the construction of a phylogenetic tree. The mitochondrial COI gene was amplified using PCR techniques. The results showed that a 519 bp COI gene fragment was obtained and sequenced, with 258 mutation sites, all of which were base substitutions, and no insertion/deletion sites. The contents of A, T, G, and C were 27.58%, 35.47%, 18.88%, and 18.07% respectively. Additionally, the content of A+T (63.05%) was significantly higher than that of G+C (36.95%). The genetic distance within species ranged from 0 to 0.071 and the average value was 0.017. The genetic distance among species ranged from 0.065 to 0.306, and the average value was 0.186, which was about 11 times that of the former. With regards to the minimum interspecific genetic distance of 0.020, the difference between the COI gene sequences could distinguish the Euphausiacea species efficiently. Four phylogenetic trees were constructed:neighbor-joining tree (NJ), maximum likelihood tree (ML), maximum parsimony tree (MP), and UPGMA tree. Their topological structures were basically the same, i.e. they can be divided into three branches. Pseudeuphausia was on the bottom of the phylogenetic tree, which was one of the earlier species of Euphausiacea. The Euphausia, which contained the most species, finally was branched out, indicating that it was a relatively newer genus of Euphausiacea. The phylogenetic relationships among 11 Euphausiacea genera have been comprehensively discussed in this paper. The results showed that the phylogenetic tree constructed based on the mitochondrial COI gene could be used to study the phylogenetic relationships between the Euphausiacea species and was of notable theoretical and practical value.

Abstract:DNA barcoding has been widely used in the fields of taxonomy, identification, phylogenetic evolution, and population genetic analysis of marine shellfish. To further evaluate the identification validity of different DNA barcoding genes in marine shellfish, sequences of COI, 16S rRNA, 18S rRNA, and 28S rRNA from Veneroida were randomly downloaded from the GenBank database, analyzed by the distance-and tree-based methods, and taxonomic relation established by the tree-based method, and compared the results with some sequences from our laboratory. According to the "10×rule" and "2%" standard criterion, 57.1% of species could be distinguished using the COI gene, whereas 16S rRNA identified 60.9%, 18S rRNA identified 16.7%, and 28S rRNA did not identify any species. We also found that there were significant barcode gaps between the genetic distances of pairwise-and within-species in most genera based on COI and 16S rRNA genes; however, there were significant overlaps, instead of barcode gaps, based on 18S rRNA and 28S rRNA. The cluster analysis showed that 87.9% of individuals clustered to a monophyletic group, with other within-species individuals clustered on the COI; and 65.6% 16S rRNA individuals clustered in monophyletic groups. Furthermore individuals without monophyletic groups clustered into sister groups, which revealed that the evolutionary relationships showed by the NJ tree constructed via COI and 16S rRNA mainly agreed with that from the morphological classification, especially that of the COI gene. In contrast, the NJ tree constructed via 18S rRNA and 28S rRNA genes showed disordered clustering relationships, including some individuals from different species cluster to monophyletic groups. In the present study, the results clearly suggested that both COI and 16S rRNA can be used as DNA barcodes in identifying species in Veneroida, particular COI, but 18S rRNA and 28S rRNA are not suitable because of the large intraspecific variation. This study provides new data for DNA barcode selection in Veneroida.

Abstract:This study analyzed the phylogeny, genetic diversity, and species identification of using the COI gene and 16S rRNA. Firstly, we obtained the complete mitochondrial genome of using Illumina sequencing. Compared with the mitochondrial genomes of the other close species, ATP8 was missing and tRNA^Met was duplicated in this genome. Based on the sequences of COI and 16S rRNA from the population, the nucleotide diversities of the COI gene and 16S rRNA were 0.00195 and 0.00073, respectively. The haplotype diversity of the COI gene was 0.76, larger than that of 16S rRNA (0.318). Secondly, a phylogenetic tree based on the mitochondrial proteins of species in Mactridae and Veneridae were constructed using the maximum likelihood (ML) method. Using this tree as a reference, we also constructed the ML phylogenetic trees using COI and 16S rRNA genes, respectively. These two trees were consistent with the reference, suggesting that these two DNA barcodes could be applied to the phylogenetic analysis. Thirdly, we analyzed the genetic distances based on sequences of the COI gene and 16S rRNA from 17 species in Mactridae and Veneridae. The average inter-and intra-species Kimura-2-parameter (K2P) distances based on COI sequences were 1.17 and 0.019, respectively. The average inter-and intra-species Kimura-2-parameter (K2P) distances based on 16S rRNA sequences were 1.117 and 0.018, respectively. The results suggested that for both the COI gene and 16S rRNA, the average inter-species genetic distances were 62 times larger than the intra-species distances. These results indicated that 16S rRNA could function as the COI gene to efficiently construct the phylogenetic tree and species identification. However, the COI gene could be used more effectively than 16S rRNA to analyze the genetic diversity of .

Abstract:The Earth's biodiversity are closely altered by a variety of human activities at all scale from local to global. These changes have a strong potential effect to biological communities, ecosystem properties, social affairs and economic development they provide. China fishery is characterized by high biodiversity which cover 10 percent of the total earth species because its role geographical position that occupies the eastern part of the Eurasian continent adjacent to the western Pacific Ocean. In recent years, it is a very realistic and important scientific problem to protect and rationally utilize the biodiversity of fisheries globally. However, insufficient protection and hard utilization of fishery isn't a single case in China. To promote the development of fishery biological diversity in China, this paper puts forward the idea of DNA bar code methods for performing in fishery biology activities. It reviewed how DNA barcode expounds the sustainable development in the fishery biological resources, species identification and classification, fishery biodiversity monitoring, foreign species evaluation, market and supervision, fishery information and so on. Besides that, it further discussed the recent prospects for the DNA barcode in the biologic study of fishery organisms, water ecological research, electronic classification technology and the new technology of meta DNA barcoding. This research had appealed the continuous researches on construction of a fishery DNA barcode database and information platform of China which need to be constructed and shared nationally and globally.