Genetic diversity in two Japanese flounder populations from China seas inferred using microsatellite markers and COI sequences

Japanese flounder is one of the most important commercial species in China; however, information on the genetic background of natural populations in China seas is scarce. The lack of genetic data has hampered fishery management and aquaculture development programs for this species. In the present study, we have analyzed the genetic diversity in natural populations of Japanese flounder sampled from the Yellow Sea (Qingdao population, QD) and East China Sea (Zhoushan population, ZS) using 10 polymorphic microsatellite loci and cytochrome c oxidase subunit I (COI) sequencing data. A total of 68 different alleles were observed over 10 microsatellite loci. The total number of alleles per locus ranged from 2 to 9, and the number of genotypes per locus ranged from 3 to 45. The observed heterozygosity and expected heterozygosity in QD were 0.733 and 0.779, respectively, and in ZS the heterozygosity values were 0.708 and 0.783, respectively. Significant departures from Hardy-Weinberg equilibrium were observed in 7 of the 10 microsatellite loci in each of the two populations. The COI sequencing analysis revealed 25 polymorphic sites and 15 haplotypes in the two populations. The haplotype diversity and nucleotide diversity in the QD population were 0.746±0.072 8 and 0.003 34±0.001 03 respectively, and in ZS population the genetic diversity values were 0.712±0.047 0 and 0.003 18±0.000 49, respectively. The microsatellite data (F_st =0.048 7, P<0.001) and mitochondrial DNA data (F_st =0.128, P<0.001) both revealed significant genetic differentiation between the two populations. The information on the genetic variation and differentiation in Japanese flounder obtained in this study could be used to set up suitable guidelines for the management and conservation of this species, as well as for managing artificial selection programs. In future studies, more geographically diverse stocks should be used to obtain a deeper understanding of the population structure of Japanese flounder in the China seas and adjacent regions.     

Genetic diversity of populations and clones of Rhopilema esculentum in China based on AFLP analysis

Amplified fragment length polymorphisms(AFLP) markers were developed to assess the genetic variation of populations and clones of Rhopilema esculentum Kishinouye(Scyphozoa,Rhizostomatidae).One hundred and seventy-nine loci from 56 individuals of two hatchery populations and two wild populations were genotyped with five primer combinations.The polymorphic ratio,Shannon’s diversity index and average heterozygosity were 70.3%,0.346 and 0.228 for the white hatchery population,74.3%,0.313,and 0.201 for the red hatchery population,79.3%,0.349,and 0.224 for the Jiangsu wild population,and 74.9%,0.328 and 0.210 for the Penglai wild population,respectively.Thus,all populations had a relatively high level of genetic diversity.A specific band was identified that could separate the white from the red hatchery population.There was 84.85% genetic differentiation within populations.Individual cluster analysis using unweighted pair-group method with arithmetic mean(UPGMA) suggested that hatchery populations and wild populations could be divided.For the hatchery populations,the white and red populations clustered separately;however,for the wild populations,Penglai and Jiangsu populations clustered together.The genetic diversity at the clone level was also determined.Our data suggest that there are relatively high genetic diversities within populations but low genetic differentiation between populations,which may be related to the long-term use of germplasm resources from Jiangsu Province for artificial seeding and releasing.These findings will benefit the artificial seeding and conservation of the germplasm resources.     

凡纳滨对虾4个选育群体遗传多样性的SSR分析

采用9对微卫星引物分析了凡纳滨对虾4个选育群体(Molokai、OI、SIS和Kona Bay)的遗传多样性。结果表明:9对微卫星引物共检测到32个等位基因,每个位点等位基因数2～7个,平均3.555 6个,平均有效等位基因数2.472 7;各位点的观测杂合度(Ho)0.026 0～0.623 4,期望杂合度(He)0.263 1～0.785 5;各群体平均观测杂合度从小到大依次为SIS(0.383 3)相似文献   

GENETIC DIVERSITY OF THE WILD AND REARED PSEUDOSCIAENA CROCEA

The genetic diversity of both wild and reared Pseudosciaena crocea (Richardson) col-lected from Guan-Jing-Yang in Ningde, China in May 1999 was investigated by random amplified poly-morphic DNA (RAPD) in the present study. The polymorphism and mean difference of the wild popula-tion as revealed by RAPD were 18.9% and 0.0960 respectively, and those of the reared stocks were rel-atively lower, with 16.7% in polymorphism and 0.0747 in mean difference. The genetic distance be-tween the two stocks was 0.0041. From the comprehensive investigation, the main reasons for the loss of genetic diversity were probably overilshing, small number of parents as broodstocks and the debatable arti-ficial ranching. Results from this study also showed that the large yellow croaker populations distributed along Fujian coastal waters including Guan-Jing-Yang still potentially wide genetic variability. It is sug-gested that genetic management and prevention should be scientifically conducted in order to maintain and improve the genetic diversity of the P. crocea population.     

Genetic differentiation of Japanese sardinella (Sardinella zunasi) populations in the Northwest Pacific revealed by ISSR analysis

Knowledge of population genetic structure plays an important role in fisheries management.In this research,In-ter-Simple-Sequence-Repeat(ISSR)markers were employed to evaluate the genetic structure of Japanese sardinella(Sardinella zun-asi)populations in the Northwest Pacific.Eighty seven individuals from 5 locations were screened using 4 highly polymorphic prim-ers.A total of 173 polymorphic loci were detected out of 191 loci amplified.Small but significant genetic differentiation was de-tected between the Chinese and Japanese populations by both AMOVA and pairwise FST analyses,which was further supported by cluster analysis.We consider that climate change during glaciations should be responsible for the genetic differentiation.Isolation by geographic distance among populations was observed,indicating that the distance might also lead to the genetic differentiation.However,no genetic structure was found within the populations off both the Chinese and Japanese coasts,indicating a high-level along-coast gene flow,which might result from ocean current transport and common ground for over-wintering.     

Genetic analysis of four populations of redlip mullet (Chelon haematocheilus) collected in China seas

Horizontal starch gel electrophoresis was used to investigate genetic structures of four populations (Dandong, Rizhao, Ningbo and Guangzhou) of redlip mullet (Chelon haematocheilus). Fourteen loci of ten enzymes (G3PDH, IDHP, LAP, LDH, MDH, MPI, PGDH, PGM, SDH, and SOD) were identified. The proportions of polymorphic loci varied from 0.07 to 0.14. The average observed and expected heterozygosities ranged from 0.02 to 0.05 and from 0.02 to 0.04 respectively among the 4 populations. The average number of efficient alleles of each locus varied from 1.02 to 1.06. The genetic distance among populations was from 0.0004 to 0.0021. The genetic distances between Dandong, Rizhao and Ningbo populations were small, while those between Guangzhou population and other three populations were relatively high. The result indicated the possible divergence of redlip mullet between the South China Sea and the other sea areas of China due to geographic isolation.     

Genetic diversity and population structure of Eleutheronema rhadinum in the East and South China Seas revealed in mitochondrial COI sequences

Eleutheronema rhadinum is a potential commercial fisheries species and is subject to intense exploitation in China. Knowledge on the population structure of E. rhadinum in Chinese coastal waters, which is important for sustainable exploitation and proper resource management, is lacking. In the present study, the genetic diversity and population structure of E. rhadinum were evaluated using a 564-base pair fragment of the mitochondrial cytochrome c oxidase subunit I （COl） gene. A total of 76 specimens were collected from three localities around the East （Qidong and Zhoushan） and South China Seas （Zhuhai）. Among these individuals, nine polymorphic sites were detected and 1 l distinct haplotypes were defined. High levels ofhaplotype diversity （h=0.759i0.035） and low levels of nucleotide diversity （re=0.001 98i0.003 26） were observed in these populations, Hierarchical analysis of molecular variance （AMOVA） indicated that 96.72% of the genetic variation occurred within the populations, whereas 3.28% occurred among populations. No significant genealogical branches or clusters were recognized on the neighbor-joining tree. Intra-group variation among populations was significant （~0~t=0.032 85, P〈0.01）. These results suggest that E. rhadinum populations in the East and South China Seas have developed divergent genetic structures. Tests of neutral evolution and mismatch distribution suggest that E. rhadinum may have experienced a population expansion. The present study provides basic information for the conservation and sustainable exploitation of this species.     

Genetic improvement on Chinese shrimp （Fenneropenaeus chinensis）： growth and viability performance in F1 hybrids of different populations

Fenneropenaeus chinensis distributed in the Yellow Sea and Bohai Sea of China and the west coast of the Korean Peninsula. Different geographical populations represent potentially different genetic resources. To learn further the characteristics of different geographical population, crosses among two wild and three farmed populations were produced. The two wild populations were from the Yellow Sea and Bohai Sea (WYP), and the west coast of the Korean Peninsula and coast (WKN). The three farmed populations included the offspring of first generation of wild shrimp from coast in Korea (FKN), the Huang Hai (the Yellow Sea in Chinese) No. 1 (HH 1), and JK98. The phenotypes growth and survival rates of these populations were compared to confirm the feasibility for crossbreeding. The body length (BL), carapace length (CL), carapace width (CW), height of the second and third abdominal segment (HST), width of the second and third abdominal segment (WST), length of the first abdominal segment (LF), length of the last abdominal segment (LL), live body weight (BW), and survival rate were measured. Different combinations were statistically performed with ANOVA and Duncan's Multiple significant difference (P<0.05) in BL, CL, HST, LL, and BW; and insignificant difference (P0.05) in other growth traits and survival rate. The results of Duncan's Multiple Range Test are that BL and CL of was the best combination in all growth traits. Therefore, hybridization can introduce the variation to base populations. The systematic selection program based on additive genetic performance may be more effective than crossbreeding.     

Phylogenetic diversity and bioactivity of culturable deep-sea-derived fungi from Okinawa Trough

Deep-sea sediments are now recognized as a home for rich and largely microbial community. Recently, it has been believed in an increasing number of studies that bacteria could be abundant in deepsea sediments of many types; however, fungi in deep-sea sediments remain relatively unknown. The phylogenetic diversity and bioactivity of culturable deep-sea-derived fungi from Okinawa Trough sediments were investigated in traditional method combined with fungal identification of molecular biology in this study. A total of 76 isolates belonged to 15 fungal taxa were recovered in a harsh condition of low nutrient and low temperature, indicating that the fungal communities in deep-sea sediments from Okinawa Trough were relatively abundant and diversified. Aspergillus, Cladosporium, and Penicillium were the dominant fungal genera, while Mycosphaerella, Purpureocillium, and Schizophyllum were relatively rare in the deep-sea sediments from Okinawa Trough. Among the six genera recovered, Mycosphaerella was firstly recovered from deep-sea sediments in this study. Moreover, about 75% of the extracts from the 15 fungal representative isolates displayed distinct bioactivity against at least one indicator bacterium or marine macrofouler, emphasizing the potentials of these deep-sea-derived fungi from Okinawa Trough as producers of bioactive metabolites. Notably, isolates Cladosporium oxysporum SCSIO z001 and Penicillium citrinum SCSIO z049 displayed a wide spectrum of bioactivities, isolates Cladosporium cladosporioides SCSIO z015, Cladosporium sphaerospermum SCSIO z030, and Penicillium verruculosum SCSIO z007 exhibited a strong anti-bacterial-growth activity, and isolate Penicillium chrysogenum SCSIO z062 displayed a strong anti-larval-settlement activity. These results suggest that these isolates deserved further study as potential sources of novel bioactive metabolites.     

Genetic improvement on Chinese shrimp （Fenneropenaeus chinensis）： growth and viability performance in F1 hybrids of different populations

Fenneropenaeus chinensis distributed in the Yellow Sea and Bohai Sea of China and the west coast of the Korean Peninsula. Different geographical populations represent potentially different genetic resources. To learn further the characteristics of different geographical population, crosses among two wild and three farmed populations were produced. The two wild populations were from the Yellow Sea and Bohai Sea （WYP）, and the west coast of the Korean Peninsula and coast （WKN）. The three farmed populations included the offspring of first generation of wild shrimp from coast in Korea （FKN）, the Huang Hai （the Yellow Sea in Chinese） No.1 （HH1）, and JK98. The phenotypes growth and survival rates of these populations were compared to confirm the feasibility for crossbreeding. The body length （BL）, carapace length （CL）. carapace width （CW）, height of the second and third abdominal segment （HST）, width of the second and third abdominal segment （WST）, length of the first abdominal segment （LF）, length of the last abdominal segment （LL）, live body weight （BW）, and survival rate were measured, Different combinations were statistically performed with ANOVA and Duncan＇s Multiple Range Test. The results show that the survival rate of JK98（♀）×WKN（♂） was the highest, followed by WYP（♀）×WKN（♂）, FKN（♀）×WYP（♂）, FKN（♀）×HHI（♂） and WYP（♀）×FKN（♂）; the body weight of FKN（♀）×HHI（♂） was the highest, followed by FKN（♀）×WYP（♂）, WYP（♀）×WKN（♂）, WYP（♀）×FKN（♂） and JK98（♀）×WKN（♂）; the total length had the same ranking as the body weight. All growth traits in hybrids JK98（♀）×WKN（♂） were the lowest among all combinations. F1 hybrids had significant difference （P〈0.05） in BL, CL, HST, LL, and BW; and insignificant difference （P〉0.05） in other growth traits and survival rate. The results of Duncan＇s Multiple Range Test are that BL and CL of J     

Neuroanatomy and morphological diversity of brain cells from adult crayfish Cherax quadricarinatus

Journal of Oceanology and Limnology - As in vertebrates, brains play key roles in rhythmic regulation, neuronal maintenance, differentiation and function, and control of the release of hormones in...     

Genetic Variation and Differentiation in Wide Ranging Populations of Razor Clam （Sinonovacula constricta） Inferred from AFLP Markers

The genetic variation and differentiation of the razor clam Sinonovacula constricts distributed along the coast of China were studied through amplified fragment length polymorphism(AFLP)analysis. Six primer combinations generated 193 fragments. The He values varied from 0. 322 to 0. 463 and the percentage of polymorphic loci ranged from 74. 1% to 98. 4%, which indicates a high level of genetic diversity. Cluster analysis by Nei's pairwise distance grouped all specimens by geographical origins. AMOVA consistently showed that genetic variation among populations was 8. 71%, and most of the variation came from the genetic variation within populations(91.29%). Genetic differentiation among the six populations was moderate; pairwise FST ranged from 0. 0282 to0. 1480, which indicated that S. Constricts populations along the coast of China are genetically connected. Among all the six populations, the Beihai population is the mostly differentiated from the others, suggesting that Hainan Island and Leizhou Peninsula act as barriers to gene flow. All populations abide isolation by distance model as indicated by Mantel test, except for ZS(Zhoushan)and YQ(Yueqing)populations. Information obtained in this study will provide guidelines for conservation and fishery management of this species in the future.     

Sequence and phylogenetic analyses of the chloroplast 16S rRNA, tufA, and rbcL genes from Bryopsis hypnoides

Using shotgun sequencing data, the complete sequences of chloroplast 16S rRNA and tufA genes were acquired from native specimens of Bryopsis hypnoides (Qingdao, China). There are two group I introns in the 16S rRNA gene, which is structurally similar to that of Caulerpa sertularioides (Bryopsidales, Chlorophyta). The chloroplast-encoded tufA gene sequence is 1 230 bp long, very AT-rich (61.5%), and is similar to previously published 16S rRNA sequences of bryopsidinean algae. Phylogenetic analyses based on chloroplast 16S rRNA and tufA gene sequence data support previous hypotheses that the Bryopsidineae, Halimedineae, and Ostreobidineae are three distinct lineages. These results also confirmed the exclusion of Avrainvillea from the family Udoteaceae. Phylogenetic analyses inferred that the genus Bryopsis as sister to Derbesia; however, this clade lacked robust nodal support. Moreover, the phylogenetic tree inferred from rbcL GenBank sequences, combined with the geographical distributions of Bryopsis species, identified a strongly supportive clade for three differently distributed Asian Bryopsis species. The preliminary results suggesting that these organisms are of distinct regional endemism.     

Characterization and diversity of magnetotactic bacteria from sediments of Caroline Seamount in the Western Pacific Ocean

Journal of Oceanology and Limnology - Magnetotactic bacteria(MTB) are a group of microorganisms capable of orientating and swimming along magnetic fields because they contain intracellular...     

辽河油田油泥微生物多样性分析及功能菌种筛选评价

分析辽河油田某区块不同来源油泥中微生物种类多样性、优势菌群和分布特征,探讨功能微生物在含油污染物的生物修复及提高原油采收率的应用可行性。采集辽河油田某区块3个油泥样品,利用第二代高通量测序技术测定油泥样品内微生物的16SrDNA V3-V4可变区序列,整理和统计各分类水平的微生物类群数,分析微生物的丰度、分布和多样性,以及不同位置油泥微生物多样性丰度的差异。结果表明:辽河油田某区块油泥中3组样品属水平的微生物类群数分别为51、135和213,不同来源样品中微生物种类及所占比例差异显著;优势菌群中含有多种已报道可作用原油的功能微生物,如芽孢杆菌属(Bacillus)和诺卡氏土壤菌属(Nocardiopsis)等;从油泥中筛选的菌株LH-03发酵液表面张力为29.3mN/m,对煤油和液体石蜡乳化层高度分别为6.1和5.7cm,经鉴定为枯草芽孢杆菌(Bacillus subtilis),与Pseudomonas aeruginosa CB-01复配使用,油泥降解实验除油率达到51.9%,石蜡降解率达到38.9%,填砂管驱油实验可在水驱基础上提高采收率12.7%。辽河油田油泥含有较丰富的微生物修复物质基础,具备通过生物刺激和强化技术实现原位生物修复的可行性。     

Microbial diversity in Huguangyan Maar Lake of China revealed by high-throughput sequencing

Huguangyan Maar Lake is a typical maar lake in the southeast of China.It is well preserved and not disturbed by anthropogenic activities.In this study,microbial community structures in sediment and water samples from Huguangyan Maar Lake were investigated using a high-throughput sequencing method.We found significant differences between the microbial community compositions of the water and the sediment.The sediment samples contained more diverse Bacteria and Archaea than did the water samples.Actinobacteria,Betaproteobacteria,Cyanobacteria,and Deltaproteobacteria predominated in the water samples while Deltaproteobacteria,Anaerolineae,Nitrospira,and Dehalococcoidia were the major bacterial groups in the sediment.As for Archaea,Woesearchaeota(DHVEG-6),unclassified Archaea,and Deep Sea Euryarchaeotic Group were detected at higher abundances in the water,whereas the Miscellaneous Crenarchaeotic Group,Thermoplasmata,and Methanomicrobia were significantly more abundant in the sediment.Interactions between Bacteria and Archaea were common in both the water column and the sediment.The concentrations of major nutrients(NO_3~-,PO_4~(3-),SiO_3~(2-)and NH_4~+)shaped the microbial population structures in the water.At the higher phylogenetic levels including phylum and class,many of the dominant groups were those that were also abundant in other lakes;however,novel microbial populations(unclassified)were often seen at the lower phylogenetic levels.Our study lays a foundation for examining microbial biogeochemical cycling in sequestered lakes or reservoirs.     

Woody species diversity and forest structure from lowland to montane forest in Hyrcanian forest ecoregion

Alborz Mountains host Caspian Hyrcanian forest ecoregion along the northern slopes and forest steppe ecoregion in highlands. Hyrcanian forest covers the southeastern part of Caucasus biodiversity hotspot and is of great biogeographic importance. Altitudinal pattern and correlation between woody species biodiversity (DIV), forest structure ((stem density (DEN), mean basal area (MBA) and mean height class (MHC)) and disturbance (DIS) were explored along 2,400 m altitudinal gradient in Hyrcanian relict forest, Central Alborz Mountains. Vegetation changes from lowland forest (LoF) to mid- altitude forest (MiF) and montane forest (MoF) in this area. The altitudinal gradient was divided into twelve 200 m elevational belts. Point centered quarter method (PCQM) with 96 sampling points and 83 vegetation samples by plot method (PM) were used to record field data. Shannon-Wiener index and Pearson coefficient were used for diversity and correlation analysis. The results showed that DEN decreased linearly, MBA and MHC showed relatively hump shaped and DIS showed a reverse hump shaped pattern of change along altitudinal gradient. Woody species diversity decreased non-steadily from LoF to MoF. Transitional vegetations of Carpinus-Fagus and Fagus-Quercus represented higher diversity of woody taxa compared to adjacent homogenous communities. Significant correlation was observed between altitude and all parameters: DEN with MBA, DIS and DIV; MBA with DIS; MHC with DIS along with DIV; and DIS with DIV at the study area scale. Surprisingly,correlation between studied parameters differed within each vegetation type. Altitude probably acts as a proxy for human and environmental driving forces in this area. Stability of warm and wet condition, season length, soil depth along with forest accessibility probably influences the altitudinal pattern of the studied parameters. Disturbance affects forest structure and consequently diversity; especially in lowlands. The obtained results recommend using both forest biodiversity and mensuration data in management process of forest ecosystems.     

Phylogenetic diversity of culturable bacteria in surface seawater from the Drake Passage,Antarctica

The Drake Passage is located between the Antarctic Peninsula and Tierra del Fuego in the south of South America. Surface seawater samples were collected at seven sites in the Drake Passage during the austral summer of 2012. The 16S rRNA sequences were analyzed from 187 isolated bacterial strains. Three phyla, 29 genera and 56 species were identified. The three phyla were Actinobacteria, Firmicutes and Proteobacteria; the Proteobacteria included α-Proteobacteria, β-Proteobacteria and γ-Proteobacteria. γ-Proteobacteria, Actinobacteria and Firmicutes were the dominant class or phyla in terms of quantity and species. Gram-positive bacteria (Actinobacteria and Firmicutes) accounted for 57.8% of all types identified. There were nine dominant genera, including Curtobacterium, Staphylococcus, and Halomonas, and 14 dominant species including Curtobacterium flaccumfaciens, Curtobacterium pusillum, and Staphylococcus sciuri. Of the strains identified, 87.2% were catalase positive or weakly positive.     

Changes in fish diversity and community structure in the central and southern Yellow Sea from 2003 to 2015

The central and southern Yellow Sea is an important overwintering ground for many fish species in the Bohai Sea and Yellow Sea. For better understanding the status of the fish community after years of heavy exploitation, variations in fish community structure and diversity were analyzed using data from bottom trawls during 2003–2015. Five fish assemblage indices all showed fluctuations without clear trends from 2003 to 2015, yet there were strong positive and significant correlations(P 0.05) among them. The top-five dominant species accounted for a high weight percentage(49.7%–82.1%) in the annual fish catch. Multivariate analysis showed that two year groups could be pooled for the fish community: Group Ⅰ consisted of the years 2006, 2007, 2008 and 2015, while Group Ⅱ consisted of the years 2003, 2004, 2005, 2009, 2010 and 2014; the groups aggregated with 63.71% similarity, indicating a high level of similarity among all years. The multivariate dispersion values were 1.455 and 0.818 for Groups Ⅰ and Ⅱ, respectively, indicating greater variances in fish assemblage structure in Group Ⅰ than that in Group Ⅱ. Similarity of percentage analysis demonstrated that the average similarities for Group Ⅰ and Group Ⅱ were 71.58% and 67.51%, respectively. Size-spectra analysis revealed no consistent trend in the intercept and slope( P 0.05); there were also no significant differences between the slope of the size-spectra and fishing ef fort. The catch per unit ef fort and mean individual weight analyses of the whole fish assemblage both showed a significantly decreasing trend over time. Overall, the results showed that the fish community structure in the central and southern Yellow Sea was relatively stable from 2003 to 2015 and the study could be used as a reference for supporting ecosystem-based fishery management.     

Genetic variation within and among range-wide populations of three ecotypes of the Japanese grenadier anchovy Coilia nasus with implications to its conservation and management

Journal of Oceanology and Limnology - Studies of range-wide populations can contribute to the comprehension of the relative roles of historical events and contemporary factors that influence...