Report of the ICSF-BOBLME India (East Coast) workshop: implementing the FAO voluntary guidelines for securing sustainable small-scale fisheries in the context of food security and poverty eradication (SSF guidelines), 6-7 March 2015, Chennai, India

The workshop titled, ICSF-BOBLME India (East Coast) Workshop on Implementing the FAO Voluntary Guidelines for Securing Sustainable Small-scale fisheries in the Context of Food Security and Poverty Eradication (SSF Guidelines) was organized by ICSFin collaboration with BOBLME project.The workshop was the third in a series of consultations held in 2015 across the globe to promote the ownership of the SSF Guidelines among different stakeholders. In the run –up to the workshop, ICSF, with support from BOBLME conducted six consultation meetings with fishworkers and fishworker organizations along the east coast of India in January and February 2015. One hundred participants from India’s eastern coastal states of West Bengal, Odisha, Andhra Pradesh, Tamil Nadu and Puducherry, including women fishworkers, representatives of fishworker organizations, representatives from Department of Fisheries and other concerned departments at state and central level, Multilateral agencies, Inter-governmental organizations, Research Institutions met at Chennai, 6-7 March, 2015. The workshop was structured to facilitate active interaction and discussion among participants, taking into account linguistic diversity and the contextual differences of the marine and inland sectors. This publication—the proceedings of the Chennai workshop—will be useful for fishworker organizations, researchers, policymakers, members of civil society and anyone interested in fisheries and livelihoods.

Genetic studies of human diversity in East Asia

East Asia is one of the most important regions for studying evolution and genetic diversity of human populations. Recognizing the relevance of characterizing the genetic diversity and structure of East Asian populations for understanding their genetic his

Molecular Phylogeny of Geographical Isolates of Bursaphelenchus xylophilus: Implications on the Origin and Spread of this Species in China and Worldwide

The genetic diversity and phylogeny of 26 isolates of Bursaphelenchus xlophilus from China, Japan, Portugal and North America were investigated based on the D2/3 domain of 28S rDNA, nuclear ribosomal Internal Transcribed Spacer (ITS) sequences, and random amplified polymorphic DNA (RAPD) analysis. The genetic diversity analysis showed that the D2/3 domain of 28S rDNA of isolates of B. xlophilus from China, Portugal, Japan and the US were identical and differed at one to three nucleotides compared to those from Canada. ITS sequences of isolates from China and Portugal were the same; they differed at one or two nucleotides compared to those of Japanese isolates and at four and 23 nucleotides compared to those front the US and Canada, respectively. The phylogenetic analysis indicated that Chinese isolates share a common ancestor with one of the two Japanese clades and that the Canadian isolates form a sister group of the clade comprised of isolates from China, Portugal,Japan, and the US. The relationship between Japanese isolates and those from China was closer than with the American isolates. The Canadian isolates were the basal group of B. xylophilus. This suggests that B. xlophilus originated in North America and that the B. xylphilus that occurs in China could have been first introduced from Japan. Further analysis based on RAPD analysis revealed that the relationship among isolates from Guangdong, Zhejiang, Shandong, Anhui provinces and Nanjing was the closest, which suggests that pine wilt disease in these Chinese locales was probably dispersed from Nanjing, where this disease first occurred in China.

Investigation of polymorphism by PCR-RFLP method in Cobia fish Rachycentron canadum in the Persian Gulf and Oman Sea

Cobia is a native fish species in Iranian waters in the Persian Gulf and Sea of Oman and has a good internal and foreign market. This fish is a fast growing species and for this reason Iranian Fisheries is considering to go for it culture practices. To go for any utilization such as fishing from wild stocks or culture activities, needs a better understanding of its peculiarities and genetic characteristics of its natural resources. Therefore, this project was discribed and conducted. In this investigation, cuts 2 or 3 cm of fin tissue of  specimen of Cobia obtained from Sistan and Bluchestan, Hormozgan, Bushehr and Khuzestan water provinces, were collected. DNA was extracted by Phenol-chlorophorm method and produced PCR product in length of 1060 and 1450 base pair of two mitochondrial genes COI and NADH2. Using 13 cutting enzymes (4 enzymes were subscriber for both of genes), 205 base pair (from 2510 base pair, equal with %3.8 from gene regains) were directly investigated. But binding patterns of enzymatic digestion of PCR products of both COI and ND genes from electrophoresis were monomorph in all samples and no polymorphism was observed. This may be attributed to the unsuitable choice of COI and ND2 genes for showing of intra specific divergence. But in general non-existence of genetic diversity or noticeable decrease of that among individuals has been reported in regions were fish migration exist and they can freely move between two regions. Therefore, non-observation of polymorphism in the study area might be the case and indicates represents the area. On the other hand, some scientists believe that the distributions of populations in different regions are greatly affected by environmental and physical and ecological factors. Althoug Cobia is a migratory fish, but with regard to the fact that the environmental conditions are different (specially temperature and salinity) between east and west of Persian Gulf and Oman sea, there is a possibility that different genetic groups of this species exist in the regions. Of course It is clear that using more samples and enzymes from other genetically regions could produce better results. Since none of the two investigated genes didn’t show genetic divergence or polymorphism amongst the individuals of one region or between different regions, therefore, statistic analysis for estimating of haplotype diversity or nucleotide diversity and drawing of relationship tree among individuals using available softwares was not possible.

Identification of biodiversity and distribution pattern of benthic Foraminifera and Ostracoda in continental shelf sediments of the Oman Sea

Biodiversity and distribution of benthic Foraminifera and Ostracoda in the continental shelf sediments of the Omman Sea was studied in order to indicating of the composition of benthic foraminiferal and ostracodal communities and determining of their relationship with the environmental factors of the Omman Sea. Sediment samples were gathered in winter 2006 from twelve stations ranging in depth from 30 to 103 meters. Environmental factors including depth, temperature, salinity, dissolved Oxygen and pH were measured with a CTD system during sampling time and grain size and total organic matter were measured in laboratory. From the overall 57 benthic foram species, there were 52 identified species belong to 25 genera of 16 families. The cosmopolitan foraminifer, Ammonia beccarii, was common in all sampling stations. The composition of benthic foram communities had a highly positive correlation with depth, salinity and total organic matter. From the overall 30 ostracod species, there were 26 identified species belong to 22 genera of 13 families. Diversity and aboundance of ostracoda of the Oman Sea decreased from east to west and from south to north but increased slightly in the northwest (near the Strait of Hormoz). Ostracoda of the genus Propontocypris were common in all sampling stations but the genera Cyprideis, Paradoxostom and Hemicytheridea were rare in the Oman Sea. Diversity and aboundance of ostracoda in northern regions were less than southern and were less than foraminifera too. The composition of ostracodal communities had a highly positive correlation with dept, salinity and grain size. Biodiversity and distribution pattern of benthic foraminifera and ostracoda were being different in various sampling stations, especially between northern and southern regions. Water depth, salinity and structure of the sediments were the most important abiotic factors controlling the distribution pattern of benthic foraminifera and ostracoda in the Omman Sea. None existence or rare observation of structural abnormalities and oil polluted individuals in the vicinity of all sampling stations, resulted to the "clean" benthic environment of the Omman Sea.

Assessment of pelagic primary and secondary production in Sefidrud River estuary

Sefid-Rood River Estuary (SRE) is the most important riverine ecosystem in the south Caspian Sea along the Iranian coast lines. The aim of this study was to examine spatial and temporal variability in Phytoplankton and Zooplankton abundance and diversity in SRE. Variability of Chlorophyll a and inorganic nutrient concentration were determined during a year (November 2004– October 2005) in five sampling stations. Primary and secondry production were determined during a year. Total chlorophyll a concentration during the investigation ranged between zero to 22.8 μgl-1 and the highest levels were consistently recorded during summer and the lowest during winter with a annual mean concentration 4.48 μgl-1. Nutrient concentration was seasonally related to river flow with annual mean concentration: NO2 0.05±0.2 mgl-1, NO3 1.13±0.57 mgl-1, NH4 0.51±0.66 mgl-1, total phosphate 0.13±0.1mgl-1 and SiO2 5.68±1.91 mgl-1. Bacillariophytes, Cyanophytes, Chlorophytes, Pyrophytes and Euglenophytes were the dominant phytoplankton groups in this shallow and turbid estuary. The diversity and abundance of phytoplankton had a seasonal pattern while Diatomas and Chrysophytes were dominant throughout the year but Cyanophytes observed only during the summer. Zooplankton community structure was dominated by copepods which 68% of the total zooplankton. In the winter and summer seasons two increased in the number of zooplankton community and usually toward the sea had occurred. Zooplankton also showed a significant spatial and temporal variation. The high turbidity and temperature prime characteristics of SRE seem to be determining factors acting directly on phytoplankton and zooplankton temporal variability and nutrient fluctuations. Everywhere in this estuary nutrients appeared to be in excess of algal requirement and did not influence a phytoplankton and zooplankton composition. Also there was a positive correlation between chlorophyll a and temperature and a negative one with DIN and TP. Primary production determined in this estuary by dark and light butter method and G.P.P. 38.27±34.12 mgcm-2h-1 and N,PP 201.6±289.9 mgcm-2d-1. secondry production determined 15/128 mgc/m3/year. Everywhere in this estuary nutrients appeared to be in excess to algal requirement and did not influence in Chl. a and primary production. The most important factor influence on Chl. a was water temperature.

Priorities for research and management on Lake Victoria

Under the worrisomely changing situation in fish species diversity, water environment characteristics, socio-economic dimensions and other ecosystems variables in Lake Victoria, there is an urgent need to put in place effective research and management packages aimed at safe guarding the sustainability of the vast resources of the lake. Priority in have been out-lined to develop strategies which would promote biological productivity and diversity, and socio-economic returns. But given the size of the lake (69,000 km2) and the complexity of dynamic forces which are driving the changes, coordinated approach for research and management among the riparian states and the international scientific community will be required. The task is not only extensive but urgent as well.

Preliminary estimates of cetacean abundance in the northern Gulf of Mexico, and of selected cetacean species in the U.S. Atlantic Exclusive Economic Zone from vessel surveys

The Southeast Fisheries Science Center (SEFSC) initiated annual, vessel-based visual sampling surveys of northern Gulf of Mexico marine mammals in 1990 and conducted a similar survey in U.S. Atlantic Exclusive Economic Zone (EEZ) waters from Miami, Florida, to Cape Hatteras, North Carolina, in 1992. The primary goal of these surveys was to meet Marine Mammal Protection Act requirements for estimating abundance and monitoring trends of marine mammal stocks in United States waters. The surveys were designed to collect: 1) marine mammal sighting data to estimate abundance and to determine distribution and diversity; and 2) environmental data to evaluate factors which may affect the distribution, abundance and diversity of marine mammals. The preliminary analyses for abundance estimation from the 1990-1993 surveys are presented in this report.

Current composition, distribution and relative abundance of the fish stocks of Lake Victoria, Uganda

An experimental bottom trawl survey was carried out in the Uganda sector of Lake Victoria during the period May 1993 through May 1995 with the aim of establishing the current composition, distribution and abundance of the fish stocks. A total of 205 successful one-hour hauls were taken using the 25.4mm mesh size codend trawl net during the 19 cruises. Fourteen fish taxa (excluding the haplochromines) were recorded with Lates niloticus constituting the bulk (97 %) of the fish retained. Haplochromines and L. nilolicus were encountered in all areas sampled while Nile tilapia (Oreochromis niloticus) and other tilapiines were restricted to waters less than 20 metres deep. An average catch of 154 kg/hr was obtained in waters less than 30 metres deep. Species diversity and relative abundance varied with depth. Only two of the fifteen fish taxa (haplochromines and L.niloticus) were recorded in waters deeper than 30 metres and the bulk of the fish by weight (92 %) was obtained in waters less than 30 metres.

System-of-system Approaches and Challenges for Multi-Site Manufacturing

In the multi-site manufacturing domain, systems-of-systems (SoS) are rarely called so. However, there exist a number of collaborative manufacturing paradigms which closely relate to system-of-system principles. These include distributed manufacturing, dispersed network manufacturing, virtual enterprises and cloud manufacturing/manufacturing-as-a-service. This paper provides an overview of these terms and paradigms, exploring their characteristics, overlaps and differences. These manufacturing paradigms are then considered in relation to five key system-of-systems characteristics: autonomy, belonging, connectivity, diversity and emergence. Data collected from two surveys of academic and industry experts is presented and discussed, with key challenges and barriers to multi-site manufacturing SoS identified.

Population differentiation of Procypris rabaudi (Tchang) in the upper reaches of the Yangtze River revealed by mitochondrial DNA and RAPD markers

Procypris rabaudi (Tchang) is a cyprinid fish endermic to middle and upper reaches of the Yangtze River. Besides in main stream and large tributaries, there exists an early matured, small-sized ecological type in a small tributary, Tang River. In this study, mitochondrial DNA cytochrome h (cyt b) gene sequence analysis and randomly amplified polymorphic DNA (RAPD) analysis were performed to investigate the differentiation of the Tang River population from the Mudong reach population of the Yangtze River, with the purpose of conservation and exploitation of this fish. In the 1140 bps of cyt b gene sequence surveyed, 20 sites were found polymorphic, which defined 23 haplotypes. Among them, four haplotypes accounted for 54.4% of all individuals, while population-specific haplotypes occurred in low frequencies. Analysis of molecular variation on cyt b data revealed no significant partition existing between Tang River population and Mudong reach population. Analyses of 132 RAPD loci suggested that genetic variation between populations was significant, though values of different F-ST were not very high. The results revealed low genetic diversity and the beginning of population differentiation, suggesting that Tang River population should be designated as a separate Management Unit.

Population genetic structure of Carchesium polypinum (Ciliophora : Peritrichia) in four chinese lakes inferred from ISSR fingerprinting: High diversity but low differentiation

Although the peritrichous ciliate Carchesium polypinum is common in freshwater, its population genetic structure is largely unknown. We used inter-simple sequence repeat (ISSR) fingerprinting to analyze the genetic structure of 48 different isolates of the species from four lakes in Wuhan, central China. Using eight polymorphic primers, 81 discernible DNA fragments were detected, among which 76 (93.83%) were polymorphic, indicating high genetic diversity at the isolate level. Further, Nei's gene diversity (h) and Shannon's Information index (I) between the different isolates both revealed a remarkable genetic diversity, higher than previously indicated by their morphology. At the same time, substantial gene flow was found. So the main factors responsible for the high level of diversity within populations are probably due to conjugation (sexual reproduction) and wide distribution of swarmers. Analysis of molecular variance (AMOVA) showed that there was low genetic differentiation among the four populations probably due to common ancestry and flooding events. The cluster analysis and principal component analysis (PCA) suggested that genotypes isolated from the same lake displayed a higher genetic similarity than those from different lakes. Both analyses separated C. polypinum isolates into subgroups according to the geographical locations. However, there is only a weak positive correlation between the genetic distance and geographical distance, suggesting a minor effect of geographical distance on the distribution of genetic diversity between populations of C. polypinum at the local level. In conclusion, our studies clearly demonstrated that a single morphospecies may harbor high levels of genetic diversity, and that the degree of resolution offered by morphology as a marker for measuring distribution patterns of genetically distinct entities is too low.

Cloning and analysis of 16 Rab genes from macronuclear DNA of Euplotes octocarinatus

Rab proteins belong to the largest family of the Ras superfamily of small GTPase that play an important role in intracellular vesicular traffic. So far, almost 60 members of Rab family have been identified in mammalian cells. To further study the diversity and function of Rab protein in evolution, unicellular protozoa ciliates, Euplotes octocarinatus, were used in this study, Rab genes were screened by PCR method from macronuclear DNA of E. octocarinatus. Sixteen Rab genes were obtained. They share 87.6 - 99.5% identities. Highly conserved GTP-binding domains were found. There are some hot regions that diverse sharply in these genes as well.

Identification, cloning, and characterization of microsatellite DNA in Euglena gracilis

Microsatellite DNA has been developed into one of the most popular genetic markers. We have identified and cloned microsatellite loci in the genome of a free-living protozoan Euglena gracilis FACHB-848, using the random amplified microsatellites method (RAMS). The digoxigenin-labelled oligonucleotides(CT)(10) and (GT)(10) served as probes to detect complementary sequences in the randomly amplified polymorphic DNA (RAPD) fingerprints produced by means of Southern blotting. Subsequently, positive RAPD fragments were cloned. From a total of 31 RAPD primer profiles, eight microsatellite loci of E. gracilis were detected and characterized. Further, six sites (i.e. EGMS1, EGMS3, EGMS4, EGMS5, EGMS6, and EGMS7) showed polymorphisms. We found a GT or CT microsatellite every 10.5 kb in the genome of E. gracilis, and similar to animal genomes, the (GT)(n) motif was much more abundant than the (CT)(n) motif. These polymorphic microsatellite DNA will serve as advantageous molecular markers for studying the genetic diversity and molecular ecology of Euglena.

Genetic variation analysis within and among six varieties of common carp (Cyprinus carpio L.) in china using microsatellite markers

Five microsatellites were used to study the genetic diversity and genetic structure of one wild and five domestic varieties of common carp in China (the Yangtze River wild common carp, Xingguo red carp, purse red carp, Qingtian carp, Russian scattered scaled mirror carp and Japanese decorative carp). All loci in this study showed marked polymorphism with the number of alleles ranging from 4 to 13. Domestic varieties (except Xingguo red carp) showed less genetic diversity than the Yangtze River wild common carp in terms of allelic diversity. Population differentiation was assessed and each combination of populations displayed significant differentiation (P < 0.05) with the exception of that between the Yangtze River wild common carp and Xingguo red carp. Genetic distance analysis (Nei's standard genetic distance and pairwise F-st distance) showed that the largest distance was between Russian scattered scaled mirror carp and the Yangtze River wild common carp and the smallest distance was between the Yangtze River wild common carp and Xingguo red carp. However, among six populations Japanese decorative carp displayed the highest level of variability in terms of heterozygosity.