Techniques for spatial analysis and visualization of benthic mapping data: final report

The mapping and geospatial analysis of benthic environments are multidisciplinary tasks that have become more accessible in recent years because of advances in technology and cost reductions in survey systems. The complex relationships that exist among physical, biological, and chemical seafloor components require advanced, integrated analysis techniques to enable scientists and others to visualize patterns and, in so doing, allow inferences to be made about benthic processes. Effective mapping, analysis, and visualization of marine habitats are particularly important because the subtidal seafloor environment is not readily viewed directly by eye. Research in benthic environments relies heavily, therefore, on remote sensing techniques to collect effective data. Because many benthic scientists are not mapping professionals, they may not adequately consider the links between data collection, data analysis, and data visualization. Projects often start with clear goals, but may be hampered by the technical details and skills required for maintaining data quality through the entire process from collection through analysis and presentation. The lack of technical understanding of the entire data handling process can represent a significant impediment to success. While many benthic mapping efforts have detailed their methodology as it relates to the overall scientific goals of a project, only a few published papers and reports focus on the analysis and visualization components (Paton et al. 1997, Weihe et al. 1999, Basu and Saxena 1999, Bruce et al. 1997). In particular, the benthic mapping literature often briefly describes data collection and analysis methods, but fails to provide sufficiently detailed explanation of particular analysis techniques or display methodologies so that others can employ them. In general, such techniques are in large part guided by the data acquisition methods, which can include both aerial and water-based remote sensing methods to map the seafloor without physical disturbance, as well as physical sampling methodologies (e.g., grab or core sampling). The terms benthic mapping and benthic habitat mapping are often used synonymously to describe seafloor mapping conducted for the purpose of benthic habitat identification. There is a subtle yet important difference, however, between general benthic mapping and benthic habitat mapping. The distinction is important because it dictates the sequential analysis and visualization techniques that are employed following data collection. In this paper general seafloor mapping for identification of regional geologic features and morphology is defined as benthic mapping. Benthic habitat mapping incorporates the regional scale geologic information but also includes higher resolution surveys and analysis of biological communities to identify the biological habitats. In addition, this paper adopts the definition of habitats established by Kostylev et al. (2001) as a “spatially defined area where the physical, chemical, and biological environment is distinctly different from the surrounding environment.” (PDF contains 31 pages)

Economic and social impacts of Integrated Aquaculture-Agriculture technologies in Bangladesh

This study estimated the adoption rate of integrated aquaculture-agriculture (IAA) technologies in Bangladesh and their impact on poverty and fish and food consumption in adopting households. We used a novel, simulation-based approach to impact assessment called Tradeoff Analysis for Multi-Dimensional Impact Assessment (TOA-MD). We used the TOA-MD model to demonstrate how it is possible to use available data to estimate adoption rates in relevant populations, and to quantify impacts on distributional outcomes such as poverty and food security, thus demonstrating ex ante the potential for further investment in technology dissemination. The analysis used baseline and end-of-project survey data from WorldFish-implemented Development of Sustainable Aquaculture Project (DSAP), promoting IAA. This dataset was used to simulate adoption and assess its impacts on poverty and food security in the target population. We found that, if adopted, IAA had a significant positive impact on reducing poverty and improving food security and income.

Standardisation of specification for different trolling lures

Fishing experiments were conducted with buffalo horn, wooden and galvanised iron jigs of different lengths and weights rigged in troll lines. It was observed that jigs with 12 cm length and 60 g weight were superior to others in luring seer fish. Fish head jigs of 60 g weight showed a higher efficiency index than those of 50 and 70 g tried in these studies.

The biology and ecology of native non-cichlids in the Victoria and Kyoga lake basins

An overview of the biology and ecology of some of the constantly less important commercial species is given below. These included Bagrus docmac, Clarias gariepinus, Protopterus aethiopicus, Labeo victorianus, Barbus spp, Mormyrids, Synodontis spp, and Schilbe intermedius. The stocks of most of these species declined due to over-exploitation and introduction of non-native fishes especially Nile perch. A few of these taxa still survive in the main lake and others in satellite lakes. The current status of these species in the Victoria lake basin is not known but the available information provided some information on some habitat and other requirements of some of these originally important species of the Victoria lake basin.

Investigation on possibility of survival and growth enhancing by selected seaweeds from Persian Gulf in post larvae shrimp Litopenaeus vannamei

The use of antibiotics in aquaculture has been limited. Scientifics seeking for natural substitutes to prevent of aquatic animals diseases. Considering seaweeds are rich of nutritions and bioactive compounds, the purpose of this study is: investigation the potential and use possibility of native seaweeds from Persian Gulf in shrimp aquculture industry to improve growth, survival of postlarvae and to resistance against pathogens such as vibriosis. For this propose 7 macroalgae species from Bushehr province coast, inclouding: green algae (C. iyengarii), brown algae (S. angutifolium and S. ilicifolium) and red algae (L. snyderiae, K. alvarezii and G. corticata) were collected and identified. Then seaweed extracts abtained by Water, Ethanol, Methanol and Chloroform solvents by soaking method. In vitro antibacterial activity of extracts against Gr+ bacteria (S. aureus and B. subtilis) and Gr- bacteria (V. harveyi, V. alginolyticus and E. coli) was conducted by Agar diffusion, MIC and MBC methods. Antioxidant activity also by DPPH and EC50 methods was investigated. According to results of these two tests four seaweeds species (S. angutifolium, L. snyderiae, K. alvarezii and G. corticata) were selected for use in shrimp postlarvae (PL22) diets by Bio-Encapsulation (Artemia enrichment). Before of enrichment, toxicity effect of extracts to Artemia nauplii were evaluated by determination of LC50 24 h method. From results of this section Ethanol extracts were selected to bioencapsulation. After encapsulation shrimp postlarvae divided to 12 groups in triplicate, namely: C-, C+, S (200), S (400), S (600), L(200), L(400), L(600), G(300), G(600), K(300) and K(600). During 30 days of reared period C- and C+ use of basal diet and unenriched Artemia, but the other groups use of basal diet and enriched Artemia. Except C-, the shrimps in first day of culture put in 107 cfu/ml v. harveyi suspension for 30 minutes, and after water exchange 10 ml of this dose was added to reared aquaria. After 30 days survival percentage, obtained weight and SGR% were investigated. To evaluate vibrio loading, every 10 days 5 postlarvae were sampled randomly for vibrio count. Results showed that vibrio count in C- was less than the others and in C+ was more than the others. In treatments vibrio count in L(200) was the most and L(600) was the less. Survival rate in C- was the most and after that G(600) with 79.4±6.6% and then S(300) and K(600) were 73.3±7.3% and 70.6±6.6% respectively that were significantly compare the other (P < 0.01). Also the C+ was the less with 33.3±6.6% that difference was significant (P< 0.01). In this study growth parameters of all groups that fed by enriched Artemia were better than C+ (P<0.05). After cultre period 10 shrimp of every aquarium disinfected and reared for 10 days like before treatment. After 10 days the shrimps were challenged by 3×108 cfu/ml V. harveyi and mortality was recorded for 7 days. The all of animals in C- were survive but more than 90% of C+ were dead. And survival in all of treatments were better the C+ (P<0.05). The study showed the ethanol extracts of selected seaweed from Persian Gulf is a good source for growth, Survival and disease control in shrimp larviculture.

Ichthyological ecoregions of Argentina

The Argentine Republic is situated in the southernmost portion of the American continent, occupying over 2,785,600 km2 not including the Antarctic territory. The country ranges from subtropical areas (21º46’S) to subantarctic regions (55º03’S), extending latitudinally over about 4,000 km. It possesses significant latitudinal and altitudinal variation (33º of latitudinal range, and heights from Bajo de San Julián in Santa Cruz province at 105 m below sea level, up to Mt. Aconcagua, 6,959 m over sea level), as well as two gradients of physical variability, extending in north-south and east-west directions. Owing to these features, the country presents a wide range of climates and soil types, being one of the countries with greatest diversity of biogeographical units (Lean et al., 1990, In: Bertonatti & Corcuera, 2000). There are four main hydrographic systems: Río de la Plata basin, the Atlantic and Pacific drainages, and several endorrheic systems. Within these basins, the ichthyofaunistic assemblage is well represented, with different magnitude in accordance with the different taxonomic groupings and regions considered. From an ichthyogeographic standpoint, and according to the works of Ringuelet (1975) and Arratia et al. (1983), Argentina is included in the Brasilic and Austral Subregions. The first of these is represented by two domains: the Andean Domain, comprising the southernmost portion of Titicaca Province, and the Paranensean Domain, including part of Alto Paraná and Paranoplatensean Provinces. The Austral Subregion is represented in Argentina by the Subandean-Cuyan and Patagonian Provinces. The present survey indicates that there are about 441 fish species in Argentina, distributed throughout the country; this number represents less than 10% of the total fish species occurring in the Neotropical Region. There is a recognizable trend of faunal impoverishment, both in North-South and East-West direction, reaching its maximum expression in the provinces of Tierra del Fuego (situated at approximately 52º30’S to 55ºS, and 65ºS to 68º50’W) and San Juan (approximately 28º50’S and 67ºW to 70º45’W), which have 4 and 5 fish species respectively. In north-south direction, one of the regional indicators of this phenomenon is the Salado river basin in Buenos Aires province, which constitutes the southern distributional boundary for the majority of the paranoplatensean ichthyofauna; 12 of the families occurring in the Paraná-Plata system are absent from this pauperized paranensean ichthyofaunal assemblage. Most of the continental fish fauna of Argentina belongs to the primary division of Myers (1949), while some elements are included in the secondary division and others in an amphibiotic or ‘marine penetration’ category. This ichthyofaunistic scope encompasses a wide range of morphological, biological, ecological and ethological types (benthic and pelagic, migrating and sedentary, haematophagous or parasites, annual species, inhabitants of plains or heights, estivation-adapted, etc.) inhabiting different regions within the national territory.

User’s Guide to ADMB2R: A Set of AD Model Builder Output Routines Compatible with the R Statistics Language

ADMB2R is a collection of AD Model Builder routines for saving complex data structures into a file that can be read in the R statistics environment with a single command.1 ADMB2R provides both the means to transfer data structures significantly more complex than simple tables, and an archive mechanism to store data for future reference. We developed this software because we write and run computationally intensive numerical models in Fortran, C++, and AD Model Builder. We then analyse results with R. We desired to automate data transfer to speed diagnostics during working-group meetings. We thus developed the ADMB2R interface to write an R data object (of type list) to a plain-text file. The master list can contain any number of matrices, values, dataframes, vectors or lists, all of which can be read into R with a single call to the dget function. This allows easy transfer of structured data from compiled models to R. Having the capacity to transfer model data, metadata, and results has sharply reduced the time spent on diagnostics, and at the same time, our diagnostic capabilities have improved tremendously. The simplicity of this interface and the capabilities of R have enabled us to automate graph and table creation for formal reports. Finally, the persistent storage in files makes it easier to treat model results in analyses or meta-analyses devised months—or even years—later. We offer ADMB2R to others in the hope that they will find it useful. (PDF contains 30 pages)

User’s Guide to C2R: A Set of C Language Output Routines Compatible with the R Statistics Language

C2R is a collection of C routines for saving complex data structures into a file that can be read in the R statistics environment with a single command.1 C2R provides both the means to transfer data structures significantly more complex than simple tables, and an archive mechanism to store data for future reference. We developed this software because we write and run computationally intensive numerical models in Fortran, C++, and AD Model Builder. We then analyse results with R. We desired to automate data transfer to speed diagnostics during working-group meetings. We thus developed the C2R interface to write an R data object (of type list) to a plain-text file. The master list can contain any number of matrices, values, dataframes, vectors or lists, all of which can be read into R with a single call to the dget function. This allows easy transfer of structured data from compiled models to R. Having the capacity to transfer model data, metadata, and results has sharply reduced the time spent on diagnostics, and at the same time, our diagnostic capabilities have improved tremendously. The simplicity of this interface and the capabilities of R have enabled us to automate graph and table creation for formal reports. Finally, the persistent storage in files makes it easier to treat model results in analyses or meta-analyses devised months—or even years—later. We offer C2R to others in the hope that they will find it useful. (PDF contains 27 pages)

User’s Guide to For2R: A Module of Fortran 95 Output Routines Compatible with the R Statistics Language

For2R is a collection of Fortran routines for saving complex data structures into a file that can be read in the R statistics environment with a single command.1 For2R provides both the means to transfer data structures significantly more complex than simple tables, and an archive mechanism to store data for future reference. We developed this software because we write and run computationally intensive numerical models in Fortran, C++, and AD Model Builder. We then analyse results with R. We desired to automate data transfer to speed diagnostics during working-group meetings. We thus developed the For2R interface to write an R data object (of type list) to a plain-text file. The master list can contain any number of matrices, values, dataframes, vectors or lists, all of which can be read into R with a single call to the dget function. This allows easy transfer of structured data from compiled models to R. Having the capacity to transfer model data, metadata, and results has sharply reduced the time spent on diagnostics, and at the same time, our diagnostic capabilities have improved tremendously. The simplicity of this interface and the capabilities of R have enabled us to automate graph and table creation for formal reports. Finally, the persistent storage in files makes it easier to treat model results in analyses or meta-analyses devised months—or even years—later. We offer For2R to others in the hope that they will find it useful. (PDF contains 31 pages)

Guidance for benthic habitat mapping: an aerial photographic approach

This document, Guidance for Benthic Habitat Mapping: An Aerial Photographic Approach, describes proven technology that can be applied in an operational manner by state-level scientists and resource managers. This information is based on the experience gained by NOAA Coastal Services Center staff and state-level cooperators in the production of a series of benthic habitat data sets in Delaware, Florida, Maine, Massachusetts, New York, Rhode Island, the Virgin Islands, and Washington, as well as during Center-sponsored workshops on coral remote sensing and seagrass and aquatic habitat assessment. (PDF contains 39 pages) The original benthic habitat document, NOAA Coastal Change Analysis Program (C-CAP): Guidance for Regional Implementation (Dobson et al.), was published by the Department of Commerce in 1995. That document summarized procedures that were to be used by scientists throughout the United States to develop consistent and reliable coastal land cover and benthic habitat information. Advances in technology and new methodologies for generating these data created the need for this updated report, which builds upon the foundation of its predecessor.

Distribution of fishing effort and resulting tuna catches from the Eastern Tropical Pacific by quarters of the year, 1951-1958

ENGLISH: This is a data report based on information collected from the logbooks of baitboats and purse-seiners engaged in the fishery for yellowfin (Neothunnus macropterus) and skipjack (Katsulvonus pelamis) tuna in the Eastern Tropical Pacific Ocean from 1951 through 1958. The detailed analysis of these data appears in other research bulletins, some already published and others in preparation. SPANISH: Este es un informe basado en los datos contenidos en la información recogida de los registros de bitácora de los barcos de carnada y rederos que se dedicaron a la pesca de atún aleta amarilla (Neothunnus macropterus) y barrilete (Katsuwonus pelamis) en el Océano Pacífico Oriental Tropical de 1951 a 1958. El análisis detallado de estos datos aparece en otros boletines de investigación, algunos de los cuales ya han sido publicados y otros están en preparación.

Abundance and distribution patters of Hawaiian odontocetes: focus on O'ahu

This dissertation is an assessment of the status of odontocetes in Hawaiian waters focussing on O´ahu. The work builds on available literature, and on data collected by the author and by others in Hawaiian waters. Abundance and distribution patterns of odontocetes were derived from stranding and aerial survey data. A stranding network operated by the National Marine Fisheries Service, Pacific Area Office collected 187 stranding reports throughout the main Hawaiian Islands between 1937 and 2002. These reports included 16 odontocete species. Number of stranding reports increased over time and was highest on O´ahu. Strandings occurred throughout the year. The difference in number of strandings per month was not significant. Fifteen of the 16 species reported in the stranding record for the main Hawaiian Islands were also reported by aerial survey studies of the area between 1993 and 1998. Only 7 of the species reported were detected during aerial transects around O′ahu between 1998 and 2000. Based on the stranding record, Kogia sp., melon-headed whales, striped dolphins and dwarf killer whale appear to be more common than suggested by aerial surveys. Conversely, pilot whales and bottlenose dolphins were more common, according to aerial surveys, than predicted by the stranding data. Aerial surveys of waters between 0 and 500m around the Island of O′ahu showed that the most abundant species by frequency of occurrence was the pilot whale (30% of sightings), followed by the spinner (16%) and bottlenose dolphin (14%). Because of small sample size, abundance estimates for odontocetes have a high level of uncertainty. The unavailability of a correction factor for g(0)<1, and the reduced visibility below the aircraft further reduced accuracy and increased the inherent underestimation in the data. The most abundant species according to distance sampling estimates were spotted dolphins, pilot whales, false killer whales and spinner dolphins. A natural factor shaping the ecology of odontocete populations is predation pressure both by other odontocetes and, more frequently, by sharks. An account of predation by a tiger shark on a spotted dolphin near Penguin Banks is used as an example of the potential mechanisms of predation by sharks on odontocetes.

Zustand und Entwicklung ausgewählter Fischbestände: Einschätzung des ICES im Herbst 2003

During the autumn session of the ICES Advisory Committee for Fisheries Management (ACFM) 58 stocks assessed in 7 Working Groups have been analyzed and reviewed, among these the demersal stocks in the North Sea and the Mackerel stock. As in previous years, ICES recommends a reduction in fishing mortality for a number of stocks or even the establishment of recovery and management plans, to safeguard a continuous development of the stocks towards safe biological limits. ICES reiterated last year’s recommendation to close the directed cod fishery and any fishery taking cod as by-catch in the North Sea, west of Scotland and in the Irish Sea. This year, the stocks of plaice in the North Sea, southern hake and southern anglers are (among others) in a critical state and in urgent need of protecting or rebuilding measures. This will again have an enormous impact on almost all mixed fisheries in the European Union.

Fish demand and supply projections

It has been predicted that the global demand for fish for human consumption will increase by more than 50% over the next 15 years. The FAO has projected that the increase in supply will originate primarily from marine fisheries, aquaculture and to a lesser extent from inland fisheries, but with a commensurate price increase. However, there are constraints to increased production in both marine and inland fisheries, such as overfishing, overexploitation limited potential increase and environmental degradation due to industrialization. The author sees aquaculture as having the greatest potential for future expansion. Aquaculture practices vary depending on culture, environment, society amd sources of fish. Inputs are generally low-cost, ecologically efficient and the majority of aquaculture ventures are small-scale and family operated. In the future, advances in technology, genetic improvement of cultured species, improvement in nutrition, disease management, reproduction control and environmental management are expected along with opportunities for complimentary activities with agriculture, industrial and wastewater linkages. The main constraints to aquaculture are from reduced access to suitable land and good quality water due to pollution and habitat degradation. Aquaculture itself carries minimal potential for aquatic pollution. State participation in fisheries production has not proven to be the best way to promote the fisheries sector. The role of governments is increasingly seen as creating an environment for economic sectors to make an optimum contribution, through support in areas such as infrastructure, research, training and extension and a legal framework. The author feels that a holistic approach integrating the natural and social sciences is called for when fisheries policy is being examined.