Manual on application of molecular tools in aquaculture and inland fisheries management. Part I : conceptual basis of population genetic approaches

The aim of this manual is to provide a comprehensive practical tool for the generation and analysis of genetic data for subsequent application in aquatic resources management in relation to genetic stock identification in inland fisheries and aquaculture. The material only covers general background on genetics in relation to aquaculture and fisheries resource management, the techniques and relevant methods of data analysis that are commonly used to address questions relating to genetic resource characterisation and population genetic analyses. No attempt is made to include applications of genetic improvement techniques e.g. selective breeding or producing genetically modified organisms (GMOs). The manual includes two ‘stand-alone’ parts, of which this is the first volume: Part 1 – Conceptual basis of population genetic approaches: will provide a basic foundation on genetics in general, and concepts of population genetics. Issues on the choices of molecular markers and project design are also discussed. Part 2 – Laboratory protocols, data management and analysis: will provide step-by-step protocols of the most commonly used molecular genetic techniques utilised in population genetics and systematic studies. In addition, a brief discussion and explanation of how these data are managed and analysed is also included. This manual is expected to enable NACA member country personnel to be trained to undertake molecular genetic studies in their own institutions, and as such is aimed at middle and higher level technical grades. The manual can also provide useful teaching material for specialised advanced level university courses in the region and postgraduate students. The manual has gone through two development/improvement stages. The initial material was tested at a regional workshop and at the second stage feedback from participants was used to improve the contents.

Manual on application of molecular tools in aquaculture and inland fisheries management. Part I : laboratory protocols, data management and analysis

The aim of this manual is to provide a comprehensive practical tool for the generation and analysis of genetic data for subsequent application in aquatic resources management in relation to genetic stock identification in inland fisheries and aquaculture. The material only covers general background on genetics in relation to aquaculture and fisheries resource management, the techniques and relevant methods of data analysis that are commonly used to address questions relating to genetic resource characterisation and population genetic analyses. No attempt is made to include applications of genetic improvement techniques e.g. selective breeding or producing genetically modified organisms (GMOs). The manual includes two ‘stand-alone’ parts, of which this is the second volume: Part 1 – Conceptual basis of population genetic approaches: will provide a basic foundation on genetics in general, and concepts of population genetics. Issues on the choices of molecular markers and project design are also discussed. Part 2 – Laboratory protocols, data management and analysis: will provide step-by-step protocols of the most commonly used molecular genetic techniques utilised in population genetics and systematic studies. In addition, a brief discussion and explanation of how these data are managed and analysed is also included. This manual is expected to enable NACA member country personnel to be trained to undertake molecular genetic studies in their own institutions, and as such is aimed at middle and higher level technical grades. The manual can also provide useful teaching material for specialised advanced level university courses in the region and postgraduate students. The manual has gone through two development/improvement stages. The initial material was tested at a regional workshop and at the second stage feedback from participants was used to improve the contents.

Responsible aquaculture and trophic level implications to global fish supply

Hunger and malnutrition remain among the most devastating problems facing the world’s poor and needy, and continue to dominate the health and well-being of the world’s poorest nations. Moreover, there are growing doubts as to the long-term sustainability of many existing food production systems, including capture fisheries and aquaculture, to meet the future increasing global demands.Of the different agricultural food production systems, aquaculture (the farming of aquatic animals and plants) is widely viewed as an important weapon in the global fight against malnutrition and poverty, particularly within developing countries where over 93% of global production is currently produced, providing in most instances an affordable and a much needed source of high quality animal protein, lipids, and other essential nutrients. The current article compares for the first time the development and growth of the aquaculture sector and capture fisheries by analyzing production by mean trophic level. Whereas marine capture fisheries have been feeding the world on high trophic level carnivorous fish species since mankind has been fishing the oceans, aquaculture production within developing countries has focused, by and large, on the production of lower trophic level species. However, like capture fisheries, aquaculture focus within economically developed countries has been essentially on the culture of high value-, high trophic level-carnivorous species. The long term sustainability of these production systems is questionable unless the industry can reduce its dependence upon capture fisheries for sourcing raw materials for feed formulation and seed inputs. In line with above, the article calls for the urgent need for all countries to adopt and adhere to the principles and guidelines for responsible aquaculture of the FAO Code of Conduct for Responsible Fisheries.

Strong population genetic structure and its management implications in the mud carp Cirrhinus molitorella, an indigenous freshwater species subject to an aquaculture and culture-based fishery

This study investigated population genetic structure and diversity of mud carp Cirrhinus molitorella, a species widely used in aquaculture and culture-based fisheries in China and Mekong River riparian countries. Seven newly developed and one published microsatellite DNA markers were used to analyse samples from six wild locations, four hatchery broodstocks and one farmed site from the Mekong, Red and Pearl Rivers. Significant genetic structure was detected in C. molitorella, with isolation-by-distance being a strong force in the Mekong. Pair-wise F_ST, Fisher's exact tests for population differentiation, permutation tests and individual-based structure analysis all support the recognition of a sample originating from Toul Krasaing Lake (Cambodia) and one between Kratie and Stung Treng (Cambodia) as distinct from the remainder of the sampled range. Samples from the main upper Mekong and the Nam Khan River were significantly differentiated, but on a time scale inferred to be short (i.e. by genetic drift, not sufficient for evolution of new microsatellite alleles). The Mekong stock of C. molitorella was strongly differentiated from those from the Red and Pearl Rivers, inferred to be on an evolutionary time scale. Finer-scale sampling is warranted to further improve the understanding of genetic interactions among fish from the Mekong and its tributaries. Detailed studies on the ecology of C. molitorella (e.g. migration pathways and preferred spawning habitats) would provide useful information to explain the patterns of genetic structure detected here, and deepen insights about evolutionary distinctiveness of the population units.

Addressing aquaculture-fisheries interactions through the implementation of the ecosystem approach to aquaculture (EAA

This review addresses how the ecosystem approach to aquaculture (EAA) can optimize aquaculture-fisheries interactions considering different spatial scales from farm, aquaculture zone and watershed through to the global market. Aquaculture and fisheries are closely related subsectors with frequent interactions, largely due to the sharing of common ecosystems and natural resources. Interactions are also born from the flow of biomass from fisheries to aquaculture through fish-based feeds (e.g. fishmeal, fish oil and trashfish), through the collection of wild seed and brookstock, and genetic resources and biomass transfer from aquaculture to fisheries through culture-based fisheries (CBF) and escapees. Negative effects include modification of habitats affecting fisheries resources and activities (e.g. mangrove clearing for shrimp ponds, seabed disturbances through anchoring of aquaculture cages or pens, damage to seagrasses, alteration to reproductive habitats, biodiversity loss). Eutrophication of waterbodies due to excess nutrient release leading to anoxia and fish mortality can also impact negatively on biodiversity and wild fish stocks. Release of diseases and chemicals also imposes some threats on fisheries. Yet there could be beneficial impacts; for example, aquaculture is increasingly contributing to capture fisheries through CBF and could contribute to restore overfished stocks. Aquaculture can offer alternative livelihoods to fisherfolk, providing increased opportunity to them and also to their families, and especially to women. Aquaculture-increased production and marketing can also enhance and indirectly improve processing and market access to similar fishery products. The ecosystem approach to aquaculture (EAA) is a strategy for the management of the sector that emphasizes intersectoral complementarities by taking into account the interactions between all the activities within ecologically meaningful boundaries and acknowledging the multiple services provided by ecosystems. The main objective of this review is to understand the status of aquaculture-fisheries interactions associated with the biological, technological, social, economic, environmental, policy, legal and other aspects of aquaculture development and to analyze how these interactions are or could be addressed with an EAA. Therefore, the review involves aspects of scoping, identification of issues, prioritizing, devising management tools and plans for minimizing negative effects and optimizing positive ones within the context of social-ecological resilience, at different relevant geographical scales. Many of the management measures suggested in this review must involve not only EAA but also an ecosystem approach to fisheries (EAF), especially to deal with issues such as fishery of wild seed and the management of fisheries to produce fishmeal/oil for pelleted feeds or for direct feeding with wet fish. The implementation of EAA and EAF should help to overcome the sectoral and intergovernmental fragmentation of resource management efforts and assist in the development of institutional mechanisms and private-sector arrangements for effective coordination among various sectors active in ecosystems in which aquaculture and fisheries operate and between the various levels of government. Ecosystem-based management involves a transition from traditional sectoral planning and decision-making to the application of a more holistic approach to integrated natural resource management in an adaptive manner.

Alien species in aquaculture and biodiversity : a paradox in food production

Aquaculture is seen as an alternative to meeting the widening gap in global rising demand and decreasing supply for aquatic food products. Asia, the epicenter of the global aquaculture industry, accounts for over 90% of the global aquaculture production quantity and about 80% of the value. Asian aquaculture, as with global aquaculture, is dependent to a significant extent on alien species, as is the case for all the major food crops and husbanded terrestrial animals. However, voluntary and or accidental introduction of exotic aquatic species (alien species) is known to negatively impact local biodiversity. In this relatively young food production industry, mitigating the dependence on alien species, and thereby minimizing potential negative impacts on biodiversity, is an imperative for a sustainable future. In this context an attempt is made in this synthesis to understand such phenomena, especially with reference to Asian inland finfish, the mainstay of global aquaculture production. It is pointed out that there is potential for aquaculture, which is becoming an increasingly important food production process, not to follow the past path of terrestrial food crops and husbanded animals in regard to their negative influences on biodiversity.

Use and exchange of genetic resources of emerging species for aquaculture and other purposes

From a genetic resources viewpoint, emerging aquaculture species and species groups are examined mainly in terms of food use. In addition, we include species that are becoming increasingly important for biodiversity conservation and related ecotourism aspects. Together with ornamental fish species, we argue that these species are facing increasing vulnerability and warrant attention. Our intention is to raise awareness of the potential for increasing production and revenues from emerging species/species groups with an emphasis on an underlying link to biodiversity conservation and ecosystem preservation, and how this information will inform policy on access to the genetic resources and the sharing of benefits derived from their use. For food purposes, the fastest growing aquaculture sector is mariculture, and within this sector groupers and wrasses are considered to be the most important because they cater to the relatively lucrative live food fish restaurant trade (LFFRT), which is rapidly expanding in selected South-East Asian countries. In the Asian region, ecotourism is an emerging sector and a prominent fish group for this purpose is considered to be mahseer. A number of mahseer species are culturally and commercially important and are often seen as a group of indigenous species that are suitable for aquaculture. This review summarizes much of the limited information related to the patterns of use and exchange of genetic resources on emerging aquatic species/species groups, with particular reference to Asia.

Fish and fisheries of large and medium-sized reservoirs in Vietnam

The study was undertaken in view of the importance of reservoir fisheries for Vietnam, and to fill gaps in the current knowledge in order to introduce affective management measures to optimise the fish yields from the reservoirs. Eight large and medium sized reservoirs , representing a cross section of reservoirs in Vietnam in the different climatic zones were studied.

Constructed wetland for treating aquaculture and industrial effluent

This project was a practical assessment of the giant reed Arundo donax in comparison with the common reed, Phragmites autralis, in gravel substrate-based horizontal subsurface flow constructed wetlands designed to treat agro-industrial effluent. Results indicated, the planted CWs were more effective at removing nutrients than the unplanted conrol CWs with A.donax produce larger amounts of biomass than P. australis planted CWs.

ICES meets marine historical ecology: placing the history of fish and fisheries in current policy context

As a discipline, marine historical ecology (MHE) has contributed significantly to our understanding of the past state of the marine environment when levels of human impact were often very different from those today.What is less widely known is that insights from MHE have made headway into being applied within the context of present-day and long-term management and policy. This study draws attention to the applied value of MHE. We demonstrate that a broad knowledge base exists with potential for management application and advice, including the development of baselines and reference levels.Using a number of case studies from around the world,we showcase the value of historical ecology in understanding change and emphasize how it either has already informed management or has the potential to do so soon.We discuss these case studies in a context of the science–policy interface around six themes that are frequently targeted by current marine and maritime policies: climate change, biodiversity conservation, ecosystem structure, habitat integrity, food security, and human governance.We encourage science–policy bodies to actively engage with contributions from MHE, as well informed policy decisions need to be framed within the context of historical reference points and past resource or ecosystem changes.

Aquaculture : a newly emergent food production sector-and perspectives of its impacts on biodiversity and conservation

The fisheries sector in the course of the last three decades have been transformed from a developed country to a developing country dominance. Aquaculture, the farming of waters, though a millennia old tradition during this period has become a significant contributor to food fish production, currently accounting for nearly 50 % of global food fish consumption; in effect transforming our dependence from a hunted to a farmed supply as for all our staple food types. Aquaculture and indeed the fisheries sector as a whole is predominated in the developing countries, and accordingly the development strategies adopted by the sector are influenced by this. Aquaculture also being a newly emerged food production sector has being subjected to an increased level of public scrutiny, and one of the most contentious aspects has been its impacts on biodiversity. In this synthesis an attempt is made to assess the impacts of aquaculture on biodiversity. Instances of major impacts on biodiversity conservation arising from aquaculture, such as land use, effluent discharge, effects on wild populations, alien species among others are highlighted and critically examined. The influence of paradigm changes in development strategies and modern day market forces have begun to impact on aquaculture developments. Consequently, improvements in practices and adoption of more environmentally friendly approaches that have a decreasing negative influence on biodiversity conservation are highlighted. An attempt is also made to demonstrate direct and or indirect benefits of aquaculture, such as through being a substitute to meet human needs for food, particularly over-exploited and vulnerable fish stocks, and for other purposes (e.g. medicinal ingredients), on biodiversity conservation, often a neglected entity.

More rapid and severe disease outbreaks for aquaculture at the tropics : implications for food security

1. Aquaculture is replacing capture fisheries in supplying the world with dietary protein. Although disease is a major threat to aquaculture production, the underlying global epidemiological patterns are unknown. 2. We analysed disease outbreak severity across different latitudes in a diverse range of aquaculture systems. 3. Disease at lower latitudes progresses more rapidly and results in higher cumulative mortality, in particular at early stages of development and in shellfish. 4. Tropical countries suffer proportionally greater losses in aquaculture during disease outbreaks and have less time to mitigate losses. 5. Synthesis and applications. Disease can present a major problem for food production and security in equatorial regions where fish and shellfish provide a major source of dietary protein. As the incidences of some infectious diseases may increase with climate change, adaptation strategies must consider global patterns in disease vulnerability of aquaculture and develop options to minimize impacts on food production.