Scoping genetic tools, their limitations and applications for wild fisheries management

FRDC has commissioned a review of the role that existing and future genetic technologies may play in addressing critical challenges facing the exploitation of wild fisheries. Wild fisheries management has been assisted by genetic research for over 50 years and in Australia, this research has been largely funded by FRDC. Both fisheries management and the methods of genetic analysis have changed significantly during this time. Given these dynamics, as well as perceptions that communication between fisheries managers and geneticists has been poor in some cases, there is a strong need to reassess the ways in which genetic research can contribute to fisheries and for all stakeholders to critically examine each other's needs and capabilities.

Ecology of aquaculture species and enhancement of stocks: proceedings of the thirtieth U.S. - Japan meeting on aquaculture, Sarasota, FL, Dec. 3-4, 2001

CONTENTS: I. U.S.-Japan Cooperation Open Ocean Aquaculture – A Venue for Cooperative Research Between the United States and Japan.............................................................................. 1 C. Helsley II. Growth, Nutrition and Genetic Diversity Daily Ration of Hatchery-Reared Japanese Flounder Paralichthys olivaceus as an Indicator of Release Place, Time and Fry Quality. In situ Direct Estimation and Possibility of New Methods by Stable Isotope............................ 7 O. Tominaga, T. Seikai, T. Tsusaki, Y. Hondo, N. Murakami, K. Nogami, Y. Tanaka and M. Tanaka Nucleic Acids and Protein Content as a Measure to Evaluate the Nutritional Condition of Japanese Flounder Paralichthys olivaceus Larvae and Juveniles........................................................................................................ 25 W. Gwak Genetic Diversity Within and Between Hatchery Strains of Flounder Paralichthys olivaceus Assessed by Means of Microsatellite and Mitochondrial DNA Sequencing Analysis...................................................................... 43 M. Sekino, M. Hara and N. Taniguchi Tracking Released Japanese Flounder Paralichthys olivaceus by Mitochondrial DNA Sequencing................................................................................ 51 T. Fujii Preliminary Aspects of Genetic Management for Pacific Threadfin Polydactylus sexfilis Stock Enhancement Research in Hawaii........................................ 55 M. Tringali, D. Ziemann and K. Stuck Enhancement of Pacific Threadfin Polydactylus sexfilis in Hawaii: Interactions Between Aquaculture and Fisheries............................................................. 75 D. Ziemann Aquaculture and Genetic Structure in the Japanese Eel Anguilla japonica..................... 87 M. Katoh and M. Kobayashi Comparative Diets and Growth of Two Scombrid Species, Chub Mackerel Scomber japonicus and Japanese Spanish Mackerel Scomberomorus niphonius, in the Central Seto Inland Sea, Japan.................................. 93 J. Shoji, M. Tanaka and Tsutomu Maehara iii Evaluating Stock Enhancement Strategies: A Multi-disciplinary Approach................... 105 T. M. Bert, R.H. McMichael, Jr., R.P. Cody, A. B. Forstchen, W. G. Halstead, K. M. Leber, J. O’Hop, C. L. Neidig, J. M. Ransier, M. D. Tringali, B. L. Winner and F. S. Kennedy III. Physiological and Ecological Applications Predation on Juvenile Chum Salmon Oncorhynchus keta by Fishes and Birds in Rivers and Coastal Oceanic Waters of Japan................................... 127 K. Nagasawa and H. Kawamura Interaction Between Cleaner and Host: The Black Porgy Cleaning Behavior of Juvenile Sharpnose Tigerfish Rhyncopelates Oxyrhynchus in the Seto Inland Sea, Western Japan............................................................................. 139 T. Shigeta, H. Usuki and K. Gushima IV. Case Studies Alaska Salmon Enhancement: A Successful Program for Hatchery and Wild Stocks............................................................................................... 149 W. Heard NMFS Involvement with Stock Enhancement as a Management Tool........................... 171 T. McIlwain Stock Enhancement Research with Anadromous and Marine Fishes in South Carolina...................................................................................... 175 T. I. J. Smith, W. E. Jenkins, M. R. Denson and M. R. Collins Comparison of Some Developmental, Nutritional, Behavioral and Health Factors Relevant to Stocking of Striped Mullet, (Mugilidae), Sheepshead (Sparidae), Common Snook (Centropomidae) and Nassau Groupers (Serranidae)........................... 191 J. W. Tucker Jr. and S. B. Kennedy Participants in the Thirtieth U.S.-Japan Meeting on Aquaculture................. Inside Back Cover iv (PDF has 204 pages.)

Improving coastal livelihoods through sustainable aquaculture practices in Hon Mun marine protected area, Nha Trang Bay, Vietnam: a report to the collaborative APEC Grouper Research and Development Network

This case study describes the present status and trends, and provides recommendations for the improvement of aquatic resources management within Hon Mun Marine Protected Area (MPA), Nha Trang Bay, Khanh Hoa Province, Vietnam. The case study also evaluates options for improving the livelihoods of local villagers through the development of ecologically sustainable aquaculture and fisheries, which include diversification following careful selection and trial of appropriate culture species, and application of “best practice” culture methods. (Pdf contains 43 pages).

Salmon stocks and fisheries in England and Wales, 2001. Preliminary assessment prepared for ICES, April 2002

This report presents a preliminary assessment of the state of salmon stocks and fisheries in England and Wales in 2001 to assist ICES in providing scientific advice to NASCO and to provide early feedback to fishery managers and anglers. The chief indicators of the state o f salmon stocks are normally the catches taken by rod and net fisheries. However, in 2001 angling was affected by the outbreak of foot and mouth disease (FMD), which restricted angling opportunities and access to rod fisheries in many parts of the country for lengthy periods. It is impossible to quantify the impact that FMD had on rod catches, although these were undoubtedly significantly reduced; net fisheries were unaffected by FMD. The declared salmon catch for 2001 (including those fish released alive by anglers) is provisionally estimated at 209 tonnes, representing some 57,000 fish, and comprising 153 tonnes (-43,000 fish) by nets and fixed engines and 56 tonnes (-14,000 fish) by rods. For direct comparison with previous years, it should be noted that the declared catch prior to the issue of a second reminder was about 49 tonnes (see below). An estimated 26 tonnes (43%) of the rod catch was released alive. These figures do not take account of catches of salmon which go unreported (including those taken illegally), and it is estimated that there may have been a total of 33 tonnes of additional fish caught in 2001; approximately 15% of all fish killed.

Annual Report of the Game and Fisheries Department for the year ended 31st December, 1953

Summary of fish production on main lakes of Uganda 1953, consumption of fish in Uganda 1953, imports and exports of fish, including reports from the different regions Fisheries by Regions (1) Lake Victoria (2) Lake Albert (3) Lake Kyoga and Waters of Eastern Uganda Lakes George, Edward, Fish Farming, Dams and miscellaneous minor waters. It includes information on: Angling which includes Trouting, Nile Perch fishing and Tiger Fishing, Ripon Falls Barbel and Tailpiece.

Status of sturgeon aquaculture and sturgeon trade in China: a review based on two recent nationwide surveys

The authors reviewed the aquacultural history of Acipenseriformes in China, related the legal status and examined the current status of the cultured species or hybrids, origins of seedlings, quantities of production, geographic distribution in farming, and the sustainability for both restocking programmes and human consumption. The census shows that since 2000, the production of cultured sturgeons in China appears to have become the largest in the world. As of 2000, the rapid growth of sturgeon farming in China mainly for commercial purposes has shifted harvests in the Amur River from caviar production to the artificial culture of sturgeon seedlings. This dramatic development has also caused a series of extant and potential problems, including insufficient market availability and the impact of exotic sturgeons on indigenous sturgeon species. Annual preservation of sufficient higher-age sturgeons should be a national priority in order to establish a sustainable sturgeon-culture industry and to preserve a gene pool of critically endangered sturgeon species to prevent their extinction.

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.

Implicit discount rates and fisheries management : is there a relationship?

Fishers are faced with multiple risks, including unpredictability of future catch rates, prices and costs. While the latter are largely beyond the control of fisheries managers, effective fisheries management should reduce uncertainty about future catches. Different management instruments are likely to have different impacts on the risk perception of fishers, and this should manifest itself in their implicit discount rate. Assuming licence and quota values represent the net present value of the flow of expected future profits, then a proxy for the implicit discount rate of vessels in a fishery can be derived by the ratio of the average level of profits to the average licence/quota value. From this, an indication of the risk perception can be derived, assuming higher discount rates reflect higher levels of systematic risk. In this paper, we apply the capital asset pricing model (CAPM) to determine the risk premium implicit in the discount rates for a range of Australian fisheries, and compare this with the set of management instruments in place. We test the assumption that rights based management instruments lower perceptions of risk in fisheries. We find little evidence to support this assumption. although the analysis was based on only limited data.

Genetic resources in wild and cultured stocks of the Asian mud crab, Scylla paramamosain

The mud crab (Scylla spp.) aquaculture industry has expanded rapidly in recent years in many countries in the Indo - West Pacific (IWP) region as an alternative to marine shrimp culture because of significant disease outbreaks and associated failures of many shrimp culture industries in the region. Currently, practices used to produce and manage breeding crabs in hatcheries may compromise levels of genetic diversity, ultimately compromising growth rates, disease resistance and stock productivity. Therefore, to avoid “genetic pollution” and its harmful effects and to promote further development of mud crab aquaculture and fisheries in a sustainable way, a greater understanding of the genetic attributes of wild and cultured mud crab stocks is required. Application of these results can provide benefits for managing wild and cultured Asian mud crab populations for multiple purposes including for commercial production, recreation and conservation and to increase profitability and sustainability of newly emerging crab culture industries. Phylogeographic patterns and the genetic structure of Asian mud crab populations across the IWP were assessed to determine if they were concordant with those of other widespread taxa possessing pelagic larvae of relatively long duration. A 597 bp fragment of the mitochondrial DNA COI gene was amplified and screened for variation in a total of 297 individuals of S. paramamosain from six sampling sites across the species’ natural geographical distribution in the IWP and 36 unique haplotypes were identified. Haplotype diversities per site ranged from 0.516 to 0.879. Nucleotide diversity estimates among haplotypes were 0.11% – 0.48%. Maximum divergence observed among S. paramamosain samples was 1.533% and samples formed essentially a single monophyletic group as no obvious clades were related to geographical location of sites. A weak positive relationship was observed however, between genetic distance and geographical distance among sites. Microsatellite markers were then used to assess contemporary gene flow and population structure in Asian mud crab populations sampled across their natural distribution in the IWP. Eight microsatellite loci were screened in sampled S. paramamosain populations and all showed high allelic diversity at all loci in sampled populations. In total, 344 individuals were analysed, and 304 microsatellite alleles were found across the 8 loci. The mean number of alleles per locus at each site ranged from 20.75 to 28.25. Mean allelic richness per site varied from 17.2 to 18.9. All sites showed high levels of heterozygosity as average expected heterozygosities for all loci ranged from 0.917 – 0.953 while mean observed heterozygosity ranged from 0.916 – 0.959. Allele diversities were similar at all sites and across all loci. The results did not show any evidence for major differences in allele frequencies among sites and patterns of allele frequencies were very similar in all populations across all loci. Estimates of population differentiation (FST) were relatively low and most probably largely reflect intra – individual variation for very highly variable loci. Results from nDNA analysis showed evidence for only very limited population genetic structure among sampled S. paramamosain, and a positive and significant association for genetic and geographical distance among sample sites. Microsatellite markers were then employed to determine if adequate levels of genetic diversity has been captured in crab hatcheries for the breeding cycle. The results showed that all microsatellite loci were polymorphic in hatchery samples. Culture populations were in general, highly genetically depauperate, compared with comparable wild populations, with only 3 to 8 alleles recorded for the same loci set per population. In contrast, very high numbers of alleles per locus were found in reference wild S. paramamosain populations, which ranged from 18 to 46 alleles per locus per population. In general, this translates into a 3 to 10 fold decline in mean allelic richness per locus in all culture stocks compared with wild reference counterparts. Furthermore, most loci in all cultured S. paramamosain samples showed departures from HWE equilibrium. Allele frequencies were very different in culture samples from that present in comparable wild reference samples and this in particular, was reflected in a large decline in allele diversity per locus. The pattern observed was best explained by significant impacts of breeding practices employed in hatcheries rather than natural differentiation among wild populations used as the source of brood stock. Recognition of current problems and management strategies for the species both for the medium and long-term development of the new culture industry are discussed. The priority research to be undertaken over the medium term for S. paramamosain should be to close the life cycle fully to allow individuals to be bred on demand and their offspring equalised to control broodstock reproductive contributions. Establishing a broodstock register and pedigree mating system will be required before any selection program is implemented. This will ensure that sufficient genetic variation will be available to allow genetic gains to be sustainably achieved in a future stock improvement program. A fundamental starting point to improve hatchery practices will be to encourage farmers and hatchery managers to spawn more females in their hatcheries as it will increase background genetic diversity in culture stocks. Combining crablet cohorts from multiple hatcheries into a single cohort for supply to farmers or rotation of breeding females regularly in hatcheries will help to address immediate genetic diversity problems in culture stocks. Application of these results can provide benefits for managing wild and cultured Asian mud crab populations more efficiently. Over the long-term, application of data on genetic diversity in wild and cultured stocks of Asian mud crab will contribute to development of sustainable and productive culture industries in Vietnam and other countries in the IWP and can contribute towards conservation of wild genetic resources.

Molecular discrimination of Perna (Mollusca: Bivalvia) species using the polymerase chain reaction and species-specific mitochondrial primers

This work was prompted by the need to be able to identify the invasive mussel species, Perna viridis, in tropical Australian seas using techniques that do not rely solely on morphology. DNA-based molecular methods utilizing a polymerase chain reaction (PCR) approach were developed to distinguish unambiguously between the three species in the genus Perna. Target regions were portions of two mitochondrial genes, cox1 and nad4, and the intergenic spacer between these that occurs in at least two Perna species. Based on interspecific sequence comparisons of the nad4 gene, a conserved primer has been designed that can act as a forward primer in PCRs for any Perna species. Four reverse primers have also been designed, based on nad4 and intergenic spacer sequences, which yield species-specific products of different lengths when paired with the conserved forward primer. A further pair of primers has been designed that will amplify part of the cox1 gene of any Perna species, and possibly other molluscs, as a positive control to demonstrate that the PCR is working.

Modelling discard ogives from Irish demersal fisheries

Annual discard ogives were estimated using generalized additive models (GAMs) for four demersal fish species: whiting, haddock, megrim, and plaice. The analysis was based on data collected on board commercial vessels and at Irish fishing ports from 1995 to 2003. For all species the most important factors influencing annual discard ogives were fleet (combination of gear, fishing ground, and targeted species), mean length of the catch and year, and, for megrim, also minimum landing size. The length at which fish are discarded has increased since 2000 for haddock, whiting, and plaice. In contrast, discarded length has decreased for megrim, accompanying a reduction in minimum landing size in 2000.

Prevalence, persistence and control of Salmonella and Listeria in shrimp and shrimp products: A review.

Shrimp are an important commodity in the international fisheries trade and there is an indication of an increase in worldwide consumption of this crustacean. Salmonella and Listeria have been isolated from shrimps and shrimp products on a regular basis since the 1980s. The continued reporting of the presence of these pathogens in fresh and frozen shrimps, and even in the lightly preserved and ready-to-eat products, indicates that the existing practices used by the manufacturers or processors are insufficient to eliminate these pathogens. This paper reviews the information available on Salmonella and Listeria in shrimp and makes recommendations on control options and avenues for future research in order to improve shrimp safety and quality.