Stock assessment for fishery management - A framework guide to the stock assessment tools of the Fisheries Management Science Programme (FMSP)

This document provides guidelines for fish stock assessment and fishery management using the software tools and other outputs developed by the United Kingdom's Department for International Development's Fisheries Management Science Programme (FMSP) from 1992 to 2004. It explains some key elements of the precautionary approach to fisheries management and outlines a range of alternative stock assessment approaches that can provide the information needed for such precautionary management. Four FMSP software tools, LFDA (Length Frequency Data Analysis), CEDA (Catch Effort Data Analysis), YIELD and ParFish (Participatory Fisheries Stock Assessment), are described with which intermediary parameters, performance indicators and reference points may be estimated. The document also contains examples of the assessment and management of multispecies fisheries, the use of Bayesian methodologies, the use of empirical modelling approaches for estimating yields and in analysing fishery systems, and the assessment and management of inland fisheries. It also provides a comparison of length- and age-based stock assessment methods. A CD-ROM with the FMSP software packages CEDA, LFDA, YIELD and ParFish is included.

The relationship between multi-species catch and effort: among fishery comparisons

The control of fishing mortality via fishing effort remains fundamental to most fisheries management strategies even at the local community or co-management level. Decisions to support such strategies require knowledge of the underlying response of the catch to changes in effort. Even under adaptive management strategies, imprecise knowledge of the response is likely to help accelerate the adaptive learning process. Data and institutional capacity requirements to employ multi-species biomass dynamics and age-structured models invariably render their use impractical particularly in less developed regions of the world. Surplus production models fitted to catch and effort data aggregated across all species offer viable alternatives. The current paper seeks models of this type that best describe the multi-species catch–effort responses in floodplain-rivers, lakes and reservoirs and reef-based fisheries based upon among fishery comparisons, building on earlier work. Three alternative surplus production models were fitted to estimates of catch per unit area (CPUA) and fisher density for 258 fisheries in Africa, Asia and South America. In all cases examined, the best or equal best fitting model was the Fox type, explaining up to 90% of the variation in CPUA. For lake and reservoir fisheries in Africa and Asia, the Schaefer and an asymptotic model fitted equally well. The Fox model estimates of fisher density (fishers km−2) at maximum yield (iMY) for floodplain-rivers, African lakes and reservoirs and reef-based fisheries are 13.7 (95% CI [11.8, 16.4]); 27.8 (95% CI [17.5, 66.7]) and 643 (95% CI [459,1075]), respectively and compare well with earlier estimates. Corresponding estimates of maximum yield are also given. The significantly higher value of iMY for reef-based fisheries compared to estimates for rivers and lakes reflects the use of a different measure of fisher density based upon human population size estimates. The models predict that maximum yield is achieved at a higher fishing intensity in Asian lakes compared to those in Africa. This may reflect the common practice in Asia of stocking lakes to augment natural recruitment. Because of the equilibrium assumptions underlying the models, all the estimates of maximum yield and corresponding levels of effort should be treated with caution.

Hierarchical analysis of production efficiency in a coastal trawl fishery

We present, pedagogically, the Bayesian approach to composed error models under alternative, hierarchical characterizations; demonstrate, briefly, the Bayesian approach to model comparison using recent advances in Markov Chain Monte Carlo (MCMC) methods; and illustrate, empirically, the value of these techniques to natural resource economics and coastal fisheries management, in particular. The Bayesian approach to fisheries efficiency analysis is interesting for at least three reasons. First, it is a robust and highly flexible alternative to commonly applied, frequentist procedures, which dominate the literature. Second,the Bayesian approach is extremely simple to implement, requiring only a modest addition to most natural-resource economist tool-kits. Third, despite its attractions, applications of Bayesian methodology in coastal fisheries management are few.

Interactions between fur seals and a squid jig fishery in southern Australia

Interactions between Australian fur seals (Arctocephalus pusillus doriferus) and the Southern Squid Jig Fishery (SSJF) were investigated in April–May 2002. Details on the number of seals present, distance from the vessel, age and gender, and their behaviour were recorded using scan sampling techniques over 26 nights from eight vessels operating out of Portland and Port Fairy on the southwest coast of Victoria. Seals were observed on all nights but none were recorded in 30% of all (777) scan observations. Of the seals attending vessels at any one time (1.89 ± 0.24), 67% were involved in activities unrelated to jigging operations with the most common behaviour category being resting/grooming. Only 3.6% of observations involved seals targeting squid caught on jig lures whereas a further 29% were of foraging on squid within 40 m of the vessel. Damage to fishing gear attributable to seals was recorded on only three occasions. There was no evidence of negative impacts on seals from vessel operations. The majority of seals foraging on squid around vessels were adult females (71%) with the remainder being almost exclusively juvenile males. The current level of interactions between Australian fur seals and vessels in the SSJF appears minor.

The fishery, biology and management of three inland water-bodies, Vietnam

This study was carried out from 1997 to 2004 and its findings have significantly enhanced our understanding on fishery, biology, and management of three inland water bodies in Vietnam. The study also provides insights into development of management guidelines and recommendations for future fisheries development in the research area.

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.

Two hundred years after a commercial marine turtle fishery: the current status of marine turtles nesting in the Cayman Islands

Large populations of marine turtles breeding in the Cayman Islands were drastically reduced in the early 1800s. However, marine turtle nesting still occurs in the islands. The present-day status of this nesting population provides insight into the conservation of marine turtles, a long-lived species. In 1998 and 1999, the first systematic survey of marine turtle nesting in the Cayman Islands found 38 nests on 22 beaches scattered through the three islands. Three species were found: the green Chelonia mydas, hawksbill Eretmochelys imbricata and loggerhead Caretta caretta turtles. Comparison with other rookeries suggests that the small number of sexually mature adults surviving Cayman’s huge perturbations may be impeding population recovery. This shows the need to implement conservation measures prior to massive reductions in population size.

Spatial abundance patterns and recruitment of a virus-affected commercial mollusc fishery

 Infectious pathogens figure prominently among those factors threatening marine wildlife. Mass mortality events caused by pathogens can fundamentally alter the structure of wild fish stocks and depress recruitment rates and yield. In the most severe instances, this can precipitate stock collapses resulting in dramatic economic losses to once valuable commercial fisheries. An outbreak of a herpes-like virus among commercially fished abalone populations in the south-west fishery of Victoria, Australia, during 2006-2007, has been associated with high mortality rates among all cohorts. Long-term records from fishery-independent surveys of blacklip abalone Haliotis rubra (Leach) enabled abundance from pre- and post-viral periods to be analysed to estimate stock density and biomass. The spatial distribution of abundance in relation to physical habitat variables derived from high-resolution bathymetric LiDAR data was investigated. Significant differences were observed in both measures between pre- and post-viral periods. Although there was some limited evidence of gradual stock improvement in recent years, disease-affected reefs have remained below productivity rates prior to the disease outbreak suggesting a reduction in larval availability or settlement success. This was corroborated by trends in sublegal sized blacklip abalone abundance that has yet to show substantial recovery post-disease. Abundance data were modelled as a function of habitat variables using a generalised additive model (GAM) and indicated that high abundance was associated with complex reef structures of coastal waters (<15 m). This study highlights the importance of long-term surveys to understand abalone recovery following mass mortality and the links between stock abundance and seafloor variability.

Contribution to the chemoreception capacity of juvenile Loggerhead sea turtles (Caretta caretta, L.)

Loggerhead sea turtle juveniles (Caretta caretta), pelagic stage, are found in waters of Madeira archipelago. Pelagic turtles are in the main growth phase of their life cycle and consequently higher energy needs. However, knowledge about the ecology of pelagic loggerhead sea turtles is still quite rudimentary, mainly about the mechanisms that lead them to find food in the vast ocean. Studies with other pelagic species, such as procellariiform birds, revealed that the olfactory system play an important role for the detection of feeding areas, through the detection of concentration peaks of DMS (dimethylsulfide), a scent compound that naturally exists in the marine environment and it is related to areas of high productivity. Based on the assumption that loggerhead sea turtles use a similar mechanism, behavioural experiments were conducted in order to analyze the chemoreception capacity to DMS (airborne chemoreception - theoretically responsible for the long distance detection of areas with food patches; and aquatic chemoreception - theoretically responsible for the short distance detection of preys). The first step was to observe if pelagic loggerheads demonstrate sensitivity to DMS and the second was to verify if they really use the DMS, in natural conditions, as an airborne cue to find areas where food patches might be available. Four juveniles of loggerhead sea turtles were tested in captivity and three wild turtles in the open ocean. The results of airborne chemoreception experiments in captivity revealed that one turtle clearly demonstrated sensitivity to DMS and the sea experiments confirmed this result. However, the experiments were not conclusive on the question whether the pelagic turtles actually use the DMS as an airborne cue to detect long distance food patches. In aquatic chemoreception experiments was not observed sensitivity to DMS by the three sea turtles tested. In the classical conditioning experiment, where DMS and food were given nearly at the same time revealed that after a certain period of time, the sea turtle tested did not associated the DMS stimulus with a possible food reward. The main cause of mortality of loggerhead sea turtles in Madeira waters is due to the accidental capture (bycatch) by deep pelagic longlines fishery which the target species is the black-scabbard (Aphanopus carbo) fish. Chub mackerel (Scomber japonicus) is one of the baits used in this fishery. Aquatic chemoreception experiments were conducted in order to evaluate the attractiveness of the chub mackerel for sea turtles. For the three sea turtles tested, the results showed that in 90% of the cases the sea turtles were extremely attracted by the underwater smell of this fish.