Stock assessment of the Queensland-New South Wales tailor fishery (Pomatomus saltatrix)

Data on catch sizes, catch rates, length-frequency and age composition from the Australian east coast tailor fishery are analysed by three different population dynamic models: a surplus production model, an age-structured model, and a model in which the population is structured by both age and length. The population is found to be very heavily exploited, with its ability to reproduce dependent on the fishery’s incomplete selectivity of one-year-old fish. Estimates of recent harvest rates (proportion of fish available to the fishery that are actually caught in a single year) are over 80%. It is estimated that only 30–50% of one-year-old fish are available to the fishery. Results from the age-length-structured model indicate that both exploitable biomass (total mass of fish selected by the fishery) and egg production have fallen to about half the levels that prevailed in the 1970s, and about 40% of virgin levels. Two-year-old fish appear to have become smaller over the history of the fishery. This is assumed to be due to increased fishing pressure combined with non-selectivity of small one-year-old fish, whereby the one-year-old fish that survive fishing are small and grow into small two-year-old fish the following year. An alternative hypothesis is that the stock has undergone a genetic change towards smaller fish; the true explanation is unknown. The instantaneous natural mortality rate of tailor is hypothesised to be higher than previously thought, with values between 0.8 and 1.3 yr–1 consistent with the models. These values apply only to tailor up to about three years of age, and it is possible that a lower value applies to fish older than three. The analysis finds no evidence that fishing pressure has yet affected recruitment. If a recruitment downturn were to occur, however, under current management and fishing pressure there is a strong chance that the fishery would need a complete closure for several years to recover, and even then recovery would be uncertain. Therefore it is highly desirable to better protect the spawning stock. The major recommendations are • An increase in the minimum size limit from 30cm to 40cm in order to allow most one-year-old fish to spawn, and • An experiment on discard mortality to gauge the proportion of fish between 30cm and 40cm that are likely to survive being caught and released by recreational line fishers (the dominant component of the fishery, currently harvesting roughly 1000t p.a. versus about 200t p.a. from the commercial fishery).

Stock assessment report on Queensland east coast red throat emperor (Lethrinus miniatus) fishery

The Red Throat Emperor fishery was assessed using an age-structured model that incorporated all available information on catch, catch per unit effort (CPUE) and age structure and a surplus production model fitted to the catch and CPUE data. The Great Barrier Reef (GBR) was divided into five regions: Townsville, Mackay, Storm Cay, Swain reefs, and Capricorn Bunker. Age structure varied greatly between regions, with fish aged 5-8 years predominating in the Townsville region, 4-7 years in the Mackay, Storm Cay and Swains regions, and 2-3 years in the Capricorn-Bunker region. These differences were explained by different age-dependent vulnerabilities to fishing between the regions. The age-structured model estimated that exploitable biomass fell to about 60% of virgin biomass in the late 1990s, due mainly to years of poor recruitment, but recovered to around 70% by 2004. Further recovery can be expected due to the fishery not meeting its total allowable commercial catch (TACC) of 700 t in recent years. The current TACC of 700 t, combined with a recreational-charter catch of around 450 t, contains little margin for error, especially in view of high year-to-year variability of recruitment of red throat emperor and stresses on the GBR from land clearing, coastal development and climate change. The state of the population needs to be monitored closely. Further data on age structures after 2000 will provide more certainty to this assessment.

Stock assessment of the Queensland east coast common coral trout (Plectropomus leopardus) fishery

Common coral trout Plectropomus leopardus is an iconic fish of the Great Barrier Reef (GBR) and is the most important fish for the commercial fishery there. Most of the catch is exported live to Asia. This stock assessment was undertaken in response to falls in catch sizes and catch rates in recent years, in order to gauge the status of the stock. It is the first stock assessment ever conducted of coral trout on the GBR, and brings together a multitude of different data sources for the first time. The GBR is very large and was divided into a regional structure based on the Bioregions defined by expert committees appointed by the Great Barrier Reef Marine Park Authority (GBRMPA) as part of the 2004 rezoning of the GBR. The regional structure consists of six Regions, from the Far Northern Region in the north to the Swains and Capricorn–Bunker Regions in the south. Regions also closely follow the boundaries between Bioregions. Two of the northern Regions are split into Subregions on the basis of potential changes in fishing intensity between the Subregions; there are nine Subregions altogether, which include four Regions that are not split. Bioregions are split into Subbioregions along the Subregion boundaries. Finally, each Subbioregion is split into a “blue” population which is open to fishing and a “green” population which is closed to fishing. The fishery is unusual in that catch rates as an indicator of abundance of coral trout are heavily influenced by tropical cyclones. After a major cyclone, catch rates fall for two to three years, and rebound after that. This effect is well correlated with the times of occurrence of cyclones, and usually occurs in the same month that the cyclone strikes. However, statistical analyses correlating catch rates with cyclone wind energy did not provide significantly different catch rate trends. Alternative indicators of cyclone strength may explain more of the catch rate decline, and future work should investigate this. Another feature of catch rates is the phenomenon of social learning in coral trout populations, whereby when a population of coral trout is fished, individuals quickly learn not to take bait. Then the catch rate falls sharply even when the population size is still high. The social learning may take place by fish directly observing their fellows being hooked, or perhaps heeding a chemo-sensory cue emitted by fish that are hooked. As part of the assessment, analysis of data from replenishment closures of Boult Reef in the Capricorn–Bunker Region (closed 1983–86) and Bramble Reef in the Townsville Subregion (closed 1992–95) estimated a strong social learning effect. A major data source for the stock assessment was the large collection of underwater visual survey (UVS) data collected by divers who counted the coral trout that they sighted. This allowed estimation of the density of coral trout in the different Bioregions (expressed as a number of fish per hectare). Combined with mapping data of all the 3000 or so reefs making up the GBR, the UVS results provided direct estimates of the population size in each Subbioregion. A regional population dynamic model was developed to account for the intricacies of coral trout population dynamics and catch rates. Because the statistical analysis of catch rates did not attribute much of the decline to tropical cyclones, (and thereby implied “real” declines in biomass), and because in contrast the UVS data indicate relatively stable population sizes, model outputs were unduly influenced by the unlikely hypothesis that falling catch rates are real. The alternative hypothesis that UVS data are closer to the mark and declining catch rates are an artefact of spurious (e.g., cyclone impact) effects is much more probable. Judging by the population size estimates provided by the UVS data, there is no biological problem with the status of coral trout stocks. The estimate of the total number of Plectropomus leopardus on blue zones on the GBR in the mid-1980s (the time of the major UVS series) was 5.34 million legal-sized fish, or about 8400 t exploitable biomass, with an 2 additional 3350 t in green zones (using the current zoning which was introduced on 1 July 2004). For the offshore regions favoured by commercial fishers, the figure was about 4.90 million legal-sized fish in blue zones, or about 7700 t exploitable biomass. There is, however, an economic problem, as indicated by relatively low catch rates and anecdotal information provided by commercial fishers. The costs of fishing the GBR by hook and line (the only method compatible with the GBR’s high conservation status) are high, and commercial fishers are unable to operate profitably when catch rates are depressed (e.g., from a tropical cyclone). The economic problem is compounded by the effect of social learning in coral trout, whereby catch rates fall rapidly if fishers keep returning to the same fishing locations. In response, commercial fishers tend to spread out over the GBR, including the Far Northern and Swains Regions which are far from port and incur higher travel costs. The economic problem provides some logic to a reduction in the TACC. Such a reduction during good times, such as when the fishery is rebounding after a major tropical cyclone, could provide a net benefit to the fishery, as it would provide a margin of stock safety and make the fishery more economically robust by providing higher catch rates during subsequent periods of depressed catches. During hard times when catch rates are low (e.g., shortly after a major tropical cyclone), a change to the TACC would have little effect as even a reduced TACC would not come close to being filled. Quota adjustments based on catch rates should take account of long-term trends in order to mitigate variability and cyclone effects in data.

Bayesian fisheries stock assessment: integrating and updating knowledge

In this thesis the use of the Bayesian approach to statistical inference in fisheries stock assessment is studied. The work was conducted in collaboration of the Finnish Game and Fisheries Research Institute by using the problem of monitoring and prediction of the juvenile salmon population in the River Tornionjoki as an example application. The River Tornionjoki is the largest salmon river flowing into the Baltic Sea. This thesis tackles the issues of model formulation and model checking as well as computational problems related to Bayesian modelling in the context of fisheries stock assessment. Each article of the thesis provides a novel method either for extracting information from data obtained via a particular type of sampling system or for integrating the information about the fish stock from multiple sources in terms of a population dynamics model. Mark-recapture and removal sampling schemes and a random catch sampling method are covered for the estimation of the population size. In addition, a method for estimating the stock composition of a salmon catch based on DNA samples is also presented. For most of the articles, Markov chain Monte Carlo (MCMC) simulation has been used as a tool to approximate the posterior distribution. Problems arising from the sampling method are also briefly discussed and potential solutions for these problems are proposed. Special emphasis in the discussion is given to the philosophical foundation of the Bayesian approach in the context of fisheries stock assessment. It is argued that the role of subjective prior knowledge needed in practically all parts of a Bayesian model should be recognized and consequently fully utilised in the process of model formulation.

Stock assessment of protogynous fish: evaluating measures of spawning biomass used to estimate biological reference points

In stock assessments, recruitment is typically modeled as a function of females only. For protogynous stocks, however, disproportionate fishing on males increases the possibility of reduced fertilization rates. To incorporate the importance of males in protogynous stocks, assessment models have been used to predict recruitment not just from female spawning biomass (Sf), but also from that of males (Sm) or both sexes (Sb). We conducted a simulation study to evaluate the ability of these three measures to estimate biological reference points used in fishery management. Of the three, Sf provides best estimates if the potential for decreased fertilization is weak, whereas Sm is best only if the potential is very strong. In general, Sb estimates the true reference points most closely, which indicates that if the potential for decreased fertilization is moderate or unknown, Sb should be used in assessments of protogynous stocks. Moreover, for a broad range of scenarios, relative errors from Sf and Sb occur in opposite directions, indicating that estimates from these measures could be used to bound uncertainty.

Stock assessment of loggerhead and leatherback sea turtles and An assessment of the impact of the pelagic longline fishery on the loggerhead and leatherback sea turtles of the Western North Atlantic

On September 7, 2000 the National Marine Fisheries Service announced that it was reinitiating consultation under Section 7 of the Endangered Species Act on pelagic fisheries for swordfish, sharks, tunas, and billfish. 1 Bycatch of a protected sea turtle species is considered a take under the Endangered Species Act (PL93-205). On June 30, 2000 NMFS completed a Biological Opinion on an amendment to the Highly Migratory Pelagic Fisheries Management Plan that concluded that the continued operation of the pelagic longline fishery was likely to jeopardize the continued existence of loggerhead and leatherback sea turtles.2 Since that Biological Opinion was issued NMFS concluded that further analyses of observer data and additional population modeling of loggerhead sea turtles was needed to determine more precisely the impact of the pelagic longline fishery on turtles. 3,4 Hence, the reinitiation of consultation. The documents that follow constitute the scientific review and synthesis of information pertaining to the narrowly defined reinitiation of consultation: the impact of the pelagic longline fishery on loggerhead and leatherback sea turtles The document is in 3 parts, plus 5 appendices. Part I is a stock assessment of loggerhead sea turtles of the Western North Atlantic. Part II is a stock assessment of leatherback sea turtles of the Western North Atlantic. Part III is an assessment of the impact of the pelagic longline fishery on loggerhead and leatherback sea turtles of the Western North Atlantic. These documents were prepared by the NMFS Southeast Fisheries Science Center staff and academic colleagues at Duke University and Dalhousie University. Personnel involved from the SEFSC include Joanne Braun-McNeill, Lisa Csuzdi, Craig Brown, Jean Cramer, Sheryan Epperly, Steve Turner, Wendy Teas, Nancy Thompson, Wayne Witzell, Cynthia Yeung, and also Jeff Schmid under contract from the University or Miami. Our academic colleagues, Ransom Myers, Keith Bowen, and Leah Gerber from Dalhousie University and Larry Crowder and Melissa Snover from Duke University, also recipients of a Pew Charitable Trust Grant for a Comprehensive Study of the Ecological Impacts of the Worldwide Pelagic Longline Industry, made significant contributions to the quantitative analyses and we are very grateful for their collaboration. We appreciate the reviews of the stock definition sections on loggerheads and leatherbacks by Brian Bowen, University of Florida, and Peter Dutton, National Marine Fisheries Service Southwest Fisheries Science Center, respectively, and the comments of the NMFS Center of Independent Experts reviewers Robert Mohn, Ian Poiner, and YouGan Wang on the entire document. We also wish to acknowledge all the unpublished data used herein which were contributed by many researchers, especially the coordinators and volunteers of the nesting beach surveys and the sea turtle stranding and salvage network and the contributors to the Cooperative Marine Turtle Tagging Program. (PDF contains 349 pages)

Stock assessment of the Atlantic menhaden, Brevoortia tyrannus, fishery

A stock assessment of the Atlantic menhaden, Brevoortia tyrannus, fishery was conducted with purse-seine landings data from 1940 to 1984 and port sampling data from 1955 to 1984. These data were analyzed to determine growth rates, maximum sustainable yield (MSY), spawner-recruit relationships, and yield per recruit. Virtual population analysis was used to estimate stock size, year class size, and fishing mortality rates. Surplus production models produced estimates of MSY from 450 to 490 kmt compared with yields of 416to 436 kmt based roughly on maximum recruitment from a weak spawner-recruit relationship. Recruitment to age-I ranged from 1.2 to 14.8 billion fish for year classes 1955-81. Recent mean recruitment to age-I for the 1975-81 year classes averaged 5.7 billion fish and compared favorably with the mean of 7.7 billion age-I fish recruited during the late 1950's. Mean recruitment from recent years suggests possible coastwide yields of 416 to 481 kmt. Continued dominance of late age-2 spawners among the spawning stock is of concern, since the stock is at greater risk through poor recruitment if recent favorable environmental conditions change. Yield-per-recruit estimates ranged from 46 g to 59 g since 1970. The high dependency of the modern fishery on prespawners has increased concerns about fluctuations in year-to-year availability and catches. To increase yield and enhance the stability of the resource, the number of age classes contributing significantly to the fishery should be increased, creating a butTer against future poor recruitment years and lessening the year-to-year fluctuations in landings. (PDF file contains 24 pages.)

Stock assessment of the gulf menhaden, Brevoortia patronus, fishery

A stock assessment of the gulf menhaden. Brevoortia patronus, fishery was conducted with data on purse-seine landings from 1946 to 1985 and port sampling data from 1964 to 1985. These data were analyzed to determine growth rates, yield-per-recruit, spawner-recruit relationships, and maximum sustainable yield (MSY). Virtual population analysis was used to estimate stock size, year-class size, and fishing mortality rates. During the period studied, an average of 27% of age-l fish and 55% of age-2 and age-3 fish were taken by the fishery, and 54% for age-I and 38% for age-2 and -3 fish were lost annually to natural causes. Annual yield-per-recruit estimates ranged from 6.9 to 19.3 g, with recent mean conditions averaging 12.2 g since 1978. Surplus production models produced estimates of MSY from 620 to 700 kilometric tons. Recruits to age-I ranged from 8.3 to 41.8 billion fish for 1964-82. Although there was substantial scatter about the fitted curves, Ricker·type spawner-recruit relationships were found suitable for use in a population simulation model. Estimates of MSY from population simulation model runs ranged from 705 to 825 kilometric tons with F -multiples of the mean rate of fishing ranging from 1.0 to 1.5. Recent harvests in excess of the historical MSY may not be detrimental to the gulf menhaden stock. However, one should not expect long-term harvesting above the historical MSY because of the short life span of gulf menhaden and possible changes from currently favorable environmental conditions supporting high recruitment.(PDF file contains 24 pages.)

Stock assessment of Lates niloticus (L.), Oreochromis niloticus (L.) and Rastrineobola argentea (Pellegrin) using fishery dependent data from the Tanzanian waters of Lake Victoria

Catch data were collected from three beaches in the Mwanza area of lake Victoria, Tanzania for Oreochromis niloticus (L.), Rastrineobola argentea (Pellegrin) and Lates niloticus (L.). Sampling took place in October 1997 and February, June and September 1998. The CPUE for O. niloticus was 3.9 to 6kg boat super(-1) and for R. argentea from 98 to 282 kg boat super(-1). There was no obvious trend in catch rates for L. niloticus. The modal length for O. niloticus recorded at Chole beach was 34cm TL. In February, fish were larger (41-45 cm) than in the other surveys. Rastrineobola argentea caught in October 1997 had modal length at 65 mm TL with some smaller fish. In February and June prominent length modes occurred at 45 and 58 mm respectively, which may represent the same cohort as the small fish caught in October 1997. In September 1998, there were two length modes at 46 and 60 mm. The 60 mm fish may represent the same cohort seen in previous surveys, suggesting growth from approximately 30 mm to 60 mm in an eleven-month period. Lates niloticus landed at Kayenze beach over the four surveys had a modal length of 46 cm TL. Fish species encountered on the three beaches during the surveys were O. niloticus, R. argentea, Bagrus docmak Forsskall, Clarias gariepinus (Burchell), Protopterus aethiopicus Heckel, Labeo victorians Boulenger, Synodontis afrofischeri Hilgendorf, Synodontis victoriae Boulanger, Schilbe intermedius (L.), Brycinus jacksonii (Boulanger), Mormyrus kannume Forsskall and Haplochromine cichlids

Stock assessment of Lates niloticus (L.), Oreochromis niloticus (L.) and Rastrineobola argentea (Pellegrin) using fisheries-dependent data from Tanzania waters of Lake Victoria

Three commercially important fish species, Lates niloticus (L.), Rastrineobola argentea (Pellegrin) and Oreochromis niloticus (L.) that are fished by artisanal fishermen of Lake Victoria, Tanzania part, were studied in Kagera, Mwanza and Mara beaches from October 1997 to July 1999. Catches, effort, exploitation and stock structure were investigated. Beaches for sampling were selected based on importance for landing the above named fish species. The number of boats found on beach that day, the number that lay idle and their means of propulsion were recorded. As many boats as possible were sampled for gear type and gear size. The catches were sorted into species and measured. Variation in the species and size composition of landings was observed between regions, between months and between gears used. The implications of the findings to management are discussed.

World meeting on stock assessment of bluefin tunas: strengths and weaknesses

The Inter-American Tropical Tuna Commission (IATTC) hosted a meeting, sponsored jointly by the IATTC and the Australian Fisheries Service, to discuss and report on the strengths and weaknesses of stock assessment techniques used on bluefin tuna stocks in the Pacific, Indian, and Atlantic Oceans and the Mediterranean Sea. The meeting was held in La Jolla, California, on Mat 25-31, 1990.

The River Lune strategic stock assessment survey 1991 with particular reference to salmonids

In the past stock assessment surveys were generally reactive in response to a particular problem e.g. a pollution incident and as such were limited in the information they provided. A programme of strategic stock assessment would be more beneficial, providing up to date information on the status and composition of the stock. On a national level this could reveal trends in population dynamics and enable comparisons to be made between key rivers and between regions. The Stock Assessment Task Group (1991) has recommended annual strategic surveys for juvenile salmonids and triennial strategic surveys for coarse fish and non- migratory salmonids. The aim of this pilot study was to gain information on species distribution and their relative abundance within the River Lune catchment, and to compare the findings with the surveys carried out between 1981-1985. This would provide valuable information on the current status of the stock and provide an indication of the resources required to conduct such strategic surveys on other river catchments in the North West Region of the National Rivers Authority.

River Lune juvenile fish stock assessment 1997 with particular reference to salmonids

This report presents data from the juvenile salmonid fish stock assessment which is part of the routine Environment Agency riverine monitoring programme. A total of 110 sites was electrofished throughout the Lune catchment between 15th July 1997 and 14th October 1997. These sites included 84 that had been previously sampled in the last comprehensive survey of the catchment, in 1991. The aim of this survey was to assess the distribution and abundance of juvenile salmon and trout in the River Lune catchment and to compare results with those of previous surveys.

River Lune juvenile fish stock assessment 2002 (annotated draft copy, Site Reports only)

This draft copy of the River Lune juvenile fish stock assessment from 2000 provides "Site Reports" from different water bodies in the Lune catchment. These Site Reports provide brief information on habitat features, fishery classification and comments on species caught and stocking. This document provides no summary or interpretation of the given data.

Report on the 1995 stock assessment of the Douglas catchment

The River Douglas has a long industrial heritage beginning in the early 18th century with its use by boats carrying goods between Wigan and Tarleton. The River and its tributaries have also historically been, and to a certain extent are still, subject to polluting inputs from the urban, agricultural and industrialised areas located within its catchment. During the early stages in the production of the River Douglas Catchment Management Plan, it became apparent that very little data existed on the populations of coarse and salmonid fish species within the River Douglas system. The data that did exist was largely anecdotal, consisting of catch reports from anglers or water bailiffs, or of dead and distressed fish following pollution incidents. This study was initiated to assess the status of coarse and salmonid fish species within the River Douglas system and so address the lack of knowledge. Eighty two sites were surveyed by electric fishing, including 14 sites using an electric fishing punt and up to four anodes. The data was analysed according to a new National Fisheries Classification Scheme. This classified the sites by the fish stock s present and compared the results with a database containing information from sites around the country that have similar habitat types. A stocking experiment was also undertaken in the River Lostock using chub reared at the Leyland Hatchery. These were marked with an identifiable blue spot in the spring of 1995 and then released into three, previously surveyed, locations in the river. These sites were then resurveyed during the summer stock assessment. This report also Site Reports with details on monitored sites, habitat features and fishery classification.