Use of individual types of fishing effort in analyzing catch and effort data by use of a generalized linear model

Fishing effort is a function of many (continuous) variables which fishers can manipulate. However, when catch and fishing effort data are analysed using a generalized linear model, individual types of fishing effort usually enter as a composite quantity. But not all quantities can be combined into a composite quantity. Use of such data this way generally leads to a loss of information and incurs a model bias. In this paper, I analyse catch and effort data for the blue swimmer crab off South Australia by a direct use of individual types of fishing effort to extract a relative index of biomass, and use the concept of homogeneous functions to present some of the results. I also give formulae for choosing a combination of different types of fishing effort to effect a specified level of catch in both absolute and relative terms. Assuming that catch follows an independent gamma, normal, negative binomial, or Poisson distribution, fitting of a generalized linear model with a log-link function to the commercial catch and effort data suggests that: (1) the exploitable biomass remained relatively constant from 1 July 1983 to 30 June 1996; (2) the relative instantaneous rate of fishing mortality of a particular sex and age (if gear selectivity was constant over time) slightly increased over time; (3) a 1% increase in the number of days fished gave about 0.85% increase in catch whereas a 1% increase in the number of people on a boat led to only about a 0.45% increase in catch. This implies that use of a composite measure of fishing effort such as boat days and man days when analysing catch and effort data is inappropriate for this fishery. Although a generalized linear model may be a reasonable first-order approximation, catch and effort data are best interpreted through a process model.     

RISK ASSESSMENT OF A SHRIMP AQUACULTURE INVESTMENT IN FLORIDA

A stochastic simulation model was developed to examine the impact of risky economic variables on the profitability of a small-scale shrimp farm. Sources of risk included input and output prices, random-kill events, and hurricane damages. Success was measured using the probability distribution of the net present value (NPV). A baseline model that assumed capital costs of $493,993, a stocking density of 100 shrimp per m², a harvest survival of 80%, and a discount rate of 8% failed to generate a positive NPV. Subsequently adding a $0.66 price premium also failed to establish a positive NPV. Further reducing initial capital costs by 50% resulted in a 2% probability of a positive NPV. Incrementally reducing the discount rate generated increasingly positive NPV probabilities ranging from a 9% probability of success (7% discount rate) to a 94% probability of success (3% discount rate). Additional analyses suggested that probabilities of financial success were also sensitive to random-kill and hurricane events.     

Vaccine-induced protective immunity against Aeromonas salmonicida tested in experimental carp erythrodermatitis

Abstract The development and applicability of a dose-controlled experimental infection with atypical Aeromonas salmonicida in carp is described. The proliferation and clinical manifestations of experimentally induced carp erythrodermatitis mimicked a natural infection. An in-vivo assay was used to evaluate the lethal properties of cell-free culture supernatants and a simple serum-free growth medium was devised for maintaining the virulence of the challenge strain. Depending on the inoculation dose, a sublethal (chronic) to a lethal (acute) infection could be induced, and a dose-response relation was observed between A. salmonicida inoculum size and carp mortality. The dose-controlled experimental infection was used as a challenge test for laboratory evaluation of the efficacy of potential vaccine candidates. The vaccine candidates tested, a cell envelope preparation, purified lipopolysaccharide and purified A-layer (ACE) protein showed no protection or only a feeble one at the best, while formalinized whole cells showed a consistent but only moderate protection. In contrast, when concentrated, detoxified culture supernatant was used, the carp were protected against a subsequent lethal challenge. These observations indicate that immunity against A. salmonicida extracellular products is of prime importance.     

Development and regression of soybean meal induced enteritis in Atlantic salmon, Salmo salar L., distal intestine: a comparison with the intestines of fasted fish

The development of a pathological condition in the distal intestine of Atlantic salmon, Salmo salar L., induced by dietary soybean meal, was studied in a 6-week feeding experiment. The fully developed condition, as observed after 3 weeks on the experimental diets, was characterized by: (1) a shortening of heights of the mucosal foldings; (2) a loss of the normal supranuclear vacuolization of the absorptive cells in the intestinal epithelium; (3) a widening of the central stroma within the mucosal foldings, with increased amounts of connective tissue; and (4) a profound infiltration of inflammatory cells in the lamina propria. The first signs of morphological changes were observed after 2 days on a diet containing a solvent extracted soybean meal, and within 7 days, all the above mentioned signs were observed. When the fish were subsequently transferred to a control diet, the mucosal folds were rebuilt from the base, resulting in an apparently functional epithelium after 3 weeks. Starved fish also exhibited characteristic changes of the mucosa, including a finely granular cytoplasm replacing the supranuclear vacuoles seen in the epithelial cells of normal fish. In addition, a pattern of irregularly spaced indentations developed in the epithelium of the simple folds. The condition induced by dietary soybean meal was classified as a no n-infectious subacute enteritis, and a pathogenesis involving immunological mechanisms is suggested.     

Analysis of juvenile tuna movements as correlated random walk

We explore how a stochastic model provides the most promising avenue towards predicting fish movement. To construct a stochastic model describing fish movement, trajectories of ten juveniles in a water tank were analyzed from a stochastic point of view. The heading angle was defined as a random variable. Our analysis found that the most probable forward heading angle was between 0° and 22.5° (probability ~78%), followed by angles between 22.5° and 45° (probability ~10%). We also found that the choice of future heading angle depends on the current heading angle. Therefore, we treated heading angle state as a first-order Markov process and constructed a correlated random walk model describing juvenile movement in a water tank. Our stochastic model simulated a trajectory similar to observed trajectories. We used the model as a tool for estimating the probability distribution of potential fish path outcomes. We derived the distribution of potential outcomes from a large number of simulations (N = 1000) and investigated these trajectories. We collected a set of juvenile trajectories that collided with the tank and estimated the probability of juvenile collisions with the tank.     

RISK ASSESSMENT IN OPEN-OCEAN AQUACULTURE: A FIRM-LEVEL INVESTMENT-PRODUCTION MODEL

ABSTRACT

We develop a framework for risk assessment in open-ocean aquaculture. The framework consists of three components: a firm-level investment-production model simulates a specific grow-out project and estimates the project's benefit-cost values, a second model calculates the risk premium for a risk-averse investor, and a third model quantifies the option value for a risk-neutral investor. We show that under uncertainty, the traditional NPV rule for making an investment should be modified. We illustrate our models using a case study of open-ocean aquaculture of Atlantic cod (Gadus morhua) in New England.     

Characterization of the isoforms of type IIb sodium-dependent phosphate cotransporter (Slc34a2) in yellow catfish, <Emphasis Type="Italic">Pelteobagrus fulvidraco</Emphasis>, and their vitamin D<Subscript>3</Subscript>-regulated expression under low-phosphate conditions

In this study, two isoforms slc34a2 genes (type IIb sodium-dependent phosphate cotransporter), slc34a2a2 and slc34a2b, were cloned from intestine and kidney of yellow catfish (Pelteobagrus fulvidraco), with rapid amplification of cDNA ends. The structure differences and the regulation effects of dietary VD₃ under low phosphorus were compared among three isoforms of slc34a2 in yellow catfish. The predicted Slc34a2a2 and Slc34a2b proteins match 65 % and 53.8 % sequence identity, with Slc34a2a1, respectively. The membrane-spanning domains were different among these three isoforms. Intestinal Slc34a2a1 and Slc34a2a2 proteins had eight and eleven transmembrane domains, while renal Slc34a2b protein had nine. The tissue distribution study showed that same as slc34a2a1, slc34a2a2 mRNA was mainly distributed in intestine and slc34a2b mRNA in kidney. The effect of vitamin D₃ (VD₃) level on slc34a2 subfamily expression under low-phosphate conditions, induced by the addition of 0 (VD0), 324 (VD1), 1243 (VD2), 3621 (VD3), 8040 (VD4), or 22700 (VD5) IU VD₃/kg feed, was assessed by qPCR. The dose-responsive expression of intestinal slc34a2a2 and high expression of intestinal slc34a2a2 in VD5 together with peak expression of kidney slc34a2b in VD3 coincided with the accumulation of body phosphate content. These data suggested that appropriate level of dietary VD₃ up-regulated slc34a2a1, slc34a2a2, and slc34a2b mRNA levels, which increased phosphate retention. In conclusion, the current study provided another possible approach to improve dietary phosphate utilization by adding appropriate level of VD₃ to a low-phosphate diet to regulate intestinal and renal slc34a2 gene expression and thus minimize the excretion of phosphorus in yellow catfish.     

A client/server architecture remote fish finder system for a set net fishery

In order to monitor the fish volume entrapped over time in a set net in real time, a new remote fish finder system based on a mobile network was developed and tested. This system was designed with a client/server architecture including an echo sounder terminal, a web server, and some end user display terminals, which allowed fishermen to monitor the fishing state of a set net via any display device. In addition, in order to transfer the echo data smoothly via a mobile network, a fish echo extraction method based on image processing and a data organization structure were proposed, which can significantly reduce the data volume for transmission, supply sufficient information to reconstruct the high resolution echogram at the user terminals, and calculate the positional and morphometric parameters of fish echoes. Furthermore, a semiautomatic data recording method for use with a database was proposed to manage the extracted fish echo data and the fishing records. The functions and capabilities of the new system were demonstrated by a sea trial.     

杭州湾北部张网对凤鲚幼鱼的损害性分析

为探究张网捕捞作业对凤鲚幼鱼的损害性,根据2017年5—10月杭州湾北部张网渔业资源调查数据,利用全长分析、幼鱼密度和质量占比等方法,对张网渔获中凤鲚幼鱼的生物学特征及幼鱼密度的变化进行了研究分析。结果表明,5—10月各月份张网渔获物中均有凤鲚幼鱼出现,6月份凤鲚幼鱼的平均全长达到最大值112.8 mm,8月份最小,仅为64.7 mm;平均体质量则是10月份最大,达4.4 g,8月份最小,仅1.7 g。5月份凤鲚幼鱼质量密度最高,达到493.1 g/kg,8月份最低,仅为70.3 g/kg;凤鲚幼鱼的数量密度则是7月份最高,为225 ind/kg,6月份最低,为63 ind/kg。渔获中凤鲚幼鱼质量占比5月份最高,为49.3%,8月份最低,仅7.0%;9月份渔获中凤鲚幼鱼数量占比最高,为21.0%,6月份最低,仅为5.3%。研究结果表明,5月和7月杭州湾北部张网对凤鲚幼鱼的损害程度最高。为保护凤鲚幼鱼资源,除调整禁渔期以外,建议组织开展张网网目尺寸试验,研究不同网目尺寸对凤鲚幼鱼释放的效果。     

Simulation Modelling for Fisheries Management

The use of simulation models in fisheries management is introduced with the particular aim of encouraging fisheries managers to participate in providing data for or constructing such models. Management models are useful both as a training tool for future managers and as a decision-making tool. The close connection between verbal statements about how a system works and the corresponding computer statements is illustrated by a simple example. The main flows of information associated with a simulation model for management are illustrated, and it is shown that fisheries managers could provide much of the information needed. Finally, an example is given of a management model used as a teaching game, illustrating the components that such models can include and the range of management decisions available for achieving a particular objective. This model is based on a reservoir which can be stocked with two species of trout; the reservoir is to be managed for maximum profit, with revenue coming from people engaging in three recreational activities - angling, sailing and boating.     

Evaluation of testing strategies for infectious salmon anaemia and implications for surveillance and control programs

Infectious salmon anaemia (ISA) is an economically important disease in New Brunswick, Canada. Current regulatory control involves detection of ISAv in broodstock, hatcheries and marine sites through a surveillance program. Prior to recent assessments of operating characteristics of diagnostic tests, the efficiency of this surveillance program was difficult to evaluate. In order to determine the optimal testing strategies for various phases of production, a cost-effectiveness analysis was done for different strategies including single testing and multiple testing with results interpreted in series or in parallel. The lowest cost testing strategy, which would achieve a group-level sensitivity (GSe) of 95% and a group-level specificity (GSp) of 95%, was determined for each production phase. Our analyses showed that the most cost-effective testing strategy depended on the production phase. If sampling is to be carried out in a freshwater facility, then broodstock should be tested by VI alone, while pre-smolts should be tested with IFAT and VI used in series. For fish reared in saltwater, parallel interpretation of results from VI and RT-PCR, or testing with VI alone, are appropriate testing strategies for broodstock. For market-fish, PCR alone is a good screening option. If one assumes the prevalence of ISAv in moribund fish is at least 50%, then a maximum of 5 fish (at a cut-point of 1 positive fish to designate a cage as positive) need to be tested at a cost of $220. If one desired to have a perfect GSp (i.e. no false positive cage designations), serial testing with IFAT and VI is a better option. However, for this strategy a maximum of 9 fish (at a cut-point of 1) need to be tested at a cost of $472.     

The Effect of Parental Vitamin K Deficiency on Bone Structure in Mummichog Fundulus heteroclitus

The effect of parental vitamin K deficiency on developing bone structure was examined in mummichog ( Fundulus heteeroclitus ) larvae. Larvae from fish fed a vitamin K-deficient diet had abnormal vertebral formation, whereas larvae from fish fed a vitamin K-rich diet showed a significantly lower incidence of abnormality 5 d post-hatch. Larvae from fish that had been fed either the vitamin K-rich or the vitamin K-deficient diet had a high rate of abnormality when reared on a vitamin K-deficient diet for 30 d. Larvae from fish fed a vitamin K-rich diet that were reared on a vitamin K-rich diet showed a low rate of abnormality. Vertebral bone structure of larvae fed a vitamin K-deficient diet for 30 d was thin and rough, and seemed to have repaired fine fractures of the bone surface. In contrast, this type of structural abnormality was not observed in any larvae fed a vitamin K (phylloquinone) rich diet. These results imply that vitamin K deficiency causes the formation of thin and weak bone, and induces bone structure abnormality both in early development and during growth.     

A parasite survey of farmed Southern bluefin tuna, Thunnus maccoyii (Castelnau)

Farmed Southern bluefin tuna (SBT) were examined for parasites. Samples of harvest fish, mortalities and some fish showing clinical signs of disease were investigated. Targeted screening was conducted for a scuticociliate, Uronema nigricans, the myxosporean Kudoa sp. and a sanguinicolid digenean, Cardicola forsteri. General parasitological investigation revealed a diverse parasite community of didymozoid digeneans, two species of copepods, a polyopisthocotylean monogenean and larval cestodes. Targeted screening for U. nigricans exposed a low prevalence, most probably due to a lack of sensitivity in the test method. Few of the parasites examined pose a risk to the health of farmed SBT.     

A novel multiplex RT‐qPCR method based on dual‐labelled probes suitable for typing all known genotypes of viral haemorrhagic septicaemia virus

Viral haemorrhagic septicaemia (VHS) is a notifiable fish disease, whose causative agent is a rhabdovirus isolated from a wide range of fish species, not only in fresh but also in marine and brackish waters. Phylogenetic studies have identified four major genotypes, with a strong geographical relationship. In this study, we have designed and validated a new procedure – named binary multiplex RT‐qPCR (bmRT‐qPCR) – for simultaneous detection and typing of all four genotypes of VHSV by real‐time RT‐PCR based on dual‐labelled probes and composed by two multiplex systems designed for European and American/Asiatic isolates, respectively, using a combination of three different fluorophores. The specificity of the procedure was assessed by including a panel of 81 VHSV isolates covering all known genotypes and subtypes of the virus, and tissue material from experimentally infected rainbow trout, resulting in a correct detection and typing of all strains. The analytical sensitivity was evaluated in a comparative assay with titration in cell culture, observing that both methods provided similar limits of detection. The proposed method can be a powerful tool for epidemiological analysis of VHSV by genotyping unknown samples within a few hours.     

团头鲂Hox基因家族的鉴定、进化与表达分析

Hox基因家族在调控动物早期胚胎发育、组织和器官生长起重要作用,因此这类基因家族被广泛应用到物种进化和发育调控的研究中。为了探究Hox基因在团头鲂中分布,进化及表达调控作用,同时为了探究Hox基因与团头鲂肌间刺发育的关系,研究基于团头鲂全基因组数据,结合生物信息学分析方法对其Hox基因家族进行鉴定、染色体分布、系统进化和表达模式分析。结果显示,在团头鲂基因组中共鉴定出49个Hox基因,根据系统进化分析分为5个亚类;其中49个Hox基因不均匀的分布在5条染色体上,并分为7个基因连锁群（HoxAa、HoxAb、HoxBa、HoxBb、HoxCa、HoxCb和HoxDa）;表达模式分析结果表明,团头鲂Hox基因家族成员具有不同的表达模式;团头鲂和斑马鱼所有Hox基因在肌肉中的表达水平存在显著差异。此外,团头鲂不同发育阶段及不同组织转录组结果显示,HoxA基因群集中,HoxA2a、HoxA3a在幼鱼阶段高表达,其他基因在肌肉、肌间刺及结缔组织中表达量低甚至不表达;HoxB基因群集中,HoxB9a、HoxB3a、HoxB8a、HoxB1b、HoxB5a、HoxB5b在幼鱼阶段高表达;HoxB7a、HoxB10a、HoxB9a在成鱼肌肉、结缔组织及肌间刺中高表达;HoxC基因群集中,HoxC3a、HoxC4a在幼鱼阶段高表达,HoxC3a、HoxC8a在成鱼的3个组织都有表达;HoxD基因群集中,HoxD9a、HoxD10a和HoxD11a在胚胎S2期表达量较高。研究表明,Hox基因在团头鲂早期胚胎时期和肌间刺的形成中有表达,提示团头鲂肌间刺的形成可能受Hox基因家族调控。     

Hypopituitarism as the possible cause of prolonged gestation in cattle]

Multiple malformations were shown in a bovine fetus delivered at slaughter after a gestation period of 469 days. Hypoplasia of the adenohypophysis and a bilateral agenesis of the adrenal cortex suggest that the failure of initiation of parturition resulted from a fetal deficiency of ACTH and glucocorticoid hormones. ACTH, GH (growth hormone) and prolactin could not be demonstrated immunohistochemically within the adenohypophysis. However, TSH immunoreactive pituitary cells were demonstrable. Nevertheless, considering the extremely reduced size of the adenohypophysis a fetal deficiency of TSH is suspected. This view is supported by a bilateral hypoplasia of the thyroid gland. Additionally, the complex fetal endocrine dysfunction had led to a growth retardation of the fetus.     

Economic analysis of tiger grouper <Emphasis Type="Italic">Epinephelus fuscoguttatus</Emphasis> and humpback grouper <Emphasis Type="Italic">Cromileptes altivelis</Emphasis> commercial cage culture in Indonesia

This study presents an economic analysis of tiger and humpback grouper at different production scales in Indonesia. The results highlight the non-viability of small-scale tiger grouper farming, with a 5-year projected negative cumulative cash flow of −IDR 18,102,650.00 and a negative net present value (NPV) of −IDR 22,059,576.28. An increased production scale of tiger grouper highlights a marginal viability for medium-scale farms (with a 5-year projected cumulative cash flow of IDR 198,320,673.00, a positive NPV of IDR 105,578,440.42; a benefit cost ratio of 1.25; an internal rate of return (IRR) of 88% and a payback period of 0.99 years), and an economically viable large-scale cage culture (with a 5-year projected cumulative cash of IDR 707,746,923.00; a NPV of IDR 406,801,749.07; a benefit cost ratio of 1.33; an internal rate of return of 157%; and a payback period of 0.57 years). The economic analysis of humpback grouper at different production scales highlighted a positive cumulative cash and NPV, a benefit cost ratio over 2, an internal rate of return over 300% and a payback period <1 year. A sensitivity analysis revealed that increased survival rate up to 80% would increase cumulative cash and NPV of small-scale tiger grouper cage culture. Additionally, improved profitability performance was associated with decreasing major production costs, increasing production and price of the product.     

A large‐scale approach can help detect general processes driving the dynamics of brown trout populations in extensive areas

Abstract – Most studies on the population dynamics of stream‐living salmonids have been conducted at the scale of a reach, a stream or a river basin. This can lead to overestimating the importance of local factors acting on a reduced scale compared to the more general factors that drive the dynamics of several populations. Two models were built on the basis of a data set from 60 sampling stations representing separated populations inhabiting a large heterogeneous area encompassing 18 years of quantifications. Our analyses showed the following: (i) Population growth rate (pgr) of a set of independent brown trout populations can be described by means of a single model; (ii) the youngest and the oldest year classes of these populations seem to be limited by the same constraints; (iii) there is a climatic control of the recruitment because of spring weather conditions, but also the abundance of oldest age class may be controlled by the climate, (iv) there is a nonlinear positive effect of winter North Atlantic Oscillation on pgr; (v) there is a 3‐year lagged positive feedback tracing the upward trend of a stock‐recruitment curve, and 1‐year lagged negative feedback showing the downward trend of the curve; (vi) a strong cohort has a positive effect on the whole population that can be detected throughout the time. Our fitted models allowed to predict the mean population densities at a regional scale with <10% error and shed light onto the main factors and associated ecological processes that control these large‐scale dynamics.     

Effects of High-Protein "Finishing" Feeds on Performance and Fat Content of Channel Catfish

A study was conducted to evaluate the effects of using high-protein "finishing" feeds on production and fat content of channel catfish. Fish were fed either: a 32% protein feed for 150 days; a 28% protein feed for 150 days; a 28% protein feed for 90 days and then a 38% protein feed for 60 days; a 28% protein feed for 90 days and then a 35% protein feed for 60 days; a 28% protein feed for 120 days and then a 38% protein feed for 30 days; or a 28% protein feed for 120 days and then a 35% protein feed for 30 days. The study was conducted in earthen ponds stocked with channel catfish at a rate of 14,826 fish/ha (35 g initial weight) and fed once daily to satiation. There were no significant differences in either feed consumption, weight gain, final weight, feed conversion ratio, survival, or percentage visceral fat of catfish regardless of treatment. Fillets from fish fed the 28% protein feed for 150 days contained more fat than fish on other treatments. There was no advantage of finishing channel catfish on high-protein diets as compared to feeding either a 28 or 32% protein feed for the entire grow-out period.