Integrating the standardization of catch-per-unit-of-effort into stock assessment models: testing a population dynamics model and using multiple data types

Standardization of catch-per-unit-of-effort (CPUE) data can be integrated into stock assessment methods. We apply this method to the stock of trevally (Pseudocaranx dentex) off the west coast of New Zealand to address: (1) whether the stock assessment model explains all of the annual variation in the CPUE data, and (2) the impact on the assessment results of how the catch-at-age data are weighted. If not all of annual variation in CPUE is explained by the stock assessment model, the assessment may be statistically inadequate. The inadequacy may be in the representation of the population dynamics, in the relationship between CPUE and abundance, or due to additional variation in CPUE left unexplained by the independent variables. Catch-at-age data often have too much influence on the estimated abundance trajectory, so the sample size used in the catch-at-age likelihood function is often reduced when applying age-structured stock assessment methods. The integrated approach automatically places more weight on the CPUE data compared to the catch-at-age data, and may therefore provide an alternative to arbitrarily downweighting catch-at-age data.     

Estimation of genetic parameters for growth traits in cultured clam Meretrix meretrix (Bivalvia: Veneridae) using the Bayesian method based on Gibbs sampling

The aim of this study was to estimate the genetic parameters of the growth performance of clam Meretrix meretrix. As part of the breeding programme, 25 full‐sib families nested within eight half‐sib families were produced, planted out and tested to assess the heritability of the total body weight (TW), shell length (SL), shell height (SH) and shell width (SW) at different growth stages. Method of analysis was implemented using the Bayesian method based on the Multiple Trait using Gibbs Sampling under Animal Model program, which was used to estimate the (co)variance components of the traits and conduct genetic analysis. A total of 25 full‐sib families, each with 30–35 individuals within family, were used for the analysis. Significant positive genetic and phenotypic correlations between SL, SW, SH and TW with each other were observed. The growth traits showed high‐magnitude heritabilities, with values ranging from 0.64 to 0.85, which indicates that these traits should respond to selection and therefore should be included in genetic improvement programmes.     

A Bayesian model for anchovy (Engraulis encrasicolus): the combined forcing of man and environment

Fishery collapses frequently result from combined pressures of the environment and man, which are difficult to discern because of the complexities involved and our limited knowledge. Models to resolve this complexity often become too sophisticated, with too many assumptions and, consequently, with little capacity to predict beyond calibration data. In this paper we implement a different procedure where the model is kept simple and uncertainty accounts for the equation imperfectness to reproduce ecological complexity. Human and environmental forcing on an anchovy ( Engraulis encrasicolus ) stock are simulated with only six parameters plus their error terms, and the uncertainty is computed with Bayesian methods. The simple structure is able to reproduce the major dynamical features of this species in the Gulf of Cádiz, including data on life stages and age structure that had no contact with the model. This is a distinct performance for a frugal approach working on a mid-trophic species and a positive instance where parsimony can simulate the interaction of man, fish and the environment, provided uncertainty is accounted for in the process.     

Aquaponics and sustainability: The comparison of two different aquaponic techniques using the Life Cycle Assessment (LCA)

Aquaponics is generally regarded as a sustainable practice, but its environmental burdens were not yet deeply investigated. In this study, Life Cycle Assessment (LCA) was used to assess the environmental impacts of two hypothetical coupled aquaponics systems (CAPS): Raft System (RAFT) and Media-Filled Beds System (MFBS). Rainbow trout (Oncorhynchus mykiss) and lettuce (Lactuca sativa) were considered as cultivated species in both systems. The Simapro^© software V.8.0 was used for calculation. The comparison between the two virtual systems indicated the floating technique as the less impacting one. Even though energy consumption appears to be higher in the floating system, LCA results were markedly influenced by the extensive use of inert materials in MFSB. In both systems, contribution analyses underlined that the main environmental impacts are related to infrastructures, electricity and fish feed. The LCA analyses carried out in this study highlights that the choice of less impacting materials, and the optimization of management practices, should be taken as priorities in order to reduce environmental impacts of this activity.     

Changes in the population of American plaice (Hippoglossoides platessoides) off Labrador and northeastern Newfoundland: A collapsing stock with low exploitation

Changes in the population dynamics of American plaice off southern Labrador and eastern Newfoundland (NAFO Subarea 2 and Division 3K) for the period 1977–1994 were investigated. Since the mid 1980s the population has declined dramatically and by the 1990s the stock had essentially collapsed. A higher proportion of what remained of the stock was found in deeper and warmer water than had previously been observed, coincident with a period of unusually cold ocean conditions. During the period of the greatest reductions in population size, the proportion of older, spawning-age fish declined much more rapidly than the younger ages and this decline was accompanied by a slight decrease in mean size at age. Also associated with these observations were declining trends in both size and age at maturity.

Although exploitation has always been low, the fishery for American plaice in NAFO Subarea 2 and Division 3K has been regulated since the early 1970s. For the period investigated the average annual commercial exploitation rate was less than 2% with negligible bycatch in other fisheries. We conclude, therefore, that the collapse of this stock was not a result of fishing mortality. The causal mechanism for the decline remains unclear although unusual environmental conditions during the period continue to be investigated in relation to the observed changes in this population.     

A geostatistical approach for the stock assessment of the edible sea urchin, Paracentrotus lividus, in four coastal zones of Southern and West Sardinia (SW Italy, Mediterranean Sea)

Quantitative surveys of the edible sea urchin, Paracentrotus lividus, were conducted in four fishing zones of Sardinia (Southern Italy, Mediterranean Sea), in Autumn 2007. A total of 120 stations were geo-located along a bathymetric gradient ranging from 0 to 10 m. A geostatistical method was used to evaluate spatial patterns in density and to estimate harvestable stocks. Variographic analyses showed that the isotropic Gaussian and spherical models successfully explained the spatial structure of sea urchin assemblages in these areas. Density maps obtained by punctual kriging showed that sea urchin populations tend to be patchy rather than uniform in their density distribution. A combination of mapping and size categories was used to generate diverse scenarios of harvestable stocks (specimens ≥50 mm in diameter) before the start of the current fishing season. We conclude that the geostatistical approach, which takes into consideration the spatial autocorrelation structure of the populations in small areas, seems to be a good estimator of P. lividus density and biomass and for the assessment of its harvestable stocks, and thus provides an initial step towards a scientific approach to the management of local sea urchin fisheries.     

Geographic influences on and the accuracy and precision of age estimates for the red bass, Lutjanus bohar (Forsskal 1775): A large tropical reef fish

The red bass is a large tropical reef fish (Lutjanidae, tropical snappers) that is harvested to varying extents throughout a widespread Indo-Pacific distribution. The aims of this study were to investigate the accuracy and precision of age estimates from transverse sections of sagittal otoliths and to assess effects on these of the geographic area of collection and otolith preparation method. Two independent validation studies suggested an approximately annual formation of annuli in otoliths, predominantly for otoliths with 4–10 annuli but also for one otolith with 29 annuli. Otolith sections produced exceptionally high annulus counts: up to 56 annuli for samples from the Great Barrier Reef (GBR), Australia; and up to 55 annuli from the Seychelles, indicating a high longevity for this species. The precision of otolith readings from the GBR (index of average percent error, IAPE = 3.21 ± 0.26 S.E.) was within commonly accepted bounds for age estimation (IAPE up to 5%) but precision of readings from the Seychelles was significantly lower (IAPE = 9.18 ± 0.47 S.E.) and outside of this “acceptable” range. Age-based biological parameters for red bass from the Seychelles should thus be applied with greater caution than those for red bass from the GBR. If basic demographic properties are assumed relatively constant across the wide geographic range sampled, however, results from the GBR could be used as more reliable preliminary data for precautionary management strategies in the Seychelles and elsewhere.     

Predicting the age of fish using general and generalized linear models of biometric data: A case study of two estuarine finfish from New South Wales, Australia

Direct ageing of fish can be a laborious and expensive task when age estimates from a large population are required, and often involves a degree of subjectivity. This study examined the application of general and generalized linear models that predict the age of fish from a range of efficiently and objectively measured covariates. The data sampled were from yellowfin bream (Acanthopagrus australis (Sparidae) (Owen, 1853)) and sand whiting (Sillago ciliata (Sillaginidae) Cuvier, 1829) populations from New South Wales, Australia. The covariates evaluated in the models were fish length, otolith weight, sex and location (the estuary from which the fish were sampled). Akaike Information Criteria were used for model selection and residual plots of the final models revealed a satisfactory fit to the observations. The best fitting model for each species included all covariates. An additional investigation considered whether general and generalized linear models that predict age from two different categories of biometric information outperform age-length keys with respect to subsequent estimates of total mortality from catch-curve analysis. The two categories of biometric information differed in the ease and cost with which the information could be collected. The first category only included fish length and location as covariates, whilst the second category also included otolith weight and sex. It was found that traditional age-length keys outperformed the predictive models that estimated age from only fish length and location, because the results from the models were prone to significant bias. However, when otolith weight and sex were added as covariates to the predictive models, some of them, including a generalized linear model with a Poisson-distributed response variable, performed similarly to the age-length key. Given that otolith weight and the sex of fish are cheaper to quantify than age from a sectioned otolith in many situations, general or generalized linear models may represent a cheaper and faster method of estimating mortality compared to age-length keys. Such models can also easily incorporate the influence of spatial, temporal and demographic variation.     

Conservation status assessment and a new method for establishing conservation priorities for freshwater mussels (Bivalvia: Unionida) in the middle and lower reaches of the Yangtze River drainage

1. The freshwater mussel (Unionida) fauna of the Yangtze River is among the most diverse on Earth. In recent decades, human activities have caused habitat degradation in the river, and previous studies estimated that up to 80% of the mussel species in the Yangtze River are Threatened or Near Threatened with extinction. However, a comprehensive and systematic evaluation of the conservation status of this fauna has yet to be completed.
2. This study evaluated the conservation status of the 69 recognized freshwater mussel species in the middle and lower reaches of the Yangtze River, using the criteria published by the International Union for Conservation of Nature (IUCN). A new method for prioritizing species for conservation was then developed and applied termed Quantitative Assessment of Species for Conservation Prioritization (QASCP), which prioritizes species according to quantifiable data on their distribution and population status, life history, and recovery importance and potential.
3. IUCN assessments showed that 35 (51%) species in the study region are Threatened or Near Threatened (11 Endangered, 20 Vulnerable, 4 Near Threatened). In addition, 16 species (23%) could not be assessed owing to data deficiency. Key threats to the freshwater mussel biodiversity of the Yangtze River include pollution, habitat loss and fragmentation, loss of access to host fish, and overharvesting of mussels and their host fish. The genera Aculamprotula, Gibbosula, Lamprotula, Pseudodon, Ptychorhynchus, and Solenaia were identified as particularly threatened.
4. Data availability allowed QASCP assessment of 44 species. Only Solenaia carinata, regionally Endangered under IUCN criteria, achieved the highest QASCP rank, i.e. First Priority. The five species assessed as Second Priority were considered either regionally Endangered (one), Vulnerable (three), or Data Deficient (one) under IUCN criteria. The 23 Third Priority species were assessed as regionally Endangered (two), Vulnerable (15), Near Threatened (two), or Least Concern (four).

     

A method for collecting eggs of Pseudocapillaria tomentosa (Nematoda: Capillariidae) from zebrafish Danio rerio and efficacy of heat and chlorine for killing the nematode's eggs

Pseudocapillaria tomentosa is a common pathogen of zebrafish (Danio rerio) in research facilities. We developed a method to collect and concentrate the nematode eggs using a modified sugar centrifugation method and documented their normal development. Embryonating stages with blastomere formation followed by elongation of the embryo prior to larva formation cumulated in developed larvae inside the eggs and hatching after 5–10 day. We then evaluated the efficacy of heat and chlorine to kill them based on a larva development assay. Eggs were exposed to 40, 50, 60 °C for 30 min and 1 h. Chlorine treatment was performed at 100, 250, 500, 1000, 3000 and 6000 ppm for 10 min. Samples exposed to 40 °C for 30 min or 1 h showed incidences of larvated eggs similar to controls. In contrast, no larvation occurred with eggs exposed to either 50 or 60 °C for 30 min or 1 h. Remarkably, in repeated assays, samples exposed to low doses of chlorine (100, 250, 500 and 1000 ppm for 10 min) showed significantly higher incidence of larvation than controls. Eggs treated with 3000 ppm for 10 min did not develop larvae, and no eggs were found after 6000 ppm treatment.