A comparison of the incidence of five pathological conditions in soft-shell clams, Mya arenaria, from environments with various pollution histories

The distribution of the occurrences and co-occurrences of five pathological conditions in samples of the soft-shell clam, Mya arenaria, from 17 locations on the east coast of the United States were compared by two different analytical techniques. 1. The relative fit of Poisson and Lagrange-Poisson distributions to the data were related to the mortality rate and spread of the pathological conditions. 2. A severity index based on a matrix of occurrences and co-occurrences, and the analysis of its eigenvectors were used to measure and to characterise the severity of the spread. These two techniques were compared with the help of a cluster analysis and discussed in the context of the pollution history of the seventeen locations studied. Although causal inferences cannot be drawn, the analyses suggested that crude oils and heavy metals had less effect on the incidence of hyperplasia and neoplasia than more refined petrochemicals. However, neoplasia was found in both clean and polluted environments.     

A theoretical individual-based model of Brown Ring Disease in Manila clams,Venerupis philippinarum

An individual-based mathematical model was developed to investigate the biological and environmental interactions that influence the prevalence and intensity of Brown Ring Disease (BRD), a disease, caused by the bacterial pathogen, Vibrio tapetis, in the Manila clam (Venerupis (= Tapes, = Ruditapes) philippinarum). V. tapetis acts as an external microparasite, adhering at the surface of the mantle edge and its secretion, the periostracal lamina, causing the symptomatic brown deposit. Brown Ring Disease is atypical in that it leaves a shell scar that provides a unique tool for diagnosis of either live or dead clams. The model was formulated using laboratory and field measurements of BRD development in Manila clams, physiological responses of the clam to the pathogen, and the physiology of V. tapetis, as well as theoretical understanding of bacterial disease progression in marine shellfish. The simulation results obtained for an individual Manila clam were expanded to cohorts and populations using a probability distribution that prescribed a range of variability for parameters in a three dimensional framework; assimilation rate, clam hemocyte activity rate (the number of bacteria ingested per hemocyte per day), and clam calcification rate (a measure of the ability to recover by covering over the symptomatic brown ring deposit), which sensitivity studies indicated to be processes important in determining BRD prevalence and intensity. This approach allows concurrent simulation of individuals with a variety of different physiological capabilities (phenotypes) and hence by implication differing genotypic composition. Different combinations of the three variables provide robust estimates for the fate of individuals with particular characteristics in a population that consists of mixtures of all possible combinations.The BRD model was implemented using environmental observations from sites in Brittany, France, where Manila clams routinely exhibit BRD signs. The simulated annual cycle of BRD prevalence and intensity agrees with observed disease cycles in cultured clam populations from this region, with maximum disease prevalence and intensity occurring from December to April. Sensitivity analyses of modeled physiological processes showed that the level of hemocyte activity is the primary intrinsic determinant of recovery of infected clams. Simulations designed to investigate environmental effects on BRD suggested that the outcome of the host–parasite interaction is dependent on food supply (high values being favorable for the host) and temperature. Results of simulations illustrate the complex interaction of temperature effects on propagation and viability of the bacterium, on the phagocytic activity of the hemocytes, and on other physiological processes of the host clam. Simulations using 1 °C and 2 °C increases in temperature generally favored disease development, indicating that climate warming might favor the spread of BRD.     

菲律宾蛤仔不同品系斑马蛤的选择反应及现实遗传力

对菲律宾蛤仔中的斑马蛤、黑斑马、白斑马三品系进行混合选择,测量了各实验组的壳长,计算了不同品系斑马蛤的选择反应和现实遗传力。结果表明:3个品系的上选组壳长均大于对照组,说明单向上选是行之有效的遗传改良方法。在不同的生长发育阶段,斑马蛤品系的选择反应(R)和现实遗传力(2Rh)出现阶段性变化,从平均水平上看,R在幼虫期为0.688±0.184,稚贝期为0.605±0.214,养成期为0.670±0.120;2Rh在幼虫期为0.392±0.081,稚贝期为0.344±088,养成期为0.380±0.058。从一周年的生长情况来看,三个品系总的R为0.654±0.179,斑马蛤、黑斑马蛤和白斑马蛤品系的R分别为0.655±0.155、0.525±0.116、0.782±0.170;三个品系总的2Rh为0.373±0.070,斑马蛤、黑斑马蛤和白斑马蛤品系的2Rh分别为0.372±0.042、0.300±0.028、0.445±0.031。不同品系间R和2Rh次序为白斑马斑马蛤黑斑马,说明各斑马蛤品系的选择效果是不同的,品系间存在着一定程度的遗传差异。     

New polymorphic microsatellite markers derived from hemocyte cDNA library of Manila clam <Emphasis Type="Italic">Ruditapes philippinarum</Emphasis> challenged by the protozoan parasite <Emphasis Type="Italic">Perkinsus olseni</Emphasis>

Manila clam Ruditapes philippinarum is one of the most important benthic animals in the coastal north Pacific region, where clam populations have been mixed genetically through trade and aquaculture activities. Accordingly, identification of the genetically different clam populations has become one of the most important issues to manage interbreeding of the local and introduced clam populations. To identify genetically different populations of clam populations, we developed 11 expressed sequence tag (EST)-microsatellite loci (i.e., simple sequence repeat, SSR) from 1,128 clam hemocyte cDNA clones challenged by the protozoan parasite Perkinsus olseni. Genotype analysis using the markers developed in this study demonstrated that clams from a tidal flat on the west coast contained 6 to 19 alleles per locus, and a population from Jeju Island had 4 to 20 alleles per locus. The expected heterozygosity of the 2 clam populations ranged from 0.472 to 0.919 for clams from the west coast, and 0.494 to 0.919 for clams from Jeju Island, respectively. Among the 11 loci discovered in this study, 7 loci significantly deviated from the Hardy-Weinberg equilibrium after Bonferroni correction. The 5 loci developed in this study also successfully amplified the SSRs of R. variegatus, a clam species taxonomically very close to R. philippinarum, from Hong Kong and Jeju Island. We believe that the 11 novel polymorphic SSR developed in this study can be utilized successfully in Manila clam genetic diversity analysis, as well as in genetic discrimination of different clam populations.     

Growth performance of the clam, Meretrix meretrix, breedingselection populations cultured in different conditions

A breeding-selection program for the clam,Meretrix meretrix,was conducted since 2004.Two of the selection populations were generated with the shell color pattern as an additional selection criterion and named as SP(purple stripes)population and SB(black dots)population.The third-generation SP and SB populations(08G3SP and 08G3SB,respectively)were cultured at two commercial clam farms and a nursery pond and their shell lengths were compared.08G3SB clams had significantly larger sizes than 08G3SP clams at commercial clam farms(p<0.05),yet 08G3SB individuals were significantly smaller than 08G3SP individuals at the nursery pond(p<0.05).Then,we examined the growth of the fourth-generation SP and SB populations(10G4SP and 10G4SB,respectively)at a commercial farm,and found that the shell lengths of the 10G4SB clams increased at a significantly higher growth rate than the 10G4SP clams(p<0.05)from May to September,when the water temperature was between 24.2–27.5 C,while 10G4SB lost the growth advantage in the other months.These results indicated that SP and SB populations responded differently to environmental factors,so it is beneficial for the clam farmers to select a suitable population according to the culture environment.Furthermore,a diallel mating of the SB and SP populations was designed to investigate whether their hybrid population would show heterosis.However,the heterosis was not shown in this study,which might result from the slight genetic divergence between SB and SP populations.     

Management strategies to optimise sustainable clam (Tapes philippinarum) harvests in Barbamarco Lagoon,Italy

Barbamarco Lagoon is a small lagoon adjoining the Northern Adriatic Sea and is the site of a commercially valuable clam (Tapes philippinarum) fishery. A three-dimensional (3D) coupled hydrodynamic–ecological model was applied to the lagoon with the objective of assessing impacts on clam food supply, commercial harvests and water quality of different clam rearing strategies, lagoon morphologies and flow regimes. Harvest and net growth to seeding ratios, total harvest value, clearance efficiencies and clam satiety were used to quantify the commercial success of different management strategies, while bottom dissolved oxygen concentrations were used as an indicator of ecosystem health. Increasing exchange with the Northern Adriatic Sea or increasing freshwater inputs into the lagoon improved clam food supply and increased both harvest production and ecosystem health in model simulations of the system. Results indicated that the high spatial and temporal variability of clam production and water quality responses must be considered for a holistic assessment of the outcomes of strategies in the context of ecological and production carrying capacity.     

A spatially resolved model of seasonal variations in phytoplankton and clam (Tapes philippinarum) biomass in Barbamarco Lagoon,Italy

Barbamarco Lagoon (area = 7 km²) is in the Po River Delta, adjoining the Northern Adriatic Sea, and supports a commercially valuable clam (Tapes philippinarum) fishery. This study investigated interactions of the lagoon with adjacent coastal waters and inland riverine inputs by modelling both the lagoon and the Northern Adriatic Sea, using a coupled three-dimensional (3D) hydrodynamic-ecological model (ELCOM-CAEDYM) adapted to include the clam population. The clam model accounted for carbon (C), nitrogen (N) and phosphorus (P) biomass in the benthos through parameterisations for filtration, excretion, egestion, respiration, mortality, and harvesting. Multiple clam size classes were included in a new population dynamics sub-model. Output from the coupled model was validated against hydrodynamic and water quality data from intensive field sampling and routine monitoring. Time scales of tidal flushing, primary production and clam grazing were investigated with the model to demonstrate that food supply to clam populations is dominated by phytoplankton inputs from the Northern Adriatic Sea. Effects of clam cultivation on nutrient concentrations and phytoplankton biomass in Barbamarco Lagoon were primarily localised, with strong tidal flushing minimising impacts of clam filtration on lagoon-wide nutrient concentrations at current clam stocking levels. Clam populations were found to alter the cycling of nutrients in the system, causing the lagoon to become a net sink for particulate organic matter and to export dissolved organic matter to the adjacent sea via tidal flushing. Ecosystem health and sensitivity of nutrient cycles to clam cultivation are important considerations for the long term sustainable management and potential expansion of the fishery.     

Effects of environmental and biological conditions on the recruitment and growth of the Manila clam <Emphasis Type="Italic">Ruditapes philippinarum</Emphasis> on the west coast of Korea

The distribution of the Manila clam Ruditapes philippinarum, which is often dominant in intertidal zones, is influenced by both environmental and biological conditions. However, there have been few comprehensive studies on the interactive effects of these two groups of factors. The present study examined the environmental and biological parameters determining the population dynamics of the clams that is a dominant component of the intertidal communities of Euhangri and Padori on the west coast of Korean peninsula. We collected R. philippinarum and other members of the macrobenthos (> 1 mm long) monthly from 0.25 m² quadrats deployed in the intertidal zones at Euhangri, Taean, and Padori during the period from August 2013 to January 2015. Physicochemical parameters of the water and sediment were measured at the same time. Water temperature and salinity is high and low in the summer to winter, respectively. While mean grain size of the sediment was higher at Euhangri than at Padori, total mean density of R. philippinarum was higher at Euhangri (325 ind./ 0.25 m² at Padori vs. 194 ind./0.25 m² at Euhangri). Settled spat (< 10 mm in length) density was much higher at Euhangri than at Padori (132 vs. 12 individuals/0.25m², respectively). R. philippinarum spats settled down on the sediment at Euhangri in October and grew continually until the following May, when they reached adult size. Spats that settled down at Padori between March and April were not able to reach the adult stage. As the density of the adult population increased, the condition index of individual clams decreased, but as the population density of the spat increased the body condition index increased. The chlorophyll a content of the sediments at Padori exceeded that at Euhangri and decreased as the population of R. philippinarum increased. The shapes of R. philippinarum shells at Euhangri were more prolate than those at Padori, and the condition index at Euhangri exceeded that at Padori, indicating better growth conditions at Euhangri. The condition index and density of R. philippinarum were affected by the amount of chlorophyll a in the water column and in the sediment. The recruitment success of spats was negatively influenced by spat density. We suggest that regulation of habitat conditions for R. philippinarum, including the food supply, will optimize production of these commercial clams.     

Cytogenetics of Anodonta cygnea (Mollusca: Bivalvia) as possible indicator of environmental adversity

Anodonta cygnea is a freshwater clam, belonging to the Unionidae family, which can be found in rivers and lagoons all over Europe and Northern America. As they appear as important case studies for ecological damage assessments, the various species of the Unionidae family have been submitted to a sort of recent studies on their chromosomal or cytogenetic status. In this study we confirmed the diploid chromosome number of 2n = 38 for this species, and established for the first time the karyotype, which comprised six metacentric, 12 submetacentric and one subtelocentric chromosome pairs. We also found a high percentage of cells with an abnormal number of chromosomes. Considering that karyotype disturbances in Unionids have been previously related with exposure to chemicals, either natural or produced by human activity, we determined the aneuploidy index for our population. The aneuploidy index is an excellent marker for pollutant presence/effect. The animals acclimatized in tap water and in natural water from the lake where the individuals were collected showed different levels of aneuploidy. The higher values were found in tap water. Chromosome analysis techniques seem a suitable tool to study the impact of contaminants referred above, and making A. cygnea a suitable organism for assessment of an eugenic damage in aquatic systems. On the other hand, our results also point out to the importance of doing the acclimatizing process of the collected animals in their own natural water.     

Relationships between environmental factors and Donax denticulatus populations in Puerto Rico

Donax denticulatus population density and size distribution were studied in five different Puerto Rican beaches for a one year period in order to determine relationships between the densities and size distributions of the clam, and twelve different physico-chemical parameters of sediments and water. Maní beach exhibits significantly higher population densities followed by Luquillo, Esperanza and Ballenas. No clams were found in Crashboat. Luquillo and Esperanza had similar population fluctuations, having peak densities in August and January. Maní had higher densities in September and May, and Ballenas in June. The only major settlement period appeared during January at Esperanza. The bigger clams (30 mm) were found in Maní only. Higher population density and bigger clams in Maní are related to waters having high concentrations of total organic carbon, particulate organic carbon and nitrates. The clam was absent from Crashboat where very low levels of phosphates and nitrates were observed. These studies indicate relationships between water and sediment quality, and densities of D. denticulatus.     

A multibiomarker approach in the clam Ruditapes decussatus to assess the impact of pollution in the Ria Formosa lagoon,South Coast of Portugal

The Ria Formosa lagoon is an ecosystem whose water quality reflects the anthropogenic influence upon the surrounding areas. In this lagoon, the clam Ruditapes decussatus has a great economical importance and has been widely used as a biomonitor. A multibiomarker approach (δ-aminolevulinic acid dehydratase, metallothionein, lipid peroxidation, acetylcholinesterase, alkali-labile phosphates, DNA damage) was applied to assess the environmental quality of this ecosystem and the accumulation of contaminants and their potential adverse effects on clams. Clams were sampled in different shellfish beds in the period between July 2007 and December 2008 and abiotic parameters (temperature, salinity, pH and dissolved oxygen of seawater and organic matter in the sediment), condition index, metals (Cd, Cu, Zn, Ni, Pb), TBTs and PAHs concentrations were measured in clam tissues. Data was integrated using Principal Component Analyses and biomarker indices: IBR (Integrated Biomarker Response) and HSI (Health Status Index). This multibiomarker approach enabled discrimination of a time and space trend between sites with different degrees of anthropogenic contamination, identifying one of them (site 2) as the most stressful and summer months as the most critical period for clams due to an increase of environmental stress (anthropogenic pressure along with extreme environmental conditions, e.g. temperature, dissolved oxygen, organic matter in the sediments, etc). The selected biomarkers provided an integrated response to assess the environmental quality of the system, proving to be a useful approach when complex mixtures of contaminants occur.     

Estimation of dynamic energy budget parameters for the Mediterranean toothcarp (Aphanius fasciatus)

Organisms adopt different sets of physiological, behavioural and morphological trade-offs in order to cope with natural environmental fluctuations. This has consequential rebounds on ecological processes and population dynamics. Such aspects become crucial for sex-dimorphic species, where sex-specific growth variation could mirror different tactics both in energy acquisition and investment between maximum female and male body size with cascading effects on population demography. To date, different approaches have been used in order to understand the causes of individual growth rate changes in ectotherm indeterminate growers, most of which failed. Here, we propose the use of a mechanistic model based on the Dynamic Energy Budget theory (DEB; Koojiman, 2010) to investigate potential differences in energy allocation strategies adopted by individuals of different genders with the Mediterranean toothcarp Aphanius fasciatus (Valenciennes, 1821) as the model species. We collected literature and field data in order to study differences in energy allocation strategies between females and males of the same species by generating projections of possible growth performances: (1) throughout their entire life span and (2) under a context of varying functional responses. Generally, the present exercise of simulations returned different patterns of growth performance among females and males of A. fasciatus, with the former being able to better optimize energetic trade-offs under optimal environmental conditions. The present DEB parameterization exercise represents an essential step towards developing a mechanistic approach to depict metabolic strategies, which are at the base of observed sexual differences, and how such differences may impair ultimate fitness at individual and, therefore, population levels.     

基于GLM模型Logistic回归的菲律宾蛤仔地理群体判别

菲律宾蛤仔(Ruditapesphilippinarum)是重要的海洋经济贝类和海水养殖品种,具有较强的表型可塑性特点,不同地理群体之间存在表型差异。本研究根据实测数据建立了胶州湾与天鹅湖菲律宾蛤仔壳长(SL)与壳高(SH)、壳宽(SW)和活体重(W)的回归方程,定量分析了两个地理群体的形态学差异。由于其近似圆形的形态使得所能测量的外部指标较少,限制了传统形态测量学在其地理群体判别中的应用。本研究提出了将传统形态测量学和广义线性模型(GLM)相结合的方法,建立了判别菲律宾蛤仔地理群体的逻辑斯蒂(Logistic)回归方程。结果表明:菲律宾蛤仔的天鹅湖群体比胶州湾群体具有更高的SH/SL和SW/SL比值,壳形椭圆较圆且隆起程度高,"凸"形明显;基于GLM模型的Logistic回归能够快速准确地判别菲律宾蛤仔的地理群体归属,判别正确率高达94.23%。本研究为双壳类物种地理群体判别提供了新的分析方法和技术手段。     

Vertical zonation and aggregated distribution of the Manila clam on subtidal sand flats in a coastal brackish lagoon along the Sea of Japan

The Manila clam, Ruditapes philippinarum, has maintained small‐sized populations in a semi‐enclosed brackish lake along the Sea of Japan, the Honjo area of Lake Nakaumi, although the environment and biota of this area have changed dramatically due to a large‐scale reclamation project. There should be underlying processes that enable the restoration of this species from small‐sized populations, such as the existence of source (i.e. reproductive) populations in other areas and depth zones of the lake. However, there has been no robust, properly designed evaluation of the distribution of the Manila clam in the subtidal sand flats. In order to elucidate the possible mechanisms that allow for the persistence of populations of the Manila clam, we examined the spatiotemporal and vertical variation in distributions of 0‐age clams in the subtidal zone of sand flats. Seasonal effects on population variations showed erratic changes among depth zones without a decreasing trend along the depth gradient. Further, many local populations became extinct even in the shallower zones due to seasonal (summer) hypoxia at deeper zones and hypoxia by the accumulation of key benthic species (Asian mussel and decaying macroalgae) in mats at shallower zones. A few surviving local populations were stable with a spatial‐fragmental (patchy) distribution, associated with fragmented accumulations of Asian mussels and macroalgae. Efforts to maintain stable populations and to restore this species in the subtidal area may depend on these small, restricted, patchy local populations. These findings suggest that high fertility and productivity of the Manila clam as well as patchy distribution of small populations may contribute to the maintenance of the population and the avoidance of extinction (by spatially diffusing the risk of extinction) in harsh environments resulting from the reclamation project.     

Infestation of the surf clam Mesodesma donacium by the spionid polychaete Polydora bioccipitalis

The surf clam Mesodesma donacium is an economically important species for Chilean and Peruvian shellfisheries. This clam is often infested by Polydora bioccipitalis, a species belonging to the Spionidae, the most common parasitic polychaete group. To study this association, clams were sampled monthly over a one-year period in northern Chile. Collected clams covered the entire available size range and were classified into four infestation levels in order to study: (1) the relationship between prevalence of infestation (PI) and host size, (2) the temporal pattern of infestation events related to seasonal temperature changes, and (3) the relationship between infestation, body condition index (BCI) and gonado-somatic index (GSI). Additionally, growth rate and digging ability of clams with different infestation levels was studied. A logistic regression model best explained the relationship between PI and host size, with the smallest infested clam being 34 mm long and PI increasing steeply thereafter. Ontogenetic shifts in the habitat of the clam and ontogenetic changes, mainly in shell morphology, seem to explain the sigmoid pattern. Periods of increased shell blistering after infestation by P. bioccipitalis showed a similar seasonal pattern with GSI and BCI of non-infested clams, suggesting either an association between infestation ability and low condition of the clam or common environmental triggers for those factors. Heavily infested clams showed a significant lower BCI, growth rate and digging ability; however, given its low number, they are unlikely to be significant in terms of the local population survival. However, the infestation could play a key role in explaining mass mortality of northern populations during El Niño events, given the latitudinal differences in PI and the fact that infestation ability could be enhanced by increased temperature and facilitated in stressed clams.     

Nutrient load estimates for Manila Bay,Philippines using population data

A major source of nutrient load to periodically hypoxic Manila Bay is the urban nutrient waste water flow from humans and industries to surface water. In Manila alone, the population density is as high as 19,137 people/km². A model based on a global point source model by Morée et al. (2013) was used to estimate the contribution of the population to nitrogen and phosphorus emissions which was then used in a water transport model to estimate the nitrogen (N) and phosphorus (P) loads to Manila Bay. Seven scenarios for 2050 were tested, with varying degrees and amounts for extent of sewage treatment, and population growth rates were also included. In scenario 1, the sewage connection and treatment remains the same as 2010; in scenario 2, sewage connection is improved but the treatment is the same; in scenario 3, the sewage connection as well as treatment is improved (70% tertiary); and in scenario 4, a more realistic situation of 70% primary treatment achieved with 100% connection to pipes is tested. Scenarios 5, 6, and 7 have the same parameters as 1, 2, and 3 respectively, but with the population growth rate per province reduced to half of what was used in 1, 2, and 3. In all scenarios, a significant increase in N and P loads was observed (varying from 27% to 469% relative to 2010 values). This was found even in scenario 3 where 70% of the waste water undergoes tertiary treatment which removes 80% N and 90% P. However, the lowest increase in N and P load into the bay was achieved in scenarios 5 to 7 where population growth rate is reduced to half of 2010 values. The results suggest that aside from improving sewage treatment, the continued increase of the human population in Manila at current growth rates will be an important determinant of N and P load into Manila Bay.

     

三种蛏的遗传多样性分析

应用AFLP技术对浙南地区分布的小荚蛏(Siliqua minimai)、缢蛏(Sinonovacula constricta)和大竹蛏(Solen grandis)3种蛏进行了基因组DNA多态性检测,并对其遗传多样性进行了分析.利用筛选出的5对引物组合,共扩增出781个清晰的位点;小荚蛏、缢蛏和大竹蛏多态位点比例依次为79.22%、84.25%和64.82%,Nei's基因多样性指数分别为0.2971、0.3070和0.2785,Shannon's多样性指数分别为0.4402、0.4575和0.4010,种内平均遗传距离为0.2585、0.2691和0.1838.研究结果表明,这3种蛏的核DNA遗传多样性水平以缢蛏为最丰富,小荚蛏次之,大竹蛏最低;并且3种蛏的共享位点很少,遗传趋异比较明显,说明3种蛏的遗传关系比较远.     

AFLP analysis revealed differences in genetic diversity of four natural populations of Manila clam(Ruditapes philippinarum) in China

1 IntroductionManila clam (Ruditapes philippinarum) is aworldwide distributed species. In China, it is foundfrom the northern to southern seashores (Wang etal., 1993; Zhuang, 2001). This species is eura-line with the salinity tolerance ranging from 20 to4…     

The Manila clam population in Arcachon Bay (SW France): Can it be kept sustainable?

The venerid clam Ruditapes philippinarum is the most prominent suspension-feeding bivalve inhabiting muddy intertidal seagrass beds in Arcachon Bay (SW France). It is exploited by fishermen, and Arcachon Bay ranks number one in France in terms of production and total biomass of this species. Previous studies revealed a decrease in the standing stock of R. philippinarum since 2003 and unbalanced length–frequency distributions with a lack of juveniles and of adults > 40 mm. Consequently, the population dynamics of this bivalve were studied at four intertidal sites and one oceanic site in Arcachon Bay. As clam size structure did not allow classical dynamics computations, field monitoring was coupled with field experiments (tagging–recapture) over two years. Monitoring of condition index and gonadal maturation stages highlighted a high variability in spawning number and intensity between sites. Recruitment events in the exploited area varied spatially but with uniformly low values. Von Bertalanffy Growth Function (VBGF) parameters (K, L_∞) were determined using Appeldoorn and ELEFAN methods. In the exploited sites in the inner lagoon, K was relatively high (mean = 0.72 yr^? 1) but L_∞ was low (mean = 41.1 mm) resulting in a moderate growth performance index (Φ′ = 2.99). Growth parameters were not correlated with immersion time and L_∞ was different between sites. Comparison of mortality coefficients (Z) between cage experiments and field monitoring suggested that fishing accounts for 65–75% of total adult mortality. Low recruitment, a low growth rate and a normal mortality rate led to low somatic production (4.1 and 8.7 g Shell-Free Dry Weight (SFDW) m^? 2 yr^? 1) and an annual P/B ratio from 0.44 to 0.92 yr^? 1. Under current conditions, the possibility of a sustainable population in Arcachon Bay will strongly depend on recruitment success and fishing management.     

A higher-order σ-coordinate non-hydrostatic model for nonlinear surface waves

A higher-order non-hydrostatic model in a σ-coordinate system is developed. The model uses an implicit finite difference scheme on a staggered grid to simultaneously solve the unsteady Navier-Stokes equations (NSE) with the free-surface boundary conditions. An integral method is applied to resolve the top-layer non-hydrostatic pressure, allowing for accurately resolving free-surface wave propagation. In contrast to the previous work, a higher-order spatial discretization is utilized to approximate the large horizontal pressure gradient due to steep surface waves or rapidly varying topographies. An efficient direct solver is developed to solve the resulting block hepta-diagonal matrix system. Accuracy of the new model is validated by linear and nonlinear standing waves and progressive waves. The model is then used to examine freak (extreme) waves. Features of downshifting focusing location and wave asymmetry characteristics are predicted on the temporal and spatial domains of a freak wave.