A Comparison of the SNP Variation in the Calcification PMCA Gene of Lottia gigantea between a Santa Barbara Population and a More Acidic Monterey Bay Population

As the atmospheric levels of CO2 rise from human activity, the carbonic acid levels of the ocean increase, causing ocean acidification. This increase in acidity breaks down the calcified bodies that many marine organisms depend upon. Upwelling regions such as Monterey Bay in California have pH levels that are not expected to reach the open ocean for a few decades. This study reviews one of the common intertidal animals of the California coast, the Owl Limpet Lottia gigantea, and its genetic variation of the plasma membrane Ca2+ ATPase (PMCA) in relation to the acidity of its environment. The PMCA protein functions in the calcification process of many organisms. Specifically in limpets, this gene functions to form its protective shell. Single-nucleotide polymorphisms (SNPs) were found among five sections of the gene to determine variation between the acidic environment population in Monterey, California and the non-acidic environment population in Santa Barbara, California. While some variation was determined, the Monterey Bay and Santa Barbara Lottia gigantea populations are not significantly distinct at the PMCA gene. Sections B, C, and D were found to be linked. Only one location in Section B was found to have an amino acid change within an exon. Section A has the strongest connection to the sampling location. Monterey individuals were seen to be more genetically recognizable, while Santa Barbara individuals showed slightly more variation. Understanding the trends of ocean acidification, upwelling region activities, and population genetics will assist in determining how the ocean environment will behave in the future.

Genetic variation between outer-coastal and fjord populations of Pacific herring (Clupea pallasii) in the eastern Gulf of Alaska

Pacific herring (Clupea pallasii) from the Gulf of Alaska were screened for temporal and spatial genetic variation with 15 microsatellite loci. Thirteen collections were examined in this study: 11 from Southeast Alaska and 2 from Prince William Sound, Alaska. Although FST values were low, a neighbor-joining tree based on genetic distance, homogeneity, and FST values revealed that collectively, the Berners Bay and Lynn Canal (interior) collections were genetically distinct from Sitka Sound and Prince of Wales Island (outer-coastal) collections. Temporal genetic variation within regions (among three years of Berners Bay spawners and between the two Sitka Sound spawners) was zero, whereas 0.05% was attributable to genetic variation between Berners Bay and Sitka Sound. This divergence may be attributable to environmental differences between interior archipelago waters and outer-coast habitats, such as differences in temperature and salinity. Early spring collections of nonspawning Lynn Canal herring were nearly genetically identical to collections of spawning herring in Berners Bay two months later—an indication that Berners Bay spawners over-winter in Lynn Canal. Southeast Alaskan herring (collectively) were significantly different from those in Prince William Sound. This study illustrates that adequate sample size is needed to detect variation in pelagic fish species with a large effective population size, and microsatellite markers may be useful in detecting low-level genetic divergence in Pacific herring in the Gulf of Alaska.

A meta-analytic approach to quantifying scientific uncertainty in stock assessments

Quantifying scientific uncertainty when setting total allowable catch limits for fish stocks is a major challenge, but it is a requirement in the United States since changes to national fisheries legislation. Multiple sources of error are readily identifiable, including estimation error, model specification error, forecast error, and errors associated with the definition and estimation of reference points. Our focus here, however, is to quantify the influence of estimation error and model specification error on assessment outcomes. These are fundamental sources of uncertainty in developing scientific advice concerning appropriate catch levels and although a study of these two factors may not be inclusive, it is feasible with available information. For data-rich stock assessments conducted on the U.S. west coast we report approximate coefficients of variation in terminal biomass estimates from assessments based on inversion of the assessment of the model’s Hessian matrix (i.e., the asymptotic standard error). To summarize variation “among” stock assessments, as a proxy for model specification error, we characterize variation among multiple historical assessments of the same stock. Results indicate that for 17 groundfish and coastal pelagic species, the mean coefficient of variation of terminal biomass is 18%. In contrast, the coefficient of variation ascribable to model specification error (i.e., pooled among-assessment variation) is 37%. We show that if a precautionary probability of overfishing equal to 0.40 is adopted by managers, and only model specification error is considered, a 9% reduction in the overfishing catch level is indicated.

Growth and survival of sockeye salmon (Oncorhynchus nerka) from Karluk Lake and River, Alaska, in relation to climatic and oceanic regimes and indices, 1922–2000

We examined whether the relationship between climate and salmon production was linked through the effect of climate on the growth of sockeye salmon (Oncorhynchus nerka) at sea. Smolt length and juvenile, immature, and maturing growth rates were estimated from increments on scales of adult sockeye salmon that returned to the Karluk River and Lake system on Kodiak Island, Alaska, over 77 years, 1924–2000. Survival was higher during the warm climate regimes and lower during the cool regime. Growth was not correlated with survival, as estimated from the residuals of the Ricker stock-recruitment model. Juvenile growth was correlated with an atmospheric forcing index and immature growth was correlated with the amount of coastal precipitation, but the magnitude of winter and spring coastal downwelling in the Gulf of Alaska and the Pacific Northwest atmospheric patterns that influence the directional bifurcation of the Pacific Current were not related to the growth of Karluk sockeye salmon. However, indices of sea surface temperature, coastal precipitation, and atmospheric circulation in the eastern North Pacific were correlated with the survival of Karluk sockeye salmon. Winter and spring precipitation and atmospheric circulation are possible processes linking survival to climate variation in Karluk sockeye salmon.

River fisheries in Africa: their relationship to flow regimes

River fisheries in Africa are important because of their contribution of animal protein to human diets. Such fisheries are highly dependent on hydrological regimes and show considerable year-to-year variation in response to natural climatic events. River flow regimes are being increasingly altered by withdrawals by man, principally for agriculture. The modification of hydrological regimes is leading to diminishing catches of fish and changes in the number and size of the species caught. Given that the trend to remove water from rivers for agriculture and power generation will continue, better appraisals of the impacts of such withdrawals are urgently needed so the policies for water allocation can be better defined. The development of tools to aid in such decision-making is equally important.

A tool for better management of water quality during periods of algal blooms: the case of the River Oise

Like other rivers in the Paris area, the Oise is subject to important seasonal algal blooms. This eutrophication generates notable problems for the production of drinking-water from a treatment plant on the river at Méry. A mathematical model has been developed to simulate variation in water quality in a pre-treatment storage basin, and another model is currently being adapted to model the River Oise. Integration of the two models should provide a comprehensive tool for predicting variations of phytoplankton and water-quality parameters associated with algal blooms. This will be a decision-aid for optimizing control of the treatment process for providing potable water.

Estimating relative abundance from catch and effort data, using neural networks

We develop and test a method to estimate relative abundance from catch and effort data using neural networks. Most stock assessment models use time series of relative abundance as their major source of information on abundance levels. These time series of relative abundance are frequently derived from catch-per-unit-of-effort (CPUE) data, using general linearized models (GLMs). GLMs are used to attempt to remove variation in CPUE that is not related to the abundance of the population. However, GLMs are restricted in the types of relationships between the CPUE and the explanatory variables. An alternative approach is to use structural models based on scientific understanding to develop complex non-linear relationships between CPUE and the explanatory variables. Unfortunately, the scientific understanding required to develop these models may not be available. In contrast to structural models, neural networks uses the data to estimate the structure of the non-linear relationship between CPUE and the explanatory variables. Therefore neural networks may provide a better alternative when the structure of the relationship is uncertain. We use simulated data based on a habitat based-method to test the neural network approach and to compare it to the GLM approach. Cross validation and simulation tests show that the neural network performed better than nominal effort and the GLM approach. However, the improvement over GLMs is not substantial. We applied the neural network model to CPUE data for bigeye tuna (Thunnus obesus) in the Pacific Ocean.

Energy efficiency in trawling operations

Diurnal variation in trawl catches and its influence on energy efficiency of trawler operations are discussed in this paper, based on data on landings of a Japanese factory trawler which operated in the Indian waters during 1992-93. The factory vessel equipped for stern trawling had a length overall of 110 m, GT of 5460 and installed engine power of 5700 hp. Operations were conducted off west coast of India between 31 and 278 m depth contours, using a 80.4 m high opening bottom trawl with an adjusted vertical opening of 7.60.9 m. The catch data was grouped according to the median towing hour, by the time of the day. CPUE obtained was 3713.4 kg.h-1 for day time operations and 1536.6 kg.h-1 for night-time operations. Mean daily catches were 31367 kg.day-1 (SE: 2743) for day time operations and 9430 kg.day-1 (SE: 966) for night-time operations. Fuel consumption were 0.399 and 0.982 kg fuel.kg fish-1, respectively for day and night-time operations. Total catch and catch components such as threadfin bream, bulls eye, hairtails, trevelly, lizard fish showed significant improvement during day-time operations while swarming crabs showed a significant improvement in the night-time operations. The difference in catch rates between day and night could be attributed to diurnal variation in the spatial distribution and schooling behaviour of the catch categories, their differential behaviour in the vicinity of trawl systems under varying light levels of day and night and consequent effect on catching efficiency and size selectivity at different stages in the capture process. The results obtained in addition to its importance in the operational planning of trawling in order to realise objectives of maximising catch per unit effort and minimising fuel consumption per unit volume of fish caught, has added significance in the use of bottom trawl surveys in stock abundance estimates.

Growth dynamics of the spinner shark (Carcharhinus brevipinna) off the United States southeast and Gulf of Mexico coasts: a comparison of methods

The age and growth dynamics of the spinner shark (Carcharhinus brevipinna) in the northwest Atlantic Ocean off the southeast United States and in the Gulf of Mexico were examined and four growth models were used to examine variation in the ability to fit size-at-age data. The von Bertalanffy growth model, an alternative equation of the von Bertalanffy growth model with a size-at-birth intercept, the Gompertz growth model, and a logistic model were fitted to sex-specific observed size-at-age data. Considering the statistical criteria (e.g., lowest mean square error [MSE], high coefficient-of-determination, and greatest level of significance) we desired for this study, the logistic model provided the best overall fit to the size-at-age data, whereas the von Bertalanffy growth model gave the worst. For “biological validity,” the von Bertalanffy model for female sharks provided estimates similar to those reported in other studies. However, the von Bertalanffy model was deemed inappropriate for describing the growth of male spinner sharks because estimates of theoretical maximum size (L∞) indicated a size much larger than that observed in the field. However, the growth coefficient (k= 0.14/yr) from the Gompertz model provided an estimate most similar to that reported for other large coastal species. The analysis of growth for spinner shark in the present study demonstrates the importance of fitting alternative models when standard models fit the data poorly or when growth estimates do not appear to be realistic.

Deepwater prawns and lobsters off the Kerala coast

Majority of the prawn catch of the Kerala coast comes from the inshore regions within the 10 fathom line. A bottom deposit formed of fine mud rich in humus is found to be the ideal condition for the penaeid prawns. Similarly the lobster is observed in large numbers at localised areas very near the coast in the crevices of rocks. Though it has been observed that prawns and lobsters exist in deep water as well under different conditions, our knowledge about these forms along the Indian coasts is very scanty, being restricted to the works of Spence Bate, Alcock, De Man and Ramadan. Recently, during the cruises of the University Research Vessel Conch off the Kerala Coast (1958-1963) two species of deep water prawns and one species of lobster were collected from depths 100 - 180 fathoms. Of these, Penaeopsis philippi is found in large numbers occupying an almost continuous bed extending from Anjengo to Mangalore, while P. rectacutus has a restricted appearance between Cochin and Calicut. However, some sort of year to year variation has also been observed regarding the abundance of the species at various stations. Peurulus sewelli has a more restricted distribution, the maximum number being found between Puvar and Cochin. Attempt has been made to correlate the occurrence of the species with the hydrological conditions at the bottom and the nature of the substratum. It is observed that Peurulus sewelli occupies a more or less hard bed formed of sand with shell fragments or stones and small percentage of silt, the bottom temperature at the stations varying from 11°C to l4°C. P. sewelli is a more or less permanent inhabitant of the edge of the continental shell off the Kerala Coast worthy of attention for detailed investigation with a view to explore the possibilities of commercial exploitation.

An experiment conducted with a floating trawl net off Cochin

The paper deals with an experiment with a floating trawl net off Cochin, using a pair of curved otter boards and a transducer mounted on the head rope of the net. 32 hauls were made with different towing speeds and warp length keeping one factor constant for varying parameters of the other factor. The working data for 32 hauls are presented and the effect in the fishing depth of the net due to the variation in one factor is mentioned. The 'fishing depth' is indicated in this paper as the distance between the head rope and the bottom. The usefulness of similar experiments with added information on the angle of leading warp at the stern for the exploitation of column fishes in Indian waters is indicated.

Use of length-weight relationship in grading processed beche-de-mer

Holothurians, belonging to the species Holothuria scabra, have been collected by diver-fishermen and processed for export. There is an active fishery for these animals in Palk Bay and Gulf of Mannar, off the north-western coast of Sri Lanka. The absence of standardized method of grading has led to unwarranted variation in sale prices and sometimes in loss of foreign exchange in Sri Lanka. In this paper an attempt is made to present a method to grade processed beche-de-mer by using the lenght-weight relationship.

Heat budget studies of the north Arabian Sea during summer and winter seasons, 1992

In this study heat budget components and momentum flux for August and January 1992 over the north Arabian Sea are computed. The marine meteorological data measured on board during the cruises of PAK-US joint project (NASEER) are used for the computation. Significant differences were found in the heat budget components as well as in the momentum flux during different monsoon periods over the north Arabian Sea. The latent heat flux was always positive and attributed to the large vapour pressure gradient. The computed moisture and latent heat fluxes in January were higher than August The highest value of latent heat flux 309 W/m2 at station 8 was evaluated. These higher latent heat fluxes were due to the large vapour pressure gradient, air-sea temperature difference, the wind speed, and the prevailing wind direction (from north and northeast). Negative values of sensible heat fluxes in both seasons indicate that the heat transfer was from the atmosphere to the ocean. The negative values of net heat gain indicate that the sea surface field became an energy sink: or the sea surface supplied more energy to the atmosphere than it received from it. Large variation in the momentum flux mainly attributed to the variation in the wind speed. Aerial averages of heat and momentum fluxes were also computed.

A method for the preparation of cooked-peeled-frozen prawns

Several consignments of cooked-peeled-frozen prawns exported from India were rejected last year due to high total plate count (TPC) at 30°C. The specified temperature of incubation for TPC in our country is 37°C. Hence the effect of incubation at 30 and 37°C on TPC was studied. It is seen that the count is higher on incubation at 30°C. A method for production of cooked-peeled-frozen prawns conforming to the specification for TPC at 30°C is standardized and is reported. It consists of recooking the cooked-peeled prawns followed by packing and freezing without further contamination. The method minimizes batch to batch or sample to sample variation in TPC.