Incorporating spatial autocorrelation into the general linear model with an application to the yellowfin tuna (Thunnus albacares) longline CPUE data

Catch-per-unit-effort (CPUE) data have often been used to obtain a relative index of the abundance of a fish stock by standardizing nominal CPUE using various statistical methods. The theory underlying most of these methods assumes the independence of the observed CPUEs. This assumption is invalid for a fish population because of their spatial autocorrelation. To overcome this problem, we incorporated spatial autocorrelation into the standard general linear model (GLM). We also incorporated into it a habitat-based model (HBM), to reflect, more effectively, the vertical distributions of tuna. As a case study, we fitted both the standard-GLM and spatial-GLM (with or without HBM) to the yellowfin tuna CPUE data of the Japanese longline fisheries in the Indian Ocean. Four distance models (Gaussian, exponential, linear and spherical) were examined for spatial autocorrelation. We found that the spatial-GLMs always produced the best goodness-of-fit to the data and gave more realistic estimates of the variances of the parameters, and that HBM-based GLMs always produced better goodness-of-fit to the data than those without. Of the four distance models, the Gaussian model performed the best. The point estimates of the relative indices of the abundance of yellowfin tuna differed slightly between standard and spatial GLMs, while their 95% confidence intervals from the spatial-GLMs were larger than those from the standard-GLM. Therefore, spatial-GLMs yield more robust estimates of the relative indices of the abundance of yellowfin tuna, especially when the nominal CPUEs are strongly spatially autocorrelated.     

The spawning cycle,fry appearance and mass collection techniques for fry of Siganus rivulatus in the Red Sea

Data on the G.S.I. of adults and appearance of fry indicated a regular lunar spawning cycle of S. rivulatus within a seasonal breeding period. A mass collection technique yielding 5000–7000 fry per day was developed.     

Stocking density and artificial habitat influence stock structure and yield from intensive nursery systems for mud crabs Scylla serrata (Forsskål 1775)

Intensive nursery systems are designed to culture mud crab postlarvae through a critical phase in preparation for stocking into growout systems. This study investigated the influence of stocking density and provision of artificial habitat on the yield of a cage culture system. For each of three batches of postlarvae, survival, growth and claw loss were assessed after each of three nursery phases ending at crab instars C1/C2, C4/C5 and C7/C8. Survival through the first phase was highly variable among batches with a maximum survival of 80% from megalops to a mean crab instar of 1.5. Stocking density between 625 and 2300 m⁻² did not influence survival or growth in this first phase. Stocking densities tested in phases 2 and 3 were 62.5, 125 and 250 m⁻². At the end of phases 2 and 3, there were five instar stages present, representing a more than 20‐fold size disparity within the populations. Survival became increasingly density‐sensitive following the first phase, with higher densities resulting in significantly lower survival (phase 2: 63% vs. 79%; phase 3: 57% vs. 64%). The addition of artificial habitat in the form of pleated netting significantly improved survival at all densities. The mean instar attained by the end of phase 2 was significantly larger at a lower stocking density and without artificial habitat. No significant effect of density or habitat on harvest size was detected in phase 3. The highest incidence of claw loss was 36% but was reduced by lowering stocking densities and addition of habitat. For intensive commercial production, yield can be significantly increased by addition of a simple net structure but rapidly decreases the longer crablets remain in the nursery.     

Hydromorphological rehabilitation improves channel morphology,instream biotopes,and macroinvertebrate communities,and thus enhances the conservation of an urban river

1. Many river rehabilitation projects have been criticized for failing to meet their goals or for being insufficiently monitored. There is, therefore, an urgent need to develop robust approaches for assessing treatment efficacy and thus guide the increasing investment in rehabilitation.
2. Instream biotopes (formerly called ‘functional habitats’ or ‘mesohabitats’ by different authors) and their macroinvertebrate assemblages were used to assess the effectiveness of entire-channel hydromorphological rehabilitation of a 1.8-km stretch of a lowland stream through the town of Market Harborough, Leicestershire, UK.
3. The project successfully enhanced the physical diversity, measured in the rehabilitated reach as the coefficients of variability for channel water depth and width, wet surface area, number of instream biotopes, and biotope diversity.
4. The project also enhanced the biodiversity conservation value, measured as macroinvertebrate total density, total biomass, richness, diversity, Ephemeroptera, Plecoptera, and Trichoptera (EPT) richness, EPT diversity, EPT count%, and EPT biomass%, all of which significantly increased following rehabilitation. Chironomidae count% and biomass% significantly decreased following rehabilitation. Rehabilitation was also successful in significantly increasing macroinvertebrate shredder, scraper, and filter-feeder group density.
5. Changes in the macroinvertebrate community metrics in the rehabilitated reach were related significantly to changes in the percentages of cover of instream biotopes and increases in biotope diversity in the rehabilitated reach.
6. Macroinvertebrate structural and functional metrics can provide quantitative data for assessing reach-level rehabilitation outcomes, if samples are collected in a pre-defined sampling protocol stratified at the instream biotope level.
7. The practical implications of this work are that the design of rehabilitation projects, if based upon the recreation of biotope heterogeneity, will succeed in improving biological value and restoring the area to near naturalness if a suitable upstream source of macroinvertebrates for natural recolonization is available. The study shows that the concept of biotopes has an important role to play in river conservation management.

     

Influence of Salinity in the Bioavailability of Zn in Sediments of the Gulf of Cádiz (Spain)

This study assesses the effect of salinity in bioavailability and toxicity of Zn by means of laboratory bioassays by observing contamination in both sediment and water, accumulation of Zn in biological tissues, and histopathological damage in the gills and guts tissues of Ruditapes philippinarum clams, which were exposed to different types of sediments from the Gulf of Cádiz (SW Spain) as well as two dilutions of toxic mud coming from an accidental mining spill. With this objective, the coefficients of distribution (K _D) for Zn between overlying water and sediments were calculated, the histopathological frequencies in the tissues of the gills and guts of clams were determined, and the biota-sediment bioaccumulation factors as well as the bioaccumulation factors were quantified in the different stations. Results showed that the greatest histopathological damages appeared when the salinity values decreased. Statistical results showed that salinity was inversely correlated with histopathological damage (p?<?0.01) for the lesion index for gills. The most outstanding results were observed in the two dilutions of toxic mud (0.3% and 7.9%) at a salinity value of 10. Salinity was inversely correlated with the concentration of Zn in biological tissues (p?<?0.05) and inversely correlated with the concentration of Zn in water and sediment. Zn mobilization to the overlying water is produced when salinity values decrease.     

Changes in amino acid levels in bacteria adhering to rumen epithelium in sheep after oral administration of very low doses of mercury

The effect of low concentrations of mercury taken in the diet (4 mg per a head and day) on the amino acid composition in the proteins of rumen bacteria adhering to the dorsal and ventral parts of the rumen was studied in six sheep. Though the mercury did not influence the amino acid concentration in hydrolyzates of epimural bacteria, low-mercury doses caused significant changes of some amino acids, as compared with the control group of animals. The levels of alanine, histidine, threonine, serine and glycine were significantly decreased and at the same time the levels of proline, valine, isoleucine, tyrosine, lysine and phenylalanine were significantly increased. It was stated in our experiment that the levels of histidine, alanine and threonine in hydrolyzates of epimural bacteria of the rumen were significantly decreased both in the sheep given the balanced feed ration with additions of mercury and nitrogen (according to the standard) and in the sheep given a low-nitrogen diet. Similarly, the levels of proline, tyrosine and phenylalanine in the hydrolizates of epimural bacteria in rumen were significantly increased both with the low-nitrogen diet and in the normal -nitrogen diet with mercury supplement. The results suggest that unexplained disorders frequently occurring in the microbial synthesis in the rumen might be caused by long-continued administration of feed contaminated with extremely low concentrations of heavy metals. The problem deserves detailed investigation in future studies, oriented to explaining the biosynthesis disorders in rumen, reducing the production ability of ruminants.     

Screening sorghum genotypes for salinity tolerant biomass production

Genetic improvement of salt tolerance is of high importance due to the extent and the constant increase in salt affected areas. Sorghum [Sorghum bicolor (L.) Moench] has been considered relatively more salt tolerant than maize and has the potential as a grain and fodder crop for salt affected areas. One hundred sorghum genotypes were screened for salinity tolerance in pots containing Alfisol and initially irrigated with a 250-mM NaCl solution in a randomized block design with three replications. Subsequently 46 selected genotypes were assessed in a second trial to confirm their responses to salinity. Substantial variation in shoot biomass ratio was identified among the genotypes. The performance of genotypes was consistent across experiments. Seven salinity tolerant and ten salinity sensitive genotypes are reported. Relative shoot lengths of seedlings were genetically correlated to the shoot biomass ratios at all stages of sampling though the relationships were not close enough to use the trait as a selection criterion. In general, the whole-plant tolerance to salinity resulted in reduced shoot Na⁺ concentration. The K⁺/Na⁺ and Ca²⁺/Na⁺ ratios were also positively related to tolerance but with a lesser r ². Therefore, it is concluded that genotypic diversity exists for salt tolerance biomass production and that Na⁺ exclusion from the shoot may be a major mechanism involved in that tolerance.