Filtering method for obtaining stock indices by shark species from species-combined logbook data in tuna longline fisheries

ABSTRACT:   A method of filtering logbook data to obtain estimates of catch per unit effort (CPUE) for sharks has been proposed which simultaneously addresses the issues of under-reporting and the lack of species-specific catch records in historical data. Logbook catch data from vessels with high shark reporting rates are used to represent catch rates for the abundant blue shark Prionace glauca and low reporting vessels' data are used for the main commercially valuable species, the shortfin mako Isurus oxyrinchus . Logbook reporting rate filter (RRF) levels are evaluated through analytical and model-based comparisons to species-specific logbook records available since 1994 and shipboard observer data. At the high reporting rates, the ≥ 80% filter avoids large numbers of false zeros and provides the best fit to observer data for blue shark. At the low reporting rates, the ≤ 40% filter best matches the observer data for makos, but this filter level includes large numbers of false zeros and sharks of other species. The ≤ 20% filter produces a dataset that is better targeted to mako catches but considerably under-estimates CPUE relative to observer records. For these reasons, other means of estimating mako catch rates are suggested for further research.     

Genetic identification of native populations of fluvial white-spotted charr <Emphasis Type="Italic">Salvelinus leucomaenis</Emphasis> in the upper Tone River drainage

ABSTRACT:   Stocking of exogenous, hatchery-reared white-spotted charr Salvelinus leucomaenis has been conducted throughout much of their range in Honshu Island, Japan, to increase angling opportunities. Although the native charr populations are thought to have declined because of hybridization with introduced fish, their distribution and genetic status have been uncertain. Fine population structures of charr in the upper Tone River drainage were examined using mitochondrial DNA and microsatellite analyses so as to clarify the presence of native populations. One common mtDNA haplotype was detected in all populations in the Ohashi River and Watarase River, and four and one tributary populations were monomorphic for such haplotypes, respectively. However, several haplotypes, considered to have originated from stocked hatchery fish, were observed in the stocked and the remaining populations. Judging from the genetic integrity over a fine geographic scale, the former were considered as indicative of native populations and the latter as admixtures with hatchery fish. Comparisons of genetic diversity, deviations from the Hardy–Weinberg equilibrium, principal component analysis, and relatedness estimations based on microsatellite DNA can also provide evidence for distinguishing native populations from those influenced by hatchery fish.     

Development of near-isogenic lines of durum wheat (Triticum durum Desf.) for glaucousness inhibitor loci Iw1, Iw3 and Iw4 derived from wild relatives

Genetic Resources and Crop Evolution - The majority of cultivated wheat varieties have glaucous spikes, leaves and leaf sheaths, and the non-glaucous phenotype is rare in modern varieties. The...     

Influence of overplanting paddy rice on irrigation water delivery performance: a case study in the Dakalt branch canal,Nile Delta of Egypt

In the North Nile Delta of Egypt, the impacts of overplanting paddy rice on water delivery performance have not been discussed quantitatively. Further, the amount of water that could have been saved if farmers would follow the planned area is unknown. In this study, water delivery performance was assessed by comparison of actual paddy rice planting and the government’s planned conditions. For both conditions, performance indicators relating to adequacy, equity, and dependability were analyzed across six locations in conjunction with the branch canal water level in 2013 and 2014. Based on the difference between the actual water supply and planned water demand, the amount of water that could have been saved for downstream uses was calculated. The average adequacy for the investigation period was good at one location, fair at 2 locations, and poor at 3 locations in both years. Further, adequacy under both actual and planned conditions was poor in late July at all locations. The planned adequacy and dependability downstream and equity among locations improved compared to the actual condition in both years. Under the condition that paddy rice area is the upper limit planned by the government, about 12.3% and 9.6% of water could be potentially saved in each year. The difference between actual and planned water delivery performance is caused by the branch canal’s low water level. Control of overplanting paddy rice and coordination of water distribution among water user associations would improve stable water level in the canal and, eventually, water delivery performance.

     

Ionomic Profiling of Rice Genotypes and Identification of Varieties with Elemental Covariation Effects

Ionomic profiles are primarily influenced by genetic and environmental factors. Identifying ionomic responses to varietal effects is necessary to understand the ionomic variations among species or subspecies and to potentially understand genetic effects on ionomic profiles. We cultivated 120 rice (Oryza sativa) varieties to seedling stage in identical hydroponic conditions and determined the concentrations of 26 elements (including 3 anions) in the shoots and roots of rice. Although the subspecies effects were limited by the genus Oryza pre-framework and its elemental chemical properties, we found significant differences in ionomic variations in most elements among the aus, indica and japonica subspecies. Principal component analysis of the correlations indicated that variations in the root-to-shoot ionomic transport mechanisms were the main causes of ionomic differences among the subspecies. Furthermore, the correlations were primarily associated with the screening of varieties for elemental covariation effects that can facilitate breeding biofortified rice varieties with safe concentrations of otherwise toxic elements. The japonica subspecies exhibited the strongest elemental correlations and elemental covariation effects, therefore, they showed greater advantages for biofortification than the indica and aus subspecies, whereas indica and aus subspecies were likely safer in metal(loid) polluted soils. We also found that geographical and historical distribution significantly defined the ionomic profiles. Overall, the results of this study provided a reference for further association studies to improve the nutritional status and minimize toxicity risks in rice production.     

Relationship between soak time and number of enmeshed animals in experimentally lost gill nets

In order to determine the effects of ghost fishing by lost gill nets, the relationship was examined between soak time and number of enmeshed animals in experimentally lost gill nets by using diving observations. Two experimental gill nets were set at 13 m depth in Tateyama Bay, Chiba Prefecture, Japan for approximately 200 days. One gill net was deployed in a small trough surrounded by artificial reefs, and the other was deployed on an adjacent open sandy bed. Twelve species of crustaceans, six species of gastropods, and five species of bony fish were enmeshed in the experimental gill nets. The number of enmeshed animals in the artificial reef gill net was substantially larger than that in the sandy bed gill net. The number of enmeshed animals in the experimental gill nets increased rapidly within one month after deployment, and then declined gradually showing fluctuations caused by the decrease in newly enmeshed animals, and the drop off from gill nets caused by the decomposition of dead animals. The decrease in the number of enmeshed animals was expressed by logarithmic equations, and based on these equations, the duration of capture function for the lost gill nets was calculated to be 284–561 days in the artificial reef gill net and 200 days in the sandy bed gill net. The duration of capture function for the lost gill nets for non-commercial by-catch species such as small crustaceans and gastropods was longer than for commercial species such as Japanese spiny lobster and bony fish.     

Dietary value of benthic diatoms for post-larval abalone <Emphasis Type="Italic">Haliotis diversicolor</Emphasis> associated with feeding transitions

ABSTRACT:   The feeding behavior and growth of post-larval Haliotis diversicolor with initial shell lengths (SL) of approximately 500 μm (Exp. 1-1 and 1-2), 800 μm (Exp. 2), and 1200 μm (Exp. 3) were studied in a laboratory setting while they fed on four species of benthic diatom Achnanthes longipes , Cocconeis sublittoralis , Cylindrotheca closterium , and Navicula ramosissima . Exp. 1-1 and 1-2 revealed no marked differences in post-larval growth rates (mean 24–39 μm SL/day) among the diatom species. However, marked differences in growth rates among the species were revealed in Exp. 2 and 3. Three species, A. longipes , Co. sublittoralis, and Cy. closterium , produced faster growth (Exp. 2 mean 29–51 μm/day, Exp. 3 mean 36–44 μm/day) than N. ramosissima (Exp. 2 mean 18 μm/day, Exp. 3 mean 23 μm/day). Post-larvae fed N. ramosissima had lower digestion efficiency (42.8%) than those fed other diatom species (90.7–100%). Diatom extracellular substances appeared to be principally used from post-settlement to 800 μm SL, and diatom cell contents were required to produce rapid growth of larger post-larvae (>800 μm SL). It is likely that the availability of each diatom for post-larvae was affected by diatom morphology, attachment strength, frustule strength, and post-larval size.     

Guanine-cytosine contents of the host and symbiont cDNA in a symbiotic coral

ABSTRACT:   Hermatypic (reef-building) corals harbor dinoflagellate endo-symbionts Symbiodinium spp. In studying gene expression in such symbiotic corals, problems arise regarding how to distinguish the coral and symbiont mRNA, and how to estimate their fractions in the mRNA population of the holobiont (symbiotic complex of the coral and Symbiodinium cells). In this study, these issues were addressed using juveniles of hermatypic coral Acropora tenuis in symbiosis with Symbiodinium cells of strain PL-TS-1. First, the guanine-cytosine (GC) contents were determined in expressed sequence tags (EST) from PL-TS-1 cells cultured in vitro and symbiont-free larvae of A. tenuis , and their average GC contents were found to be significantly different. The average GC content of the EST from the holobiont was much closer to that of A. tenuis larvae, suggesting that the majority (>90%) of mRNA isolated from the holobiont originated in the host. In protein-coding sequences, little overlap was observed between the GC-content distributions of PL-TS-1 cells and A. tenuis larvae. All of the coding sequences ( n  = 59) found in the A. tenuis EST had GC contents below 0.5, whereas the GC content exceeded 0.5 in the majority (43/44) of coding sequences from the nuclear genome of PL-TS-1 cells.