The Vector Autoregressive Spatio-Temporal (VAST) software package for R, which enables researchers to analyze fishery data using a spatio-temporal generalized linear mixed model, has recently attracted attention as a new approach and is now commonly used globally to predict spatial changes in species distribution and temporal variations in a population range and density, based on spatial and temporal autocorrelation among catch rates and correlations with various biotic and abiotic environmental factors. However, a Japanese overview of the package including the spatio-temporal model has not yet been published. The main purpose of this paper is to provide an overview of VAST, describing the model structure, methods of estimating parameters and predicting abundance indices, and technical terms associated with the spatio-temporal model. We also demonstrate how VAST can be applied to studies on highly migratory species such as the Pacific bluefin tuna Thunnus orientalis, Pacific saury Cololabis saira, and North Pacific shortfin mako shark Isurus oxyrinchus. We hope that this overview of VAST and its application to actual species will assist Japanese end-users in understanding VAST and thus contribute to the wider application of this package in Japan and improved assessments of domestic fishery stocks.
This work examined a modified bottom trawling method for pair-trawl fishery off Shimane Prefecture. Wing, side, and baiting nets were either made of small-diameter twine (modified-1), or enlarged mesh (modified-2), which nettings were made of ultra-high-molecular-weight polyethylene twine. The hydrodynamic force acting on modified-2 net was reduced by 29.6%, and the sum of hydrodynamic and frictional force was reduced by 9.9%, compared with the conventional net. The shape obtained for both conventional and modified-2 nets was almost the same when tested at towing speed of 3 knots through flume tank experiment and computer simulation. The handrope tension of modified-2 reduced by 19.3% compared with the conventional net, when assessed in a sea trial at towing speed of 3 knots.
Snow crab Chionoecetes opilio is among the most important species for the Danish seine fishery in the western Sea of Japan. The caught males are divided into “kata-gani” and “mizu-gani” based on shell condition, which reflects the time elapsed since last molt. The former have a hard shell, indicating more than one year since last molt; the latter are postmolt (new and soft shell) males. The kata-gani are classified into “tate-gani” (adult, terminally molted males) and “momo-gani” (adolescent, pubertally molted males). The occurrence rates of momo-gani and terminal molt are important in estimating male stock abundance. We investigated kata-gani and mizu-gani collected in the Sea of Japan off Kyoto Prefecture to examine occurrence rates of momo-gani and terminal molt probability. The annual occurrence rate of momo-gani fluctuated sharply, with clear decreases in the monthly frequency between fishery seasons. The terminal-molt rates of males entering the 90-109 mm and 110-119 mm carapace width groups were significantly elevated. Tate-gani stock estimation by three scenarios of different terminal-molt rates indicated that carapace size of tate-gani became smaller as a result of increasing individual number of the small instar group and total stock weight was reduced by higher terminal-molt rates.
Mass mortality of cultured young bluefin tuna Thunnus orientalis, with the loss of approximately 2,400 individuals, occurred in Asou bay, Tsushima, Nagasaki, Japan in April 2017. Blood fluke eggs were observed in the gills of dead fish, but fish without severe infection also died. At the time, a noxious red tide of Heterosigma akashiwo was also detected (13-90 cells mL−1). However, the density of blood fluke eggs in the fish gills, or concentration of H. akashiwo cells in the area alone, was not high enough to have caused the mortality. Since both blood fluke eggs and H. akashiwo are known to have deleterious effects on the respiratory function of fish, the mass mortality was most likely caused by their synergistic effects.
Experimental cultivation of Sargassum fusiforme, Undaria pinnatifida and Meristotheca papulosa was conducted at six sites with different water temperature conditions from the Seto Inland Sea to eastern Bungo Channel (Uwa Sea). Among the sites, the maximum difference in water temperature was 5℃ observed during February to March. Growth of S. fusiforme was better at the sites in the Uwa Sea except for Ainan, the southernmost site in the Uwa Sea, than at the sites in the Seto Inland Sea where the water temperature was mostly lower than 15℃ during the cultivation period. In Ainan, the warmest site, most of S. fusiforme thalli were lost up to February. Undaria grew in the Seto Inland Sea and northern Uwa Sea, but thalli were also lost at the southern Uwa Sea sites. Scars marked on basal parts of these algae left on culturing ropes indicated signs of having been browsed by herbivorous fish. Meristotheca papulosa, which was cultured in cages, exhibited better growth at the warmer Uwa Sea sites. M. papulosa did not grow and died during winter at the sites of the Seto Inland Sea, though it exhibited a slight growth in spring when the mean water temperature exceeded 15℃.
The effects of removing long-spined sea urchin species of the genus Diadema on regeneration of seaweeds were investigated in barren rocky areas in Haidaura Bay, Mie Prefecture, central Japan from February 2010 to December 2019. Diadema spp. were removed by diving and capturing from ships. Algal coverage and density of sea urchins, turban shells and abalone were monitored. Reduced density of Diadema spp. resulted in increased algal coverage in the area where sea urchins had been removed. In addition, the density of sea urchins other than Diadema spp. and the total number of sea urchin species increased under low Diadema spp. densities. Turban shells and abalone started to appear after the algal coverage increased.
We conducted sensory evaluation and physicochemical analyses of grilled Japanese eel Anguilla japonica farmed by hatchery-based aquaculture (HBA) following controlled captive reproduction. A total of 4939 artificial glass eels were reared in a commercial farm in Shizuoka, Japan for 12 months among which 50 adults (201 g average body weight) were grilled without sauce in a continuous two-sided grilling machine. Eels cultured by capture-based aquaculture (CBA) from seedlings of wild-caught glass eels in the same farm, were used as controls. Sensory evaluation showed that HBA grilled eels had a more fatty taste and harder texture than CBA grilled eels did. Chemical analyses revealed no significant difference in crude fat content between HBA and CBA eels, but the CBA eels contained more n-3 polyunsaturated fatty acids, possibly influencing the evaluation of fatty taste. Texture analysis indicated significantly harder flesh and skin in HBA than CBA eels, corresponding to the sensory evaluation. This information should be useful for product development of HBA eels.
Research was conducted on oyster consumers to evaluate their assessment of the quality of external appearance of unshelled oysters. The purpose was to support the product development process of unshelled oysters in an ever-maturing oyster bar market. On the basis of a conjoint analysis using a latent class model, we divided the respondents into three classes: Class 1 was reluctant to consume unshelled oysters and Class 2 was more active in consuming unshelled oysters. Regarding Class 3, the willingness to pay for common domestic unshelled oysters that were distributed to domestic oyster bars was estimated at 687 yen/unit (base price). Additionally, we estimated from the analysis that respondents in Class 3 preferred a slightly smaller body size in terms of shell fullness, and a larger shell (11 cm), although smaller shells (6.5 cm and 7.75 cm) were also acceptable. Further, the optimum ratio of height to length of the shell was estimated to be 1:1.5 (shell length: shell height) within this class. However, the body and mantle conditions were insignificant at all levels in all three classes.
The diversity of consumption of major fresh fish and shellfish was quantified using the Shannon index for the capital cities of the 47 prefectures in Japan. Geographical characteristics of the diversities were analyzed using global and local Moran's I statistics. The Shannon index shows a downward trend for Japan as a whole between 2000 and 2017. The result of the Global Moran's I statistics shows a downward trend in the concentration of cities with high or low diversity in specific regions. The Local Indicator of Spatial Association (LISA) cluster map, in which the result of local Moran's I statistics is mapped, shows that 11 cities in the Kansai and Setouchi regions are hot-spots of diversity (i.e., a wide variety of fish species are usually consumed in households), while 6 cities (Shizuoka, Kofu, Maebashi, Nagano, Aomori and Sapporo) are cold-spots with low diversity.