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Nonlinear phenomena are universal in ecology. However, their inference and prediction are generally difficult because of autocorrelation and outliers. A traditional least squares method for parameter estimation is capable of improving short-term prediction by estimating autocorrelation, whereas it has weakness to outliers and consequently worse long-term prediction. In contrast, a traditional robust regression approach, such as the least absolute deviations method, alleviates the influence of outliers and has potentially better long-term prediction, whereas it makes accurately estimating autocorrelation difficult and possibly leads to worse short-term prediction. We propose a new robust regression approach that estimates autocorrelation accurately and reduces the influence of outliers. We then compare the new method with the conventional least squares and least absolute deviations methods by using simulated data and real ecological data. Simulations and analysis of real data demonstrate that the new method generally has better long-term and short-term prediction ability for nonlinear estimation problems using spawner–recruitment data. The new method provides nearly unbiased autocorrelation even for highly contaminated simulated data with extreme outliers, whereas other methods fail to estimate autocorrelation accurately.

DOI： 10.1038/s41598-021-91327-8

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Species identification based on morphological characteristics includes species misidentification, leading to estimation bias in stock assessment and posing challenges difficult to be resolved. The spawning eggs of spotted mackerel Scomber australicus and chub mackerel S. japonicus in the western North Pacific are used for stock assessment as an index of spawning biomass and are classified based on egg diameter by past evidence. However, the difference in the distribution of egg diameters between the two species has become so ambiguous that the spawning eggs of chub mackerel may be classified as spotted mackerel. This can be explained by the larger distribution of egg diameters in chub mackerel with increasing stock abundance, resulting in overlap with the distribution of egg diameters in spotted mackerel. This leads to species misidentification and biased estimates of spotted mackerel abundance. To overcome this bias, it is necessary to develop a standardization method to remove the effect of species misidentification. Here, we demonstrate that a recently-developed spatio-temporal model can easily and efficiently reduce estimation bias for egg density and stock abundance in the spotted mackerel, using 15 years data for spawning eggs. We incorporated species identification error as the effect of the egg density of chub mackerel on the catchability of spotted mackerel in the spatio-temporal model. The index estimated from the model decreased temporal fluctuation substantially. When using the index accounting for species misidentification, the retrospective bias of abundance estimates for spotted mackerel decreased by about half compared with using the indices that ignored species misidentification. These results suggest that incorporating species misidentification bias is an essential process for improving stock assessment.

DOI： 10.1016/j.fishres.2020.105825

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Pacific saury (Cololabis saira) has a 2-year life span and age-1 fish migrates from the central and western North Pacific to Japanese waters from summer to winter. To understand interannual abundance variability of Pacific saury in the North Pacific, we examined the extended Japanese standardized catch per unit effort (esCPUE) with generalized linear models (GLMs) during 1982–2018. Explanatory variables included proxies of total and non-traditional fishing effort (Ettl and Ent) and environmental factors. Each environmental variable was averaged for years t -1 and t, corresponding to esCPUE in year t, as esCPUE represented two-year classes. Ettl and Ent were averaged for years t - 2 and t-1, assuming fishing of year t affects biomass in year t + 1. We compared four GLMs with different explanatory variables: (a) environmental factors only, (b) fishing effort (without interactions) only, (c) environmental factors and fishing effort (without interactions) and (d) environmental factors and fishing effort (with interactions, i.e., time-varying effects). Explanatory variables of the best GLM in terms of AICc included the following: Ent with different effects between 1982–2015 and 2016–2018, sea surface water temperature (SST) of the Kuroshio Recirculation Area (KRA) in winter, North Pacific Gyre Oscillation (NPGO) in winter, Southern Oscillation Index in winter, and the biomass of Japanese sardine. The NPGO, a proxy of zooplankton abundance, and KRA-SST may affect the early growth and survival rates of Pacific saury. We hypothesized the abundance variability of Pacific saury was driven by environmental factors and fishing, the latter of which more adversely affected since 2016.

DOI： 10.1111/fog.12513

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY  

Regime shifts of climatic and environmental conditions potentially affect the productivity of fishery resources, posing challenges in stock management. The stocks of the Japanese flying squid (Todarodes pacificus) are suspected to suffer from regime shifts, but detecting the occurrence of regime shifts in this species is generally difficult and unreliable because the short-lived nature of this species inherently confounds the effect of regime shifts with observation and process errors. Here we developed a new state-space assessment model to evaluate the influence of regime shifts on the spawner-recruit relationship of the Japanese flying squid. The model simultaneously estimates the population dynamics of multiple stocks that could share some life history parameters, thereby stabilizing parameter inference. We demonstrate that two regime shifts in productivity around 1991 and 2015 caused two- to threefold changes of maximum sustainable yields. The model with regime shifts clarifies the relationship between fishing pressure and spawner abundance that is difficult to detect in a model with no regime shift. The state-space approach is a promising tool for accurately assessing stock status by separating the recruitment process from observation errors and is expected to contribute to the effective management of marine biological resources sensitive to regime shifts.

DOI： 10.1002/1438-390X.12062

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A maximum sustainable yield (MSY) obtained by maintaining or restoring fish stock levels is a tangible benefit of ecosystem services. Snow crab (Chionoecetes opilio) off Tohoku, Japan has been managed by a total allowable catch since 1996, although the abundance has not increased. Surprisingly, there was no increase after 2011, when fishing pressure was greatly reduced because of the Great East Japan earthquake. This implies that some of the crab's biological characteristics, such as recruits, natural mortality coefficient (M) and terminal molting probabilities (p), might have changed. We developed “just another state-space stock assessment model” to estimate the MSY of the snow crab off Tohoku considering interannual variations in M and p. The multimodel inference revealed that M increased from 0.2 in 1997 to 0.59 in 2018, although it did not vary according to instars, sex or terminal molt. The parameter p also increased by 1.34–2.46 times depending on the instar growth stages from 1997 to 2018. We estimated the MSYs in three scenarios, which changed drastically if M and p were set as they were in the past or at the current values estimated from this study. This result indicated that the MSY of snow crab would also vary with time based on their time-varying biological characteristics.

DOI： 10.1002/1438-390X.12068

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Stock assessment approaches are often oversimplified due to lack of biological knowledge and insufficient data. In spite of world-wide attention, fishery-targeted coastal dolphin species in Japan have lacked in-depth quantitative stock assessments because of limited time series of population size and an absence of associated biological information. We consequently developed integrated population models that analysed multiple sources of data simultaneously with published biological information within a Bayesian framework. We estimate population status and trends for three main species targeted by fisheries, bottlenose dolphins Tursiops truncatus, Risso's dolphins Grampus griseu, and short-finned pilot whales Globicephala macrorhynchus, using single-species age-aggregated and age-structured population dynamics models. Models were fit to absolute abundance estimates from systematic line-transect surveys, four series of abundance indices calculated from fisher's logbooks, and historical catch records. Published biological information was used to develop prior distributions for the biological parameters. We assessed the possible effects of ecological disturbance and competition using state-space and multispecies models. The multispecies model was selected by the model selection both for the age-aggregated and the age-structured approaches. Single-species assessments found that population size declined 4.2% (Risso's dolphin) to 8.0% (bottlenose dolphin) for three species since the late 1800s based on median posterior values, while the state-space and multispecies models found that environmental disturbance and an interaction among species could have reduced population size more substantially. Policy implications. Simple single-species models are often used to provide conservation and management advice for wild animals but, in this case, results from such models are overly optimistic because they overlook important ecological process. In contrast, current population status could be less favorable if environmental disturbance and interspecific competition actually control population dynamics. Even if that is not the case, considering ecological process in the model will provide more precautionary ways. Our approach of combining multiple modelling frameworks is applicable to many other management systems, and offers increased confidence in estimated status and trends over assessments that consider only a single model.

DOI： 10.1111/1365-2664.13982

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Standardization of catch per unit effort is an effective way to not only extract temporal abundance trends but also understand distribution shifts of fish resources. Chub mackerel in the Northwest Pacific has recently been of great concern to fishermen and fisheries managers because the total catch has been increasing, and fishing grounds have expanded from the Japanese exclusive economic zone eastward to high-sea areas. Understanding the spatiotemporal dynamics of chub mackerel is urgently needed for evaluating the current status (i.e., abundance and distribution) and considering future exploitation. Here we constructed two recruitment indices from pelagic trawl survey data of the Pacific chub mackerel. For recruitment indices of age-0 fish, we integrated an algorithm for automatic area stratification into the delta-GLM that combines two separate generalized linear models (for encounter probability and positive catch rates) to simultaneously investigate changes in relative abundance and distribution. Recruitment indices were high in the recent years of 2013, 2016, and 2017, especially at around 160 °E longitude within the high-sea areas, suggesting simultaneous changes in abundance and distribution. Furthermore, we found that our approach had better predictive ability, especially for positive catch rates, than that of a generalized additive model by cross validation, and the obtained standardized indices mitigated potential bias in stock assessment estimates. Our integrated approach will be useful for understanding the spatiotemporal dynamics of fishes and standardizing abundance indices for stock assessment and management.

DOI： 10.1016/j.fishres.2019.105315

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：INTER-RESEARCH  

Despite extensive studies of phenological shifts associated with climate change, a few unresolved issues remain. In particular, little is known about the phenological shifts of marine organisms, and simultaneous evaluations of phenological and distributional shifts in reproduction are needed. Chub mackerel Scomber japonicus in the western North Pacific is a small pelagic fish species with its main spawning ground around the Izu Islands. Since its spawning patterns are af - fected by the sea surface temperature (SST), changes in the spawning time and spawning ground are expected if the SST has increased around the Izu Islands. Here, to elucidate phenological and distributional shifts in reproduction associated with climate change and the underlying causes, we first examined the long-term changes in spawning patterns and spawning ground using a geostatistical model with 40 yr time series data for spawning eggs of chub mackerel in the western North Pacific. We then tested the prediction that increasing SST impacts the timing and distribution of chub mackerel reproduction. We found that the spawning period was extended owing to a delay in the end of spawning. The geographic location of the spawning ground moved northward after the 2000s, and this was probably related to the change in SST. In addition, SST in the spawning ground after the 2000s was not significantly different from the SST in the previous spawning ground. Therefore, the environmental change associated with climate change likely influences phenological and distributional shifts in reproduction simultaneously and underlines the importance of focusing on spatio-temporal changes in reproduction.

DOI： 10.3354/meps13037

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PERGAMON-ELSEVIER SCIENCE LTD  

Synchrony of species alternations in the northern Humboldt (NHCS) and Kuroshio (KCS) Current systems was examined by comparing time series data of landings and population statistics of major small pelagic fish species along with climate indices from 1960 to 2015. Target species were anchovy Engraulis ringens, sardine Sardinops sagax, jack mackerel Trachurus murphyi and chub mackerel Scomber japonicus in the NHCS, and anchovy E. japonicus, sardine S. melanostictus, jack mackerel T. japonicus and chub mackerel in the KCS. The time series of total biomass and spawning stock biomass (SSB) of anchovy and sardine for the NHCS and the KCS were well correlated, as were the landings data. Landings of small pelagic fish including jack mackerel and chub mackerel indicated that multi-species alternations may also be synchronous at a community level between the two current systems. Peak landings of jack mackerel and chub mackerel were observed between peaks of anchovy and sardine in both current systems, although the relationships between jack mackerel and chub mackerel differed between the current systems. The species alternations between anchovy and sardine are most reasonably attributable to environmentally-induced changes in the biomass as a major mechanism, although the effect of fishing activity cannot be excluded. Future studies will be required to compare biological characteristics of multiple small pelagic fish species in the pelagic food chain in each current system.

DOI： 10.1016/j.dsr2.2018.11.018

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：CANADIAN SCIENCE PUBLISHING  

Catchability plays a central role in fisheries stock assessment. Since catchability often varies with time depending on population density, environmental factors, and anthropogenic effects, assuming constant catchability in population models can lead to biased abundance estimates. Here we present a novel way to simultaneously estimate time-varying catchability and abundance by integrating a short-term (month-based) removal method and a long-term (year-based) age-structured population dynamics model. We applied this approach to commercial fishery data for a Japanese pufferfish (Takifugu rubripes) population and found that the models with time-varying catchability greatly outperformed the models with constant catchability in terms of predictive ability and model consistency. The temporal variation in catchability was parsimoniously predicted by fishing effort and population size, indicating the existence of effort-and density-dependent catchability. Our approach, integrating population dynamics at different timescales, will help avoid inadvertent overexploitation and contribute to sustainable harvesting by enhancing the estimation accuracy of time-varying catchability and abundance.

DOI： 10.1139/cjfas-2018-0114

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：OXFORD UNIV PRESS  

Age-structured models have played an important role in fisheries stock assessment. Although virtual population analysis (VPA) was once the most widely used stock assessment model for when catch-at-age information is available, (hierarchical) statistical catch-at-age analysis (SCAA) is about to take that position. However, the estimation performance of different age-structured models has not been evaluated sufficiently, especially in cases where there are few available abundance indices. We examined the performance of VPA and SCAA using simulation data in which only the abundance indices of spawning stock biomass and recruitment were available. The simulation demonstrated that VPA with the ridge penalty selected by minimizing retrospective bias provided near-unbiased abundance estimates without catch-at-age error and moderately biased estimates with catch-at-age error, whereas SCAA with random-walk selectivity suffered from problems in estimating parameters and population states. Without sufficient information on abundance trends, naïvely using SCAA with many random effects should be done cautiously, and comparing results from various age-structured models via simulation tests will be informative in selecting an appropriate stock assessment model.

DOI： 10.1093/icesjms/fsy126

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY  

Pacific saury (Cololabis saira) has a short life span of 2 years and tends to exhibit marked population fluctuations. To examine the importance of sea surface temperature (SST) and mixed layer depth (MLD) as oceanographic factors for interannual variability of saury recruitment in early life history, we analyzed the relationship between abundance index (survey CPUE (catch per unit of effort)) of age-1 fish and the oceanographic factors in the spawning and nursery grounds of the previous year when they were born, for the period of 1979–2006, in the central and western North Pacific. Applying the mixture of two linear regression models, the variability in the survey CPUE was positively correlated with previous year's winter SST in the Kuroshio Recirculation region (KR) throughout the survey period except 1994–2002. In contrast, the survey CPUE was positively correlated with the previous year's spring MLD (a proxy of spring chlorophyll a (Chl-a) concentration) in the Kuroshio-Oyashio Transition and Kuroshio Extension (TKE) during 1994–2002. This period is characterized by unusually deep spring MLD during 1994–1997 and anomalous climate conditions during 1998–2002. We suggest that saury recruitment variability was generally driven by the winter SST in the KR (winter spawning/nursery ground), or by the spring Chl-a concentration (a proxy of prey for saury larvae) in the TKE (spring spawning/nursery ground). These oceanographic factors could be potentially useful to predict abundance trends of age-1 saury in the future if the conditions leading to the switch between SST and MLD as the key input variable are elucidated further.

DOI： 10.1111/fog.12265

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The abundance and recruitment of anchovy Engraulis spp. and sardine Sardinops spp. alternate in a synchronized way across the Pacific. Convergent cross mapping (CCM) indicated that climate change drives the alternation of the two species in the California Current System. However, climate indices patterns in the western North Pacific contrast with those in the eastern North Pacific, despite synchronous species alternations occurring. Therefore, it is of great interest to clarify whether climate change, or any other factors, affects the population dynamics of Japanese anchovy and Japanese sardine in the western North Pacific. Using CCM, we tested whether climate change and interspecific interactions affect the population dynamics of these two species. We found that climate change affected recruitment, and we clarified the spatiotemporal pattern of this effect. This result supports the existing hypotheses that population dynamics are regulated by climate change in the western North Pacific. The present study also detected interspecific interactions between sardine and anchovy, which might promote the alternation of the two species, and has not been reported in other regions.

DOI： 10.1111/fog.12254

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER JAPAN KK  

The abundance index used in a tuned virtual population analysis (VPA) is usually assumed to be proportional to actual abundance. However, the actual abundance and abundance index do not always have a linear relationship. Such nonlinearity can cause biases in abundance estimates as well as retrospective biases arising from systematic differences in abundance estimates when more data are successively added. Severe retrospective biases can damage the reliability of stock assessments. In this study, we use an approach to estimate an additional parameter that controls the nonlinearity in a tuned VPA. A performance test using simulated data revealed that the tuned VPA was able to accurately estimate the nonlinearity parameter and thus yielded less biased abundance estimates and smaller retrospective biases. We also found that estimating the nonlinearity parameters was effective even under other model misspecification scenarios, such as disregarding historical increases in catchability and time-varying natural mortality. Moreover, we applied this approach to some Japanese fish stocks and evaluated its validity. We found that estimating the nonlinearity parameters in the tuned VPA enhances the reliability of fisheries stock assessments.

DOI： 10.1007/s12562-017-1159-0

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：CANADIAN SCIENCE PUBLISHING  

Standardized catch per unit effort (CPUE) is a fundamental component of fishery stock assessment. In multispecies fisheries, catchability can differ depending on which species is being targeted, and so the yearly trend extracted from the standardized CPUE is likely to be biased. We have, therefore, developed a method for predicting the unobserved variable related to targeted species from among multispecies composition data using a mixture regression model for the transformed residuals. In contrast with traditional methods, the proposed method predicts the target variable in CPUE standardization without removing a subset of the data. Keeping the entire data set avoids information loss, and so CPUE standardization with the predicted target variable should yield an unbiased estimate of the yearly trend. Simple simulation tests demonstrate that our method outperforms traditional methods. We illustrate the use of our method by applying it to CPUE data on arabesque greenling (Pleurogrammus azonus) caught in multispecies trawl fisheries in Hokkaido, Japan.

DOI： 10.1139/cjfas-2016-0460

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Proper fisheries management is difficult in fisheries targeting small pelagic fish that are subject to climate-induced oceanic regime shifts. A favourable regime tends to induce capa - city investments, but the results of these investments turn out to be irreducible overcapacity under the next unfavourable regime. The Japanese purse seine fishery studied here, which targets small pelagic fish, is a typical example of such overcapacity. However, we demonstrate that this fishery represents a best practice of properly designed effort management in recent years through its quantitative evaluation. Generalized liner mixed models (GLMMs) applied to daily logbook data revealed that effort restrictions on daily purse seine operations (in terms of the duration and the total number of operations per ship and day) significantly reduced total fishing efforts on chub mackerel. Stochastic simulations based on the parameters estimated in GLMMs quantified the extent of the potential catch reduction by the effort reductions at approximately 20%. Combined with the effect of another concurrently implemented management measure, i.e. day closures, the net effects of the effort management on the total catch reduction were estimated at 30%. Because the quota uptake percentages in this fishery were 60-80% during the study period, we conclude that the effort management helped avoid overshooting of the quota and consequent seasonal closures.

DOI： 10.3354/meps12688

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：OXFORD UNIV PRESS  

Tuned virtual population analyses are widely used for fisheries stock assessments. However, accurately estimating abundances and fishing mortality coefficients in the terminal year using tuned virtual population analyses is generally difficult, particularly when there is a limited number of available abundance indices. We propose a new method of integrating the tuned virtual population analyses with a ridge regression approach. In our method, penalization in the ridge regression is applied to the age-specific fishing mortalities in the terminal year, and the penalty parameter is automatically selected by minimizing the retrospective bias. Therefore, our method is able to simultaneously obtain a stable estimation of fishing mortality coefficients in the terminal year and reduce retrospective bias. Simulation tests based on the northern Japan Sea stock of walleye pollock (Gadus chalcogrammus) in the Sea of Japan demonstrated that this method yielded less biased estimates of abundances and avoided overestimations of fishing mortality coefficients in the terminal year. In addition, despite limited abundance indices, our method can perform reliable abundance estimations even under hyperstability and hyperdepletion conditions.

DOI： 10.1093/icesjms/fsx089

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY  

In modeling biological and ecological processes from data, it is essential to deal with data selection bias properly in order to obtain reliable and reasonable predictions. To incorporate the mechanism of selection bias into a statistical analysis, a propensity score (PS) is widely employed as an inverse probability weight in order to obtain a consistent estimation of a binary response variable of interest. However, the estimation performance often becomes unstable due to the mis-estimation of the PS. In order to obtain a consistent estimation as well as to stabilize the estimation performance, we propose a new regression model that incorporates the PS as an explanatory variable. Moreover, we show that the proposed model has a the property of double robustness, which enables us to obtain a consistent estimation of the response without suffering from selection bias if either the PS model or the proposed model is correctly specified. The robust bias correction model also accommodates heterogeneity of data distributions based on an asymmetric logistic model, which in turn improves model fitting and prediction accuracy. The PS in our regression model enables us to estimate consistently the global fish stock status even if the information of the stock status available is biased.

DOI： 10.1002/ecs2.2038

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER JAPAN KK  

Limited access to aquatic populations hinders estimation of their status and establishment of effective management measures. We propose a modified surplus production model to cope with this problem. The model provides population parameters and biological reference points from a time series of annual accessible abundance data. Simulation tests showed that the model provided biological reference point estimates with little bias when sufficiently long time series were available. Even for short time series, we could obtain nearly unbiased estimates by providing information on the exploitation rate at the maximum sustainable yield (FMSY). As an application, we fit the modified surplus production model to 7-year accessible biomass estimates of a local population of Japanese spiky sea cucumber Apostichopus japonicus using a Bayesian approach. The results indicated that the stock in the area studied was likely to have experienced recent overfishing and had a high probability of being overfished in the future.

DOI： 10.1007/s12562-017-1078-0

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Language：English   Publisher：OXFORD UNIV PRESS  

We present the first quantitative review of the stock status relative to the stock biomass (B) and the exploitation rate (U) that achieved the maximum sustainable yield (MSY) (B MSY and U MSY, respectively) for 37 Japanese stocks contributing 61% of the total marine capture production in Japan. B MSY and U MSY were estimated by assuming three types of stock-recruitment (S-R) relationships and an age-structured population model or by applying a surplus production model. The estimated stock status shows that approximately half of the stocks were overfishing (U/U MSY > 1), and approximately half of the stocks were overfished (B/B MSY < 0.5) during 2011-2013. Over the past 15 years, U decreased and B slightly increased on average. The rate of decrease in the U of the stocks managed by the total allowable catch (TAC) was significantly greater than that of the other stocks, providing evidence of the effectiveness of TAC management in Japan. The above statuses and trends were insensitive to the assumption of the S-R relationship. The characteristics of Japanese stocks composed mainly of resources with relatively high natural mortality, i.e. productivity, suggest that Japanese fisheries have great potential of exhibiting a quick recovery and increasing their yield by adjusting the fishing intensity to an appropriate level.

DOI： 10.1093/icesjms/fsx002

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We investigated the impacts of extensive anthropogenic (high seas driftnet squid fishery) and natural (late 1990s major climate regime shift) events on dominant epipelagic fish, squid, and shark in the central North Pacific Transition Region based on a driftnet survey covering the years 1979–2006. Fishing was conducted by Japan, Korea and Taiwan to target neon flying squid in the period 1979–1992, resulting in a decline in stocks of the target species and non-target species (Pacific pomfret and juvenile blue shark), which were by-catch of this fishery. The catch was found to be at the maximum sustainable yield (MSY) level for neon flying squid, the underfished level for juvenile blue shark, but the overfished level for Pacific pomfret. The MSY of Pacific pomfret indicated that this species is more susceptible to exploitation than previously considered. In response to the late 1990s regime shift, neon flying squid and Pacific saury showed low stock levels in 1999–2002 and 1998–2002, respectively, as a result of reduced productivity in their nursery grounds (the Subtropical Frontal Zone and Kuroshio Extension Bifurcation Region, respectively). On the other hand, Pacific pomfret showed no decreasing trend in stock during the low- and intermediate-productivity regimes because of the high productivity of their main spawning/nursery ground (Transition Zone Chlorophyll Front), which was independent of the regime shifts. Thus, squid and saury appear to be more susceptible to the regime shift than pomfret. We discuss the implications for stock management of the species-specific responses to the fishery and the regime shift.

DOI： 10.1016/j.pocean.2015.03.007

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATL ACAD SCIENCES  

Food contamination caused by radioisotopes released from the Fukushima Dai-ichi nuclear power plant is of great public concern. The contamination risk for food items should be estimated depending on the characteristics and geographic environments of each item. However, evaluating current and future risk for food items is generally difficult because of small sample sizes, high detection limits, and insufficient survey periods. We evaluated the risk for aquatic food items exceeding a threshold of the radioactive cesium in each species and location using a statistical model. Here we show that the overall contamination risk for aquatic food items is very low. Some freshwater biota, however, are still highly contaminated, particularly in Fukushima. Highly contaminated fish generally tend to have large body size and high trophic levels.

DOI： 10.1073/pnas.1519792113

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Binary data are popular in ecological and environmental studies; however, due to various uncertainties and complexities present in data sets, the standard generalized linear model with a binomial error distribution often demonstrates insufficient predictive performance when analysing binary and proportional data. To address this difficulty, we propose an asymmetric logistic regression model that uses a new parameter to account for data complexity. We observe that this parameter controls the model's asymmetry and is important for adjusting the weights associated with observed data in order to improve model fitting. This model includes the ordinary logistic regression model as a special case. It is easily implemented using a slight modification of glm or glmer in statistical software R. Simulation studies suggest that our new approach outperforms a traditional approach in terms of both predictive accuracy and variable selection. In a case study involving fisheries data, we found that the annual catch amount had a greater impact on stock status prediction, and improved predictive capability was supported with a smaller AIC compared to a generalized linear model. In summary, our method can enhance the applicability of a generalized linear model to various ecological problems using a slight modification, and significantly improves model fitting and model selection.

DOI： 10.1111/2041-210X.12473

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Language：Japanese   Publisher：The Mammal Society of Japan  

Behavioral classification and observational error correction methods are often needed when analyzing mammal behavior using GPS. The switching state-space model (SSSM) has been proposed for this problem. However, various positioning intervals have been used to attempt to balance the research purposes and battery life of the GPS. Thus, we may come to different conclusions regarding the appropriate positioning intervals using the same analysis. In this study, we used Asiatic black bear (<i>Ursus thibetanus</i>) behavior data. We generated various time interval positioning data from the real positioning data, to verify the effect of the interval on the SSSM estimates. By combining the SSSM with activity sensors, we can classify the behavior into transiting, resting, and foraging, using 5- to 120-minute intervals. Moreover, time-spatial scales (which recognize the core area) increased as the positioning interval increased. We compared the relative moving distances for the different positioning intervals. Our analysis of the habitat selection performed better using short positioning intervals of 30 minutes or less. We expect that new knowledge will be obtained by applying SSSM with short interval positioning data (e.g., at 5- to 30-minute intervals).

DOI： 10.11238/mammalianscience.56.5

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY  

Restricting human access to a specific wildlife species, community, or ecosystem, i.e., input control, is one of the most popular tools to control human impacts for natural resource management and wildlife conservation. However, quantitative evaluations of input control are generally difficult, because it is unclear how much human impacts can actually be reduced by the control. We present a model framework to quantify the effectiveness of input control using day closures to reduce actual fishing impact by considering the observed fishery dynamics. The model framework was applied to the management of the Pacific stock of the chub mackerel (Scomber japonicus) fishery, in which fishing was suspended for one day following any day when the total mackerel catch exceeded a threshold level. We evaluated the management measure according to the following steps: (1) we fitted the daily observed catch and fishing effort data to a generalized linear model (GLM) or generalized autoregressive state-space model (GASSM), (2) we conducted population dynamics simulations based on annual catches randomly generated from the parameters estimated in the first step, (3) we quantified the effectiveness of day closures by comparing the results of two simulation scenarios with and without day closures, and (4) we conducted additional simulations based on different sets of explanatory variables and statistical models (sensitivity analysis). In the first step, we found that the GASSM explained the observed data far better than the simple GLM. The model parameterized with the estimates from the GASSM demonstrated that the day closures implemented from 2004 to 2009 would have decreased exploitation fractions by ∼ 10% every year and increased the 2009 stock biomass by 37-46% (median), relative to the values without day closures. The sensitivity analysis revealed that the effectiveness of day closures was particularly influenced by autoregressive processes in the fishery data and by positive relationships between fishing effort and total biomass. Those results indicated the importance of human behavioral dynamics under input control in quantifying the conservation benefit of natural resource management and the applicability of our model framework to the evaluation of the input controls that are actually implemented.

DOI： 10.1890/14-1216.1

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PERGAMON-ELSEVIER SCIENCE LTD  

Assessment of the current status of marine ecosystems is necessary for the sustainable utilization of ecosystem services through fisheries and other human activities under changing environmental conditions. Understanding of historical changes in marine ecosystems can help us to assess their current status. In this study, we analyzed Japanese commercial fishery catch data and scientific survey data of the diet of northern fur seal (. Callorhinus ursinus, NFS) to investigate potential long-term ecosystem changes in the western North Pacific Ocean off northeastern Japan over the past 60 years. Total commercial catches experienced peaks around 1960 and during the 1980s, decreasing to low levels around 1970 and after 1990. Catches were substantively impacted by the Tohoku earthquake and tsunami in 2011. Species composition of the commercial catch changed over time, resulting in changes in the mean trophic level (MTL) of the catches. Trends in observed commercial catches were affected by many factors, including species population fluctuations potentially related to large-scale environmental shifts, migration and distribution patterns of species related to local oceanography, changes in fishing technology, and the introduction of fishery management frameworks. The composition of NFS diet also changed over time: although overall changes were small, MTL derived from NFS stomach contents declined from the early 1970s to the late 1980s. This fall in the MTL of the diet of NFS is suggestive of a shift in pelagic fish fauna from a "mackerel-dominant regime" to a "sardine-dominant regime". Inconsistencies between changes in species composition and MTLs of the commercial catch and NFS diet resulted from differences in commercial fishing targeting and NFS foraging behavior strategies. Although commercial catch is a valuable source of information for investigating historical changes in fisheries, biological resources, and ecosystems, catch data should be interpreted carefully and other relevant information available should also be considered.

DOI： 10.1016/j.dsr2.2014.10.027

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Language：Japanese   Publisher：The Ecological Society of Japan  

Ecologists frequently need to detect causalities among events from time series data. It can be difficult to detect causality from time series data created from complex, deterministic, nonlinear systems, which are universal. Convergent cross mapping is a novel method for detecting causality in such situations. This review explains the mechanism, how to use the method, and future issues with this method.

DOI： 10.18960/seitai.65.3_241

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Other Link： https://agriknowledge.affrc.go.jp/RN/2010901124

Language：Japanese   Publisher：The Japanese Society of Fisheries Science  

&nbsp;&nbsp;This study explored optimum sets of coefficients used in the management procedure (MP) currently applied to the fishery stocks in Japan when estimates of the total stock biomass are not available. The MP determines annual allowable biological catch (ABC) every year using the trend of relative stock abundance and the estimated current stock status categorized into &ldquo;high&rdquo;, &ldquo;middle&rdquo;, and &ldquo;low&rdquo;. We conducted extensive population dynamics simulations with a variety of uncertainty of population parameters, observation errors, and historical trends of relative stock abundances under the MP. Performance of the MP varied with the combination of adjusting coefficients used in the MP (management rules). We quantified the difference by using scores given to each simulation result under a single management objective arbitrarily given. The total scores calculated among the different management rules illustrated the trade-off between the average catch and risk of over-fishing, and provided a single optimum management rule that maximized the score. We also observed, even under the same management objective, how the optimum management rule depends on simulation parameters, the methods used to estimate current stock status, and years to be considered in calculating ABC.<br>

DOI： 10.2331/suisan.81.206

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Other Link： https://agriknowledge.affrc.go.jp/RN/2010891461

Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER JAPAN KK  

This study used a delta-lognormal model to analyze monthly catches of age-0 Pacific bluefin tuna by the troll fishery. The model included fixed effects of month, area, and month-area interaction, and random effects of port, year and port-year interaction. The catch patterns by month and area predicted by the statistical model (standardized catch) revealed that main fishing grounds along the Tsushima Warm Current generally shifted from north to south as the season turned from autumn to winter. In contrast, the standardized catch along the Kuroshio Current did not show such clear spatiotemporal patterns. The standardized catch along the Tsushima Warm Current is significantly associated with average monthly sea surface temperatures in the fishing grounds and consistent with migration routes revealed by tagging experiments in previous studies. These associations indicate the spatiotemporal catch pattern in the Tsushima Warm Current region partly reflects seasonal migration. Knowledge of the possible associations among fish migration, environmental factors and spatiotemporal distribution of the catch will contribute to future management of this species.

DOI： 10.1007/s12562-014-0806-y

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER  

Offshore lingcod (Ophiodon elongatus) in British Columbia (BC) make seasonal migrations that differ by sex: in winter most adult males aggregate in shallow water and most adult females aggregate in deep water, while in summer both sexes distribute equally in deep and shallow water. We developed a semi-age structured delay-difference model that accommodates sex-, and age/depth-specific seasonal migration and examined the sensitivity of biological reference points for BC offshore lingcod to migration pattern and the allocation of fishing effort across seasons and depths. When a migration pattern with a homogeneous distribution of males and females in shallow and deep water throughout the year was assumed, the estimated maximum sustainable yield (MSY), biomass at MSY (BMSY), and percent spawning per recruitment at MSY (%SPRMSY) were robust to changes in effort allocation. However, when a migration pattern that assumed a winter distribution of 95% of adult males in shallow water and 95% of adult females in deep water was used, the estimated MSY, BMSY, and %SPRMSY were markedly sensitive to changes in effort allocation. These results suggest that incorporating sex-, age/depth-, and season-specific structuring in stock assessment models could enable improved evaluations of management options for BC lingcod and other species with sex- and season-specific migrations. © 2013 Elsevier B.V.

DOI： 10.1016/j.fishres.2013.10.022

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER  

Integrated analysis is widely used for fisheries stock assessment. The analysis has several merits, including its prevention of the loss of information and its enabling of the evaluation of uncertainties that arise when integrating individual data, such as size composition data and abundance indices. However, the data integration itself causes one of the most difficult problems: conflicts among data sources. This paper provides an illustrative explanation of how data conflict can occur under model mis-specification on selectivity in a multi-fishery integrated stock assessment model through simulation with known parameters. We demonstrated that estimation bias can be caused under various scenarios of model mis-specifications on selectivity. Relative likelihood profiles decomposed into the likelihood components from different data sources revealed data conflicts among multiple datasets under the model mis-specifications, whereas the relative likelihood profiles displayed no severe data conflicts without any model mis-specifications. Data conflicts occurred because a single estimation model without correct selectivity assumptions cannot explain the observed multiple data sources simultaneously. We also found that almost all of the parameters estimated in the integrated model were potentially affected by the model mis-specification in any single component of selectivity for a specific fishery. If we accumulate empirical knowledge on the general patterns of conflicts and what types of data sources are robust against typical model mis-specifications, the relative likelihood profiles could be utilized more efficiently in diagnostics to identify potential model mis-specifications and to obtain more accurate estimates of the quantities of interest for stock management. © 2014 Elsevier B.V.

DOI： 10.1016/j.fishres.2014.02.003

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Language：Japanese  

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Other Link： https://agriknowledge.affrc.go.jp/RN/2010872719

Language：Japanese   Publisher：The Mammal Society of Japan  

Recently, conflicts between Asiatic black bears (<i>Ursus thibetanus</i>) and humans are increasing as bears expand their distribution. However, little is known about the biology of bears inhabiting near settlements. We fitted GPS collars on 7 bears during 2010–11, and by fitting the Switching State-Space Model, we smoothed error-prone GPS tracks and categorized bear behavior into transit, active stay, and inactive stay. Additionally, we investigated habitat characteristics by exploring active-stay core areas. On the whole, bears lived near settlements in summer and more distantly from settlements in autumn. However, there were exceptional bears staying more distantly in summer and near settlements in autumn. Near settlements, bears mainly foraged <i>Juglans mandshurica</i> and <i>Castanea crenata</i> in late summer and <i>Diospyros kaki</i> in autumn. In distant areas, bears foraged ants and <i>Prunus</i> spp. in late summer and <i>Quercus mongolica</i> in autumn. Bears' nocturnal activity became higher near settlements. Our results indicated that bears come close to settlements in particular seasons according to seasonal changes in food availability. Bears were more likely to be near settlements if there were intensively distributed foods derived from humans nearby.

DOI： 10.11238/mammalianscience.54.19

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：MAMMALOGICAL SOC JAPAN  

Diet preferences of three captive northern fur seals for seven prey items (Okhotsk atka mackerel, rainbow trout, common mackerel, walleye pollock, Pacific sand lance, horse mackerel, and Japanese common squid) were measured through repeated two-choice tests. Preference indices estimated from the paired consumption data using the normal Bradley-Terry model revealed the existence of diet preferences and their individual variation. The three seals generally preferred Okhotsk atka mackerel, rainbow trout, and common mackerel, but showed individual differences for less preferred food items. The preferred items had moderate food size and high energy content per one item. Once diet preferences were determined, animals were given rainbow trout laced with lithium chloride (LiCl) to induce conditioned taste aversion (CTA). Four to five LiCl treatments were required for CTA, but could only induce temporary aversion of rainbow trout in favor of horse mackerel. Choice tests after CTA demonstrated a decrease in preference indices for rainbow trout in the three animals, but the ranking and preference indices of rainbow trout did not fall below those for horse mackerel. These results suggest that preference and aversion are relative phenomena, and the success of CTA is dependent on the reduction of preference relative to other food items.

DOI： 10.3106/041.038.0308

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Language：English   Publisher：WILEY-BLACKWELL  

DOI： 10.1002/biom.12048

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This paper proposes a new and flexible statistical method for marginal increment analysis that directly accounts for periodicity in circular data using a circular-linear regression model with random effects. The method is applied to vertebral marginal increment data for Alaska skate Bathyraja parmifera. The best fit model selected using the AIC indicates that growth bands are formed annually. Simulation, where the underlying characteristics of the data are known, shows that the method performs satisfactorily when uncertainty is not extremely high. © 2013 The Authors. Journal of Fish Biology © 2013 The Fisheries Society of the British Isles.

DOI： 10.1111/jfb.12062

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Language：Japanese   Publisher：The Japanese Society of Fisheries Science  

&nbsp;&nbsp;Asymmetric shell marking (type A) in the Manila clam <i>Ruditapes philippinarum</i> is known to be a heritable dominant characteristic. We collected local samples from a wide range of the Japanese Archipelago and China, and found that the frequency of type A was heterogeneous among the samples. The frequency was significantly higher (14.5-28.1%) in samples collected in Hokkaido and the Kanto area (Tokyo Bay, Sagami Bay and Numazu) than those (0-9.9%) in the other samples collected in Tohoku and west of Hamana Lake including China. Non-native clam individuals had been released in the Banzu area of Tokyo Bay for nearly two decades, ceasing in 2007. The clam samples collected at Banzu in 2005 were subdivided into small (<20 mm in shell length) and large (&ge;25 mm) size groups, and a significantly higher frequency of type A was observed in the small group (22%) than in the large group (0%). On the other hand, clam samples collected at the same area in 2011-2012 presented a high frequency of type A (17.2-20.3%) regardless of the size. Samples collected from other areas of Tokyo Bay where no exogenous individuals had been released were observed to have maintained a high frequency of type A (17.9-26.4%). This simple phenotypic marker indicates that the Manila clam population in Japan is genetically structured and exogenous individuals introduced to Tokyo Bay may have had little effect on diminishing the frequency of type A.<br>

DOI： 10.2331/suisan.79.190

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Other Link： https://agriknowledge.affrc.go.jp/RN/2010851676

Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY  

Overdispersed count data are very common in ecology. The negative binomial model has been used widely to represent such data. Ecological data often vary considerably, and traditional approaches are likely to be inefficient or incorrect due to underestimation of uncertainty and poor predictive power. We propose a new statistical model to account for excessive overdisperson. It is the combination of two negative binomial models, where the first determines the number of clusters and the second the number of individuals in each cluster. Simulations show that this model often performs better than the negative binomial model. This model also fitted catch and effort data for southern bluefin tuna better than other models according to AIC. A model that explicitly and properly accounts for overdispersion should contribute to robust management and conservation for wildlife and plants. © 2012 The Society of Population Ecology and Springer.

DOI： 10.1007/s10144-012-0319-4

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY  

Line transect sampling is one of the most widely used methods for estimating the size of wild animal populations. An assumption in standard line transect sampling is that all the animals on the trackline are detected without fail. This assumption tends to be violated for marine mammals with surfacing/diving behaviors. The detection probability on the trackline is estimated using duplicate sightings from double-platform line transect methods. The double-platform methods, however, are insufficient to estimate the abundance of long-diving animals because these animals can be completely missed while the observers pass. We developed a more flexible hazard probability model that incorporates information on surfacing/diving patterns obtained from telemetry data. The model is based on a stochastic point process and is statistically tractable. A simulation study showed that the new model provides near-unbiased abundance estimates, whereas the traditional hazard rate and hazard probability models produce considerably biased estimates. As an illustration, we applied the model to data on the Baird's beaked whale (Berardius bairdii) in the western North Pacific. © 2011, The International Biometric Society.

DOI： 10.1111/j.1541-0420.2011.01689.x

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

Population indices quantify changes in relative population sizes, which underpin much of basic ecology and conservation science. However, temporal changes in population counts may vary among survey sites for both ecological and artificial reasons, confounding existing population indices estimated without accounting for such variations. We created a smoothed hierarchical model, and compared its performance against the conventional approaches (generalized linear models and generalized additive models) and a non-smoothed hierarchical model using simulation data with a known nonlinear trend. The smoothed hierarchical model always estimated population indices with the best accuracy and precision; the performance of other models deteriorated substantially with increasing variation in trends of population counts among sites, causing inaccurate estimation of population growth rates. The estimated variations in trends of population counts among sites for 233 out of 518 North American breeding bird species were larger than the value used in the simulation where there was a considerable difference in the performance between hierarchical models and the conventional approaches. These estimated variations in trends of population counts among sites were particularly large in gregarious waterbirds. These results suggest that the smoothed hierarchical model developed in this study should play an important role in accurately assessing population indices, particularly for gregarious waterbirds, using count data from large-scale, long-term surveys in the field. © 2011 Elsevier Ltd.

DOI： 10.1016/j.ecolind.2011.06.008

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER TOKYO  

When ecological traits differ seasonally among biological groups, environmental adaptation is expected. However, current analytical methods for such seasonal data ignore the circular nature of data and therefore are likely to be flawed. We propose a simple bootstrap hypothesis test which statistically quantifies the presence/absence of differences in peak months for multiple groups taking the circular nature of the data into account. The test is based on a robust distribution-free method. Simulations showed that the test gives a satisfactory performance. The test is illustrated using data for anchovy and sardine egg abundances in the western North Pacific. © 2011 The Society of Population Ecology and Springer.

DOI： 10.1007/s10144-011-0280-7

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATL MARINE FISHERIES SERVICE SCIENTIFIC PUBL OFFICE  

We propose an extended form of the von Bertalanffy growth function (VBGF), where the allocation of surplus energy to reproduction is considered. Any function can be used in our model to describe the ratio of energy allocation for reproduction to that for somatic growth. As an example, two models for energy allocation were derived: a step-function and a logistic function. The extended model can jointly describe growth in adult and juvenile stages. The change in growth rate between the two stages can be either gradual or steep; the latter gives a biphasic VBGF. The results of curve fitting indicated that a consideration of reproductive energy is meaningful for model extension. By controlling parameter values, our comprehensive model gives various growth curve shapes ranging from indeterminate to determinate growth. An increase in the number of parameters is unavoidable in practical applications of this new model. Additional information on reproduction will improve the reliability of model estimates.

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

Organic farming has the potential to reverse biodiversity loss in farmland and benefit agriculture by enhancing ecosystem services. Although the mixed success of organic farming in enhancing biodiversity has been attributed to differences in taxa and landscape context, no studies have focused on the effect of macro-scale factors such as climate and topography. This study provides the first assessment of the impact of macro-scale factors on the effectiveness of within-farm management on biodiversity, using spiders in Japan as an example. A multilevel modelling approach revealed that reducing pesticide applications increases spider abundance, particularly in areas with high precipitation, which were also associated with high potential spider abundance. Using the model we identified areas throughout Japan that can potentially benefit from organic farming. The alteration of local habitat-abundance relations by macro-scale factors could explain the reported low spatial generality in the effects of organic farming and patterns of habitat association. © 2011 Blackwell Publishing Ltd/CNRS.

DOI： 10.1111/j.1461-0248.2011.01699.x

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：INTER-RESEARCH  

Interannual changes in abundance of the autumn cohort of neon flying squid Ommastraphes bartramii during 1979 to 2006 were examined in relation to the large-scale climate shift in the central North Pacific Ocean. Catch per unit of effort (CPUE) of driftnet surveys, which is assumed to reflect the squid stock level, was very low during 1999 to 2002, which was an anomalous climate period. Given that the autumn cohort uses productive areas near and north of the transition zone chlorophyll front (TZCF) as favorable nursery and feeding grounds, we examined 3 covariates-(1) the winter position of the TZCF in the neon flying squid nursery ground, (2) the summer position of the TZCF in the feeding ground and (3) fishing mortality-to estimate which covariates were significantly correlated with low CPUE time periods. Multiple linear regression analysis suggested that only the effect of winter position of the TZCF in the nursery ground best predicted the change in the CPUE. The anomalous climate conditions caused a significant reduction in net primary production over an extended area within the subtropical frontal zone (STFZ), which is the main nursery ground for the autumn cohort. Hence, we assume that food availability for juvenile neon flying squid could be critical for the level of stock recruitment of this cohort. Furthermore, the sea level anomaly (SLA), which is considered to be a useful index of variability in the upper ocean structure, significantly correlated to the CPUE during spawning and nursery periods in the STFZ. Our study supports the hypothesis that the bottom-up effect of the climate shift can be manifested rapidly in neon flying squid, indicating that squid abundance can act as a productivity integrator and a real-time ecosystem indicator that respond to large-scale environment changes. © Inter-Research 2011.

DOI： 10.3354/meps09365

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY  

The abundance of the northern form of the short-finned pilot whale, Globicephala macrorhynchus, in the Pacific waters of northern Japan was estimated from a line transect survey conducted in 2006 and data from seven previous surveys collected between 1985 and 1997. To overcome the difficulty of small sample size and inconsistency in survey design, we used an adjustment method using multiple covariates and sensitivity analysis by considering several scenarios. Abundance estimates showed similar long-term trends among scenarios. The northern form of G. macrorhynchus was more abundant in 1985 than in 1991-2006. The annual catch of the northern form of G. macrorhynchus exceeded the potential biological removal (PBR), especially in the 1980s. Thus, the commercial take in the early 1980s was suspected as a partial cause of a serious abundance decrease. These results provide valuable information for interpreting the impacts of coastal whaling, and to develop future management plans. © 2010 by the Society for Marine Mammalogy.

DOI： 10.1111/j.1748-7692.2010.00410.x

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Language：Japanese   Publisher：The Ecological Society of Japan  

Similarity indices are frequently used in ecological analyses to compare community structure between ecosystems and experimental treatments. However, many ecological analyses have used classical similarity indices, even though new similarity indices and statistical tests have been proposed. In this review, we introduce representative and useful similarity indices and statistical tests for analyzing ecological communities. We recommend using the statistical software R with the "vegan" package to analyze similarity indices. We synthesized the frequency with which similarity indices have been used for ecological studies and found that classical similarity indices, such as the Jaccard index, have been used by researchers in the past decade. Here, we emphasize that the Chao index is one of the best options among similarity indices when considering the probability of rare species in communities. To test for differences in community similarity, PERMANOVA is one of the best tests for ecological analyses. Ecologists should use adequate similarity indices and tests.

DOI： 10.18960/seitai.61.1_3

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Other Link： https://agriknowledge.affrc.go.jp/RN/2010811727

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We compare the sensitivity of the estimated effective strip half-width with respect to choice of hazard probability function (Q). This is done by fitting the model underan erroneous assumption about the parametric form of Q, and comparing the estimated and true effective strip half-width. An 'infinite sample size' setting is employed, where fitting the model by maximum likelihood amounts to minimising the Kullback Leibler distance between the assumed and true models. The experiment is carried out in a situation that is relevant to minke whale sighting surveys both in the Antarctic and in the northeastern Atlantic. It is found that the hazard probability model is fairly robust with respect to the choice of parametric class for Q. The largest observed bias in the resulting effective strip half-width is less than 10%, while for most situations there is almost no bias.

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY  

Patchiness structure and mortality rates of Pacific saury Cololabis saira larvae were estimated in the frontal area of the Kuroshio Extension in spring 2000 and 2001. Drogued GPS buoys, which were used as Lagrangian reference points, were deployed to mark dense patches of saury larvae and a series of samplings was conducted using a neuston net around the buoys during the night over a period of several days. A total of 225 tows were conducted and 11 690 specimens were sampled during four buoy tracking. Despite the occurrence of water diffusion, patchiness density, distance between adjacent patches and patch size estimated by geostatistical analysis did not drastically change during the buoy tracking and these parameters were robust for the difference of variogram models and the threshold larval density defining patchiness. Such a stability of the patchiness allowed the estimation of larval mortality from the decrease of larval density for different size classes with respect to individual growth based on the samples taken repeatedly during the buoy tracking. Although low or negative values were obtained for the larvae right after hatching, probably due to continuous hatching, the estimates of mortality then increased and became stable in the range of 23-37% day-1 with a small standard deviation until their knob length reached to 36 mm. In situ information on the patchiness structure and larval mortality provides crucial parameters for simulating the recruitment process of small pelagic fishes in high-resolution hydrodynamic models.

DOI： 10.1111/j.1365-2419.2009.00514.x

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：CANADIAN SCIENCE PUBLISHING  

A simple age verification method is presented for centrum edge analysis (CEA) of elasmobranch species. In this method, a binomial model is linked with a von Mises distribution for circular data, taking the characteristics of the CEA data into account. The periodicity of growth band pairs is categorized as no cycle, an annual cycle, or a biannual cycle. Three models are then constructed according to different periodicities. We use the Akaike information criterion (AIC) to determine which model is the best. The models were applied to the shortfin mako shark (Isurus oxyrinchus) data collected in the North Pacific to identify the best periodicity model. The AIC best-fitting model was one involving an annual cycle. The general performance of the method was evaluated using simulated data of various sample sizes, formation times, and durations of growth band pairs. The simulation trials showed that the performance of the method was satisfactory with moderate sample sizes. This method should improve the accuracy of age determination and could be applied to all species that have periodic growth band pairs.

DOI： 10.1139/F09-039

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER  

The effects of bait species (mackerel and squid) and color (blue-dyed and non-dyed) on the loggerhead turtle Caretta caretta bycatch in a pelagic longline fishery in the western North Pacific were assessed in shallow-set longline fishing experiments. The loggerhead turtle catches were analyzed using a generalized linear model (GLM) with a Poisson distribution. The potential factors (bait species, bait color, other species catch, and sea surface temperature) affecting loggerhead turtle catch were incorporated as explanatory variables. The model analyses indicated that bait species affected loggerhead turtle catch, while bait color did not. The model predicted that catch rates of loggerhead turtles were 75% less on mackerel bait to squid bait. This study demonstrated that fish bait choice was very effective in reducing loggerhead turtle bycatch in pelagic longline fisheries, but that the use of blue-dyed bait was not. Similar model analyses were also performed on target and by-product fish species, such as swordfish Xiphias gladius, striped marlin Tetrapturus audax, bigeye tuna Thunnus obesus, blue shark Prionace glauca, and shortfin mako shark Isurus oxyrinchus, and other non-target species. The remarkable differences between bait species and color that were found for loggerhead turtles were not found for these species catches. © 2009 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.fishres.2009.01.003

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER STATISTICAL ASSOC & INT BIOMETRIC SOC  

Quantifying resource selection is of primary interest in animal ecology. Many analyses of resource selection assume spatial and temporal independence of the sampling unit. Autocorrelation between observations, which is a general property of ecological variables, causes difficulties for most standard statistical procedures of resource selection because autocorrelated data violate the assumption of independence. To overcome this problem, we develop a mixed-effects model to estimate resource selection functions from data that are autocorrelated because of unobserved grouping behavior by animals. In the application of the expectation-maximization (EM) algorithm, the computation of the conditional expectation of the complete-data log-likelihood function does not have a closed-form solution requiring numerical integration. A Monte Carlo EM algorithm with Gibbs sampling can be used effectively in such situations to find exact maximum likelihood estimates. We propose a simple automated Monte Carlo EM algorithm with multiple sequences in which the Monte Carlo sample size is increased when the EM step is swamped by Monte Carlo errors. We demonstrate that the model can detect inherent autocorrelation and provide reasonable variance estimates when applied to nocturnal bird migration data. This approach could also be applied to ecological processes with various types of spatially and temporally autocorrelated data, circumventing serious problems caused by dangerous pseudoreplication. © 2008 American Statistical Association and the International Biometric Society.

DOI： 10.1198/108571108X337817

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Other Link： https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-19780156/

Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER JAPAN KK  

The management of Japanese domestic fisheries for small cetaceans has been based on a traditional approach that involves only the best set of assumptions and data. However, uncertainty, which is pervasive and inevitable for most fisheries resources, often leads the traditional approach to serious failure. Here is presented the basic framework of a simulation-based approach with a simple Bayesian method that is applicable to Japanese fisheries for small cetaceans. For illustration, the simulation model was applied to Dall's porpoise data in order to investigate the robustness of several management procedures against uncertainty. The simulation showed that the current management procedure, based on only the best values, could fail to manage the stocks at a considerably high probability. However, the use of the conservative management procedure, potential biological removal, permits the sustainable harvesting of Dall's porpoise for at least 100 years into the future, even under uncertainty. In conjunction with a firm structure for implementation of management procedures, the spread of simulation-based approaches will quickly enable successful sustainable management of small cetaceans. © 2008 Japanese Society of Fisheries Science.

DOI： 10.1111/j.1444-2906.2008.01582.x

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：INTER-RESEARCH  

Central-place foragers that must return to a breeding site to deliver food to offspring are faced with trade-offs between prey patch quality and distance from the colony. Among colonial animals, pinnipeds and seabirds may have different provisioning strategies, due to differences in their ability to travel and store energy. We compared the foraging areas of lactating Antarctic fur seals and chinstrap penguins breeding at Seal Island, Antarctica, to investigate whether they responded differently to the distribution of their prey (Antarctic krill and myctophid fish) and spatial heterogeneity in their habitat. Dense krill concentrations occurred in the shelf region near the colony. However, only brooding penguins, which are expected to be time-minimizers because they must return frequently with whole food for their chicks, foraged mainly in this proximal shelf region. Lactating fur seals and incubating penguins, which can make longer trips to increase energy gain per trip, and so are expected to be energy-maximizers, foraged in the more distant (>20 km from the island) slope and oceanic regions. The shelf region was characterized by more abundant, but lower-energy-content immature krill, whereas the slope and oceanic regions had less abundant but higher-energy-content gravid krill, as well as high-energy-content myctophids. Furthermore, krill in the shelf region undertook diurnal vertical migration, whereas those in the slope and oceanic regions stayed near the surface throughout the day, which may enhance the capture rate for visual predators. Therefore, we suggest that the energy-maximizers foraged in distant, but potentially more profitable feeding regions, while the time-minimizers foraged in closer, but potentially less profitable regions. Thus, time and energy constraints derived from different provisioning strategies may result in sympatric colonial predator species using different foraging areas, and as a result, some central-place foragers use suboptimal foraging habitats, in terms of the quality or quantity of available prey. © Inter-Research 2007.

DOI： 10.3354/meps06873

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

A study of common minke and Bryde's whales was conducted in the western North Pacific in the 2000 and 2001 summer seasons to estimate prey selection of cetaceans as this is an important parameter in ecosystem models. Whale sighting and sampling surveys and prey surveys using quantitative echosounder and mid-water trawl were carried out concurrently in the study. Biomasses of Japanese anchovy, walleye pollock and krill, which were major prey species of common minke and Bryde's whales, were estimated using an echosounder. The results suggested that common minke whale showed prey selection for Japanese anchovy while they seemed to avoid krill in both the offshore and coastal regions and walleye pollock in the continental shelf region. Selection for shoaling pelagic fish was similar to that in the eastern North Atlantic. Bryde's whale showed selection for Japanese anchovy in August 2000 and July 2001, while it showed prey selection for krill in May and June in 2001. © 2007 The Authors.

DOI： 10.1111/j.1365-2419.2006.00426.x

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Population sizes of long-diving marine mammals can be estimated with minimal bias using line transect sampling techniques in conjunction with data on surfacing/diving, even though the detection probability on the trackline is considerably less than 1. Using a simulation, it was investigated whether population sizes can be accurately estimated when only the mean cue production rate, without information on surfacing/diving patterns, is available. In addition, a new model that incorporates information on surfacing/diving patterns into the estimation procedure was developed. The simulation showed that the new model can provide less biased abundance estimates, whereas neglecting surfacing/diving patterns can result in serious underestimates of abundance, in particular for long-diving animals.

DOI： 10.1111/j.1444-2906.2006.01193.x

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Language：English   Publishing type：Research paper (scientific journal)  

In the high seas of the North Pacific, large-scale squid driftnet fisheries targeted the autumn cohort of neon flying squid (Ommastrephes bartramii) from May to mid-September. Total annual catches during 1982-1992 ranged from 102,000 to 209,000 t (149,000 t on average). To assess the effect of intensive commercial driftnet fishing on this cohort, we assessed the stock based on past driftnet fishing data. We used three different methods to estimate stock size during the high fishing season (July) for the driftnet fishing ground between 170°E and 145°W during 1982-1992. We found remarkable agreement in average stock estimates based on the three methods, with estimates of 380,000 t by the swept area method, 367,000 t by the DeLury method, and 333,000 t by the non-equilibrium surplus-production method. Of the three estimates, the swept area estimate was likely to be the most reliable because of the more realistic assumptions and reduced uncertainty of parameters in this method. The relative fishing mortality F/FMSY derived from the production model was 0.8-1.2, which was around the appropriate (maximum sustainable yield) fishing level (1.0), even during 1987-1990 when catches were large. The proportional escapement (number of squid alive at the end of the fishing season as a proportion of those that would have been alive had there been no fishing) was 18-64%, with an average of 42%, which was around the management target of 40%, even during this period. Thus, the large-scale driftnet fishery is considered to have been sustainable. Possible adverse effects of the driftnet fishery on food webs in the North Pacific are discussed. © 2006 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.fishres.2006.01.003

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Infant abuse by males has been observed in many pinniped species, but its adaptive significance and defense mechanism remain uncertain. We studied harassment and abduction of pups by nonterritorial male northern fur seals (Callorhinus ursinus) on St. Paul Island, Alaska, from 1993 to 1998. Juvenile, subadult, and adult males entered the breeding area and sniffed, bit, grabbed, or mounted pups. They also abducted pups to other places on land or to sea. Three pup mortalities caused by drowning, skull damage, or separation from the mother leading to emaciation were observed during the study period. Nonterritorial males did not exhibit a preference for the sexes of pups they attacked, and never consumed dead pups. Intrusions of juvenile and subadult males into breeding areas increased in the late breeding season, when harassment and abduction of pups occurred frequently. Frequency of intrusion and harassment of pups by adult nonterritorial males was lower than that by juvenile and subadult males, and did not increase in the late breeding season. On average, each pup was harassed or abducted 3.8 times in a breeding season. Pups changed their behavior to avoid nonterritorial males as pups moved out of the central breeding area in the late breeding season. Territorial males protected pups indirectly through territory defense, but their vigilance against juvenile and subadult males diminished in the late breeding season. Adult females protected their pups against juvenile and subadult males only while they were attending pups within the breeding territories. However, formation of breeding aggregation in rocky habitats may contribute to reducing the risk of harassment of pups by nonterritorial males because it provides pups with protection by territorial males as well as shelters created by irregular terrain. © 2005 American Society of Mammalogists.

DOI： 10.1644/04-MAMM-A-031R2.1

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Language：Japanese   Publisher：The Mammal Society of Japan  

DOI： 10.11238/mammalianscience.45.1

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Authorship：Lead author,　Corresponding author  

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Language：Japanese   Publisher：The Mammal Society of Japan  

DOI： 10.11238/mammalianscience.44.129

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Language：English   Publishing type：Research paper (scientific journal)  

Long-diving marine mammals, such as sperm whales and Baird's beaked whales are frequently missed in line transect sampling even though they are on the trackline. The methods so far developed to estimate the proportion of animals missed on the trackline are complicated or sensitive to model assumptions. A simpler model is developed in the present study. The model requires an estimate of mean surfacing rate that is independent of the line transect survey and does not require any complicated survey design and non-robust parameters, such as scan rate of the binoculars of observers. In addition, it can flexibly take account of systematic heterogeneity using covariates. The abundance is estimated using the Horvitz-Thompson estimator. The simulation test showed that the proposed method is promising.

DOI： 10.1111/j.0919-9268.2003.00743.x

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In conventional line transect theory, it is assumed that all animals on the line are detected. This article introduces an extended and generalized hazard probability model without the need for such an assumption. The proposed method needs a survey design with independent observers having the same visual region and assumes an explicit distinction of simultaneous and delayed duplicates. It can take account of random heterogeneity caused by surfacing behavior as well as systematic heterogeneity by covariate effects. Furthermore, it can be easily extended to cases in which data from incompletely independent observers are available. The abundance estimate is based on the Horvitz-Thompson estimator in unequal detectability sampling scheme. Simulation studies suggest that the proposed method has good performance. The method is applied to a real data set on Antarctic minke whales in the illustration.

DOI： 10.1111/1541-0420.00061

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An archival tag equipped with sensors for temperature, depth and luminous intensity is an excellent method to elucidate behaviour and migration of marine organisms. Herein, what we believe is the first successful archival tag experiment with swordfish in the world is reported. The swordfish, which was harpooned with an archival tag encased in a plastic capsule, was released in July 1999 off the east coast of Japan. The fish was recaptured by a harpoon fishing vessel in June 2000, only 103 km from the tagging location and weighed approximately 120-kg. By comparing the water temperature data of the archival tag with oceanographic data, a cyclic seasonal migration between the food-rich Oyashio cold current area (40-45°N) during summer and the subtropical wintering area (10-20°N) was suggested. During most of the days of observation and for the majority of the time within a day, tagged fish swam in cold water (3-6°C) and deeper than approximately 200 m; at night, fish generally stayed near the warmer surface waters (21-27°C). The greatest swimming depth was approximated to be 900 m, deduced from ambient water temperature data. The swimming depth and behaviour pattern changed in response to the ambient water temperature.

DOI： 10.1071/MF01245

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER TOKYO  

The Ecopath model for the western North Pacific was constructed and some preliminary analyses were carried out in order to examine the usefulness of the model for multi-species management Our Ecopath model consisted of 30 species groups based on the information that is mainly collected from published literature. Some Ecosim simulations showed non-trivial interaction between cetaceans and fishes and relative biomass of some cetaceans and fishes changed dramatically when their present harvest rates were changed in future. Fitting our model to the available abundance indices of some fishes indicated that the vulnerability parameter in the model was likely to be high. Further, additional simple simulation suggested that we could achieve targeted biomass of mackerel by adjusting the future harvest rate of cetaceans in place of that of mackerel. This indicates that multi-species management in the western North Pacific area might bring efficient fishing strategy. However, the results were very sensitive to setting of the vulnerability parameter. Therefore, Ecopath and Ecosim should not be considered as tools for multi-species management until uncertainty of important parameters is properly incorporated into Ecopath/Ecosim and the difference between them and a single-species model becomes dear. Nevertheless, those results from ecosystem models such as Ecopath and Ecosim are suggestive and valuable when they are brought up along with the result of single-species assessment.

DOI： 10.2331/fishsci.68.sup1_154

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Authorship：Lead author,　Corresponding author  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：The Biometric Society of Japan  

The analysis of paired comparison experiments with frequency data such as win-loss records is usually dealt with using the Bradley-Terry model, wherein the number of wins is supposed to have a binomial distribution. This assumption of probability distribution is inappropriate and inconvenient in quantitative analysis with continuous variables such as preference tests of consumers in biology. In this paper, a practical method is proposed to apply the Bradley-Terry model to the repeated pair-comparison experiments with quantitative data. It is obtained by the nonlinear least squares method under the assumption of the additive normal error structure. Some simple methods for the estimation of precision and for the hypothesis testing are also given. An application to the food preference test of a captive northern fur seal suggests the validity and advantage of the method.

DOI： 10.5691/jjb.21.2_1

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Language：Japanese   Publisher：公益社団法人 日本水産学会  

<p>§1. まえがき</p><p>§2. 2002年までの研究</p><p>§3. 日本水産学会85年史の資源管理の研究（2003-2016）</p><p>（白木原国雄）</p><p>§4. まとめ：最近の動向と将来展望</p><p>（岡村 寛）</p>

DOI： 10.2331/suisan.84.S58

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Language：Japanese   Publisher：水産総合研究センター  

編集：水産総合研究センター 中央水産研究所

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Language：Japanese   Publisher：JAPANESE SOC FISHERIES SCIENCE  

DOI： 10.2331/suisan.WA2456-1

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Language：Japanese   Publisher：The Japanese Society of Fisheries Science  

DOI： 10.2331/suisan.WA2456-3

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Language：Japanese   Publisher：The Japanese Society of Fisheries Science  

DOI： 10.2331/suisan.WA2456-1

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Language：Japanese   Publisher：The Japanese Society of Fisheries Science  

DOI： 10.2331/suisan.WA2405

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Language：Japanese   Publisher：The Japanese Society of Fisheries Science  

DOI： 10.2331/suisan.WA2456-4

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Language：Japanese   Publisher：JAPANESE SOC FISHERIES SCIENCE  

DOI： 10.2331/suisan.wa2314-1

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Language：Japanese   Publisher：The Japanese Society of Fisheries Science  

DOI： 10.2331/suisan.WA2314-1

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Language：Japanese   Publishing type：Rapid communication, short report, research note, etc. (scientific journal)   Publisher：The Japanese Society of Fisheries Science  

DOI： 10.2331/suisan.WA2314-6

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Language：Japanese   Publisher：水産研究・教育機構東北区水産研究所資源管理部(八戸庁舎)  

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Language：Japanese   Publisher：水産総合研究センター  

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Language：Japanese   Publisher：水産総合研究センター  

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Language：Japanese   Publisher：The Mammal Society of Japan  

DOI： 10.11238/mammalianscience.49.147

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Language：Japanese   Publisher：水産海洋学会  

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Language：Japanese   Publisher：海洋出版  

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Language：Japanese   Publisher：水産総合研究センター  

多くの鯨類のように、高度回遊性を持ち、飼育の困難な生物の正確な資源状態を知ることは容易ではない。一方で近年、単一種に基づいた生物種の管理の限界が認識され、生態系全体を考慮した資源評価・管理への需要が高まってきている。生態系モデルは一般に多くの不確実性を被るので、生態系を考慮したアプローチでは、各生物の資源状態をできるだけ正確に精度良く把握する必要がある。また、不確実性の大きいデータから効率よく情報を引き出し、生物資源の状態を正しく把握するためには、統計モデルの活用が重要となる。本論文の構成は次の通りである。第1章では、過去の海産哺乳類の資源評価・管理の歴史と現状、および近年の水産資源に対する生態系モデル研究の概要を述べた。第2章では、鯨類資源の分布・系群構造把握のための共変量モデルの開発と北太平洋ミンククジラへの適用を行った。北太平洋ミンククジラの空間的な分布、季節的な変動を推定した結果、複数系群が存在するという証拠は得られなかった。密度の季節変動は、ミンククジラの回遊の様子をよく再現しており、本方法の有効性が確認された。回帰モデルを利用した時空間分布の把握は、他の水産資源の分布・回遊の把握にも有効に働くと考えられ、本方法を広く水産生物の動態の分析に応用することが可能である。第3章では、目視調査線上の見落とし率の補正を含む新しい個体数推定法の開発を行い、シミュレーションや実際のデータへの適用により本方法の有効性を確認した。従来の調査線上の発見確率推定法では、発見したクジラの追跡などの調査デザインの変更や、潜水時間に関する外部データの必要性、情報の不完全な使用、近似尤度の使用などいくつかの問題点があった。そのような問題点を改良・修正することにより、柔軟で一般化した推定量を与える方法を開発した。第4章では、鰭脚類の実験データから、定量的に動物の嗜好性を調べる方法の開発を行った。従来のモデルでは、消費量の情報を直接扱えない、1種類の餌のみが利用される全勝データを扱えないなどの欠点により、検出力の低下、偏りの問題が想定されるが、それらの欠点を解消した方法を開発した。さらにパラメータの精度と嗜好性に関するいくつかの仮説を検定するためのシンプルな方法を提示した。第5章では、生態系モデル・エコパスを三陸生態系に適用し、鯨類と漁業の競合関係の検証を行った。パラメータの設定によっては、競合関係の存在が支持され、パラメータの精度の良い推定、不確実性の取り込みの重要性が確認された。最後に、第6章において、本論文で開発した統計モデルの長所・短所、生態系モデル開発の重要性および将来の展望について議論した。

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Other Link： https://agriknowledge.affrc.go.jp/RN/2010692577

Language：Japanese   Publisher：生物研究社  

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Language：Japanese   Publisher：水産総合研究センター  

本稿では、小標本における標準誤差や信頼区間の推定の問題点とその原因、修正方法、仮説検定への影響について述べる。特にブートストラップ法を小標本に適用した場合の影響は無視できないことがあるため、ブートストラップ法については詳しく検討する。水産分野においては実験や観測から大標本を得ることが実際上不可能で、小標本から推定値を得たり判断を下したりしなければならないことがある。水産分野において特に注意すべき点についても述べる。

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Other Link： https://agriknowledge.affrc.go.jp/RN/2010671193

Language：Japanese   Publisher：水産総合研究センター  

本研究では乗船科学オブザーバー調査によって新たに得られた大西洋と太平洋メカジキ標本を用いて、吻内部の2型の出現頻度が海域間や雌雄間及び体長区分で差異があるかどうか、2型間に遺伝学的な差があるかどうかについて検討するとともに、大西洋の南北標本間で発見された遺伝的差異が長い期間にわたって安定しているかどうかについて解析した結果を報告する。

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Other Link： https://agriknowledge.affrc.go.jp/RN/2010671199

Language：Japanese   Publisher：遠洋水産研究所  

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Other Link： https://agriknowledge.affrc.go.jp/RN/2010580356

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Language：Japanese   Publisher：遠洋水産研究所  

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Other Link： https://agriknowledge.affrc.go.jp/RN/2010560765