Empirical validation of integrated stock assessment models to ensuring risk equivalence: A pathway to resilient fisheries management.

The Precautionary Approach to Fisheries Management requires an assessment of the impact of uncertainty on the risk of achieving management objectives. However, the main quantities, such as spawning stock biomass (SSB) and fish mortality (F), used in management metrics cannot be directly observed. This requires the use of models to provide guidance, for which there are three paradigms: the best assessment, model ensemble, and Management Strategy Evaluation (MSE). It is important to validate the models used to provide advice. In this study, we demonstrate how stock assessment models can be validated using a diagnostic toolbox, with a specific focus on prediction skill. Prediction skill measures the precision of a predicted value, which is unknown to the model, in relation to its observed value. By evaluating the accuracy of model predictions against observed data, prediction skill establishes an objective framework for accepting or rejecting model hypotheses, as well as for assigning weights to models within an ensemble. Our analysis uncovers the limitations of traditional stock assessment methods. Through the quantification of uncertainties and the integration of multiple models, our objective is to improve the reliability of management advice considering the complex interplay of factors that influence the dynamics of fish stocks.

Abundance and potential sources of floating polystyrene foam macro- and microplastics around Japan.

Polystyrene foam is widely used due to its lightweight, impact resistance, and excellent thermal insulation properties. Meanwhile, weak adhesion between beads in polystyrene foam leads to fragmentation, generating a substantial amount of microplastics (<5 mm). Such polystyrene foam debris littered on beaches diminishes the aesthetic value of coastal areas, negatively impacting tourism. Due to its density lower than other plastics, polystyrene foam macroplastics float on the sea surface and, thus, they are significantly influenced by wind drag during oceanic transport. In contrast, polystyrene foam microplastics drifting beneath the sea surface are carried mostly by ocean currents. These properties of polystyrene foam macroplastics and microplastics hinder the elucidation of their transport, distribution, and fate in nature, despite their potential to adversely impact marine ecosystems. To elucidate the generation, transport, and fragmentation processes of polystyrene foam ocean plastics, we conducted concurrent visual observations and surface net towing from seven training vessels around Japan during 2014-2020. Overall, the abundances of polystyrene foam ocean plastics were higher in the Sea of Japan than in the North Pacific south of Japan. The average abundances of polystyrene foam microplastics and macroplastics were 0.33 pieces/m3 and 0.45 pieces/km, respectively, over the entire sea area around Japan. In the Sea of Japan, the peak abundances of polystyrene foam macroplastics occurred in upstream of the Tsushima Current, while the peak for microplastics occurred downstream, suggesting that continuous fragmentation occurred during transport between the two peaks. Backward-in-time particle tracking model experiments suggested that the sources of polystyrene foam macroplastics observed in the Sea of Japan included aquaculture buoys and styrene debris beached around the Tsushima Strait. The present study demonstrated that reducing the release of polystyrene foam aquaculture floats will likely diminish the abundance of ocean plastics in the Sea of Japan.

Hyper-expansion of large DNA segments in the genome of kuruma shrimp, Marsupenaeus japonicus.

BACKGROUND: Higher crustaceans (class Malacostraca) represent the most species-rich and morphologically diverse group of non-insect arthropods and many of its members are commercially important. Although the crustacean DNA sequence information is growing exponentially, little is known about the genome organization of Malacostraca. Here, we constructed a bacterial artificial chromosome (BAC) library and performed BAC-end sequencing to provide genomic information for kuruma shrimp (Marsupenaeus japonicus), one of the most widely cultured species among crustaceans, and found the presence of a redundant sequence in the BAC library. We examined the BAC clone that includes the redundant sequence to further analyze its length, copy number and location in the kuruma shrimp genome. RESULTS: Mj024A04 BAC clone, which includes one redundant sequence, contained 27 putative genes and seemed to display a normal genomic DNA structure. Notably, of the putative genes, 3 genes encode homologous proteins to the inhibitor of apoptosis protein and 7 genes encode homologous proteins to white spot syndrome virus, a virulent pathogen known to affect crustaceans. Colony hybridization and PCR analysis of 381 BAC clones showed that almost half of the BAC clones maintain DNA segments whose sequences are homologous to the representative BAC clone Mj024A04. The Mj024A04 partial sequence was detected multiple times in the kuruma shrimp nuclear genome with a calculated copy number of at least 100. Microsatellites based BAC genotyping clearly showed that Mj024A04 homologous sequences were cloned from at least 48 different chromosomal loci. The absence of micro-syntenic relationships with the available genomic sequences of Daphnia and Drosophila suggests the uniqueness of these fragments in kuruma shrimp from current arthropod genome sequences. CONCLUSIONS: Our results demonstrate that hyper-expansion of large DNA segments took place in the kuruma shrimp genome. Although we analyzed only a part of the duplicated DNA segments, our result suggested that it is difficult to analyze the shrimp genome following normal analytical methodology. Hence, it is necessary to avoid repetitive sequence (such as segmental duplications) when studying the other unique structures in the shrimp genome.

Empirical Bayes inference of pairwise F(ST) and its distribution in the genome.

Populations often have very complex hierarchical structure. Therefore, it is crucial in genetic monitoring and conservation biology to have a reliable estimate of the pattern of population subdivision. F(ST)'s for pairs of sampled localities or subpopulations are crucial statistics for the exploratory analysis of population structures, such as cluster analysis and multidimensional scaling. However, the estimation of F(ST) is not precise enough to reliably estimate the population structure and the extent of heterogeneity. This article proposes an empirical Bayes procedure to estimate locus-specific pairwise F(ST)'s. The posterior mean of the pairwise F(ST) can be interpreted as a shrinkage estimator, which reduces the variance of conventional estimators largely at the expense of a small bias. The global F(ST) of a population generally varies among loci in the genome. Our maximum-likelihood estimates of global F(ST)'s can be used as sufficient statistics to estimate the distribution of F(ST) in the genome. We demonstrate the efficacy and robustness of our model by simulation and by an analysis of the microsatellite allele frequencies of the Pacific herring. The heterogeneity of the global F(ST) in the genome is discussed on the basis of the estimated distribution of the global F(ST) for the herring and examples of human single nucleotide polymorphisms (SNPs).

Simultaneous estimation of mixing rates and genetic drift under successive sampling of genetic markers with application to the mud crab (Scylla paramamosain) in Japan.

In stock enhancement programs, it is important to assess mixing rates of released individuals in stocks. For this purpose, genetic stock identification has been applied. The allele frequencies in a composite population are expressed as a mixture of the allele frequencies in the natural and released populations. The estimation of mixing rates is possible, under successive sampling from the composite population, on the basis of temporal changes in allele frequencies. The allele frequencies in the natural population may be estimated from those of the composite population in the preceding year. However, it should be noted that these frequencies can vary between generations due to genetic drift. In this article, we develop a new method for simultaneous estimation of mixing rates and genetic drift in a stock enhancement program. Numerical simulation shows that our procedure estimates the mixing rate with little bias. Although the genetic drift is underestimated when the amount of information is small, reduction of the bias is possible by analyzing multiple unlinked loci. The method was applied to real data on mud crab stocking, and the result showed a yearly variation in the mixing rate.

An integrated-likelihood method for estimating genetic differentiation between populations.

The aim of this article is to develop an integrated-likelihood (IL) approach to estimate the genetic differentiation between populations. The conventional maximum-likelihood (ML) and pseudolikelihood (PL) methods that use sample counts of alleles may cause severe underestimations of FST, which means overestimations of theta=4Nm, when the number of sampling localities is small. To reduce such bias in the estimation of genetic differentiation, we propose an IL method in which the mean allele frequencies over populations are regarded as nuisance parameters and are eliminated by integration. To maximize the IL function, we have developed two algorithms, a Monte Carlo EM algorithm and a Laplace approximation. Our simulation studies show that the method proposed here outperforms the conventional ML and PL methods in terms of unbiasedness and precision. The IL method was applied to real data for Pacific herring and African elephants.

Isolation and characterization of halophilic lactic acid bacteria isolated from "terasi" shrimp paste: a traditional fermented seafood product in Indonesia.

Lactic acid bacteria from "terasi" shrimp paste, a highly popular fermented seafood in Indonesia were isolated and characterized. Viable cell counts were 10(4) to 10(6) cfu/g on MRS medium. All the isolates were catalase-negative, gram-positive cocci and were able to grow at 15% NaCl. Numerical phenotypic analysis showed that the isolates clustered into one group. However, they could be classified into two types: the Tetragenococcus halophilus group and the T. muriaticus group as revealed by a restriction fragment length polymorphism (RFLP) analysis and sequencing of the 16S rRNA gene. This study is the first to show that both species of Tetragenococcus are distributed in Indonesian fermented foods.

Abundance estimation of diving animals by the double-platform line transect method.

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.