A spatial ecosystem and populations dynamics model (SEAPODYM) – Modeling of tuna and tuna-like populations

An enhanced version of the spatial ecosystem and population dynamics model SEAPODYM is presented to describe spatial dynamics of tuna and tuna-like species in the Pacific Ocean at monthly resolution over 1° grid-boxes. The simulations are driven by a bio-physical environment predicted from a coupled ocean physical–biogeochemical model. This new version of SEAPODYM includes expanded definitions of habitat indices, movements, and natural mortality based on empirical evidences. A thermal habitat of tuna species is derived from an individual heat budget model. The feeding habitat is computed according to the accessibility of tuna predator cohorts to different vertically migrating and non-migrating micronekton (mid-trophic) functional groups. The spawning habitat is based on temperature and the coincidence of spawning fish with presence or absence of predators and food for larvae. The successful larval recruitment is linked to spawning stock biomass. Larvae drift with currents, while immature and adult tuna can move of their own volition, in addition to being advected by currents. A food requirement index is computed to adjust locally the natural mortality of cohorts based on food demand and accessibility to available forage components. Together these mechanisms induce bottom-up and top-down effects, and intra- (i.e. between cohorts) and inter-species interactions. The model is now fully operational for running multi-species, multi-fisheries simulations, and the structure of the model allows a validation from multiple data sources. An application with two tuna species showing different biological characteristics, skipjack (Katsuwonus pelamis) and bigeye (Thunnus obesus), is presented to illustrate the capacity of the model to capture many important features of spatial dynamics of these two different tuna species in the Pacific Ocean. The actual validation is presented in a companion paper describing the approach to have a rigorous mathematical parameter optimization [Senina, I., Sibert, J., Lehodey, P., 2008. Parameter estimation for basin-scale ecosystem-linked population models of large pelagic predators: application to skipjack tuna. Progress in Oceanography]. Once this evaluation and parameterization is complete, it may be possible to use the model for management of tuna stocks in the context of climate and ecosystem variability, and to investigate potential changes due to anthropogenic activities including global warming and fisheries pressures and management scenarios.     

基于捕捞努力量的中西太平洋鲣鱼围网渔业入渔预测分析

中西太平洋是全球主要的鲣鱼（Katsuwonus pelamis）围网作业渔场,渔场极易受到海洋环境的影响,但渔场分布在众多岛国的管辖海域,如何科学指导企业准确入渔是重要的研究课题。本文根据1995-2012年中西太平洋鲣鱼围网捕捞生产统计数据,选取产量最高的22个海区（5°×5°）,结合Niño3.4区海表温度距平值（SSTA）和作业海域表温（SST）,研究中西太平洋鲣鱼围网渔场的空间分布规律,同时,以各海区捕捞努力量（作业次数）所占的百分比为入渔指标,建立基于环境因子的入渔决策模型。研究认为,中西太平洋鲣鱼捕捞努力量在纬度方向上主要分布于5°S~5°N,其累计捕捞努力量占所有作业海区的87.4%,其中以130°~140°E经度范围为最高,其捕捞努力量占22个海区的45.08%。入渔指标与Niño3.4区的SSTA、作业海域SST均符合正态模型（P<0.01）,Niño3.4区的SSTA最适值为0.25℃,作业海域SST最适值在29.5℃左右。对预测和实际排名前十的海域进行统计发现,预测值与实际值基本一致。研究认为,所建立的入渔预测模型可有效指导企业的渔业生产,为提高企业生产效率提供支撑。     

Patterns in the spatial distribution of Peruvian anchovy (Engraulis ringens) revealed by spatially explicit fishing data

Peruvian anchovy (Engraulis ringens) stock abundance is tightly driven by the high and unpredictable variability of the Humboldt Current Ecosystem. Management of the fishery therefore cannot rely on mid- or long-term management policy alone but needs to be adaptive at relatively short time scales. Regular acoustic surveys are performed on the stock at intervals of 2 to 4 times a year, but there is a need for more time continuous monitoring indicators to ensure that management can respond at suitable time scales. Existing literature suggests that spatially explicit data on the location of fishing activities could be used as a proxy for target stock distribution. Spatially explicit commercial fishing data could therefore guide adaptive management decisions at shorter time scales than is possible through scientific stock surveys. In this study we therefore aim to (1) estimate the position of fishing operations for the entire fleet of Peruvian anchovy purse–seiners using the Peruvian satellite vessel monitoring system (VMS), and (2) quantify the extent to which the distribution of purse–seine sets describes anchovy distribution. To estimate fishing set positions from vessel tracks derived from VMS data we developed a methodology based on artificial neural networks (ANN) trained on a sample of fishing trips with known fishing set positions (exact fishing positions are known for approximately 1.5% of the fleet from an at-sea observer program). The ANN correctly identified 83% of the real fishing sets and largely outperformed comparative linear models. This network is then used to forecast fishing operations for those trips where no observers were onboard. To quantify the extent to which fishing set distribution was correlated to stock distribution we compared three metrics describing features of the distributions (the mean distance to the coast, the total area of distribution, and a clustering index) for concomitant acoustic survey observations and fishing set positions identified from VMS. For two of these metrics (mean distance to the coast and clustering index), fishing and survey data were significantly correlated. We conclude that the location of purse–seine fishing sets yields significant and valuable information on the distribution of the Peruvian anchovy stock and ultimately on its vulnerability to the fishery. For example, a high concentration of sets in the near coastal zone could potentially be used as a warning signal of high levels of stock vulnerability and trigger appropriate management measures aimed at reducing fishing effort.     

印度洋鲣鱼围网资源渔场时空变化及其与ENSO的关系

鲣鱼是印度洋重要的金枪鱼种类之一,其资源丰度与海洋环境关系密切。本研究根据1980-2010年印度洋鲣鱼围网生产统计数据以及海洋环境与厄尔尼诺-南方涛动（ENSO）指数等,对印度洋鲣鱼围网资源渔场时空分布,以及厄尔尼诺年和拉尼娜年等不同尺度气候条件下鲣鱼资源渔场时空变动及其与海洋环境因子的关系进行分析。研究结果表明,1980-2010年印度洋鲣鱼围网渔获量基本保持不断增加的趋势,但CUPE值变化幅度较大,最低仅为0.68 t/d（1997年）,最高达到1.58 t/d（2002年）。同时鲣鱼资源丰度（CPUE）与Ni?o3.4区指数存在显著的负相关关系,即厄尔尼诺年,鲣鱼CPUE 随之下降,拉尼娜年,CPUE 随之上升。ENSO现象对鲣鱼渔场时空分布也有显著影响,厄尔尼诺发生时,鲣鱼围网作业渔场重心会向东、向北移动,而拉尼娜年则向西、向南移动。     

A multi‐stock,length‐based assessment model for New Zealand rock lobster (Jasus Edwardsii)

We describe a multi‐stock, length‐based Bayesian assessment model for New Zealand spiny lobster (Jasus edwardsii) fisheries. This model allows simultaneous modelling of two or more stocks with a mixture of common and stock‐specific parameters: recruitment is always stock‐specific, but any other parameter can be specified as either common or stock‐specific. Common parameters are estimated from a wider base than they would be in a single‐stock model. The model's time step is flexible and can be changed during the period being modelled to accommodate better data quality in recent data. Other options include the capacity to estimate movements among stocks, allow density‐dependent growth, and choose among likelihood functions for the various data sets, between finite and instantaneous fishing dynamics and between two forms of selectivity curve.     

Weak and strong constraint data assimilation in the inverse Regional Ocean Modeling System (ROMS): Development and application for a baroclinic coastal upwelling system

We describe the development and preliminary application of the inverse Regional Ocean Modeling System (ROMS), a four dimensional variational (4DVAR) data assimilation system for high-resolution basin-wide and coastal oceanic flows. Inverse ROMS makes use of the recently developed perturbation tangent linear (TL), representer tangent linear (RP) and adjoint (AD) models to implement an indirect representer-based generalized inverse modeling system. This modeling framework is modular. The TL, RP and AD models are used as stand-alone sub-models within the Inverse Ocean Modeling (IOM) system described in [Chua, B.S., Bennett, A.F., 2001. An inverse ocean modeling system. Ocean Modell. 3, 137–165.]. The system allows the assimilation of a wide range of observation types and uses an iterative algorithm to solve nonlinear assimilation problems. The assimilation is performed either under the perfect model assumption (strong constraint) or by also allowing for errors in the model dynamics (weak constraints). For the weak constraint case the TL and RP models are modified to include additional forcing terms on the right hand side of the model equations. These terms are needed to account for errors in the model dynamics.Inverse ROMS is tested in a realistic 3D baroclinic upwelling system with complex bottom topography, characterized by strong mesoscale eddy variability. We assimilate synthetic data for upper ocean (0–450 m) temperatures and currents over a period of 10 days using both a high resolution and a spatially and temporally aliased sampling array. During the assimilation period the flow field undergoes substantial changes from the initial state. This allows the inverse solution to extract the dynamically active information from the synthetic observations and improve the trajectory of the model state beyond the assimilation window. Both the strong and weak constraint assimilation experiments show forecast skill greater than persistence and climatology during the 10–20 days after the last observation is assimilated.Further investigation in the functional form of the model error covariance and in the use of the representer tangent linear model may lead to improvement in the forecast skill.     

Application of the ALE technique for underwater explosion analysis of a submarine liquefied oxygen tank

The design of submarines has continually evolved to improve survivability. Explosions may induce local damage as well as global collapse to a submarine. Therefore, it is important to realistically estimate the possible damage conditions due to underwater explosions in the design stage. The present study applied the Arbitrary Lagrangian–Eulerian (ALE) technique, a fluid–structure interaction approach, to simulate an underwater explosion and investigate the survival capability of a damaged submarine liquefied oxygen tank. The Lagrangian–Eulerian coupling algorithm, the equations of state for explosives and seawater, and the simple calculation method for explosive loading were also reviewed. It is shown that underwater explosion analysis using the ALE technique can accurately evaluate structural damage after attack. This procedure could be applied quantitatively to real structural design.     

Body size–abundance distributions of nano- and micro-phytoplankton guilds in coastal marine ecosystems

This study focuses on body size–abundance distributions of nano- and micro-phytoplankton guilds in coastal marine areas of the Southern Adriatic–Ionian region. The aim of the study was to evaluate the occurrence of common patterns of body size–abundance distributions in relation to physical, chemical and biological environmental forcing factors and to taxonomic composition of phytoplankton guilds. This paper is based on data collected during four oceanographic cruises carried out seasonally along the Southern Apulian coast (Adriatic and Ionian Seas, SE Italy) as a part of the INTERREG II Italy–Greece Program. The study was performed at 21 stations located on 7 transects perpendicular to the coastline, with 3 stations per transect at a distance of 3, 9 and 15 NM from the coastline. At each station, profiles of the major physical features of the water were determined and water samples were collected for phytoplankton and nutrient analysis. Overall, 320 nano- and micro-phytoplankton taxa were identified, 76% of which at species level, with phytoplankton cells ranging in size from 0.008 to 4697.54 ng. Body size–abundance distributions showed some common features: they were relatively invariant (average similarity 65%) with respect to taxonomic composition (average similarity 32%), right skewed (90%), leptokurtic (77%) and log normal (76%). Moreover, abiotic, biotic and spatial ecosystem components accounted for up to 75% of body size–abundance distribution variation. The results of this study suggest that body size–abundance distributions are an intrinsic property of marine phytoplankton communities, emphasising functional dependence on ecological constraints related to trophic factors and intra-guild coexistence relationships.     

A video-based technique for mapping intertidal beach bathymetry

Measuring the location of the shoreline and monitoring foreshore changes through time are core tasks carried out by coastal engineers for a wide range of research, monitoring and design applications. With the advent of digital imaging technology, shore-based video systems provide continuous and automated data collection, encompassing a much greater range of time and spatial scales than were previously possible using field survey methods.A new video-based technique is presented that utilises full-colour image information, which overcomes problems associated with previous grey-scale methods, which work well at steep (reflective) sites, but are less successful at flatter (dissipative) sites. Identification of the shoreline feature is achieved by the automated clustering of sub-aqueous and sub-aerial pixels in ‘Hue–Saturation–Value’ (HSV) colour space, and applying an objective discriminator function to define their boundary (i.e., ‘shoreline’) within a time-series of consecutive geo-referenced images. The elevation corresponding to the detected shoreline features is calculated on the basis of concurrent tide and wave information, which is incorporated in a model that combines the effects of wave set-up and swash, at both incident and infragravity frequencies.Validation of the technique is achieved by comparison with DGPS survey results, to assess the accuracy of the detection and elevation methods both separately and together. The uncertainties associated with the two sub-components of the model tend to compensate for each other. The mean difference between image-based and surveyed shoreline elevations was less than 15 cm along 85% of the 2-km study region, which corresponded to an horizontal offset of 6 m. The application of the intertidal bathymetry mapping technique in support of CZM objectives is briefly illustrated at two sites in The Netherlands and Australia.     

Impacts of Kelvin wave forcing in the Peru Humboldt Current system: Scenarios of spatial reorganizations from physics to fishers

Because climate change challenges the sustainability of important fish populations and the fisheries they support, we need to understand how large scale climatic forcing affects the functioning of marine ecosystems. In the Humboldt Current system (HCS), a main driver of climatic variability is coastally-trapped Kelvin waves (KWs), themselves originating as oceanic equatorial KWs. Here we (i) describe the spatial reorganizations of living organisms in the Humboldt coastal system as affected by oceanic KWs forcing, (ii) quantify the strength of the interactions between the physical and biological component dynamics of the system, (iii) formulate hypotheses on the processes which drive the redistributions of the organisms, and (iv) build scenarios of space occupation in the HCS under varying KW forcing. To address these questions we explore, through bivariate lagged correlations and multivariate statistics, the relationships between time series of oceanic KW amplitude (TAO mooring data and model-resolved baroclinic modes) and coastal Peruvian oceanographic data (SST, coastal upwelled waters extent), anchoveta spatial distribution (mean distance to the coast, spatial concentration of the biomass, mean depth of the schools), and fishing fleet statistics (trip duration, searching duration, number of fishing sets and catch per trip, features of the foraging trajectory as observed by satellite vessel monitoring system). Data sets span all or part of January 1983 to September 2006. The results show that the effects of oceanic KW forcing are significant in all the components of the coastal ecosystem, from oceanography to the behaviour of the top predators – fishers. This result provides evidence for a bottom-up transfer of the behaviours and spatial stucturing through the ecosystem. We propose that contrasting scenarios develop during the passage of upwelling versus downwelling KWs. From a predictive point of view, we show that KW amplitudes observed in the mid-Pacific can be used to forecast which system state will dominate the HCS over the next 2–6 months. Such predictions should be integrated in the Peruvian adaptive fishery management.     

An elastic–viscous–plastic sea ice model formulated on Arakawa B and C grids

The elastic–viscous–plastic (EVP) sea ice rheology has been introduced in the large-scale Louvain-la-Neuve sea-Ice Model, version 2 (LIM2), and its performance has been evaluated. Centred difference versions of the rheology have been implemented on both an Arakawa B grid and a C grid, and their performance have been intercompared in coupled simulations with the Nucleus for European Modelling of the Ocean (NEMO) model. Integrations with both implementations lead to fairly similar results which compare well with observations and with previous LIM simulations. The C grid version, however, offers a number of advantages: (a) easier ice coupling with NEMO, which is itself defined on a C grid; (b) possibility of representing ice transport across one-cell-wide straits and passages; (c) better representation of inertial-plastic compressive waves. For these reasons, we recommend the use of the C grid EVP formulation of the ice dynamics in future LIM applications.     

Euler–Lagrange equations for the spectral element shallow water system

We present the derivation of the discrete Euler–Lagrange equations for an inverse spectral element ocean model based on the shallow water equations. We show that the discrete Euler–Lagrange equations can be obtained from the continuous Euler–Lagrange equations by using a correct combination of the weak and the strong forms of derivatives in the Galerkin integrals, and by changing the order with which elemental assembly and mass averaging are applied in the forward and in the adjoint systems. Our derivation can be extended to obtain an adjoint for any Galerkin finite element and spectral element system.We begin the derivations using a linear wave equation in one dimension. We then apply our technique to a two-dimensional shallow water ocean model and test it on a classic double-gyre problem. The spectral element forward and adjoint ocean models can be used in a variety of inverse applications, ranging from traditional data assimilation and parameter estimation, to the less traditional model sensitivity and stability analyses, and ensemble prediction. Here the Euler–Lagrange equations are solved by an indirect representer algorithm.     

Comparison of nominal and standardized catch per unit effort data in quantifying habitat suitability of skipjack tuna in the equatorial Pacific Ocean

In the western and central Pacific Ocean, upper strata waters exhibit highly dynamic oceanographic features under ENSO variability. This has been proved to be responsible for the dynamic change of both abundance and zonal distribution of skipjack tuna(Katsuwonus pelamis). Although causality has been suggested by researchers using physical–biological interaction models, cumulative evidence needs to be obtained and the tenability of assertion needs to be tested from an ecological habitat perspecti...     

The sequential megafaunal collapse hypothesis: Testing with existing data

Springer et al. [Springer, A.M., Estes, J.A., van Vliet, G.B., Williams, T.M., Doak, D.F., Danner, E.M., Forney, K.A., Pfister, B., 2003. Sequential megafaunal collapse in the North Pacific Ocean: an ongoing legacy of industrial whaling? Proceedings of the National Academy of Sciences 100 (21), 12,223–12,228] hypothesized that great whales were an important prey resource for killer whales, and that the removal of fin and sperm whales by commercial whaling in the region of the Bering Sea/Aleutian Islands (BSAI) in the late 1960s and 1970s led to cascading trophic interactions that caused the sequential decline of populations of harbor seal, northern fur seal, Steller sea lion and northern sea otter. This hypothesis, referred to as the Sequential Megafaunal Collapse (SMC), has stirred considerable interest because of its implication for ecosystem-based management. The SMC has the following assumptions: (1) fin whales and sperm whales were important as prey species in the Bering Sea; (2) the biomass of all large whale species (i.e., North Pacific right, fin, humpback, gray, sperm, minke and bowhead whales) was in decline in the Bering Sea in the 1960s and early 1970s; and (3) pinniped declines in the 1970s and 1980s were sequential. We concluded that the available data are not consistent with the first two assumptions of the SMC. Statistical tests of the timing of the declines do not support the assumption that pinniped declines were sequential. We propose two alternative hypotheses for the declines that are more consistent with the available data. While it is plausible, from energetic arguments, for predation by killer whales to have been an important factor in the declines of one or more of the three populations of pinnipeds and the sea otter population in the BSAI region over the last 30 years, we hypothesize that the declines in pinniped populations in the BSAI can best be understood by invoking a multiple factor hypothesis that includes both bottom–up forcing (as indicated by evidence of nutritional stress in the western Steller sea lion population) and top–down forcing (e.g., predation by killer whales, mortality incidental to commercial fishing, directed harvests). Our second hypothesis is a modification of the top–down forcing mechanism (i.e., killer whale predation on one or more of the pinniped populations and the sea otter population is mediated via the recovery of the eastern North Pacific population of the gray whale). We remain skeptical about the proposed link between commercial whaling on fin and sperm whales, which ended in the mid-1960s, and the observed decline of populations of northern fur seal, harbor seal, and Steller sea lion some 15 years later.     

Physical modeling of untrenched submarine pipeline instability

Wave-induced instability of untrenched pipeline on sandy seabed is a ‘wave–soil–pipeline’ coupling dynamic problem. To explore the mechanism of the pipeline instability, the hydrodynamic loading with U-shaped oscillatory flow tunnel is adopted, which is quite different from the previous experiment system. Based on dimensional analysis, the critical conditions for pipeline instability are investigated by altering pipeline submerged weight, diameter, soil parameters, etc. Based on the experimental results, different linear relationships between Froude number (Fr) and non-dimensional pipeline weight (G) are obtained for two constraint conditions. Moreover, the effects of loading history on the pipeline stability are also studied. Unlike previous experiments, sand scouring during the process of pipe’s losing stability is detected in the present experiments. In addition, the experiment results are compared with the previous experiments, based on Wake II model for the calculation of wave-induced forces upon pipeline. It shows that the results of two kinds of experiments are comparable, but the present experiments provide better physical insight of the wave–soil–pipeline coupling effects.     

Developing an intermediate-complexity projection model for China's fisheries: A case study of small yellow croaker(Larimichthys polyactis) in the Haizhou Bay,China

Projection models are commonly used to evaluate the impacts of fishing. However, previously developed projection tools were not suitable for China's fisheries as they are either overly complex and data-demanding or too simple to reflect the realistic management measures. Herein, an intermediate-complexity projection model was developed that could adequately describe fish population dynamics and account for management measures including mesh size limits, summer closure, and spatial closure. A two-patch operating model was outlined for the projection model and applied to the heavily depleted but commercially important small yellow croaker(Larimichthys polyactis) fishery in the Haizhou Bay, China, as a case study. The model was calibrated to realistically capture the fisheries dynamics with hindcasting. Three simulation scenarios featuring different fishing intensities based on status quo and maximum sustainable yield(MSY) were proposed and evaluated with projections. Stochastic projections were additionally performed to investigate the influence of uncertainty associated with recruitment strengths and the implementation of control targets. It was found that fishing at FMSY level could effectively rebuild the depleted stock biomass, while the stock collapsed rapidly in the status quo scenario. Uncertainty in recruitment and implementation could result in variabilities in management effects; but they did not much alter the management effects of the FMSY scenario. These results indicate that the lack of science-based control targets in fishing mortality or catch limits has hindered the achievement of sustainable fisheries in China. Overall, the presented work highlights that the developed projection model can promote the understanding of the possible consequences of fishing under uncertainty and is applicable to other fisheries in China.     

Numerical simulation of the hydrodynamic behaviour of submerged plane nets in current

The aim of this paper is to investigate the shape and tension distribution of fishing nets in current. A numerical model is developed, based on lumped mass method to simplify the net. The motion equation is set up for each lumped mass. The Runge–Kutta–Verner fifth-order and sixth-order method is used to solve these simultaneous equations, and then the displacement and tension of each lumped mass are obtained. In order to verify the validity of the numerical method, model tests have been carried out. The results by the numerical simulation agree well with the experimental data.     

Beach Wizard: Nearshore bathymetry estimation through assimilation of model computations and remote observations

A data–model assimilation method (called “Beach Wizard”) is presented with which the nearshore subtidal bathymetry can be accurately estimated based on video-derived observations of wave roller dissipation and variation of the intertidal shoreline, and/or radar-derived observations of wave celerity. Using many consecutive images, these observed properties are compared with numerical model results, and through a simple, optimal least-squares estimator approach the estimated bathymetry is adjusted gradually for each image in order to improve the fit between model output and observations. The key advantages of the technique are that it is based on multiple sources of information (i.e., different remote sensors and/or data products), depends on only a few free parameters (to which the model results are insensitive), and shows good skill. Herein, the technique is applied to a synthetic case and two sets of field data from sites at Duck, NC (USA) and Egmond (The Netherlands). The method, which may be extended with observations of other properties from other sources than the three described in this paper, can deliver coastal state information (i.e., simultaneous updates of bathymetry, waves, and currents) with high temporal and spatial resolution and can be used in conjunction with or instead of in-situ measured data.     

The simulation of the geometry of a tuna purse seine under current and drift of purse seiner

It was necessary to obtain a more practical interactive precise model of the three-dimensional (3-D) geometry during purse seine operations considering movements of fishing vessel and details of the sea condition. The changes in the shape of a purse seine from shooting to pursing during pelagic skipjack fishing was recorded in the Southwest Pacific Ocean by photographs of the scanning sonar with in situ measurements of water flow by a current meter. The modeling of 3-D geometry during purse seining was established using finite element methods, as resultant force vector from flow drag, buoyancy, sinking force, tension of pulling or pursing acting on net panels in connection with drift of fishing vessel with time elapsed from the start of shooting to the end of pursing. The simulation results were matched closely by field measurements as a heart-like shape in upper net near floatline and a water-drop shape in purse line following drift of ship towards inside net circle during pursing. This model of a purse seine can be extended to almost any kind of purse seine generating real fishing parameters and to modeling fish capture process.