Inna Senina - Academia.edu (original) (raw)
Papers by Inna Senina
Deep Sea Research Part II: Topical Studies in Oceanography, 2015
Tuna catches represent a major economic and food source in the Pacific Ocean, yet are highly vari... more Tuna catches represent a major economic and food source in the Pacific Ocean, yet are highly variable. This variability in tuna catches remains poorly explained. The relationships between the distributions of tuna and their forage (micronekton) have been mostly derived from model estimates. Observations of micronekton and other mid-trophic level organisms, and their link to regional oceanography, however are scarce and constitute an important gap in our knowledge and understanding of the dynamics of pelagic ecosystems. To fill this gap, we conducted two multidisciplinary cruises (Nectalis1 and Nectalis2) in the New Caledonian Exclusive Economic Zone (EEZ) at the southeastern edge the Coral Sea, in 2011 to characterize the oceanography of the region during the cool (August) and the hot (December) seasons. The physical and biological environments were described by hydrology, nutrients and phytoplankton size structure and biomass. Zooplankton biomass was estimated from net sampling and acoustics and micronecton was estimated from net sampling, the SEAPODYM ecosystem model, a dedicated echosounder and non-dedicated acoustics. Results demonstrated that New Caledonia is located in an oligotrophic area characterized by low nutrient and low primary production which is dominated by a high percentage of picoplankton cyanobacteria Prochlorococcus (>90%). The area is characterized by a large-scale north-south temperature and salinity gradient. The northern area is influenced by the equatorial Warm Pool and the South Pacific Convergence Zone and is characterized by higher temperature, lower salinity, lower primary production and micronekton biomass. The southern area is influenced by the Tasman Sea and is characterized by cooler temperature, higher salinity, higher primary production and micronekton biomass. Interactions between the dynamic oceanography and the complex topography creates a myriad of mesoscale eddies, inducing patchy structures in the frontal area. During the cool season, a tight coupling existed between the ocean dynamics and primary production, while there was a stronger decoupling during the hot season. There was little difference in the composition of mid-trophic level organisms (zooplankton and micronekton) between the two seasons. This may be due to different turnover times and delays in the transmission of primary production to upper trophic levels. Examination of various sampling gears for zooplankton and micronekton showed that net biomass 4 estimates and acoustic-derived estimates compared reasonably well. Estimates of micronekton from net observations and the SEAPODYM model were in the same range. The non-dedicated acoustics adequately reproduced trends observed in zooplankton from nets, but the acoustics could not differentiate between zooplankton and micronekton and absolute biomasses could not be calculated. Understanding the impact of mesoscale features on higher trophic levels will require further investigation and patchiness induced by eddies raises the question of how to best sample highly dynamic areas via sea experiments.
Canadian Journal of Fisheries and Aquatic Sciences, 2019
SEAPODYM is a model developed for investigating spatiotemporal dynamics of fish populations under... more SEAPODYM is a model developed for investigating spatiotemporal dynamics of fish populations under the influence of both fishing and the environment. The model simulates age-structured population dynamics using advection–diffusion–reaction equations describing movement, recruitment, and natural and fishing mortality. The dynamic processes are constrained by environmental data and distributions of prey species. Model parameter estimation using fishing data was implemented earlier based on a maximum likelihood estimation (MLE) approach and adjoint technique. Here, we describe the integration of tagging data into the existing MLE approach with application to skipjack tuna (Katsuwonus pelamis) in the Pacific Ocean. We find that tagging data improve estimates of species habitat parameters and movement rates and hence allow better representation of spatial dynamics of fish population. Due to estimated lower diffusion and higher advection rates, the model predicts less non-observed “cryptic...
Geo-referenced catch and fishing effort data of the bigeye tuna fisheries in the Indian Ocean ove... more Geo-referenced catch and fishing effort data of the bigeye tuna fisheries in the Indian Ocean over 1952-2014 were analysed and standardized to facilitate population dynamics modelling studies. During this sixty-two years historical period of exploitation, many changes occurred both in the fishing techniques and the monitoring of activity. This study includes a series of processing steps used for standardization of spatial resolution, conversion and standardization of catch and effort units, raising of geo-referenced catch into nominal catch level, screening and correction of outliers, and detection of major catchability changes over long time series of fishing data, i.e., the Japanese longline fleet operating in the tropical Indian Ocean. A total of thirty fisheries were finally determined from longline, purse seine and other-gears data sets, from which 10 longline and four purse seine fisheries represented 96% of the whole historical catch. The geo-referenced records consists of catch, fishing effort and associated length frequency samples of all fisheries.
The development of the ecosystem approach and models for the management of ocean marine resources... more The development of the ecosystem approach and models for the management of ocean marine resources requires easy access to standard validated datasets of historical catch data for the main exploited species, together with the model estimates achieved from these data, allowing models inter-comparison and evaluation of model skills. North Atlantic albacore tuna is exploited all year round by longline and in summer and autumn by surface fisheries and fishery statistics compiled by the International Commission for the Conservation of Atlantic Tunas (ICCAT). Catch and effort with geographical coordinates at monthly spatial resolution of 1° or 5° squares were extracted for this species with a careful definition of fisheries and data screening. Length frequencies of catch were also extracted according to the definition of fisheries for the period 1956-2010. Using these data, an application of the spatial ecosystem and population dynamics model (SEAPODYM) was developed for the North Atlantic albacore population and fisheries and provided the first spatially explicit estimate of albacore density in the North Atlantic by life stage. These densities by life stage (larval recruits, young immature fish adult mature fish and total biomass) are provided in gridded file (Netcdf) at resolution of 2° x 2° x month.
Climate Change Impacts on Fisheries and Aquaculture, 2017
In the Pacific Islands region, fisheries and aquaculture make vital contributions to economic dev... more In the Pacific Islands region, fisheries and aquaculture make vital contributions to economic development, government revenue, food security and livelihoods. Climate change is expected to have profound effects on the status and distribution of coastal and oceanic habitats, the fish and invertebrates they support and, as a result, the productivity of fisheries and aquaculture. In particular, declines in the productivity of demersal and invertebrate coastal fisheries, and more eastward distribution of tuna, are expected to present the greatest challenges for reef-dependent communities and economies. Some aquaculture commodities, such as species with calcareous shells, will also be impacted by climate change and ocean acidification. Based on preliminary tuna distribution modeling, Kiribati, Tuvalu, Tokelau, Cook Islands and French Polynesia are likely to have future opportunities to increase access fees from foreign fishing vessels and gain further benefits through greater engagement in the value chain. However, the progressive eastward shift in skipjack tuna could have some negative effects on the contributions of tuna fishing to government revenue, and tuna processing to GDP, for nations in the western Pacific. Climate change also has significant implications for food security and livelihoods. The projected decreases in coastal fisheries production will widen the gap between fish available for growing human populations and sustainable harvests, with shortages expected in some Pacific nations by 2035. There will also be a need to diversify livelihoods among fisheries and aquaculture operations in the region as some are negatively affected, and others favored, by global warming and ocean acidification. In some cases, building the resilience of coastal communities to climate change will involve reducing dependence on marine resources.
Progress in Oceanography, 2018
The distribution of marine species is often modeled using Eulerian approaches, in which changes t... more The distribution of marine species is often modeled using Eulerian approaches, in which changes to population density or abundance are calculated at fixed locations in space. Conversely, Lagrangian, or individual-based, models simulate the movement of individual particles moving in continuous space, with broader-scale patterns such as distribution being an emergent property of many, potentially adaptive, individuals. These models offer advantages in examining dynamics across spatiotemporal scales and making comparisons with observations from individual-scale data. Here, we introduce and describe such a model, the Individual-based Kinesis, Advection and Movement of Ocean ANimAls model (Ikamoana), which we use to replicate the movement processes of an existing Eulerian model for marine predators (the Spatial Ecosystem and Population Dynamics Model, SEAPODYM). Ikamoana simulates the movement of either individual or groups of animals by physical ocean currents, habitat-dependent stochastic movements (kinesis), and taxis movements representing active searching behaviours. Applying our model to Pacific skipjack tuna (Katsuwonus pelamis), we show that it accurately replicates the evolution of density distribution simulated by SEAPODYM with low time-mean error and a spatial correlation of density that exceeds 0.96 at all times. We demonstrate how the Lagrangian approach permits easy tracking of individuals' trajectories for examining connectivity between different regions, and show how the model can provide independent estimates of transfer rates between commonly used assessment regions. In particular, we find that retention rates in most assessment regions are considerably smaller (up to a factor of 2) than those estimated by this population of skipjack's primary assessment model. Moreover, these rates are sensitive to ocean state (e.g. El Nino vs La Nina) and so assuming fixed transfer rates between regions may lead to spurious stock estimates. A novel feature of the Lagrangian approach is that individual schools can be tracked through time, and we demonstrate that movement between two assessment regions at broad temporal scales includes extended transits through other regions at finer-scales. Finally, we discuss the utility of this modeling framework for the management of marine reserves, designing effective monitoring programmes, and exploring hypotheses regarding the behaviour of hard-to-observe oceanic animals.
Earth System Science Data Discussions, 2016
Geo-referenced catch and fishing effort data of the bigeye tuna fisheries in the Indian Ocean ov... more Geo-referenced catch and fishing effort data of the bigeye tuna fisheries in the Indian Ocean over 1952–2014 were analysed and standardized to facilitate population dynamics modelling studies. During this sixty-two years historical period of exploitation, many changes occurred both in the fishing techniques and the monitoring of activity. This study includes a series of processing steps used for standardization of spatial resolution, conversion and standardization of catch and effort units, raising of geo-referenced catch into nominal catch level, screening and correction of outliers, and detection of major catchability changes over long time series of fishing data, i.e., the Japanese longline fleet operating in the tropical Indian Ocean. A total of thirty fisheries were finally determined from longline, purse seine and other-gears data sets, from which 10 longline and four purse seine fisheries represented 96 % of the whole historical catch. The geo-referenced records...
Collecte Localisation Satellites, Jan 28, 2014
The development of the ecosystem approach and models for the management of ocean marine resources... more The development of the ecosystem approach and models for the management of ocean marine resources requires easy access to standard validated datasets of historical catch data for the main exploited species. They are used to measure the impact of biomass removal by fisheries and to evaluate the models skills, while the use of standard dataset facilitates models inter-comparison. North Atlantic albacore tuna is exploited all year round by longline and in summer and autumn by surface fisheries and fishery statistics compiled by the International Commission for the Conservation of Atlantic Tunas (ICCAT). Catch and effort with geographical coordinates at monthly spatial resolution of 1° or 5° squares were extracted for this species with a careful definition of fisheries and data screening. In total, thirteen fisheries were defined for the period 1956-2010, with fishing gears longline, troll, mid-water trawl and bait fishing. However, the spatialized catch effort data available in ICCAT database represent a fraction of the entire total catch. Length frequencies of catch were also extracted according to the definition of fisheries above for the period 1956-2010 with a quarterly temporal resolution and spatial resolutions varying from 1°x 1° to 10°x 20°. The resolution used to measure the fish also varies with size-bins of 1, 2 or 5 cm (Fork Length). The screening of data allowed detecting inconsistencies with a relatively large number of samples larger than 150 cm while all studies on the growth of albacore suggest that fish rarely grow up over 130 cm. Therefore, a threshold value of 130 cm has been arbitrarily fixed and all length frequency data above this value removed from the original data set.
Zhurnal obshcheĭ biologii
The authors present an approach for explicit modeling of spatio-temporal dynamics of predator-pre... more The authors present an approach for explicit modeling of spatio-temporal dynamics of predator-prey community. This approach is based on a reaction-diffusion-adjection PD (prey dependent) system. Local kinetics of population is determined by logistic reproduction function of prey, constant natural mortality of predator and Holling type 2 trophic function. Searching behavior of predator is described by the advective term in predator balance equation assuming the predator acceleration to be proportional to the prey density gradient. The model was studied with zero-flux boundary conditions. The influence of predator searching activity on the community dynamics, in particular, on the emergence of spatial heterogeneity, has been investigated by linear analysis and numerical simulations. It has been shown how searching activity may effect the persistence of species, stabilizing predator-prey interactions at very low level of pest density. It has been demonstrated that obtaining of such dyn...
Canadian Journal of Fisheries and Aquatic Sciences, 2015
An application of the Spatial Ecosystem And POpulation DYnamics Model (SEAPODYM) is developed for... more An application of the Spatial Ecosystem And POpulation DYnamics Model (SEAPODYM) is developed for the North Atlantic albacore (Thunnus alalunga) population. We investigate the spatiotemporal dynamics of this species, distinguishing the influences of environment and international fishing. Incorporating historical data (1960–2008), a maximum likelihood approach allows the estimation of biological parameters (thermal and oxygen tolerance) and stock spatial distribution varying over time. Juvenile albacore are predicted in warm surface waters, whereas adults inhabit cooler and deeper waters. Positive correlations between juveniles and tropical large-scale climate indices highlight the importance of environmental drivers when estimating stock recruitment biology and spatiotemporal distribution. A methodology is proposed to use SEAPODYM outputs to estimate stock abundance and maximum sustainable yield (MSY). MSY is computed taking into account the spatial dynamics of the species and the e...
Deep Sea Research Part II: Topical Studies in Oceanography, 2015
The potential impact of climate change under the IPCC AR4-A2 scenario (close to the AR5-RCP8.5 sc... more The potential impact of climate change under the IPCC AR4-A2 scenario (close to the AR5-RCP8.5 scenario) on south Pacific albacore tuna (Thunnus alalunga) is simulated with the Spatial Ecosystem And Population Dynamics Model (SEAPODYM) and environmental forcing variables provided by the Earth Climate model IPSL-CM4. Parameters controlling the habitat and dynamics of the population were optimized by fitting the model, using maximum likelihood, to a complete fishing data set for the historical fishing period since 1950. Albacore undertake clear seasonal migrations between feeding and spawning grounds, as evidenced by seasonal catch and size composition changes. This seasonality was well predicted by the SEAPODYM albacore simulations. The total biomass estimate of south Pacific albacore was predicted to have decreased from $ 1.8 million tonnes (Mt) at the beginning of industrial fisheries in 1950 to 1.25 Mt in 2006, in good agreement with an independent estimate from stock assessment analysis. A simulation without fishing indicated an equivalent contribution of environmental variability and fishing to the historical decrease of the stock biomass. The parameterized SEAPODYM model was used to project the dynamics of the population until the end of the 21st century with an average fishing effort based on recent years. Under this fishing and climate change scenario, the population was predicted to decrease and to stabilize after 2035 just below 0.8 Mt, i.e., 55% below the initial biomass of 1960. After 2080 however, the trend was reversed when a new spawning ground emerged in the north Tasman Sea. A test simulation highlighted the sensitivity of the model results to projected dissolved oxygen concentration for which there is large uncertainty in the tropical region. A second test simulation showed that genetic selection favouring albacore with preferences for higher optimal ambient spawning temperature would maintain a reduced level of spawning in current tropical spawning areas, suppress the emergence of an area of spawning in the north Tasman Sea and therefore keep stock abundance at low 2035 levels.
ICES Journal of Marine Science, 2014
In the pelagic foodweb, micronekton at the mid-trophic level (MTL) are one of the lesser known co... more In the pelagic foodweb, micronekton at the mid-trophic level (MTL) are one of the lesser known components of the ocean ecosystem despite being a major driver of the spatial dynamics of their predators, of which many are exploited species (e.g. tunas). The Spatial Ecosystem and Population Dynamics Model is one modelling approach that includes a representation of the spatial dynamics of several epi- and mesopelagic MTL functional groups. The dynamics of these groups are driven by physical (temperature and currents) and biogeochemical (primary production, euphotic depth) variables. A key issue to address is the parameterization of the energy transfer from the primary production to these functional groups. We present a method using in situ acoustic data to estimate the parameters with a maximum likelihood estimation approach. A series of twin experiments conducted to test the behaviour of the model suggested that in the ideal case, that is, with an environmental forcing perfectly simula...
Nature Climate Change, 2013
Pacific Island countries have an extraordinary dependence on fisheries and aquaculture. Maintaini... more Pacific Island countries have an extraordinary dependence on fisheries and aquaculture. Maintaining the benefits from the sector is a difficult task, now made more complex by climate change. Here we report how changes to the atmosphere-ocean are likely to affect the food webs, habitats and stocks underpinning fisheries and aquaculture across the region. We found winners and losers-tuna are expected to be more abundant in the east and freshwater aquaculture and fisheries are likely to be more productive. Conversely, coral reef fisheries could decrease by 20% by 2050 and coastal aquaculture may be less efficient. We demonstrate how the economic and social implications can be addressed within the sector-tuna and freshwater aquaculture can help support growing populations as coral reefs, coastal fisheries and mariculture decline.
... Melanie Abecassis 1 , Patrick Lehodey 2 , Inna Senina 2 , Jeffrey Polovina 3 , ... Current es... more ... Melanie Abecassis 1 , Patrick Lehodey 2 , Inna Senina 2 , Jeffrey Polovina 3 , ... Current estimates of the parameters are presented in Table 2. As a result of the lack of information on gear for all fisheries other than the Hawaii-based ones, a number of parameters had to be fixed ...
Progress in Oceanography, 2008
An enhanced version of the spatial ecosystem and population dynamics model SEAPODYM is presented ... more 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°g rid-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 [
Progress in Oceanography, 2008
A Spatial Ecosystem and Population Dynamic Model (SEAPODYM) is used in a data assimilation study ... more A Spatial Ecosystem and Population Dynamic Model (SEAPODYM) is used in a data assimilation study aiming to estimate model parameters that describe dynamics of Pacific skipjack tuna population on ocean-based scale. The model based on advection-diffusion-reaction equations explicitly predicts spatial dynamics of large pelagic predators, while taking into account data on several mid-trophic level components, oceanic primary productivity and physical environment. In order to improve its quantitative ability, the model was parameterized through assimilation with commercial fisheries data, and optimization was carried out using maximum likelihood estimation approach. To address the optimization task we implemented an adjoint technique to obtain an exact, analytical evaluation of the likelihood gradient. We conducted a series of computer experiments in order to (i) determine model sensitivity with respect to variable parameters and, hence, investigate their observability; (ii) estimate observable parameters and their errors; and (iii) justify the reliability of the computed solution. Parameters describing recruitment, movement, habitat preferences, natural and fishing mortality of skipjack population were analysed and estimated. Results of the study suggest that SEAPODYM with achieved parameterization scheme can help to investigate the impact of fishing under various management scenarios, and also conduct forecasts of a given species stock and spatial dynamics in a context of environmental and climate changes.
Progress in Oceanography, 2010
The modeling of mid-trophic organisms of the pelagic ecosystem is a critical step in linking the ... more The modeling of mid-trophic organisms of the pelagic ecosystem is a critical step in linking the coupled physical-biogeochemical models to population dynamics of large pelagic predators. Here, we provide an example of a modeling approach with definitions of several pelagic mid-trophic functional groups. This application includes six different groups characterized by their vertical behavior, i.e., occurrence of diel migration between epipelagic, mesopelagic and bathypelagic layers. Parameterization of the dynamics of these components is based on a temperature-linked time development relationship. Estimated parameters of this relationship are close to those predicted by a model based on a theoretical description of the allocation of metabolic energy at the cellular level, and that predicts a species metabolic rate in terms of its body mass and temperature. Then, a simple energy transfer from primary production is used, justified by the existence of constant slopes in log-log biomass size spectrum relationships. Recruitment, ageing, mortality and passive transport with horizontal currents, taking into account vertical behavior of organisms, are modeled by a system of advection-diffusionreaction equations. Temperature and currents averaged in each vertical layer are provided independently by an Ocean General Circulation Model and used to drive the mid-trophic level (MTL) model. Simulation outputs are presented for the tropical Pacific Ocean to illustrate how different temperature and oceanic circulation conditions result in spatial and temporal lags between regions of high primary production and regions of aggregation of mid-trophic biomass. Predicted biomasses are compared against available data. Data requirements to evaluate outputs of these types of models are discussed, as well as the prospects that they offer both for ecosystem models of lower and upper trophic levels.
Deep Sea Research Part II: Topical Studies in Oceanography, 2015
Tuna catches represent a major economic and food source in the Pacific Ocean, yet are highly vari... more Tuna catches represent a major economic and food source in the Pacific Ocean, yet are highly variable. This variability in tuna catches remains poorly explained. The relationships between the distributions of tuna and their forage (micronekton) have been mostly derived from model estimates. Observations of micronekton and other mid-trophic level organisms, and their link to regional oceanography, however are scarce and constitute an important gap in our knowledge and understanding of the dynamics of pelagic ecosystems. To fill this gap, we conducted two multidisciplinary cruises (Nectalis1 and Nectalis2) in the New Caledonian Exclusive Economic Zone (EEZ) at the southeastern edge the Coral Sea, in 2011 to characterize the oceanography of the region during the cool (August) and the hot (December) seasons. The physical and biological environments were described by hydrology, nutrients and phytoplankton size structure and biomass. Zooplankton biomass was estimated from net sampling and acoustics and micronecton was estimated from net sampling, the SEAPODYM ecosystem model, a dedicated echosounder and non-dedicated acoustics. Results demonstrated that New Caledonia is located in an oligotrophic area characterized by low nutrient and low primary production which is dominated by a high percentage of picoplankton cyanobacteria Prochlorococcus (>90%). The area is characterized by a large-scale north-south temperature and salinity gradient. The northern area is influenced by the equatorial Warm Pool and the South Pacific Convergence Zone and is characterized by higher temperature, lower salinity, lower primary production and micronekton biomass. The southern area is influenced by the Tasman Sea and is characterized by cooler temperature, higher salinity, higher primary production and micronekton biomass. Interactions between the dynamic oceanography and the complex topography creates a myriad of mesoscale eddies, inducing patchy structures in the frontal area. During the cool season, a tight coupling existed between the ocean dynamics and primary production, while there was a stronger decoupling during the hot season. There was little difference in the composition of mid-trophic level organisms (zooplankton and micronekton) between the two seasons. This may be due to different turnover times and delays in the transmission of primary production to upper trophic levels. Examination of various sampling gears for zooplankton and micronekton showed that net biomass 4 estimates and acoustic-derived estimates compared reasonably well. Estimates of micronekton from net observations and the SEAPODYM model were in the same range. The non-dedicated acoustics adequately reproduced trends observed in zooplankton from nets, but the acoustics could not differentiate between zooplankton and micronekton and absolute biomasses could not be calculated. Understanding the impact of mesoscale features on higher trophic levels will require further investigation and patchiness induced by eddies raises the question of how to best sample highly dynamic areas via sea experiments.
Canadian Journal of Fisheries and Aquatic Sciences, 2019
SEAPODYM is a model developed for investigating spatiotemporal dynamics of fish populations under... more SEAPODYM is a model developed for investigating spatiotemporal dynamics of fish populations under the influence of both fishing and the environment. The model simulates age-structured population dynamics using advection–diffusion–reaction equations describing movement, recruitment, and natural and fishing mortality. The dynamic processes are constrained by environmental data and distributions of prey species. Model parameter estimation using fishing data was implemented earlier based on a maximum likelihood estimation (MLE) approach and adjoint technique. Here, we describe the integration of tagging data into the existing MLE approach with application to skipjack tuna (Katsuwonus pelamis) in the Pacific Ocean. We find that tagging data improve estimates of species habitat parameters and movement rates and hence allow better representation of spatial dynamics of fish population. Due to estimated lower diffusion and higher advection rates, the model predicts less non-observed “cryptic...
Geo-referenced catch and fishing effort data of the bigeye tuna fisheries in the Indian Ocean ove... more Geo-referenced catch and fishing effort data of the bigeye tuna fisheries in the Indian Ocean over 1952-2014 were analysed and standardized to facilitate population dynamics modelling studies. During this sixty-two years historical period of exploitation, many changes occurred both in the fishing techniques and the monitoring of activity. This study includes a series of processing steps used for standardization of spatial resolution, conversion and standardization of catch and effort units, raising of geo-referenced catch into nominal catch level, screening and correction of outliers, and detection of major catchability changes over long time series of fishing data, i.e., the Japanese longline fleet operating in the tropical Indian Ocean. A total of thirty fisheries were finally determined from longline, purse seine and other-gears data sets, from which 10 longline and four purse seine fisheries represented 96% of the whole historical catch. The geo-referenced records consists of catch, fishing effort and associated length frequency samples of all fisheries.
The development of the ecosystem approach and models for the management of ocean marine resources... more The development of the ecosystem approach and models for the management of ocean marine resources requires easy access to standard validated datasets of historical catch data for the main exploited species, together with the model estimates achieved from these data, allowing models inter-comparison and evaluation of model skills. North Atlantic albacore tuna is exploited all year round by longline and in summer and autumn by surface fisheries and fishery statistics compiled by the International Commission for the Conservation of Atlantic Tunas (ICCAT). Catch and effort with geographical coordinates at monthly spatial resolution of 1° or 5° squares were extracted for this species with a careful definition of fisheries and data screening. Length frequencies of catch were also extracted according to the definition of fisheries for the period 1956-2010. Using these data, an application of the spatial ecosystem and population dynamics model (SEAPODYM) was developed for the North Atlantic albacore population and fisheries and provided the first spatially explicit estimate of albacore density in the North Atlantic by life stage. These densities by life stage (larval recruits, young immature fish adult mature fish and total biomass) are provided in gridded file (Netcdf) at resolution of 2° x 2° x month.
Climate Change Impacts on Fisheries and Aquaculture, 2017
In the Pacific Islands region, fisheries and aquaculture make vital contributions to economic dev... more In the Pacific Islands region, fisheries and aquaculture make vital contributions to economic development, government revenue, food security and livelihoods. Climate change is expected to have profound effects on the status and distribution of coastal and oceanic habitats, the fish and invertebrates they support and, as a result, the productivity of fisheries and aquaculture. In particular, declines in the productivity of demersal and invertebrate coastal fisheries, and more eastward distribution of tuna, are expected to present the greatest challenges for reef-dependent communities and economies. Some aquaculture commodities, such as species with calcareous shells, will also be impacted by climate change and ocean acidification. Based on preliminary tuna distribution modeling, Kiribati, Tuvalu, Tokelau, Cook Islands and French Polynesia are likely to have future opportunities to increase access fees from foreign fishing vessels and gain further benefits through greater engagement in the value chain. However, the progressive eastward shift in skipjack tuna could have some negative effects on the contributions of tuna fishing to government revenue, and tuna processing to GDP, for nations in the western Pacific. Climate change also has significant implications for food security and livelihoods. The projected decreases in coastal fisheries production will widen the gap between fish available for growing human populations and sustainable harvests, with shortages expected in some Pacific nations by 2035. There will also be a need to diversify livelihoods among fisheries and aquaculture operations in the region as some are negatively affected, and others favored, by global warming and ocean acidification. In some cases, building the resilience of coastal communities to climate change will involve reducing dependence on marine resources.
Progress in Oceanography, 2018
The distribution of marine species is often modeled using Eulerian approaches, in which changes t... more The distribution of marine species is often modeled using Eulerian approaches, in which changes to population density or abundance are calculated at fixed locations in space. Conversely, Lagrangian, or individual-based, models simulate the movement of individual particles moving in continuous space, with broader-scale patterns such as distribution being an emergent property of many, potentially adaptive, individuals. These models offer advantages in examining dynamics across spatiotemporal scales and making comparisons with observations from individual-scale data. Here, we introduce and describe such a model, the Individual-based Kinesis, Advection and Movement of Ocean ANimAls model (Ikamoana), which we use to replicate the movement processes of an existing Eulerian model for marine predators (the Spatial Ecosystem and Population Dynamics Model, SEAPODYM). Ikamoana simulates the movement of either individual or groups of animals by physical ocean currents, habitat-dependent stochastic movements (kinesis), and taxis movements representing active searching behaviours. Applying our model to Pacific skipjack tuna (Katsuwonus pelamis), we show that it accurately replicates the evolution of density distribution simulated by SEAPODYM with low time-mean error and a spatial correlation of density that exceeds 0.96 at all times. We demonstrate how the Lagrangian approach permits easy tracking of individuals' trajectories for examining connectivity between different regions, and show how the model can provide independent estimates of transfer rates between commonly used assessment regions. In particular, we find that retention rates in most assessment regions are considerably smaller (up to a factor of 2) than those estimated by this population of skipjack's primary assessment model. Moreover, these rates are sensitive to ocean state (e.g. El Nino vs La Nina) and so assuming fixed transfer rates between regions may lead to spurious stock estimates. A novel feature of the Lagrangian approach is that individual schools can be tracked through time, and we demonstrate that movement between two assessment regions at broad temporal scales includes extended transits through other regions at finer-scales. Finally, we discuss the utility of this modeling framework for the management of marine reserves, designing effective monitoring programmes, and exploring hypotheses regarding the behaviour of hard-to-observe oceanic animals.
Earth System Science Data Discussions, 2016
Geo-referenced catch and fishing effort data of the bigeye tuna fisheries in the Indian Ocean ov... more Geo-referenced catch and fishing effort data of the bigeye tuna fisheries in the Indian Ocean over 1952–2014 were analysed and standardized to facilitate population dynamics modelling studies. During this sixty-two years historical period of exploitation, many changes occurred both in the fishing techniques and the monitoring of activity. This study includes a series of processing steps used for standardization of spatial resolution, conversion and standardization of catch and effort units, raising of geo-referenced catch into nominal catch level, screening and correction of outliers, and detection of major catchability changes over long time series of fishing data, i.e., the Japanese longline fleet operating in the tropical Indian Ocean. A total of thirty fisheries were finally determined from longline, purse seine and other-gears data sets, from which 10 longline and four purse seine fisheries represented 96 % of the whole historical catch. The geo-referenced records...
Collecte Localisation Satellites, Jan 28, 2014
The development of the ecosystem approach and models for the management of ocean marine resources... more The development of the ecosystem approach and models for the management of ocean marine resources requires easy access to standard validated datasets of historical catch data for the main exploited species. They are used to measure the impact of biomass removal by fisheries and to evaluate the models skills, while the use of standard dataset facilitates models inter-comparison. North Atlantic albacore tuna is exploited all year round by longline and in summer and autumn by surface fisheries and fishery statistics compiled by the International Commission for the Conservation of Atlantic Tunas (ICCAT). Catch and effort with geographical coordinates at monthly spatial resolution of 1° or 5° squares were extracted for this species with a careful definition of fisheries and data screening. In total, thirteen fisheries were defined for the period 1956-2010, with fishing gears longline, troll, mid-water trawl and bait fishing. However, the spatialized catch effort data available in ICCAT database represent a fraction of the entire total catch. Length frequencies of catch were also extracted according to the definition of fisheries above for the period 1956-2010 with a quarterly temporal resolution and spatial resolutions varying from 1°x 1° to 10°x 20°. The resolution used to measure the fish also varies with size-bins of 1, 2 or 5 cm (Fork Length). The screening of data allowed detecting inconsistencies with a relatively large number of samples larger than 150 cm while all studies on the growth of albacore suggest that fish rarely grow up over 130 cm. Therefore, a threshold value of 130 cm has been arbitrarily fixed and all length frequency data above this value removed from the original data set.
Zhurnal obshcheĭ biologii
The authors present an approach for explicit modeling of spatio-temporal dynamics of predator-pre... more The authors present an approach for explicit modeling of spatio-temporal dynamics of predator-prey community. This approach is based on a reaction-diffusion-adjection PD (prey dependent) system. Local kinetics of population is determined by logistic reproduction function of prey, constant natural mortality of predator and Holling type 2 trophic function. Searching behavior of predator is described by the advective term in predator balance equation assuming the predator acceleration to be proportional to the prey density gradient. The model was studied with zero-flux boundary conditions. The influence of predator searching activity on the community dynamics, in particular, on the emergence of spatial heterogeneity, has been investigated by linear analysis and numerical simulations. It has been shown how searching activity may effect the persistence of species, stabilizing predator-prey interactions at very low level of pest density. It has been demonstrated that obtaining of such dyn...
Canadian Journal of Fisheries and Aquatic Sciences, 2015
An application of the Spatial Ecosystem And POpulation DYnamics Model (SEAPODYM) is developed for... more An application of the Spatial Ecosystem And POpulation DYnamics Model (SEAPODYM) is developed for the North Atlantic albacore (Thunnus alalunga) population. We investigate the spatiotemporal dynamics of this species, distinguishing the influences of environment and international fishing. Incorporating historical data (1960–2008), a maximum likelihood approach allows the estimation of biological parameters (thermal and oxygen tolerance) and stock spatial distribution varying over time. Juvenile albacore are predicted in warm surface waters, whereas adults inhabit cooler and deeper waters. Positive correlations between juveniles and tropical large-scale climate indices highlight the importance of environmental drivers when estimating stock recruitment biology and spatiotemporal distribution. A methodology is proposed to use SEAPODYM outputs to estimate stock abundance and maximum sustainable yield (MSY). MSY is computed taking into account the spatial dynamics of the species and the e...
Deep Sea Research Part II: Topical Studies in Oceanography, 2015
The potential impact of climate change under the IPCC AR4-A2 scenario (close to the AR5-RCP8.5 sc... more The potential impact of climate change under the IPCC AR4-A2 scenario (close to the AR5-RCP8.5 scenario) on south Pacific albacore tuna (Thunnus alalunga) is simulated with the Spatial Ecosystem And Population Dynamics Model (SEAPODYM) and environmental forcing variables provided by the Earth Climate model IPSL-CM4. Parameters controlling the habitat and dynamics of the population were optimized by fitting the model, using maximum likelihood, to a complete fishing data set for the historical fishing period since 1950. Albacore undertake clear seasonal migrations between feeding and spawning grounds, as evidenced by seasonal catch and size composition changes. This seasonality was well predicted by the SEAPODYM albacore simulations. The total biomass estimate of south Pacific albacore was predicted to have decreased from $ 1.8 million tonnes (Mt) at the beginning of industrial fisheries in 1950 to 1.25 Mt in 2006, in good agreement with an independent estimate from stock assessment analysis. A simulation without fishing indicated an equivalent contribution of environmental variability and fishing to the historical decrease of the stock biomass. The parameterized SEAPODYM model was used to project the dynamics of the population until the end of the 21st century with an average fishing effort based on recent years. Under this fishing and climate change scenario, the population was predicted to decrease and to stabilize after 2035 just below 0.8 Mt, i.e., 55% below the initial biomass of 1960. After 2080 however, the trend was reversed when a new spawning ground emerged in the north Tasman Sea. A test simulation highlighted the sensitivity of the model results to projected dissolved oxygen concentration for which there is large uncertainty in the tropical region. A second test simulation showed that genetic selection favouring albacore with preferences for higher optimal ambient spawning temperature would maintain a reduced level of spawning in current tropical spawning areas, suppress the emergence of an area of spawning in the north Tasman Sea and therefore keep stock abundance at low 2035 levels.
ICES Journal of Marine Science, 2014
In the pelagic foodweb, micronekton at the mid-trophic level (MTL) are one of the lesser known co... more In the pelagic foodweb, micronekton at the mid-trophic level (MTL) are one of the lesser known components of the ocean ecosystem despite being a major driver of the spatial dynamics of their predators, of which many are exploited species (e.g. tunas). The Spatial Ecosystem and Population Dynamics Model is one modelling approach that includes a representation of the spatial dynamics of several epi- and mesopelagic MTL functional groups. The dynamics of these groups are driven by physical (temperature and currents) and biogeochemical (primary production, euphotic depth) variables. A key issue to address is the parameterization of the energy transfer from the primary production to these functional groups. We present a method using in situ acoustic data to estimate the parameters with a maximum likelihood estimation approach. A series of twin experiments conducted to test the behaviour of the model suggested that in the ideal case, that is, with an environmental forcing perfectly simula...
Nature Climate Change, 2013
Pacific Island countries have an extraordinary dependence on fisheries and aquaculture. Maintaini... more Pacific Island countries have an extraordinary dependence on fisheries and aquaculture. Maintaining the benefits from the sector is a difficult task, now made more complex by climate change. Here we report how changes to the atmosphere-ocean are likely to affect the food webs, habitats and stocks underpinning fisheries and aquaculture across the region. We found winners and losers-tuna are expected to be more abundant in the east and freshwater aquaculture and fisheries are likely to be more productive. Conversely, coral reef fisheries could decrease by 20% by 2050 and coastal aquaculture may be less efficient. We demonstrate how the economic and social implications can be addressed within the sector-tuna and freshwater aquaculture can help support growing populations as coral reefs, coastal fisheries and mariculture decline.
... Melanie Abecassis 1 , Patrick Lehodey 2 , Inna Senina 2 , Jeffrey Polovina 3 , ... Current es... more ... Melanie Abecassis 1 , Patrick Lehodey 2 , Inna Senina 2 , Jeffrey Polovina 3 , ... Current estimates of the parameters are presented in Table 2. As a result of the lack of information on gear for all fisheries other than the Hawaii-based ones, a number of parameters had to be fixed ...
Progress in Oceanography, 2008
An enhanced version of the spatial ecosystem and population dynamics model SEAPODYM is presented ... more 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°g rid-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 [
Progress in Oceanography, 2008
A Spatial Ecosystem and Population Dynamic Model (SEAPODYM) is used in a data assimilation study ... more A Spatial Ecosystem and Population Dynamic Model (SEAPODYM) is used in a data assimilation study aiming to estimate model parameters that describe dynamics of Pacific skipjack tuna population on ocean-based scale. The model based on advection-diffusion-reaction equations explicitly predicts spatial dynamics of large pelagic predators, while taking into account data on several mid-trophic level components, oceanic primary productivity and physical environment. In order to improve its quantitative ability, the model was parameterized through assimilation with commercial fisheries data, and optimization was carried out using maximum likelihood estimation approach. To address the optimization task we implemented an adjoint technique to obtain an exact, analytical evaluation of the likelihood gradient. We conducted a series of computer experiments in order to (i) determine model sensitivity with respect to variable parameters and, hence, investigate their observability; (ii) estimate observable parameters and their errors; and (iii) justify the reliability of the computed solution. Parameters describing recruitment, movement, habitat preferences, natural and fishing mortality of skipjack population were analysed and estimated. Results of the study suggest that SEAPODYM with achieved parameterization scheme can help to investigate the impact of fishing under various management scenarios, and also conduct forecasts of a given species stock and spatial dynamics in a context of environmental and climate changes.
Progress in Oceanography, 2010
The modeling of mid-trophic organisms of the pelagic ecosystem is a critical step in linking the ... more The modeling of mid-trophic organisms of the pelagic ecosystem is a critical step in linking the coupled physical-biogeochemical models to population dynamics of large pelagic predators. Here, we provide an example of a modeling approach with definitions of several pelagic mid-trophic functional groups. This application includes six different groups characterized by their vertical behavior, i.e., occurrence of diel migration between epipelagic, mesopelagic and bathypelagic layers. Parameterization of the dynamics of these components is based on a temperature-linked time development relationship. Estimated parameters of this relationship are close to those predicted by a model based on a theoretical description of the allocation of metabolic energy at the cellular level, and that predicts a species metabolic rate in terms of its body mass and temperature. Then, a simple energy transfer from primary production is used, justified by the existence of constant slopes in log-log biomass size spectrum relationships. Recruitment, ageing, mortality and passive transport with horizontal currents, taking into account vertical behavior of organisms, are modeled by a system of advection-diffusionreaction equations. Temperature and currents averaged in each vertical layer are provided independently by an Ocean General Circulation Model and used to drive the mid-trophic level (MTL) model. Simulation outputs are presented for the tropical Pacific Ocean to illustrate how different temperature and oceanic circulation conditions result in spatial and temporal lags between regions of high primary production and regions of aggregation of mid-trophic biomass. Predicted biomasses are compared against available data. Data requirements to evaluate outputs of these types of models are discussed, as well as the prospects that they offer both for ecosystem models of lower and upper trophic levels.