Modelling secondary production in the Norwegian Sea with a fully coupled physical/primary production/individual-based Calanus finmarchicus model system

The copepod Calanus finmarchicus is the dominant species of the meso-zooplankton in the Norwegian Sea, and constitutes an important link between the phytoplankton and the higher trophic levels in the Norwegian Sea food chain. An individual-based model for C. finmarchicus, based on super-individuals and evolving traits for behaviour, stages, etc., is two-way coupled to the NORWegian ECOlogical Model system (NORWECOM). One year of modelled C. finmarchicus spatial distribution, production and biomass are found to represent observations reasonably well. High C. finmarchicus abundance is found along the Norwegian shelf-break in the early summer, while the overwintering population is found along the slope and in the deeper Norwegian Sea basins. The timing of the spring bloom is generally later than in the observations. Annual Norwegian Sea production is found to be 29 million tonnes of carbon and a production to biomass (P/B) ratio of 4.3 emerges. Sensitivity tests show that the modelling system is robust to initial values of behavioural traits and with regards to the number of super-individuals simulated given that this is above about 50,000 individuals. Experiments with the model system indicate that it provides a valuable tool for studies of ecosystem responses to causative forces such as prey density or overwintering population size. For example, introducing C. finmarchicus food limitations reduces the stock dramatically, but on the other hand, a reduced stock may rebuild in one year under normal conditions

Miniaturized data loggers and computer programming improve seabird risk and damage assessments for marine oil spills in Atlantic Canada

Obtaining useful information on marine birds that can aid in oil spill (and other hydrocarbon release) risk and damage assessments in offshore environments is challenging. Technological innovations in miniaturization have allowed archival data loggers to be deployed successfully on marine birds vulnerable to hydrocarbons on water. A number of species, including murres (both Common, Uria aalge, and Thick-billed, U. lomvia) have been tracked using geolocation devices in eastern Canada, increasing our knowledge of the seasonality and colony-specific nature of their susceptibility to oil on water in offshore hydrocarbon production areas and major shipping lanes. Archival data tags are starting to resolve questions around behaviour of vulnerable seabirds at small spatial scales relevant to oil spill impact modelling, specifically to determine the duration and frequency at which birds fly at sea. Advances in data capture methods using voice activated software have eased the burden on seabird observers who are collecting increasingly more detailed information on seabirds during ship-board and aerial transects. Computer programs that integrate seabird density and bird behaviour have been constructed, all with a goal of creating more credible seabird oil spill risk and damage assessments. In this paper, we discuss how each of these technological and computing innovations can help define critical inputs into seabird risk and damage assessments, and when combined, can provide a more realistic understanding of the impacts to seabirds from any hydrocarbon release

Emergent global patterns of ecosystem structure and function from a mechanistic general ecosystem model

Anthropogenic activities are causing widespread degradation of ecosystems worldwide, threatening the ecosystem services upon which all human life depends. Improved understanding of this degradation is urgently needed to improve avoidance and mitigation measures. One tool to assist these efforts is predictive models of ecosystem structure and function that are mechanistic: based on fundamental ecological principles. Here we present the first mechanistic General Ecosystem Model (GEM) of ecosystem structure and function that is both global and applies in all terrestrial and marine environments. Functional forms and parameter values were derived from the theoretical and empirical literature where possible. Simulations of the fate of all organisms with body masses between 10 µg and 150,000 kg (a range of 14 orders of magnitude) across the globe led to emergent properties at individual (e.g., growth rate), community (e.g., biomass turnover rates), ecosystem (e.g., trophic pyramids), and macroecological scales (e.g., global patterns of trophic structure) that are in general agreement with current data and theory. These properties emerged from our encoding of the biology of, and interactions among, individual organisms without any direct constraints on the properties themselves. Our results indicate that ecologists have gathered sufficient information to begin to build realistic, global, and mechanistic models of ecosystems, capable of predicting a diverse range of ecosystem properties and their response to human pressures

An Individual-based Probabilistic Model for Fish Stock Simulation

We define an individual-based probabilistic model of a sole (Solea solea) behaviour. The individual model is given in terms of an Extended Probabilistic Discrete Timed Automaton (EPDTA), a new formalism that is introduced in the paper and that is shown to be interpretable as a Markov decision process. A given EPDTA model can be probabilistically model-checked by giving a suitable translation into syntax accepted by existing model-checkers. In order to simulate the dynamics of a given population of soles in different environmental scenarios, an agent-based simulation environment is defined in which each agent implements the behaviour of the given EPDTA model. By varying the probabilities and the characteristic functions embedded in the EPDTA model it is possible to represent different scenarios and to tune the model itself by comparing the results of the simulations with real data about the sole stock in the North Adriatic sea, available from the recent project SoleMon. The simulator is presented and made available for its adaptation to other species.Comment: In Proceedings AMCA-POP 2010, arXiv:1008.314

Biological processes and links to the physics

Analysis of the temporal and spatial variability of biological processes and identification of the main variables that drive the dynamic regime of marine ecosystems is complex. Correlation between physical variables and long-term changes in ecosystems has routinely been identified, but the specific mechanisms involved remain often unclear. Reasons for this could be various: the ecosystem can be very sensitive to the seasonal timing of the anomalous physical forcing; the ecosystem can be contemporaneously influenced by many physical variables and the ecosystem can generate intrinsic variability on climate time scales. Marine ecosystems are influenced by a variety of physical factors, e.g., light, temperature, transport, turbulence. Temperature has a fundamental forcing function in biology, with direct influences on rate processes of organisms and on the distribution of mobile species that have preferred temperature ranges. Light and transport also affect the physiology and distribution of marine organisms. Small-scale turbulence determines encounter between larval fish and their prey and additionally influences the probability of successful pursuit and ingestion. The impact of physical forcing variations on biological processes is studied through long-term observations, process studies, laboratory experiments, retrospective analysis of existing data sets and modelling. This manuscript reviews the diversity of physical influences on biological processes, marine organisms and ecosystems and their variety of responses to physical forcing with special emphasis on the dynamics of zooplankton and fish stocks

Developing alternatives for optimal representation of seafloor habitats and associated communities in Stellwagen Bank National Marine Sanctuary

The implementation of various types of marine protected areas is one of several management tools available for conserving representative examples of the biological diversity within marine ecosystems in general and National Marine Sanctuaries in particular. However, deciding where and how many sites to establish within a given area is frequently hampered by incomplete knowledge of the distribution of organisms and an understanding of the potential tradeoffs that would allow planners to address frequently competing interests in an objective manner. Fortunately, this is beginning to change. Recent studies on the continental shelf of the northeastern United States suggest that substrate and water mass characteristics are highly correlated with the composition of benthic communities and may therefore, serve as proxies for the distribution of biological biodiversity. A detailed geo-referenced interpretative map of major sediment types within Stellwagen Bank National Marine Sanctuary (SBNMS) has recently been developed, and computer-aided decision support tools have reached new levels of sophistication. We demonstrate the use of simulated annealing, a type of mathematical optimization, to identify suites of potential conservation sites within SBNMS that equally represent 1) all major sediment types and 2) derived habitat types based on both sediment and depth in the smallest amount of space. The Sanctuary was divided into 3610 0.5 min2 sampling units. Simulations incorporated constraints on the physical dispersion of sampling units to varying degrees such that solutions included between one and four site clusters. Target representation goals were set at 5, 10, 15, 20, and 25 percent of each sediment type, and 10 and 20 percent of each habitat type. Simulations consisted of 100 runs, from which we identified the best solution (i.e., smallest total area) and four nearoptimal alternates. We also plotted total instances in which each sampling unit occurred in solution sets of the 100 runs as a means of gauging the variety of spatial configurations available under each scenario. Results suggested that the total combined area needed to represent each of the sediment types in equal proportions was equal to the percent representation level sought. Slightly larger areas were required to represent all habitat types at the same representation levels. Total boundary length increased in direct proportion to the number of sites at all levels of representation for simulations involving sediment and habitat classes, but increased more rapidly with number of sites at higher representation levels. There were a large number of alternate spatial configurations at all representation levels, although generally fewer among one and two versus three- and four-site solutions. These differences were less pronounced among simulations targeting habitat representation, suggesting that a similar degree of flexibility is inherent in the spatial arrangement of potential protected area systems containing one versus several sites for similar levels of habitat representation. We attribute these results to the distribution of sediment and depth zones within the Sanctuary, and to the fact that even levels of representation were sought in each scenario. (PDF contains 33 pages.

The consumption of zooplankton by early life stages of fish in the North Sea

Previous work has shown that during the 1970s, fish and carnivorous macrozooplankton together consumed ~22 gC m-2 year-1 of mesozooplankton, principally copepods. Consumption declined to ~17 gC m-2 year-1 during the 1990s, mainly because of a reduction in fish production. The zooplankton production required to meet this demand seems to be approximately accounted for by estimates of new primary production, but there are additional sinks for zooplankton production attributable to predation by, for example, gelatinous species. Additionally, the consumption of zooplankton by early life stages of fish is difficult to assess and could be larger than implied by the earlier analysis. Here, the role of fish early life stages in zooplankton consumption is reassessed, and found to be approximately double that previously estimated. Some 28% of the zooplankton consumption by fish is now estimated to be attributable to early life stages, resulting in an estimate of zooplankton consumption by the fish community as a whole 14% higher. Taken overall, the consumption of zooplankton production by fish and other planktivorous predators is now estimated to be 19-25 gC m-2 year-1

An acoustic view of ocean mixing

Knowledge of the parameter K (turbulent diffusivity/"mixing intensity") is a key to understand transport processes of matter and energy in the ocean. Especially the almost vertical component of K across the ocean stratification (diapycnal diffusivity) is vital for research on biogeochemical cycles or greenhouse gas budgets. Recent boost in precision of water velocity data that can be obtained from vessel-mounted acoustic instruments (vmADCP) allows identifying ocean regions of elevated diapycnal diffusivity during research cruises - in high horizontal resolution and without extra ship time needed. This contribution relates acoustic data from two cruises in the Tropical North East Atlantic Oxygen Minimum Zone to simultaneous field observations of diapycnal diffusivity: pointwise measurements by a microstructure profiler as well as one integrative value from a large scale Tracer Release Experiment

Transformation of context-dependent sensory dynamics into motor behavior

Latorre R, Levi R, Varona P (2013) Transformation of Context-dependent Sensory Dynamics into Motor Behavior. PLoS Comput Biol 9(2): e1002908. doi:10.1371/journal.pcbi.1002908The intrinsic dynamics of sensory networks play an important role in the sensory-motor transformation. In this paper we use conductance based models and electrophysiological recordings to address the study of the dual role of a sensory network to organize two behavioral context-dependent motor programs in the mollusk Clione limacina. We show that: (i) a winner take-all dynamics in the gravimetric sensory network model drives the typical repetitive rhythm in the wing central pattern generator (CPG) during routine swimming; (ii) the winnerless competition dynamics of the same sensory network organizes the irregular pattern observed in the wing CPG during hunting behavior. Our model also shows that although the timing of the activity is irregular, the sequence of the switching among the sensory cells is preserved whenever the same set of neurons are activated in a given time window. These activation phase locks in the sensory signals are transformed into specific events in the motor activity. The activation phase locks can play an important role in motor coordination driven by the intrinsic dynamics of a multifunctional sensory organThis work was supported by MINECO TIN2012-30883 and IPT-2011-0727-020000

Coupling the PLANKTOM5.0 marine ecosystem model to the OCCAM 1º ocean general circulation model for investigation of the sensitivity of global biogeochemical cycles to variations in ecosystem complexity and physical environment

The earliest marine ecosystem models consisted of a simple representation of the main features of marine ecosystems, including, typically, variables for phytoplankton, zooplankton, nutrient and detritus (NPZD models). These have been incorporated into ocean general circulation models to give a basic representation of ecosystem function, providing predictions of bulk quantities such as global primary production, export and biomass which can be compared with available observations. A recent trend has been to increase the number of phytoplankton and zooplankton groups modelled, as analogues of different plankton groups observed to exist in the ocean, for example diatoms and cocolithophores (the so-called plankton functional type or PFT approach). It is usually assumed that the increase in complexity of the model will result in simulated ecosystems which more faithfully reproduce observations than NPZD models, but this has not been demonstrated systematically. The robustness of the PFT models to changes in model parameters and to changes to the physical environment in which it is embedded, have not been investigated. As a first step towards these goals, we incorporate a state-of-the-art PFT model, PLANKTOM5.0 into the OCCAM ocean general circulation model. A 6 year simulation is performed, covering the years 1989-1994 with identical parameter choices to an existing run of PLANKTOM5.0 coupled to the OPA general circulation model. This document describes the development of the coupled model and the 6 year simulation. Comparison with the OPA model and sensitivity of the solution to parameter choices will be described in a forthcoming journal paper