ICHTHYOP: a Lagrangian tool for modelling ichthyoplankton dynamics

Ichthyop : locations of 5000 virtual particles after a month of drifting. These particles were released 120 km offshore Brest in the Iroise sea, on mid May 2010. Particle color stands for depth.

The third version of the tool is a Lagrangian platform structured as an Individual Based Model. It uses velocity, temperature and salinity two or three-dimensional fields archived from simulations of different coastal models such as MARS( Model for Applications at Regional Scale), ROMS ( Regional Oceanic Modelling System) ou OPA NEMO. This latest version is able to use PREVIMER model results and real time forecasts through OpenDAP data access mechanism (see access conditions).

It executes actions that might affect the position of the individuals: advection, migration, dispersion, buoyancy, etc. and the state of the individuals: larval growth, recruitment, water temperature sensitivity, etc.
The application is organized in such a way that an advanced user could easily plug in its own hydrodynamic dataset or actions.

The tool offers two running modes. The first one provides a user-friendly GUI for setting-up and running the simulation and visualizing the transport of virtual eggs and larvae, either creating animated GIF or exporting the trajectories to KMZ format (Google Earth). The second one is a batch mode that gives full power to computation. Both modes produce output files that store information about the simulated dynamics of individuals (time, longitude, latitude, depth, length, etc.). Output files are in NetCDF format and can be post-processed easily. Routines in R can be sent upon request for plotting trajectories or computing the numbers of individuals transported from pre-defined release (spawning) areas to pre-defined destination (recruitment) areas.

ICHTHYOP Tool is (version 2) is described in details in the following paper:

description détaillée d'ICHTHYOP Lett et al. (2008)

Download

Ichthyop has been developped in collaboration with IRD how also distribute the tool.

The program is written in Java and requires the Java Runtime Environment (JRE). The tool is distributed as a package that contains the program code, libraries and basic examples.

For downloading version 3.0 of ICHTHYOP click here.

Any correspondence should be addressed to info@previmer.org

References

• Brochier T, Colas F, Lett C, Echevin V, Cubillos LA, Tam J, Chlaida M, Mullon C, Fréon P (2009) Small pelagic fish reproductive strategies in upwelling systems: a natal homing evolutionary model to study environmental constraints. Prog Oceanogr 83:261-269Abstract

• Brochier T, Lett C, Tam J, Fréon P, Colas F, Ayón P (2008) An individual-based model study of anchovy early life history in the northern Humboldt Current system. Prog Oceanogr 79:313-325. Abstract

• Brochier T, Ramzi A, Lett C, Machu E, Berraho A, Fréon P, Hernández-León S (2008) Modelling sardine and anchovy ichthyoplankton transport in the Canary Current System. J Plankton Res 30:1133-1146. Abstract

• Huggett J, Fréon P, Mullon C, Penven P (2003) Modelling the transport success of anchovy Engraulis encrasicolus eggs and larvae in the southern Benguela: the effect of spatio-temporal spawning patterns. Mar Ecol Prog Ser 250:247-262. Abstract

• Lett C, Roy C, Levasseur A, van der Lingen CD, Mullon C (2006) Simulation and quantification of enrichment and retention processes in the southern Benguela upwelling ecosystem. Fish Oceanogr 15:363-372. Abstract

• Lett C, Penven P, Ayón P, Fréon P (2007) Enrichment, concentration and retention processes in relation to anchovy (Engraulis ringens) eggs and larvae distributions in the northern Humboldt upwelling ecosystem. J Mar Syst 64:189-200. Abstract

• Lett C, Veitch J, van der Lingen CD, Hutchings L (2007) Assessment of an environmental barrier to transport of ichthyoplankton from the southern to the northern Benguela ecosystems. Mar Ecol Prog Ser 347:247-259. Abstract

• Lett C, Verley P, Mullon C, Parada C, Brochier T, Penven P, Blanke B (2008) A Lagrangian tool for modelling ichthyoplankton dynamics. Environ Modell Softw 23:1210-1214. Abstract

• Martins RS, Roberts MJ, Chang N, Verley P, Moloney CL, Vidal EAG (2010) Effect of yolk utilization on the specific gravity of chokka squid (Loligo reynaudii) paralarvae: implications for dispersal on the Agulhas Bank, South Africa. ICES J Mar Sci 67:1323-1335.Abstract

• Miller DCM, Moloney CL, van der Lingen CD, Lett C, Mullon C, Field JG (2006) Modelling the effects of physical-biological interactions and spatial variability in spawning and nursery areas on transport and retention of sardine Sardinops sagax eggs and larvae in the southern Benguela ecosystem. J Mar Syst 61:212-229. Abstract

• Mullon C, Cury P, Penven P (2002) Evolutionary individual-based model for the recruitment of anchovy (Engraulis capensis) in the southern Benguela. Can J Fish Aquat Sci 59:910-922. Abstract

• Mullon C, Fréon P, Parada C, van der Lingen C, Huggett J (2003) From particles to individuals: modelling the early stages of anchovy (Engraulis capensis/encrasicolus) in the southern Benguela. Fish Oceanogr 12:396-406. Abstract

• Nicolle A, Garreau P, Liorzou B (2009) Modelling for anchovy recruitment studies in the Gulf of Lions (Western Mediterranean Sea). Ocean Dyn 59:953-968. Abstract

• Parada C, van der Lingen CD, Mullon C, Penven P (2003) Modelling the effect of buoyancy on the transport of anchovy (Engraulis capensis) eggs from spawning to nursery grounds in the southern Benguela: an IBM approach. Fish Oceanogr 12:170-184. Abstract

• Parada C, Mullon C, Roy C, Fréon P, Hutchings L, van der Lingen CD (2008) Does vertical migratory behaviour retain fish larvae onshore in upwelling ecosystems? A modelling study of anchovy in the southern Benguela. Afr J Mar Sci 30:437-452 Abstract

• Parada, C, Armstrong, D, Ernst, B, Hinckley, S, Orensanz, J.M. (Lobo). 2010. Spatial dynamics of snow crab (Chionoecetes opilio) in the Eastern Bering Sea-Putting together the pieces of the puzzle. Bulletin of Marine Sciences. Vol 86, Number 2, 413-437(25)

• Putman NF, Shay TJ, Lohmann KJ (2010) Is the geographic distribution of nesting in the Kemp’s ridley turtle shaped by the migratory needs of offspring? Integr Comp Biol 50:305-314. Abstract

• Roberts MJ, Mullon C (2010) First Lagrangian ROMS–IBM simulations indicate large losses of chokka squid Loligo reynaudii paralarvae from South Africa’s Agulhas Bank. Afr J Mar Sci 32:71-84 Abstract

• Velo-Suárez L, Reguera B, González-Gil S, Lunven M, Lazure P, Nézan E, Gentien P (2010) Application of a 3D Lagrangian model to explain the decline of a Dinophysis acuminata bloom in the Bay of Biscay. J Mar Syst 83:242–252 Abstract

Future references

• Soto-Mendoza, S., Parada, C., Castro, L., Colas, F., Schneider, W. Modeling transport and survival of anchoveta eggs and yolk sac larvae in the coastal zone off central-south Chile: assessing spatial and temporal spawning parameters. Submitted to Progress in Oceanography (August 2009) Special issue. (accepted).

• Parada, C., Colas, F., Castro, L., Soto, S. Contribution of vertical migration to onshore transport of anchovy larvae (Engraulis ringens) in Central Chile upwelling ecosystem: Seasonal variability. Manuscript to Progress in Oceanography Special issue. (accepted).

• Parada, C., Ernst, B., Hinckley, S., Orensanz, J.M. (Lobo), Armstrong, D., Curchitser, E., Hermann, A. Patterns of Connectivity and Potential Settlement Regions of Snow Crab (Chionoecetes opilio) Larvae in the Eastern Bering Sea. (accepted).

• Ospina-Álvarez, A; Palomera, I., Parada, C. Changes in egg buoyancy through development and its effects on the vertical distribution of
  anchovy eggs. Manuscript to Fisheries Research (accepted).

• Yannicelli, B., Castro, L., Parada, C., Colas, F., Schneider, W., Donoso, D., Distribution of Pleuroncodes monodon larvae over the continental shelf of south Central Chile: evidence for partial local retention and transport. Manuscript to Progress in Oceanography Special issue. (submitted).