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Ichthyop: a Lagrangian tool for modelling ichthyoplankton dynamics

About Ichthyop

ICHTHYOP tool has been developed to study how physical factors (e.g., currents, water temperature) and biological factors (e.g., egg buoyancy, larva growth) affect the dynamics of fish eggs and larvae. It gathers physicians and biologists together around a common tool, easily available and user-friendly.

The third version of the tool is a Lagrangian platform structured as an Individual Based Model. It uses velocity, temperature and salinity three-dimensional fields archived from simulations of ROMS, MARS or NEMO.
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 functioning 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 (version 2) is fully described in Lett et al. (2008). Please refer to this publication if you use the tool.

Download

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 ICHTHYOP click here

History

Previous/modified versions of this tool have been used to investigate the effects of physical and biological factors on the dynamics of anchovy (Engraulis encrasicolus, Engraulis ringens) and sardine (Sardinops sagax) ichthyoplankton in the southern Benguela and in the northern Humboldt upwelling systems. These works associated Institut de Recherche pour le Développement (IRD, teams R079 GEODES and R097 ECO-UP) from France, University of Cape Town (UCT) and Marine & Coastal Management (MCM) from South Africa, and Instituto del Mar del Perú (IMARPE) from Peru. References for published works are provided below.

Acknowledgments

We are grateful to PREVIMER for financial support. We also thank the Laboratoire de Physique des Océans (LPO) and the DYNECO department of IFREMER.

Contact

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 83:261-269 Abstract

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

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